Genomic affinity following restoration of a locally extirpated species: a case study of desert bighorn sheep in Texas - Emily A. Wright; Joseph D. Manthey; Michael R. Buchalski; Bonnie R. McKinney; David A. Ray; Caleb D. Phillips; Robert D. Bradley (Conservation Genetics, 2024)

Genetic structure of Atlantic Puffins (Fratercula arctica) breeding in Atlantic Canada - Quinn B. Carvey; Scott A. Pavey; Antony W. Diamond; Gail K. Davoren; Raphael A. Lavoie; Nathalie M. LeBlanc; Matthew J. Legard; Gregory J. Robertson; Emily S. Runnells; Christina Petalas; Heather L. Major (Conservation Genetics, 2024)

Urbanisation has impacted the population genetic structure of the Eurasian red squirrel in Japan within a short period of 30 years - Yu Takahata; Kenta Uchida; Nobuyuki Kutsukake; Tatsuki Shimamoto; Yushin Asari; Yohey Terai (Conservation Genetics, 2024)
Human activities often induce maladaptive effects in urban wildlife, such as increased inbreeding and decreased gene flow, consequently leading to a loss of biodiversity. Although maladaptive effects are commonly reported in urban wildlife, some wildlife species are not affected. Understanding the conditions and factors that affect the genetic structure of wildlife is crucial for its conservation in urban environments. Eurasian red squirrels Sciurus vulgaris in Obihiro City, Hokkaido, Japan, have settled in large residential lots with a high risk of vehicle collisions for approximately 30 years, raising the possibility that the urban population would be genetically isolated from nearby rural populations and may experience a rapid decrease in genetic diversity. In this study, we analysed the population structure, genetic distance, and nucleotide diversity of squirrels in the Obihiro area using genome-wide single nucleotide polymorphisms (SNPs). Principal component analysis and ADMIXTURE showed that urban and rural squirrel populations formed distinct clusters with intermediate urban and rural boundary populations. Genetic distances between the urban populations were greater than that of other pairs. Nucleotide diversities were lower in urban populations than in other populations, suggesting limited gene flow between urban and other populations, possibly due to urbanisation. The change in the genetic characteristics of urban squirrel populations during this short period demonstrates the strong impact of urbanisation. Our findings suggest that a genome-wide approach to the genetic structure of wildlife contributes to its conservation in urban environments.

Machine learning approaches to assess microendemicity and conservation risk in cave-dwelling arachnofauna - Hugh G. Steiner; Shlomi Aharon; Jesús Ballesteros; Guilherme Gainett; Efrat Gavish-Regev; Prashant P. Sharma (Conservation Genetics, 2024)

Genetic support for discrete conservation units of the fossorial rodent Geomys pinetis - Sarah I. Duncan; Robert A. McCleery; Celine M. Carneiro; J. T. Pynne; Elizabeth I. Parsons; L. Mike Conner; Steven B. Castleberry; Robert A. Gitzen; James D. Austin (Conservation Genetics, 2024)

Genetic diversity in the traditional cultivars and wild ancestor of near-threatened Japanese iris (Iris ensata Thunb.) - Makiko Mimura; Marina Takeuchi; Takayuki Kobayashi; Shun K. Hirota; Yoshihisa Suyama; Hirofumi Yamaguchi; Toshihito Tabuchi (Conservation Genetics, 2024)
Wild relatives of cultivars are crucial sources of genetic variation for further enhancement, yet they face potential threats due to contemporary environmental changes. Iris ensata var. spontanea , a wild progenitor of the Japanese iris cultivars ( I. ensata var. ensata ), is extensively cultivated in Japanese gardens, is distributed across mesic meadows and wetlands in Japan and East Asia. This species is currently threatened owing to habitat loss linked to land use alterations. We assessed genetic diversity and phylogenetic relationships in 32 wild accessions and the 14 principal Edo Group of Japanese iris cultivars, originally bred during the Edo period (1600–1868). In the phylogenetic tree, the cultivars formed a cluster with reduced inbreeding coefficients, suggesting a singular origin and interbreeding between the genetically distinct accessions. Conversely, wild accessions exhibited greater overall genetic diversity and higher inbreeding coefficients than cultivars, indicating frequent inbreeding within divergent natural populations. Our findings highlight the distinct genetic reservoirs of both wild accessions and Edo cultivars, although the former may face inbreeding challenges. Urgent conservation action is needed to ensure the genetic diversity of wild populations as natural resources.

Population genetic structure of the European pond turtle (Emys orbicularis) at the northern edge of the Pannonian Basin - Peter Mikulíček; Petr Papežík; Stanislav Danko; Róbert Dankovics; Daniel Gruľa; Bálint Halpern; Peter Havaš; Botond Heltai; Enikő Horváth; Tomáš Kušík; Peter Puchala; Maria Schindler; et al. (Conservation Genetics, 2024)
Populations of plants and animals at the edge of a species’ range may exhibit lower genetic diversity due to a combination of historical (e.g., postglacial dispersal) and contemporary (e.g., low effective population size, strong genetic drift or bottlenecks) processes. In this study, we analysed the genetic structure of populations of the European pond turtle ( Emys orbicularis ) in the northern part of the Pannonian Basin (Slovakia, Hungary, Austria), which represents the edge of the species’ range. Using mitochondrial DNA (mtDNA) and microsatellite markers, we aimed to assign individuals and populations into phylogeographic lineages and to determine genetic variation and population structure. Our study revealed that most individuals from natural populations belong to mtDNA lineage II (widely distributed haplotype IIa, and likely endemic haplotypes IIl and IIo), which is typical for the whole Pannonian region. However, non-native haplotypes were detected in one Slovak population (haplotype Ib) and in the Austrian Donau Auen National Park (haplotype IVa). Microsatellite markers revealed high variability comparable to that in other parts of the range, suggesting that marginal populations may not necessarily have reduced genetic diversity. A genetically mixed population was found in the Donau Auen National Park, consisting of turtles belonging to mtDNA lineage II (taxonomically assessed as subspecies E. orbicularis orbicularis ) and lineage IV (taxonomically assessed as E. orbicularis hellenica ), which is native to the circum-Adriatic region. The admixture suggests intense hybridization and introgression between the two lineages (subspecies).

Genetic assessment and monitoring of wild, captive, and reintroduced northern leopard frog populations - Parinaz Khalilzadeh; Lea Randall; David Coltman; Lindsay Anderson; David Lesbarrères (Conservation Genetics, 2024)
The northern leopard frog ( Lithobates pipiens ) has undergone dramatic declines in population size and range over recent decades in western Canada and the United States. In British Columbia, only a single population remains at the Creston Valley Wildlife Management Area. Yet, the continuing viability of this population is uncertain. In this paper, the current genetic structure of northern leopard frog populations in western Canada was assessed using microsatellite markers. Historical samples from the extinct population of Fort Steele in British Columbia were compared with the Creston Valley population to understand changes in population genetic parameters over time. Genotypic data from four populations (Creston Valley, Drain K, Prince Spring, and Cypress Hill) sampled in 2004 and 2019 were compared. To evaluate changes in the genetic diversity of the Creston Valley population over time, allelic richness and expected heterozygosity of the population were compared at three time points using genotypes from 2000, 2004, and 2019. Northern leopard frog populations in western Canada showed high genetic differentiation, with genetic diversity decreasing from east to west. Although there weren’t notable changes in genetic parameters between 2004 and 2019, there was evidence of a decline in diversity between 2000 and 2019. The extinct population of Fort Steele had private alleles, while the current Creston Valley population did not, suggesting a genetic bottleneck in the Creston Valley population. Therefore, genetic rescue, specifically for the endangered Creston Valley population, can be considered as an action to support recovery. Additionally, continued genetic monitoring will help in the effective management of the species by providing information on the success of conservation actions.

Deep genetic divergence underlies within-island eco-morphological variation in the endangered day gecko Phelsuma borbonica: implications for conservation - Josselin Cornuault; Mickaël Sanchez; Thomas Duval; Antoine Fouquet; Christophe Thébaud (Conservation Genetics, 2024)

Conservation genetics of the endangered California Freshwater Shrimp (Syncaris pacifica): watershed and stream networks define gene pool boundaries - Abdul M. Ada; Amy G. Vandergast; Robert N. Fisher; Darren Fong; Andrew J. Bohonak (Conservation Genetics, 2024)
Understanding genetic structure and diversity among remnant populations of rare species can inform conservation and recovery actions. We used a population genetic framework to spatially delineate gene pools and estimate gene flow and effective population sizes for the endangered California Freshwater Shrimp Syncaris pacifica . Tissues of 101 individuals were collected from 11 sites in 5 watersheds, using non-lethal tissue sampling. Single Nucleotide Polymorphism markers were developed de novo using ddRAD-seq methods, resulting in 433 unlinked loci scored with high confidence and low missing data. We found evidence for strong genetic structure across the species range. Two hierarchical levels of significant differentiation were observed: (i) five clusters (regional gene pools, F ST = 0.38–0.75) isolated by low gene flow were associated with watershed limits and (ii) modest local structure among tributaries within a watershed that are not connected through direct downstream flow (local gene pools, F ST = 0.06–0.10). Sampling sites connected with direct upstream-to-downstream water flow were not differentiated. Our analyses suggest that regional watersheds are isolated from one another, with very limited (possibly no) gene flow over recent generations. This isolation is paired with small effective population sizes across regional gene pools (N e = 62.4–147.1). Genetic diversity was variable across sites and watersheds ( H e = 0.09–0.22). Those with the highest diversity may have been refugia and are now potential sources of genetic diversity for other populations. These findings highlight which portions of the species range may be most vulnerable to future habitat fragmentation and provide management consideration for maintaining local effective population sizes and genetic connectivity.

Correction: Beyond Bonferroni: less conservative analyses for conservation genetics - Shawn R. Narum (Conservation Genetics, 2024)

Population genetics of caribou in the Alaska-Yukon border region: implications for designation of conservation units and small herd persistence - Karen H. Mager; Michael J. Suitor; Thanh Khoa Nguyen; My Hanh Hoang; Jim D. Herriges; Jeffrey B. Stetz; Kelsey L. Russell (Conservation Genetics, 2024)
Better knowledge of genetic relationships between the Fortymile caribou herd and its neighbors is needed for conservation decision-making in Canada. Here, we contribute the first fine-scale analysis of genetic population structure in nine contiguous caribou herds at the geographic boundaries between Barren-ground and Northern Mountain caribou, and at the Alaska-Yukon border. Using pairwise differentiation metrics, STRUCTURE, and discriminant analysis of principal components (DAPC) to analyze 15 microsatellite loci in 379 caribou, we found complex patterns of genetic differentiation. The Fortymile was the only herd assigned to more than one genetic cluster, indicative of its history as a larger herd whose range expansions and gene flow to other herds were likely important to maintaining diversity across a functioning genetic metapopulation. Some small herds (Chisana, Klaza, and White Mountains) were genetically distinct, while others (Hart River, Clear Creek, Mentasta) exhibited little differentiation from herds they occasionally overlap, including herds assigned to different conservation units (DUs). This genetic connectivity does not result from demographic connectivity, as episodic contact during rut, rather than herd switching, is the likely mechanism. Unusually, one small herd (White Mountains) maintained genetic differentiation despite rut overlap with Fortymile. Our data reveal that some herds with different ecological and behavioral attributes are demographically independent but nonetheless genetically connected. Thus, we suggest that managing caribou for an appropriate level of genetic connectivity, while also supporting herd persistence, will be essential to conserve caribou genetic diversity in the region.

Genetic structure of restored Brook Trout populations in the Southern Appalachian Mountains indicates successful reintroductions - Rebecca J. Smith; David C. Kazyak; Matt A. Kulp; Barbara A. Lubinski; Benjamin M. Fitzpatrick (Conservation Genetics, 2024)

Genomic patterns of native palms from the Leeward Antilles confirm single-island endemism and guide conservation priorities - James A. R. Clugston; Quirijn Coolen; Erik Houtepen; André S. J. van Proosdij; Ayress D. Grinage; M. Patrick Griffith (Conservation Genetics, 2024)
Systematic study of the palm (Arecaceae) flora from the Leeward Antilles marked both Sabal antillensis and Sabal lougheediana as endemic to Curaçao and Bonaire respectively. Although both species are emergent, obvious and charismatic elements of the Antillean flora, they were only described within the last decade. Sabal lougheediana is in demographic crisis as a result of constant ungulate pressure prohibiting seedling establishment, while S. antillensis is thriving as a result of careful management. Given the surprisingly recent discovery of these two species, and the severity of the conservation concern, genomic data can help inform whether these taxa are in fact well-circumscribed species, and help to guide further conservation actions. To investigate genomic diversity, we employed RADSeq data from samples throughout the range of both species. Results show significant genetic distance and fixation between the two taxa as currently circumscribed, as well as reduced genetic diversity and increased inbreeding in both species. Multivariate analysis of genetic distance and Bayesian clustering analysis both show clear and significant separation of the two taxa. Parallel assay of ex situ collections informs how future development of germplasm reserves can help support conservation of both species. We provide recommendations to help conserve these two unique and distinct species.

Isolation, small population size, and management influence inbreeding and reduced genetic variation in K’gari dingoes - Susan M. Miller; Linda Behrendorff; Benjamin L. Allen; Rose L. Andrew; Guy Ballard; J. William O. Ballard; Kylie M. Cairns; Gabriel C. Conroy; Peter J. S. Fleming; Catherine E. Grueber; Jane Oakey; Deane A. Smith; et al. (Conservation Genetics, 2024)
Small island populations are vulnerable to genetic decline via demographic and environmental stochasticity. In the absence of immigration, founder effects, inbreeding and genetic drift are likely to contribute to local extinction risk. Management actions may also have a greater impact on small, closed populations. The demographic and social characteristics of a species can, however, delay the impact of threats. K’gari, a ~ 1 660 km 2 island off the Australian east coast and UNESCO World Heritage Site (Fraser Island 1842–2023), supports an isolated population of approximately 70–200 dingoes that represent an ideal opportunity to explore the small island paradigm. To examine temporal and spatial patterns of genetic diversity in this population we analysed single nucleotide polymorphism (SNP) genotype data (72 454 SNPS) for 112 K’gari dingoes collected over a 25-year period (1996 to 2020). Genetic diversity was lower in K’gari dingoes than mainland dingoes at the earliest time point in our study and declined significantly following a management cull in 2001. We did not find any spatial genetic patterns on the island, suggesting high levels of genetic connectivity between socially discrete packs. This connectivity, combined with the social structure and behaviour of dingoes, may act in concert to buffer the population from the impacts of genetic drift in the short term. Nevertheless, a general decline in genetic variation via inbreeding and drift has occurred over the past 20 years which we suggest should be considered in any future management planning for the population. Monitoring patterns of genetic variation, together with a clearer understanding of the social ecology of K’gari dingoes, will aid in the development of measurable genetic targets set over ecologically meaningful timelines, and help ensure continued survival of this culturally important population.

Loss of genetic diversity and isolation by distance and by environment in populations of a keystone ungulate species - Fernanda de Góes Maciel; Sean O’Rourke; Melissa Jones; William Hemstrom; Michael Ryan Miller; Gabriela Schmaedecke; Leandro Reverberi Tambosi; Mozart Sávio Pires Baptista; Alexine Keuroghlian; Alessandra Ferreira Dales Nava; Marcello Schiavo Nardi; Anah Tereza de Almeida Jácomo; et al. (Conservation Genetics, 2024)

Early detection of rare and elusive endangered species using environmental DNA: a case study for the Eurasian otter and the white-clawed crayfish in northwestern Italy - Lorenzo Ballini; Dario Ottonello; Valentina Repetto; Chiara Natali; Giacomo Chini; Livia Tolve; Claudio Ciofi; Sara Fratini; Alessio Iannucci (Conservation Genetics, 2024)
Monitoring, management and conservation of rare and elusive species often requires early detection of individuals, especially for re-introduced and endangered taxa. Environmental DNA (eDNA) approaches can enhance the detection power of traditional biomonitoring methods for low-density, newly-established populations. In this study, we used species-specific Real Time PCR TaqMan assays to assess the presence of two endangered freshwater species, the white-clawed crayfish Austropotamobius pallipes and the Eurasian otter Lutra lutra at eight sites in four river catchments in Liguria (northwestern Italy). The Eurasian otter was considered extinct in the study area since the 1980s. However, recent, although scattered sightings indicated a recolonisation by a few individuals. The white-clawed crayfish populations declined drastically and became increasingly dispersed in the western part of Liguria. Our eDNA analysis confirmed the presence of both species in some of the selected rivers and detected Eurasian otter DNA where the species was not recorded through traditional monitoring methods. This study confirms eDNA-based monitoring approaches as valuable tools to assess the presence of rare and elusive species and help implement protection plans at a local scale.

Absence of genetic structure among ecologically diverse populations indicate high plasticity in a pantropical seabird - Mariana Scain Mazzochi; Vitória Muraro; Nelson Jurandi Rosa Fagundes; Leandro Bugoni (Conservation Genetics, 2024)

Genomic and common garden data reveal significant genetic differentiation in the endangered San Fernando Valley spineflower Chorizanthe parryi var. fernandina - Deborah L. Rogers; Loraine Kohorn Washburn; Cheryl Birker; Michelle A. Labbé; Matthew A. Campbell; Andrea D. Schreier (Conservation Genetics, 2024)
San Fernando Valley spineflower ( Chorizanthe parryi var. fernandina [S. Watson] Jeps.) (Polygonaceae) is an herbaceous annual plant, endemic to California, and until rediscovered in 1999 had been thought to be extinct for almost seven decades. Historically documented at 10 locations, it currently persists at 2, separated by approximately 27 km. State listed as endangered, a description of its genetic diversity and structure is of conservation interest. After determining a lack of variation in ploidy, we examined genetic variation from samples within both populations: a common garden study for potentially adaptive genetic variation in selected growth and phenological traits and analysis of single nucleotide polymorphisms identified through restriction-site associated DNA sequencing. Both measures indicated that this highly restricted taxon nevertheless harbors substantial levels of genetic diversity and has significant between- and within-population genetic structure. Combining approaches from population genomics and common garden studies provided more insight into the patterns and basis of genetic diversity than is typical for studies of non-model species. Although local adaptation was not specifically studied (i.e., via reciprocal transplant studies), the differences determined from these two independent lines of evidence indicate that mixing gene pools between populations is not recommended at this time. Further, with significant differences revealed among subpopulations, we caution against mixing genotypes across subpopulations for the most part, and without much more evidence that this would not pose a risk of outbreeding depression. The importance of supporting pollinator health and diversity is highlighted. With genetic diversity—particularly with an annual species—being dynamic, fluctuating with the usual processes and with contributions from the soil seedbank, we recommend periodic resampling to monitor genetic diversity and structure. Climate change is anticipated to contribute to this variability.

Admixture and reproductive skew shape the conservation value of ex situ populations of the Critically Endangered eastern black rhino - Franziska Elsner-Gearing; Petra Kretzschmar; Susanne Shultz; Mark Pilgrim; Deborah Ann Dawson; Gavin John Horsburgh; Jírí Hruby; Jane Hopper; Tony King; Catherine Walton (Conservation Genetics, 2024)
Small populations of endangered species risk losing already eroded genetic diversity, important for adaptive potential, through the effects of genetic drift. The magnitude of drift can be mitigated by maximising the effective population size, as is the goal of genetic management strategies. Different mating systems, specifically those leading to reproductive skew, exacerbate genetic drift by distorting contributions. In the absence of an active management strategy, reproductive skew will have long-term effects on the genetic composition of a population, particularly where admixture is present. Here we examine the contrasting effects of conservation management strategies in two ex situ populations of the Critically Endangered eastern black rhino (Diceros bicornis michaeli) , one managed as a semi-wild population in South Africa (SAx), and one managed under a mean-kinship breeding strategy in European zoos. We use molecular data to reconstruct pedigrees for both populations and validate the method using the zoo studbook. Using the reconstructed pedigree and studbook we show there is male sex-specific skew in both populations. However, the zoo’s mean-kinship breeding strategy effectively reduces reproductive skew in comparison to a semi-wild population with little genetic management. We also show that strong male reproductive skew in SAx has resulted in extensive admixture, which may require a re-evaluation of the population’s original intended role in the black rhino meta-population. With a high potential for admixture in many ex situ populations of endangered species, molecular and pedigree data remain vital tools for populations needing to balance drift and selection.

Genetic structure and diversity of semi-captive populations: the anomalous case of the Asian elephant - Gilles Maurer; Marie-Pierre Dubois; Zaw Min Oo; Vatsana Chanthavong; Baptiste Mulot; Olivier Gimenez; Finn Kjellberg (Conservation Genetics, 2024)
Wild species living in captivity are subject to loss of genetic diversity, inbreeding depression, and differentiation among populations. Only very few species have been under human care for centuries but have not been selectively bred, have free-ranging movements most of the time, and retain porous barriers to gene flow between wild and captive populations. Such captive populations are expected to retain high levels of genetic diversity and anthropogenic factors should result in a limited genetic differentiation from wild populations. Asian elephants have been trained and used by humans for at least 4000 years as war animals, mounts of kings and draught animals. In Myanmar and Laos, elephants are still being used for hauling timber in the forest while retaining traditional management practices including seasonal release, free mating and movement. However, habitat fragmentation, isolation and reduced gene flows are threatening both semi-captive and wild pools. We genotyped 167 semi-captive elephants from Laos and Myanmar using a panel of 11 microsatellite loci to estimate the genetic diversity and population structure. We found that elephants of both countries presented high levels of genetic diversity and a low degree of inbreeding, if any. This agrees with the expected high level of genetic diversity in semi-captive populations. We found a weak differentiation along a geographical gradient from southern Laos to northern Myanmar but no differentiation between wild-caught and captive-born pools. The potential value for conservation of a large population of semi-captive elephants has been recognized but the conservation community has yet to fully explore the potential role semi-captive elephants could play in maintaining gene flows.

Correction: Revisiting conservation units for the endangered mountain yellow-legged frog species complex (Rana muscosa, Rana sierrae) using multiple genomic methods - Allison Q. Byrne; Andrew P. Rothstein; Lydia L. Smith; Hannah Kania; Roland A. Knapp; Daniel M. Boiano; Cheryl J. Briggs; Adam R. Backlin; Robert N. Fisher; Erica Bree Rosenblum (Conservation Genetics, 2024)

Genetic connectivity in the Arizona toad (Anaxyrus microscaphus): implications for conservation of a stream dwelling amphibian in the arid Southwestern United States - Sara J. Oyler-McCance; Mason J. Ryan; Brian K. Sullivan; Jennifer A. Fike; Robert S. Cornman; J. Tomasz Giermakowski; Shawna J. Zimmerman; Rachel L. Harrow; Shaula J. Hedwall; Blake R. Hossack; Ian M. Latella; Robert E. Lovich; et al. (Conservation Genetics, 2024)
The Arizona Toad ( Anaxyrus microscaphus ) is restricted to riverine corridors and adjacent uplands in the arid southwestern United States. As with numerous amphibians worldwide, populations are declining and face various known or suspected threats, from disease to habitat modification resulting from climate change. The Arizona Toad has been petitioned to be listed under the U.S. Endangered Species Act and was considered “warranted but precluded” citing the need for additional information – particularly regarding natural history (e.g., connectivity and dispersal ability). The objectives of this study were to characterize population structure and genetic diversity across the species’ range. We used reduced-representation genomic sequencing to genotype 3,601 single nucleotide polymorphisms in 99 Arizona Toads from ten drainages across its range. Multiple analytical methods revealed two distinct genetic groups bisected by the Colorado River; one in the northwestern portion of the range in southwestern Utah and eastern Nevada and the other in the southeastern portion of the range in central and eastern Arizona and New Mexico. We also found subtle substructure within both groups, particularly in central Arizona where toads at lower elevations were less connected than those at higher elevations. The northern and southern parts of the Arizona Toad range are not well connected genetically and could be managed as separate units. Further, these data could be used to identify source populations for assisted migration or translocations to support small or potentially declining populations.

eDNA metabarcoding reveals a rich but threatened and declining elasmobranch community in West Africa’s largest marine protected area, the Banc d’Arguin - Carolina de la Hoz Schilling; Rima W. Jabado; Ana Veríssimo; Luca Caminiti; Ebaye Sidina; Cheikhna Yero Gandega; Ester A. Serrão (Conservation Genetics, 2024)
Elasmobranchs (sharks and rays) are the most threatened marine vertebrates, particularly in tropical and subtropical areas. Their population status is often poorly understood due to insufficient information. Despite reportedly harbouring critical elasmobranch habitats, the Banc d’Arguin National Park (PNBA) in Mauritania lacks comprehensive and updated information on the diversity of elasmobranch species in the area. We developed a baseline inventory based on morphological and molecular identification and metabarcoding. DNA barcoding of tissue samples from elasmobranch processing sites and freshly sampled specimens was used to build a genetic reference database of local elasmobranch species. The richness and diversity of species in the PNBA were described via metabarcoding of seawater eDNA samples using an elasmobranch-specific assay and our reference database. We detected 27 species, including 12 new species records for the PNBA. We further uncover potentially undescribed species of Gymnura and Torpedo , while taxonomic corrections are noted for previously reported species. In particular, the reportedly abundant Mustelus mustelus was absent from tissue and eDNA samples, while M. punctulatus was detected instead. Taxa that have anecdotally become regionally extinct or rare (e.g., sawfishes, wedgefishes, lemon sharks) were not detected, highlighting local species diversity shifts within the last few decades. Results show that 67.9% of elasmobranch species in the PNBA are threatened with extinction according to the IUCN Red List of Threatened Species. This study emphasises the importance of taxonomic identification in support of species management and provides a baseline to inform future studies and conservation measures to avoid further species losses.

Genomic data identify genetic structure in Enoploctenus cyclothorax (Araneae: Ctenidae), revealing two distinct taxonomic units in the southern region of the Brazilian Atlantic Forest - Mariana Costa Terra; Antonio Domingos Brescovit; Rogério Fernandes de Souza; Ana Lúcia Dias; Matheus Pires Rincão; Renata da Rosa (Conservation Genetics, 2024)

The importance of understanding clonal structure for species listing and recovery: case studies from the rare oconee bells (Shortia brevistyla and Shortia galacifolia; Diapensiaceae) and the federally endangered bunched arrowhead (Sagittaria fasciculata; Alismataceae) - Skyler Fox; Lauren Eberth; J. Banks Floyd; Calla Pederson; Lily Stafford; Nora Tillmanns; Lo Vodo; Ashley B. Morris (Conservation Genetics, 2024)

Remnant kenngoor (Phascogale calura) retain genetic connectivity and genetic diversity in a highly fragmented landscape - Rhiannon S. J. de Visser; Michelle Hall; Kym Ottewell; Jennifer C. Pierson; Angela Sanders; J. Anthony Friend; Laurence Berry; Carolyn Hogg; Renee A. Catullo (Conservation Genetics, 2024)
Kenngoor ( Phascogale calura ) persist in < 1% of their original distribution, occupying highly fragmented remnant habitat in south-west Western Australia, with very little known of the genetic diversity of the remaining wild populations. Recently, the species has been translocated to managed reserves to improve its conservation. Understanding genetic structure and patterns of genetic diversity is crucial to inform conservation translocations for species recovery. This study aims to (1) assess genetic structure and genetic diversity across remaining wild locations, (2) assess long-term genetic outcomes of a mixed-source wild-to-wild translocation, and (3) estimate global effective population size. We genotyped 209 samples from 13 locations of fragmented remnant habitat using reduced representation sequencing. An isolation by distance model best explained genetic structure across the survey areas, with evidence of fine scale divergence of two northern locations. Allelic richness and autosomal heterozygosity measures indicated that diversity is spread uniformly across locations, and no locations showed signs of inbreeding or strong genetic drift. The mixed-source translocation has retained the diversity of the wider species ten years post-translocation. Overall, our results suggest that connectivity between survey areas has largely been maintained and that no location has substantially lower genetic diversity, despite the highly fragmented nature of remnant kenngoor habitat. Future translocations should aim to represent a mixture of genetically divergent locations to maintain the diversity present at the species level. Ongoing conservation management will be required to ensure the long-term viability of the species in this fragmented landscape.

Effective population size of adult and offspring cohorts as a genetic monitoring tool in two stand-forming and wind-pollinated tree species: Fagus sylvatica L. and Picea abies (L.) Karst. - Heike Liesebach; Pascal Eusemann; Aki M. Höltken; Ute Tröber; Oleksandra Kuchma; Manuel Karopka; Frank Becker; Ralf Kätzel; Barbara Fussi (Conservation Genetics, 2024)
Genetic diversity is considered to be a prerequisite for adaptation and adaptability as it is a key element of biological diversity. However, the monitoring of genetic diversity has tended to be ignored in biodiversity monitoring. We report a comprehensive genetic monitoring effort in two dominant forest tree species, which was started with a baseline survey in 12 European beech populations and 10 Norway spruce populations in Germany. The standardized experimental design is based on collecting samples of at least 250 adult trees, and 400 natural regeneration and 400 seed samples and their genotyping with 15–16 high-resolution SSR markers. In addition to commonly used mean values across the markers to quantify genetic diversity, we placed special emphasis on various marker-based, pedigree-based and demographic models for estimating the contemporary effective population size N e of the different generations. In both beech and spruce, no variation in genetic diversity with mean values across markers was detectable between the studied stands and between age cohorts. We detected that stable allelic diversity in progeny generations is ensured by sufficient gene flow from surrounding forests. However, estimates of effective population size show marked differentiation among populations and among age cohorts. Natural regeneration samples appear to converge on the parent generation, while seed samples show a clear bottleneck effect. The N e parameter can be used to derive conclusions for sustainable natural regeneration management in forest stands and for seed stand approvals including adequate seed collections for appropriate artificial regenerations.The sibship frequency-based method for N e estimates is presented as much more robust than the widely used LD estimates, which often fail for samples with too weak relatedness. Despite the distinct kinship structure in our monitoring plots, the contemporary effective population size proves to be an essential parameter for assessing the integrity of the reproductive system.

Sampling through space and time: multi-year analysis reveals dynamic population genetic patterns for an amphibian metapopulation - Chloe E. Moore; Meryl C. Mims (Conservation Genetics, 2024)
Metapopulations are dynamic, and population genetics can reveal both spatial and temporal metapopulation variation. Yet, population genetic studies often focus on samples collected within a single time period or combine samples taken across time periods due to limited resources and the assumption that these approaches capture patterns and processes occurring over decadal and longer temporal scales. However, this may leave important fine-scale temporal variation in genetic composition undetected, particularly for metapopulations in which dynamic populations are expected. We investigated temporal patterns of population genetic diversity, effective population size, and differentiation across three sample periods for a dryland amphibian metapopulation. We sampled nine distinct Arizona treefrog ( Hyla (Dryophytes) wrightorum ) breeding ponds in 2014, 2018/2019, and 2021 and genotyped 17 microsatellite loci to quantify spatial and temporal population genetic dynamics. Genetic diversity within and between populations varied significantly among years. Most notably, we identified a concerning decline in allelic richness across populations, with an average − 26.11% difference between a population’s first and last sample period. Effective population sizes were generally small (N e < 100) and variable within and among populations over time, with many populations falling below common conservation thresholds by the final sample period. Trends in global genetic diversity, as measured by heterozygosity, and population differentiation were relatively consistent across all sampling periods. Overall, we found that “snapshot” or single-time sampling approaches may miss temporal variability in genetic composition that has important conservation implications, including early warning signs of decline in genetic diversity.

Towards a genomic resolution of the Phengaris alcon species complex - Kay Lucek; Lucas Blattner; Camille Cornet; Yannick Chittaro; Andreas Erhardt; Andreas Jaun; Bernhard Jost; Nathalie Winiger; Hans-Peter Wymann; Goran Dušej (Conservation Genetics, 2024)
Taxonomic entities below the species level often pose difficulties for conservation practice, especially when they are ecologically distinct from the nominal species. Genomic tools provide the opportunity to study and potentially resolve such cryptic diversity. The Alcon blue butterfly Phengaris alcon species complex is such a cryptic example, comprising different ecotypes or even subspecies, one of them is the high elevation taxon P. rebeli from the European Alps. We sequenced a first reference genome for Phengaris alcon . Furthermore, we generated whole genome resequence data for individuals of three Swiss ecotypes, i.e., the low elevation P. alcon , the mid elevation and high elevation alpine P. rebeli and integrated genomic data from across Europe to study the relationship among these ecotypes. At a European scale, our results suggest that for the P. alcon complex, biogeography and the evolutionary context of diversification is more multifaceted than previously suggested, falling in the range of more recent ecological speciation. In Switzerland, the three ecotypes were genetically isolated with only limited current gene flow between them. Past gene flow, however, could have given rise to the mid elevation ecotype. Our findings emphasise that high elevation P. rebeli in the Alps should be treated as a distinct species. Our study highlights how the availability of reference genome assemblies allows to address so far open taxonomic questions in conservation research and that broadscale studies are needed to understand the biogeographic history of apparent diversification.

Genetic diversity and inbreeding in an endangered island-dwelling parrot population following repeated population bottlenecks - Daniel Gautschi; Robert Heinsohn; Luis Ortiz-Catedral; Dejan Stojanovic; Melinda Wilson; Ross Crates; Nicholas A. Macgregor; Penny Olsen; Linda Neaves (Conservation Genetics, 2024)
Genetic diversity and population structure can have important implications for the management of threatened species. This is particularly true for small, isolated populations that have experienced significant declines or population bottlenecks. The Norfolk Island green parrot Cyanoramphus cookii is an endangered species at risk of inbreeding and loss of genetic diversity due to its restricted range and the population bottlenecks experienced in recent decades. To assess the severity of inbreeding and loss of genetic diversity in the population we analyzed single nucleotide polymorphisms (SNPs) for 157 unique genetic samples collected from nestlings and randomly captured adult birds between 2015 and 2022. We also assessed the population for genetic structure, calculated sex ratios, and looked for evidence of past population bottlenecks. Our analysis revealed that 17.83% of individuals sampled were highly inbred ( F > 0.125), although expected heterozygosity ( H E ) did not significantly differ from observed heterozygosity ( H O ) and the average inbreeding coefficient was low. The estimated effective population size ( N e ) was 43.8 and we found no evidence of genetic structure. Demographic simulations provided support for scenarios including multiple population bottlenecks, when compared to those with a single population bottleneck or no past bottlenecks. We discuss the implications of our findings for the future management of the species including any potential attempt to establish an insurance population via translocation. Our study highlights the importance of considering population genetics when determining appropriate management actions for threatened species and the need to assess non-model species on an individual basis.

Using genomic data to estimate population structure of Gopher Tortoise (Gopherus polyphemus) populations in Southern Alabama - Alexander R. Krohn; Brian Folt; Joseph J. Apodaca; Craig Guyer; Jeffrey M. Goessling (Conservation Genetics, 2024)

Using recent genetic history to inform conservation options of two Lesser Caymans iguana (Cyclura nubila caymanensis) populations - Thea F. Rogers; Ewan H. Stenhouse; Hannah Wilson; Morgan Pendaries; Michael W. Bruford; Matthias Goetz; Pablo Orozco-terWengel (Conservation Genetics, 2024)
The Sister Islands rock iguana ( Cyclura nubila caymanensis ) is critically endangered and endemic to the Caribbean islands Little Cayman and Cayman Brac. The Cayman Brac population and indeed the entire species is under threat from habitat destruction, invasive species, and anthropogenic impacts on the island. We assessed the genetic diversity, estimated effective population sizes, and tested for differentiation of populations between these two islands to inform potential future translocation should this be needed for the Cayman Brac population. Two mitochondrial DNA markers (cytochrome b and NADH subunit 4) and seven DNA microsatellite markers were used to assess the genetic diversity, genetic structure, demographic history, and effective population size of the two iguana populations. Mitochondrial DNA showed no genetic differentiation between populations; however, we found little to moderate divergence with microsatellites. We compared multiple demographic scenarios and revealed that ongoing gene flow is likely. The demographic history implied a significant genetic bottleneck around 10,000 years ago, coinciding with the sea level rise at the close of the last glacial period, and the start of the Holocene. Estimates of current effective population sizes indicate a small-scale number of breeders on each island of similar magnitude to the census mature population size (between 100 and 800 individuals). The relatively low differentiation between populations supports the possible development of active genetic management plans to manage the declining populations of the Sister Islands rock iguana.

Cross ocean-basin population genetic dynamics in a pelagic top predator of high conservation concern, the oceanic whitetip shark, Carcharhinus longimanus - Cassandra L. Ruck; Mahmood S. Shivji; Rima W. Jabado; Andrea M. Bernard (Conservation Genetics, 2024)

Integrating genomics into the genetic management of the endangered mountain yellow-legged frog - Cynthia C. Steiner; Leah Jacobs; Emma Choi; Jamie Ivy; Aryn Wilder; Natalie E. Calatayud; Debra M. Shier (Conservation Genetics, 2024)

Population genomics of the ‘rediscovered’ threatened New Zealand storm petrel (Fregetta maoriana) support a single breeding colony - Anika N. Correll Trnka; Chris P. Gaskin; Matt J. Rayner; Brent Stephenson; Fiona Robertson; Bruce C. Robertson; Anna W. Santure (Conservation Genetics, 2024)

Clonal distribution and spatial genetic structure of the reef-building coral Galaxea fascicularis - Yuichi Nakajima; Patricia H. Wepfer; Satoshi Mitarai (Conservation Genetics, 2024)

Conservation genomics of an endangered floodplain dragonfly, Sympetrum pedemontanum elatum (Selys), in Japan - Wataru Higashikawa; Mayumi Yoshimura; Atsushi J. Nagano; Kaoru Maeto (Conservation Genetics, 2024)

Distinct spatial patterns of genetic structure and diversity in the butterfly Marbled White (Melanargia galathea) inhabiting fragmented grasslands - Evelyn Terzer; Max Schmid; Barbara Bauert; Daniela Weidmann-Csencsics; Stefan Birrer; Janine Bolliger; Sabine Brodbeck; Felix Gugerli (Conservation Genetics, 2024)
We adopted a landscape-scale approach to analyze the genetic patterns (diversity, structure, and differentiation) of the Marbled White ( Melanargia galathea ). This butterfly species is characteristic of semi-dry grasslands, which have substantially declined in Switzerland during past decades. We sampled individuals on a regular grid of the established Biodiversity Monitoring program of Switzerland over five consecutive years, obtaining 1639 genotyped individuals from 185 locations. Results showed that M. galathea populations cluster into five spatially aggregated clusters that largely coincide with the biogeographic regions of Switzerland. Genetic diversity (allelic richness) was higher in the South of the Alps, likely related to immigration dynamics that suggest recolonisation from the South after the last glaciation. Demographic history resulted in distinct isolation by distance (IBD) and by cumulative elevational difference (isolation by altitude, IBA) at large scale, while regional IBD and IBA were less pronounced. This pattern was likely induced by the barrier effect of the high mountains of the Alps impeding continuous northward migration after the last glacial maximum. A temporal analysis revealed that regional genetic diversity did not change strongly during the five sampling years. This result indicates that the genetic diversity pattern in M. galathea has not been noticeably affected by historical land-use change or that the sampling period of five years is too short to detect any changes. Our findings highlight the regionally, topography-induced distinct genetic clusters, relevant for consideration as conservation units and likely reflecting genetic structures similar to those found in other butterfly species of conservation concern.

Phylogeographic analysis points toward invasion of the Timanfaya National Park (Lanzarote; Canary Islands) by a translocated native plant (Rumex lunaria) - Mario A. González Carracedo; Mariano Hernández Ferrer; Raimundo Cabrera; María Bernardos; José A. Pérez Pérez (Conservation Genetics, 2024)
Rumex lunaria is an endemic shrub of the Canary Islands, which is colonizing the Timanfaya National Park (TNP) in Lanzarote. Whether the arrival of R. lunaria to Lanzarote has been natural or by human intervention is still a matter of debate. To address this question, 100 specimens of R. lunaria were collected from the seven main Canary Islands, and genetic analysis of four chloroplast DNA loci were performed, covering a total length of 4809 nucleotide positions. Multiple alignments revealed 49 nucleotide substitutions, which define 30 different haplotypes. Island-specific haplotypes were found in Tenerife, La Gomera, La Palma and Gran Canaria, with the greatest diversity found in the first island. Interestingly, the unique haplotype detected in El Hierro is shared with almost all plants from Lanzarote (95%), including all individuals sampled in the TNP. The most frequent haplotype present in Gran Canaria was detected in only one sample from Lanzarote (5%). These results were corroborated by a robust phylogenetic analysis, which supports the hypothesis of a common origin of R. lunaria populations from El Hierro and the vast majority of those from Lanzarote. In addition, this study rules out the genetic singularity of the R. lunaria specimens that are colonizing the TNP.

Revisiting conservation units for the endangered mountain yellow-legged frog species complex (Rana muscosa, Rana sierrae) using multiple genomic methods - Allison Q. Byrne; Andrew P. Rothstein; Lydia L. Smith; Hannah Kania; Roland A. Knapp; Daniel M. Boiano; Cheryl J. Briggs; Adam R. Backlin; Robert N. Fisher; Erica Bree Rosenblum (Conservation Genetics, 2024)
Insights from conservation genomics have dramatically improved recovery plans for numerous endangered species. However, most taxa have yet to benefit from the full application of genomic technologies. The mountain yellow-legged frog species complex, Rana muscosa and Rana sierrae, inhabits the Sierra Nevada mountains and Transverse/Peninsular Ranges of California and Nevada. Both species have declined precipitously throughout their historical distributions. Conservation management plans outline extensive ongoing recovery efforts but are still based on the genetic structure determined primarily using a single mitochondrial sequence. Our study used two different sequencing strategies – amplicon sequencing and exome capture – to refine our understanding of the population genetics of these imperiled amphibians. We used buccal swabs, museum tissue samples, and archived skin swabs to genotype frog populations across their range. Using the amplicon sequencing and exome capture datasets separately and combined, we document five major genetic clusters. Notably, we found evidence supporting previous species boundaries within Kings Canyon National Park with some exceptions at individual sites. Though we see evidence of genetic clustering, especially in the R. muscosa clade, we also found evidence of some admixture across cluster boundaries in the R. sierrae clade, suggesting a stepping-stone model of population structure. We also find that the southern R. muscosa cluster had large runs of homozygosity and the lowest overall heterozygosity of any of the clusters, consistent with previous reports of marked declines in this area. Overall, our results clarify management unit designations across the range of an endangered species and highlight the importance of sampling the entire range of a species, even when collecting genome-scale data.

Correction: Population structure and history of North Atlantic Blue whales (Balaenoptera musculus musculus) inferred from whole genome sequence analysis - Sushma Jossey; Oliver Haddrath; Livia Loureiro; Jason T. Weir; Burton K. Lim; Jacqueline Miller; Stephen W. Scherer; Anders Goksøyr; Roger Lille-Langøy; Kit M. Kovacs; Christian Lydersen; Heli Routti; et al. (Conservation Genetics, 2024)

Monitoring genome-wide diversity over contemporary time with new indicators applied to Arctic charr populations - Atal Saha; Sara Kurland; Verena E. Kutschera; David Díez-del-Molino; Diana Ekman; Nils Ryman; Linda Laikre (Conservation Genetics, 2024)
Genetic diversity is fundamental to the adaptive potential and survival of species. Although its importance has long been recognized in science, it has a history of neglect within policy, until now. The new Global Biodiversity Framework recently adopted by the Convention on Biological Diversity, states that genetic diversity must be maintained at levels assuring adaptive potential of populations, and includes metrics for systematic monitoring of genetic diversity in so called indicators. Similarly, indicators for genetic diversity are being developed at national levels. Here, we apply new indicators for Swedish national use to one of the northernmost salmonid fishes, the Arctic charr ( Salvelinus alpinus ). We sequence whole genomes to monitor genetic diversity over four decades in three landlocked populations inhabiting protected alpine lakes in central Sweden. We find levels of genetic diversity, inbreeding and load to differ among lakes but remain stable over time. Effective population sizes are generally small (< 500), suggesting a limited ability to maintain adaptive variability if genetic exchange with nearby populations became eliminated. We identify genomic regions potentially shaped by selection; SNPs exhibiting population divergence exceeding expectations under drift and a putative selective sweep acting within one lake to which the competitive brown trout ( Salmo trutta ) was introduced during the sampling period. Identified genes appear involved in immunity and salinity tolerance. Present results suggest that genetically vulnerable populations of Arctic charr have maintained neutral and putatively adaptive genetic diversity despite small effective sizes, attesting the importance of continued protection and assurance of gene flow among populations.

Population genetic structure of Morelet’s and American crocodiles in Belize: hybridization, connectivity and conservation - Clare J. Wilkie; Marisa Tellez; Gareth Jones; Martin J. Genner (Conservation Genetics, 2024)

Population structure and history of North Atlantic Blue whales (Balaenoptera musculus musculus) inferred from whole genome sequence analysis - Sushma Jossey; Oliver Haddrath; Livia Loureiro; Jason T. Weir; Burton K. Lim; Jacqueline Miller; Stephen W. Scherer; Anders Goksøyr; Roger Lille-Langøy; Kit M. Kovacs; Christian Lydersen; Heli Routti; et al. (Conservation Genetics, 2024)
Knowledge of genetic diversity and structure is essential for developing conservation strategies for endangered species. Blue whales were hunted to near extinction in the mid-twentieth century. Not-withstanding almost 380,000 animals killed globally, much remains unknown about their population structure and migration patterns. Herein, we use whole genome sequencing to elucidate the poorly understood population genetics of North Atlantic (NA) blue whales. We generated a de novo genome assembly for a NA blue whale to analyze 19 other whole genomic sequences and 31 complete mitochondrial genomes. Present-day and historical samples (earliest from 1876) from the Atlantic and Antarctic Oceans were included to understand the impact of whaling on the genetic diversity of this species. We found low but statistically significant population structuring and high genetic diversity. Demographic modeling using fastsimcoal2 rejected an absence of gene flow between eastern and western NA blue whales and suggested an asymmetric west to east gene flow. Introgression estimated using D-statistics between blue and fin whales ( Balaenoptera physalus ), was observed in all present-day samples. This gene flow was found to be unidirectional from fin whales to blue whales and accounts for ~ 3.5% of the NA blue whale’s genome. Our sequencing and population structure analyses provide a genomic baseline to inform ongoing conservation strategies for this iconic species.

What mandrills leave behind: using fecal samples to characterize the major histocompatibility complex in a threatened primate - Anna Weber; Jackie Lighten; Cock van Oosterhout; Amour Guibinga Mickala; Stephan Ntie; Patrick Mickala; David Lehmann; Katharine Abernethy; Nicola Anthony (Conservation Genetics, 2024)

Contemporary reproductive patterns of Snake River Oncorhynchus nerka in Pettit Lake - Kendra R. Eaton; Kurt A. Tardy; Rebecca M. Croy (Conservation Genetics, 2024)

Genome-wide analysis of the harbour porpoise (Phocoena phocoena) indicates isolation-by-distance across the North Atlantic and potential local adaptation in adjacent waters - Marijke Autenrieth; Katja Havenstein; Binia De Cahsan; Julia Canitz; Harald Benke; Anna Roos; Christophe Pampoulie; Guðjón Már Sigurðsson; Ursula Siebert; Morten Tange Olsen; Vincent Biard; Mads Peter Heide-Jørgensen; et al. (Conservation Genetics, 2024)
The harbour porpoise ( Phocoena phocoena ), a highly mobile cetacean species of the Northern Hemisphere, inhabits basins that vary broadly in salinity, temperature, and food availability; such variation can drive divergent adaptation among local populations. To shed light on range-wide population structure and local adaptation, we generated ddRAD sequencing data spanning the entire North Atlantic and the Baltic Sea, as well as the Black Sea as an outgroup, and mapped this data to the high-quality draft genome of the species. We identified 11,978 genome-wide SNPs from 150 individuals, which we used for population genetic inferences. Our results support genetic differentiation between North Atlantic and Baltic Sea populations, with Kattegat as a transition zone. Across the North Atlantic the population differentiation is subtle from west to east, congruent with an isolation-by-distance pattern, but indicates a separation of southern North Sea harbour porpoises. We identified genomic outlier regions, i.e., scaffold regions where SNPs with high F ST across North Atlantic populations co-occur. Together with the draft genome annotation, these regions could point towards candidate genes for differential local adaptation processes among populations. Furthermore, they enable the development of a SNP panel for routine population assignment which will be useful in a conservation and management context. We identified six outlier loci putatively under positive selection, based on the population structure inferred from the complete SNP set. Our study highlights the value of genome resources in conservation and management and provides a crucial additional resource for the study of harbour porpoise evolution and phylogeny.

Evolutionary history of the salt marsh harvest mouse mitogenome is concordant with ancient patterns of sea level rise - Cody M. Aylward; Laureen Barthman-Thompson; Douglas A. Kelt; Benjamin N. Sacks; Mark J. Statham (Conservation Genetics, 2024)
Coastal wetland ecosystems support unique biodiversity and are imminently threatened by climate change-driven sea level rise. However, the impact of climate change on their demographic and evolutionary histories is poorly understood. To improve our understanding, we examined how past climatic events have shaped the evolutionary history of the salt marsh harvest mouse ( Reithrodontomys raviventris ), an endangered species and a salt marsh habitat specialist, completely restricted to coastal wetlands in the San Francisco Estuary (SFE). We used whole mitochondrial genome sequences of 102 salt marsh harvest mice to characterize phylogeography and demographic history. Then, we predicted the ancient distribution of salt marsh habitat and examined correspondence between divergence, demographic history, and changes in ancient marsh habitat caused by sea level rise. A Bayesian Skyline Plot revealed demographic expansions during periods of sea level rise, particularly during the formation of the modern SFE (~ 10 kya), and rapid decline consistent with recent anthropogenic landscape change. Bayesian estimates of divergence time were consistent with subspecies divergence ~ 10 kya, and subpopulation divergence ~ 5 kya, consistent with multiple episodes of vicariance caused by Holocene sea level rise. Spatial Analysis of Molecular Variance and Φ ST revealed a mismatch between the morphological and molecular subspecies assignment of two populations. Our study implicates sea level rise as a force of demographic change and evolutionary divergence in coastal marsh ecosystems. Our study also aids conservation of an endangered species by clarifying genetic subspecies boundaries and highlighting the unique nature of isolated populations that are increasingly threatened by modern sea level rise.

Changes in the spatio-temporal genetic structure of Baltic sea trout (Salmo trutta L.) over two decades: direct and indirect effects of stocking - Oksana Burimski; Anti Vasemägi; Riho Gross (Conservation Genetics, 2024)
Several countries have implemented stocking programmes to enhance abundance and fish production by releases of hatchery-reared fish. However, due to fluctuations in population size, stocking history, and potential indirect effects of straying of hatchery-reared fish, it is often difficult to predict how these factors will affect genetic diversity and differentiation patterns among wild populations. This study characterized the population genetic structure and temporal variability of four Estonian sea trout populations by evaluating the degrees of direct and indirect genetic impacts of stocking over two decades using 14 microsatellite loci. Our results demonstrate considerable temporal change combined with weak genetic structuring among studied sea trout populations. We found a reduction of the overall level of genetic differentiation combined with the tendency for increased genetic diversity, and an effective number of breeders ( N b ) over the study period. Furthermore, we found that immigration rates ( m ) from hatchery stocks were highest in the population subjected to direct stocking and in non-stocked populations that were located geographically closer to the stocked rivers. This work suggests that hatchery releases have influenced the genetic diversity and structuring of studied sea trout populations. However, the impact of hatchery releases on the adaptive variation and fitness-related traits in wild trout populations remains to be revealed by more informative genetic markers. This study illustrates the dynamic nature of the population genetic structure of sea trout and the value of long-term genetic monitoring for management and conservation.

A comprehensive strategy for the conservation of forest tree genetic diversity: an example with the protected Pinus nigra subsp. salzmannii (Dunal) Franco in France - C. Scotti-Saintagne; A. de Sousa Rodrigues; A. Roig; B. Fady (Conservation Genetics, 2024)

Combining genomic and field analyses to reveal migratory status in a burrowing owl population - Lynne A. Trulio; Debra A. Chromczak; Philip G. Higgins; Sandra Menzel; Christen M. Bossu; Kristen Ruegg (Conservation Genetics, 2024)

Conservation implications of diverse demographic histories: the case study of green peafowl (Pavo muticus, Linnaeus 1766) - Ajinkya Bharatraj Patil; Nagarjun Vijay (Conservation Genetics, 2024)

Rivers have shaped the phylogeography of a narrowly distributed cycad lineage in Southwest China - Li-Xin Wu; Yi-Qing Wang; Si-Yue Xiao; Yue-Hua Wang; Jian Liu; Xun Gong; Xiu-Yan Feng (Conservation Genetics, 2024)

Conservation genomics of Dioon holmgrenii (Zamiaceae) reveals a history of range expansion, fragmentation, and isolation of populations - Brian L. Dorsey; Silva H. Salas-Morales; Timothy J. Gregory (Conservation Genetics, 2024)
Many Cycad species may not survive the current extinction crisis, despite belonging to the oldest living seed plant lineage. Conservation of endangered and threatened species will require a combination of in situ and ex situ programs, both of which will benefit from better knowledge of species’ population genetic structure, as will assessments of threatened status. Here we develop a cost-effective method of obtaining population-level genomic data from across the range of the Mexican cycad, Dioon holmgreni , and use these data to characterize the genetic structure and diversity of the species. We also reconstruct aspects of the demographic history of the species and evaluate the taxonomic cohesion of populations across the range using genomic and morphological data. We find that D. holmgrenii harbors moderate genetic diversity across genetically and geographically isolated populations that each possess a substantial percentage of private alleles. We further find that the history of this species likely includes a widespread range expansion followed by fragmentation due to population contraction. These results argue for conservation of all populations and their unique alleles but also suggest an unexpected ability of this species to maintain genetic diversity despite dramatic reductions in population size.

Comparative population genetics of habitat-forming octocorals in two marine protected areas: eco-evolutionary and management implications - Mathilde Horaud; Rosana Arizmendi-Meija; Elisabet Nebot-Colomer; Paula López-Sendino; Agostinho Antunes; Simon Dellicour; Frédérique Viard; Raphael Leblois; Cristina Linares; Joaquim Garrabou; Jean-Baptiste Ledoux (Conservation Genetics, 2024)
Current efforts to halt the decline of biodiversity are based primarily on protecting species richness. This narrow focus overlooks key components of biological diversity, particularly the infra-species genetic diversity, which is critical to consider with respect to genetic adaptation in changing environments. While comparative population genetics is recognized as a relevant approach to improve biodiversity management, it is still barely considered in practice. Here, a comparative population genetics study was conducted on two key habitat-forming octocoral species, Corallium rubrum and Paramuricea clavata , to contribute to management of two Marine Protected Areas (MPAs) in the northwestern Mediterranean. Contrasting patterns of genetic diversity and structure were observed in the two species, although they share many common biological features and live in similar habitats. Differential genetic drift effects induced by species-specific reproductive strategies and demographic histories most likely explain these differences. The translation of our results into management strategies supports the definition of four management units. We identified a coldspot of genetic diversity, with genetically isolated populations, and a hotspot of genetic diversity that has a central role in the system’s connectivity. Interestingly, they corresponded to the most recent and the oldest protected areas, respectively. This case study shows how moving from a “species pattern” perspective to an “eco-evolutionary processes” perspective can help assess and contribute to the effectiveness of biodiversity management plans.

Introgressive hybridization levels of Tilapiine species in Lake Victoria basin, Kenya inferred from microsatellite and mitochondrial DNA genotyping based on next-generation sequencing - Gerald Kwikiriza; Thapasya Vijayan; Papius Dias Tibihika; Manuel Curto; Gerold Winkler; Juliet Kigongo Nattabi; John Kariuki; Harald Meimberg (Conservation Genetics, 2024)
Despite their high abundance and species richness, tilapiines have been compromised by various factors especially overfishing, climate change, and uncontrolled fish transfers and introductions. Fish introductions have negatively impacted native tilapiine populations through competition, predation, hybridization, and introgression compromising their genetic integrity. The hybridization levels of different tilapiines in the Lake Victoria basin remain relatively understudied. The study utilized nuclear microsatellite and mitochondrial DNA (mtDNA) genetic markers to investigate hybridization signals and compare the genetic diversity of different tilapiines in Lake Victoria, Kenya, using next-generation sequencing. Low levels of hybridization from Oreochromis niloticus into other Oreochromis species were detected by Bayesian clustering analysis and principal coordinate analysis (PCoA). The results contribute to the need for conservation measures for these fish species.

Exploring genetic diversity and population structure of the Little Tern (Sternula albifrons) in Taiwan based on mtDNA and ddRAD sequencing data - Mei Shuet Kong; Chung-Hang Hung; Ling-Lan Hsu; Hsiao-Wei Yuan; Wei-Jen Chen (Conservation Genetics, 2024)

Conservation genomics of the threatened Trispot Darter (Etheostoma trisella) - Kayla M. Fast; Brook L. Fluker; Bernard R. Kuhajda; Patrick E. O’Neil; Stuart W. McGregor; Matthew S. Piteo; Michael W. Sandel (Conservation Genetics, 2024)

Exploring cross-species genetic diversity: unveiling new insights in Megalobrama through whole genome-wide simple sequence repeats - Kai Liu; Nan Xie; Yuxi Wang (Conservation Genetics, 2024)

Connectivity patterns of bottlenose dolphins (Tursiops truncatus) in the north-east Mediterranean: implications for local conservation - Stefania Gaspari; Charlotte Dooley; Kypher Shreves; Cátia S. E. Silva; Natasha Chapman; Tilen Genov; Joan Gonzalvo; Draško Holcer; Andre E. Moura (Conservation Genetics, 2024)

Genomic analysis of geographical structure and diversity in the capercaillie (Tetrao urogallus) - Lídia Escoda; Josep Piqué; Ladislav Paule; Kévin Foulché; Emmanuel Menoni; Jose Castresana (Conservation Genetics, 2024)
The capercaillie is widespread throughout the boreal forests of northern Eurasia, but faces serious conservation challenges in the southernmost mountain ranges, where the populations are fragmented and some are critically endangered. To develop effective conservation strategies for these populations, it is essential to have information on both their genetic diversity and the genetic structure of the species. In this work, we used a reduced representation (ddRAD) genomic sequencing technique to analyze the genetic structure of the capercaillie across its European range and to assess the inbreeding levels in some of the most threatened populations. Our population structure analysis suggested the existence of two evolutionarily significant units, one formed by the two populations from the Iberian Peninsula and the other by the populations from the rest of Europe. Genetic diversity showed a significant decrease in the Iberian populations with respect to the other European populations. An isolation-with-migration model supported these results and allowed us to estimate the parameters of the population tree. The inbreeding coefficients estimated for the Iberian capercaillies showed relatively low levels in the Pyrenees. However, some individuals with very high inbreeding values were detected in the Cantabrian Mountains, suggesting that some of its subpopulations are substantially isolated. The population structure results and the genomic monitoring method we used to assess inbreeding levels may be crucial for the conservation and recovery of the most endangered capercaillie populations.

Genetic diversity within late-summer run and half-pounder steelhead (Oncorhynchus mykiss) in the Rogue River, Oregon - David I. Dayan; Steve Mazur; Laura J. Green; Andrew J. Wells; Marc A. Johnson; Daniel J. Van Dyke; Peter A. Samarin; Ryan D. Battleson; Kathleen G. O’Malley (Conservation Genetics, 2024)

In situ conservation of Helosciadium nodiflorum: a crop wild relative of celery in Germany - Inga Mewis; Nadine Bernhardt; Maria Bönisch; Jonathan Brassac; Annette Naumann; Matthias Zander; Uta Schirmak; Marion Nachtigall; Christian Ulrichs (Conservation Genetics, 2024)
Crop wild relatives (CWR) represent valuable sources of traits that can enhance the abiotic and biotic stress tolerance of crops. Due to climate change and expansion of land use, they may suffer from population decline, which increases the risk of losing these resources. The in situ conservation of CWR is receiving growing attention to preserve their intraspecific diversity. In contrast to the safeguarding of seeds ex situ, the preservation of taxa in their natural habitat facilitates the development of new adaptations to changing environmental conditions. However, studies aiming at the establishment of their in situ conservation are rare. Therefore, we identified and genotyped Helosciadium nodiflorum occurrences in Germany. Helosciadium nodiflorum is an endangered CWR of cultivated celery ( Apium graveolens ). For 20 occurrences the number of individuals, the number of sexually reproducing individuals, and potential threats were recorded. Genetic differences were examined using 17 newly developed simple sequence repeats (SSR). Population genetic analyses, like the inference of the compositional genetic differentiation, of population structure, and a Discriminant Analysis of Principal Components were conducted. The analyses revealed that most occurrences were genetically distinct. Geographically closely located populations are often also genetically more similar. Several populations revealed a composite genome indicative of hybridizations between distinct populations. Populations that experienced fixation were also identified. Based on the genetic diversity, the location in different ecogeographic units, and the support of local stakeholders, we recommend the establishment of 15 genetic reserves for H. nodiflorum in Germany.

Asymmetrical gene flow between coastal and inland dunes in a threatened digger wasp - Femke Batsleer; Matthieu Gallin; Moyra Delafonteyne; Daan Dekeukeleire; Filiep T’Jollyn; Pieter Vantieghem; An Vanden Broeck; Joachim Mergeay; Dirk Maes; Dries Bonte (Conservation Genetics, 2024)

Do river basins shape genetic structure in the Kempholey night frog, India? - Hebbar Priti; Anand Anisha; Thunga Pavankumar; Kotambylu Vasudeva Gururaja; Neelavar Anantharam Aravind; Gudasalamani Ravikanth (Conservation Genetics, 2024)

Inconsistent estimates of hybridization frequency in newts revealed by SNPs and microsatellites - Aurélien Miralles; Jean Secondi; Maciej Pabijan; Wiesław Babik; Christophe Lemaire; Pierre-André Crochet (Conservation Genetics, 2024)
Hybridization between the European smooth and palmate newts has recurrently been mentioned in the literature. The only two studies that attempted to quantify the frequency of hybridization and gene admixture between these two species came to strikingly opposite conclusions. According to Arntzen et al. (1998, 42 allozymes), hybrids are rare in nature and introgression negligible, while according to Johanet et al. (2011, 6 microsatellites), introgressive hybridization is significant and widespread across the shared distribution range. To clarify this question, we implemented high-throughput SNP genotyping with diagnostic biallelic SNPs on 965 specimens sampled across Europe. Our results are in line with Arntzen et al., since only two F1 hybrids were identified in two distinct French localities, and no further hybrid generations or backcrosses. Moreover, reanalysis of 78 of the samples previously studied by Johanet et al. (2011) using our SNPs panel could not reproduce their results, suggesting that microsatellite-based inference overestimated the hybridization frequency between these two species. Since we did not detect methodological issues with the analyses of Johanet et al., our results suggest that SNP approaches outperform microsatellite-based assessments of hybridization frequency, and that conclusions previously published on this topic with a small number of microsatellite loci should be taken with caution, and ideally be repeated with an increased genomic coverage.

Sibship analysis revealed the reproductive strategy and current population status of the silver carp (Hypophthalmichthys molitrix) from the middle and lower reaches of the Yangtze River, China - Ping Yang; Cheng Chen; Dan Yu; Minzheng Li; Huanzhang Liu (Conservation Genetics, 2024)

Genomic data reveal shift in geographic source of an illegally traded songbird - Meng Yue Wu; Han Wei Chong; Yen Yi Tan; Bryan T. M. Lim; Anna M.S. Wong; Rachel Rui Ying Oh; Jessica G.H. Lee; Elize Y.X. Ng; Frank E. Rheindt (Conservation Genetics, 2024)

Conservation implications for the world’s most widely distributed cavefish species complex based on population genomics (Typhlichthys, Percopsiformes) - Pamela B. Hart; Matthew L. Niemiller; Jonathan W. Armbruster; Prosanta Chakrabarty (Conservation Genetics, 2024)

Evaluating possible anthropogenic impacts on gene flow and loss of genetic diversity in endangered Madla Cave Meshweaver spiders (Hahniidae, Cicurina madla) - Guilherme H. F. Azevedo; Jennifer Blair; Marshal Hedin (Conservation Genetics, 2024)

Population genetic structure of a timberline oak (Quercus semecarpifolia Sm.) of western Himalayas and conservation implications - Harish S. Ginwal; Anita Rawat; Chander Shekhar; Maneesh S. Bhandari; Haripriya Kavidayal; Rajeev Shankhwar; Abhishek Yadav; Rama Kant; Santan Barthwal; Rajendra K. Meena (Conservation Genetics, 2024)

Pollen dispersal and mating patterns determine resilience for a large-yet-fragmented population of Cariniana estrellensis - Thaisa Y. K. Kubota; John E. Hallsworth; Alexandre M. da Silva; Mario L. T. Moraes; Jose Cambuim; Cláudia W. Corseuil; Alexandre M. Sebbenn (Conservation Genetics, 2024)

Genetic analysis of federally endangered Cape Sable seaside sparrow subpopulations in the Greater Everglades, USA - Caitlin E. Beaver; Thomas Virzi; Margaret E. Hunter (Conservation Genetics, 2024)
The federally endangered Cape Sable seaside sparrow ( Ammospiza maritima mirabilis ) is endemic to the Greater Everglades ecosystem in southern Florida, inhabiting fragmented marl prairies in six individual subpopulations. The subspecies is threatened by loss of breeding habitat from fire and water management. Genetic information is severely limited for the subspecies but could help inform decisions regarding subpopulation protections and potential translocations for genetic rescue. To provide genetic data and inform management efforts, feather samples were collected across five subpopulations (designated A–E) and protocols were tested to optimize DNA extraction yields. We assessed four mitochondrial DNA markers (N = 36–69) and 12 nuclear microsatellite loci (N = 55) in 108 sparrows. Mitochondrial DNA sequences revealed low haplotype diversity, with NADH dehydrogenase-2 haplotypes matching to most other extant subspecies and to the Atlantic coast subspecies. Nuclear diversity was low compared to other subspecies, but similar across subpopulations. Samples grouped as one population when analyzed by Principal Component Analysis, Bayesian modelling and genetic distance metrics. Limited genetic emigration was detected from one putative migrant. Relatedness was significantly different for sparrows in the most geographically distant subpopulation (A), likely reflecting high self-recruitment and natal site fidelity ( P = 0.003). The low to moderate effective population size (N E = 202.4; N E :N C = 0.06) and generation time estimates indicated that unique genetic variation could be lost quickly during stochastic events. The sample sizes were limited, which reduced the power to comprehensively address recent population size reductions and any subsequent loss of genetic diversity.

Neutral genetic diversity follows a latitudinal gradient in the endangered plant Arnica montana L.: a range-wide study - Loris Capria; Sascha Liepelt; Klaus Eimert; Ilona Leyer; Eva Mosner (Conservation Genetics, 2024)
Arnica montana is a clonal, self-incompatible herb of economic and intrinsic ecological value which is declining in large parts of its range. With the employment of microsatellite markers, we characterized the population structure and distribution of genetic diversity of 40 populations of A. montana sampled throughout Europe. We detected a clear geographical pattern of isolation and strong population structure, indicating limited gene flow. We also observed a negative latitudinal gradient in genetic diversity. Such patterns can be explained by paleo-historical colonization routes following the last glacial maximum, with regions characterized by higher genetic diversity corresponding to former glacial refugia. We recommend the implementation of conservation measures such as assisted gene flow in the populations characterized by low genetic diversity under consideration of the observed population structure. For the populations where high levels of genetic diversity are still retained, we recommend the maintenance of suitable habitat conditions. Our study emphasises the importance of conducting large-scale population genetic studies that consider postglacial recolonization history when planning active conservation measures such as assisted gene flow.

Assessment of population structure and genetic diversity of wild and captive populations of Ammotragus lervia provide insights for conservation management - Cristian Pizzigalli; Teresa Luísa Silva; Teresa Abáigar; Giorgio Bertorelle; Jorge Cassinello; José Carlos Brito (Conservation Genetics, 2024)
The aoudad ( Ammotragus lervia ) is a Vulnerable bovid endemic of North Africa. Although legally protected in almost every country of its native distribution, the aoudad continues to be hunted for meat and trophy in both North Africa and the countries where it has been introduced. The species was subject to past translocations planned irrespectively of the genetic diversity and local adaptations of source and receiving populations, and no management or conservation units have ever been designed. We aim to provide here important insights on the taxonomy of the aoudad subspecies and the genetic diversity of most of its wild and captive populations. We collected 127 invasive and non-invasive samples from five of the six subspecies of aoudad recognized to date. We could successfully retrieve genetic data for 74 samples. Of those, 36 provided both nuclear (11 microsatellites) and mitochondrial ( Cyt-b ) data, 31 just nuclear data, and six just mitochondrial data. We implement Bayesian approaches to infer the population structure and phylogenetic relationships between the different populations/subspecies and backtrack the maternal lineages of introduced individuals in European populations. Our results support the presence of four genetically different wild populations, corresponding to three distinct mitochondrial lineages plus a fourth group restricted to Egypt identified by the nuclear markers. We also provide genetic evidence on the affiliation of some introduced European populations with respect to the native ones. The genetic diversity instead of variation within all wild populations was low. This might be a consequence of small effective population size and/or high inbreeding degree, probably related to hunting, decline in habitat availability and quality (i.e. overgrazing, and frequent drought), and high inbreeding degree. Our results provide important information for the aoudad conservation, including reintroductions and reinforcement actions of wild populations, and the exchange of individuals among captive stocks.

Towards a standardised set of data analyses for long-term genetic monitoring of grouse using non-invasive sampling: a case study on western capercaillie - Teresa Zeni; Marlene Haider; Stephanie Vallant; Reinhard Lentner; Florian M. Steiner; Birgit C. Schlick-Steiner (Conservation Genetics, 2024)
Genetic monitoring has become a popular instrument in the conservation of endangered species, allowing to estimate size and genetic structure of wild populations. Long-term monitoring projects are essential to recognize demographic changes and impact of human activities. Since 2011, an extensive monitoring project on the population size and trends, as well as spatial distribution and survival rates, of two grouse species including the western capercaillie, Tetrao urogallus , has been conducted in Tyrol, in the eastern part of the European Alps, where T. urogallus males are huntable under specific regulations. In this case study, we aimed to compile a set of analyses to be employed in evaluating data from dropping and feather samples for conservation studies. Using eleven microsatellite and two sex markers, we genotyped 251 faeces and feathers of T. urogallus collected in East Tyrol in spring 2019. We analysed population structure and mobility patterns, including sex differences in genetic diversity and mobility. The relationship between habitat parameters and genetic diversity was investigated using multiple linear regressions. We showed that the investigated T. urogallus population is well mixed and likely well connected to neighbouring populations. We also found sex-specific mobility patterns that support female-biased dispersal. As the last step, we demonstrated the general feasibility of a modelling approach using habitat parameters. With this pilot study, further analysis of data is possible for the whole monitoring project, giving a better insight in the grouse populations in Tyrol.

The impact of habitat loss and population fragmentation on genomic erosion - Alessandro V. Pinto; Bengt Hansson; Ioannis Patramanis; Hernán E. Morales; Cock van Oosterhout (Conservation Genetics, 2024)
Habitat loss and population fragmentation pose severe threats to biodiversity and the survival of many species. Population isolation and the decline in effective population size lead to increased genetic drift and inbreeding. In turn, this reduces neutral diversity, and it also affects the genetic load of deleterious mutations. Here, we analyse the effect of such genomic erosion by designing a spatially explicit, individual based model in SLiM, simulating the effects of the recorded habitat loss in Mauritius over the past ~ 250 years. We show that the loss of neutral diversity (genome-wide heterozygosity) was barely noticeable during the first 100 years of habitat loss. Changes to the genetic load took even more time to register, and they only became apparent circa 200 years after the start of habitat decline. Although a considerable number of deleterious mutations were lost by drift, others increased in frequency. The masked load was thus converted into a realised load, which compromised individual fitness and population viability after much of the native habitat had been lost. Importantly, genomic erosion continued after the metapopulation had stabilised at low numbers. Our study shows that historic habitat loss can pose a sustained threat to populations also in future generations, even without further habitat loss. The UN’s Decade on Ecosystem Restoration needs to lead to transformative change to save species from future extinction, and this requires the urgent restoration of natural habitats.

Genetic diversity, structure, and demographic histories of unique and ancient wolf lineages in India - Yellapu Srinivas; Yadvendradev Jhala (Conservation Genetics, 2024)

Functional connectivity in northern swamp deer (Rucervus duvaucelii duvaucelii) population across a fragmented, human-dominated landscape along Gangetic Plains of north India: implications for conservation in non-protected areas - Shrutarshi Paul; Sohini Saha; Parag Nigam; Garima Pandey; Bilal Habib; Dhananjai Mohan; Bivash Pandav; Samrat Mondol (Conservation Genetics, 2024)

Inbreeding depression in Sable Island feral horses is mediated by intrinsic and extrinsic variables - Julie Colpitts; Philip Dunstan McLoughlin; Jocelyn Poissant (Conservation Genetics, 2024)

Michael (Mike) William Bruford (6th June 1963–13th April 2023) - Benoit Goossens; Pablo Orozco-terWengel (Conservation Genetics, 2023)

Correction: Genetic structure and north-south decrease of genetic diversity in the Patagonian maqui berry (Aristotelia chilensis [Molina] Stuntz): implications for its conservation and use - Matías Cona; Alexandra Chávez; Pedro León-Lobos; Juan Carlos Marín; Patricio Hinrichsen (Conservation Genetics, 2023)

Evolutionary divergence and adaptive capacity in morphologically distinct song sparrow subspecies - Chloe S. Mikles; Peter Arcese; Irby J. Lovette; Stepfanie M. Aguillon; Yvonne L. Chan; Phred M. Benham; Katherine Carbeck; Jennifer Walsh (Conservation Genetics, 2023)

Mitochondrial DNA diversity of the eastern black rhinoceros (Diceros bicornis michaeli) in Tanzania: implications for future conservation - Ronald V. K. Mellya; J. Grant C. Hopcraft; Ernest M. Eblate; Linus Kariuki; Moses Otiende; Idrissa S. Chuma; Emmanuel S. Macha; Dickson Wambura; Elizabeth Kilbride; Barbara K. Mable (Conservation Genetics, 2023)
There has been a drastic decline in the number of eastern black rhinoceros ( Diceros bicornis michaeli ) across Africa, leaving individuals restricted to small, isolated populations that are vulnerable to extinction. Focusing on highly threatened populations in Tanzania, this study investigated the genetic impacts of past management interventions on mitochondrial control region diversity in extant subpopulations, assessed whether there has been evidence of dispersal of females between populations based on haplotype sharing, and related current haplotype diversity to historical patterns. Across extant subpopulations in Tanzania, six maternal haplotypes were identified, with an overall haplotype diversity of h = 0.72 but lower overall nucleotide diversity within populations (π = 0.017) compared to historical populations (π = 0.021). Translocated populations did not share haplotypes with native populations, even though all haplotypes from translocated individuals had been found among historic samples from Kenya. This suggests that translocations have been successful at restoring previous diversity to the region but that the current Intensive Protection Zone (IPZ) management practices have restricted the movement of females between subpopulations. Extant haplotypes were distributed among three East African haplogroups described in previous studies, suggesting that multiple lineages have been preserved despite the loss of historical haplotypes. Our recommendation is to enhance the utilisation of previous translocations by enabling the natural movements of individuals between subpopulations. Such a change in management strategy could be less costly both economically and in terms of animal welfare than the alternative of using genetic data to target specific animals for translocation in order to supplement diversity.

Characterising a genetic stronghold amidst pervasive admixture: Morelet’s crocodiles (Crocodylus moreletii) in central Yucatan - José António L. Barão-Nóbrega; Mauricio González-Jáuregui; Sergio Padilla-Paz; Kathryn H. Maher; Arely Martínez-Arce; José Rogelio Cedeño-Vázquez; Robert Jehle (Conservation Genetics, 2023)
When backcrosses are fertile, interbreeding between endangered taxa can lead to the admixture of gene pools under threat. One such case pertains to the Mesoamerican crocodile Crocodylus moreletii , a species which shows strong signatures of both recent hybridisation and historic intogression with the American crocodile C. acutus across large parts of its range . In the present paper, we use RAD-seq derived SNPs (4980 nuclear and seven mtDNA loci) to demonstrate that C. moreletii populations inhabiting the region of Calakmul in central Yucatan (Mexico) are rather unaffected by hybridization, despite being surrounded by coastal areas where pervasive admixture has previously been documented. All (based on fastSTRUCTURE) and 96% (based on NGSadmix) of 84 genotyped individuals from 18 sampled waterbodies (locally termed aguadas) were free from nuclear introgression of C . acutus DNA at at threshold of 0.95. Seven individuals (8%) possessed a C. acutus mtDNA haplotype, five of which were derived from two adjacent, rather peripheral aguadas. Spatial inferences based on a DAPC and fineRADstructure further showed that the region of Calakmul is inhabited by three genetic clusters spanning across a set of distinct aguadas each. Taken together, our findings reveal that central Yucatan contains the currently largest documented stronghold of C. moreletii populations only marginally affected by introgression, which has major implications for the conservation management of this important flagship species.

Genetic insights into pepper-bark tree (Warburgia salutaris) reproduction in South Africa - K. L. Glennon; J. J. Le Roux; D. I. Thompson (Conservation Genetics, 2023)
Genetic diversity in over-exploited and threatened species has important, but often neglected, implications for conservation. In South Africa, the bark of the regionally endangered pepper-bark tree, Warburgia salutaris , is extensively harvested for subsistence medicine. We developed 11 polymorphic microsatellite markers to examine the genetic diversity and structure among 227 W. salutaris individuals sampled from across much of its range in South Africa’s Kruger National Park (KNP) and 31 trees growing in local nurseries. We also tested the cross-amplification success of these markers in two closely related species, Warburgia elongata (IUCN listed as Endangered) and W. stuhlmannii (IUCN listed as Vulnerable). Contrary to our expectations, we found evidence of clonality and for high genetic diversity in all wild KNP sub-populations of W. salutaris . We identified between 114 and 149 unique multi-locus genotypes in the 258 individuals included in our analyses. Bayesian assignment tests identified three distinct genetic clusters that are represented by the sampled KNP sub-population of W. salutaris , with minimal geographic structure and some admixture. Three genetic clusters were also identified among all sampled individuals, i.e., KNP and nursery trees. Nursery W. salutaris germplasm comprised unique genotypes with similar levels of observed heterozygosity to the wild population. High levels of clonality and reported self-incompatibility, along with short distance pollination, likely explain the lack of recent sexual recruitment (i.e., reduced fruit set and lack of seedlings) in the wild population. These findings will be useful to identify sub-populations where genets may be sampled to maximize genetic diversity within subpopulations for restoration throughout KNP.

Optimizing targeted gene flow to maximize local genetic diversity: when and how to act under various scenarios of environmental change - Adam S. Smart; Ben L. Phillips (Conservation Genetics, 2023)
Targeted gene flow is an emerging conservation approach which involves introducing a cohort of individuals with particular traits to locations where they can produce a conservation benefit. This technique is being proposed to adapt recipient populations to a known threat, but questions remain surrounding how best to maximize conservation outcomes during periods of continuous directional environmental change. Here we introduce a new management objective—to keep the recipient population extant and with maximum diversity of local alleles—and we explore how varying the timing and size of an introduction can maximise this objective. Our results reveal a trade-off between keeping a population extant and maintaining a high level of genetic diversity, but management levers can often optimize this so that nearly 100% of the allelic diversity is preserved. These optimum outcomes sets are highly sensitive to the predicted rate of environmental shift, as well as the level of outbreeding depression in the system.

Genomics of founders for conservation breeding: the Jasper caribou case - Maria Cavedon; Lalenia Neufeld; Laura Finnegan; Dave Hervieux; Anita Michalak; Agnes Pelletier; Jean Polfus; Helen Schwantje; Geoff Skinner; Robin Steenweg; Caeley Thacker; Jocelyn Poissant; et al. (Conservation Genetics, 2023)
Conservation breeding programs are increasingly used as recovery actions for wild animals; bringing founders into captivity to rear captive populations for future reintroduction into the wild. The International Union for the Conservation of Nature recommends that founders should come from genetically close populations and should have sufficient genetic diversity to avoid mating among relatives. Genomic data are highly informative for evaluating founders due to their high resolution and ability to capture adaptive divergence, yet, their application in that context remains limited. Woodland caribou are federally listed as a Species at Risk in Canada, with several populations facing extirpation, such as those in the Rocky Mountains of Alberta and British Columbia (BC). To prevent local extirpation, Jasper National Park (JNP) is proposing a conservation breeding program. We examined single nucleotide polymorphisms for 144 caribou from 11 populations encompassing a 200,000 2 km area surrounding JNP to provide information useful for identifying appropriate founders for this program. We found that this area likely hosts a caribou metapopulation historically characterized by high levels of gene flow, which indicates that multiple sources of founders would be appropriate for initiating a breeding program. However, population structure and adaptive divergence analyses indicate that JNP caribou are closest to populations in the BC Columbia range, which also have suitable genetic diversity for conservation breeding. We suggest that collaboration among jurisdictions would be beneficial to implement the program to promote recovery of JNP caribou and possibly other caribou populations in the surrounding area, which is strategically at the periphery of the distribution of this endangered species.

The genetic diversity, phylogeography, and population structure of Pacific harbor seals reveal isolation at the southern end of their distribution - Eva María Fernández-Martín; Yolanda Schramm; Gisela Heckel; Alicia Abadía-Cardoso (Conservation Genetics, 2023)

Identification of conservation priority units in the Asian elephant, Elephas maximus - Kris Budd; Joe C. Gunn; Lauren L. Sullivan; Lori S. Eggert (Conservation Genetics, 2023)

The common ground in landscape effects on gene flow in two newt species in an agroecosystem - Karen Cox; Robbert Schepers; An Van Breusegem; Jeroen Speybroeck (Conservation Genetics, 2023)

Genetic diversity, gene flow, and source-sink dynamics of cougars in the Pacific Northwest - Claudia Wultsch; Katherine A. Zeller; Lindsay S. Welfelt; Richard A. Beausoleil (Conservation Genetics, 2023)

Pooled whole genome sequencing of the endangered Banff Springs Snail, Physella johnsoni, reveals genetic separation to P. gyrina and cryptic micro-geographical genetic structure - Brenna C.M. Stanford; Dwayne A.W. Lepitzki; Mark K. Taylor; Sean M. Rogers (Conservation Genetics, 2023)

Landscape genetics of the protected Spanish Moon Moth in core, buffer, and peripheral areas of the Ordesa y Monte Perdido National Park (Central Pyrenees, Spain) - Inés González-Castellano; Neus Marí-Mena; Gernot Segelbacher; Carlos Lopez-Vaamonde; Jorge González-López; Jaime Fagúndez; Marta Vila (Conservation Genetics, 2023)
Conservation managers need to know the degree of connectivity showed by the populations to be preserved, especially when protected areas and/or species are involved. One of the conservation projects carried out by the Ordesa y Monte Perdido National Park (Central Pyrenees, Spain) is the monitoring of the protected Spanish Moon Moth, Graellsia isabellae (Lepidoptera, Saturniidae), in several sites within the actual park, buffer zone, and peripheral area. Here we studied the genetic diversity, geographical structure, and connectivity of this iconic insect in those areas with the aim of producing evidence-based recommendations that might help the National Park staff in their decision-making. For this, we non-lethally sampled 402 adult moths from 17 sites and worked at two geographic scales: Western/Central Pyrenees and the area monitored by the staff of the National Park. The multilocus genotypes obtained for nine nuclear microsatellite markers allowed us to quantify genetic variation, investigate population structure, and calculate recent migration rates. Our results revealed a large-scale (ca. 125 km) west–east cline in allele frequencies that causes low overall genetic differentiation ( F ST = 0.038) and similar levels of diversity among sites. Habitat connectivity revealed as an important element determining dispersal for G. isabellae , given the patchy distribution of the host plant ( Pinus sylvestris ) in the study area. Gene flow within and outside the National Park was proved, with a particular site of the buffer zone (Bujaruelo) acting as a source of migrants to other localities within and outside the National Park. This finding underlines the importance of considering buffer zones to preserve genetic diversity within protected areas, and that safeguarding the connectedness of pine patches is key to the conservation of this iconic moth.

Genomic and morphological assessment of the status of Kuenzler’s hedgehog cactus (Echinocereus fendleri var. kuenzleri) - James B. Beck; Kevin M. Fehlberg; Shannon D. Fehlberg (Conservation Genetics, 2023)

Genetic diversity and origin of captive lion (Panthera leo) in South Africa: an assessment and comparison to wild populations - Susan M. Miller; Antoinette Kotze; Cindy K. Harper; Jacqueline M. Bishop; Vivienne L. Williams; Charné Rossouw; Johanita Schoeman; Marli de Bruyn; Desiré Lee Dalton; S. A. Jeanetta Selier (Conservation Genetics, 2023)
South Africa has a large captive lion ( Panthera leo ) sector, but detailed knowledge on the origin of individuals and any potential genetic value to conservation targets is lacking. In 2021, the South African government committed to closing the sector and have since appointed a Ministerial Lion Task Team (2022) to initiate this process. Some have suggested that captive lions could be integrated into wild populations as part of the process but information on the genetic origins and diversity of captive lions is critical if this is to be explored further. Both the Biodiversity Management Plan for lions in South Africa (2015) and a High-Level Ministerial report for the South African government (2021) have called for more information on the genetic composition of captive lions. To determine the probable origin of captive lions in South Africa we summarised existing survey responses from captive facilities (collected 2017–2018) and CITES permit data (issued 1991–2019). Survey data suggest that most lions were sourced from within the South African captive sector. However, many CITES permits were also issued for the import of lions from across Africa and beyond, indicating possible mixed origins within the sector. To evaluate genetic relationships between captive and wild lions in South Africa we standardised existing microsatellite marker data from three laboratories and analysed genotypes of captive lions from 31 properties. A comparison of captive and wild lion genotypes revealed that the genetic composition of captive lions is currently comparable to existing wild South African lions. Captive lions cluster with similar probabilities to three of four regional reference populations of wild lions included in the study and no major signatures of inbreeding were identified. However, captive lions are highly genetically interconnected across properties and represent a smaller effective population size compared to Kruger National Park, the largest population of wild lions in South Africa, suggesting some risk of future inbreeding. There were also signatures of genetic drift which should be investigated further as it will likely compromise any potential conservation genetic value of captive lions in the future. The findings of this study should be considered when planning the fate of individuals within South Africa’s captive lion sector and within the broader context of African lion conservation.

Diversity and structure of Bettongia tropica: using population genetics to guide reintroduction and help prevent the extinction of an endangered Australian marsupial - Stephanie J. Todd; Donald T. McKnight; Brad C. Congdon; Jennifer Pierson; Manuela Fischer; Sandra Abell; Jessica Koleck (Conservation Genetics, 2023)
Conservation translocations can restore populations and prevent extinction of threatened species. Sourcing adequate genetic diversity is an essential consideration when planning reintroductions, because it influences individual fitness and long-term persistence of populations, yet available populations of threatened species may lack diversity. We estimated population genetic parameters for one of Australia’s most threatened mammals, the northern bettong, Bettongia tropica , to select source populations for reintroduction. Individuals from sites across the species’ extant range in the Wet Tropics of north Queensland were genotyped, using 6,133 informative SNPs. We found that samples clustered into four populations: an isolated northern population at Mt Spurgeon and three connected southern populations in the Lamb Range. Most of the species’ genetic diversity was dispersed across the Lamb Range populations in approximately equal proportions. Populations showed an isolation-by-distance effect, even over short distances within continuous habitat. Admixture of populations was high at distances < 7 km but low at distances > 11 km, and there was asymmetrical gene flow between the two closest neighboring populations. All populations had small effective sizes and experienced drift, but connectivity appears to have mitigated drift and stabilized population sizes within the Lamb Range. The Mt Spurgeon population had a very small effective population size and low genetic diversity. We use our findings to weigh up the risks and benefits of mixing sources for reintroduction, and we recommend a mixed source approach. We do not currently recommend sourcing individuals from Mt Spurgeon and conservation efforts to preserve this population are urgently required.

Landscape genetics in a highly threatened environment: how relevant to ants is the physiognomic mosaic of the cerrado savanna? - Marianne Azevedo-Silva; Marina C. Côrtes; Carolina S. Carvalho; Gustavo M. Mori; Anete P. Souza; Paulo S. Oliveira (Conservation Genetics, 2023)

Genetic structure and north-south decrease of genetic diversity in the Patagonian maqui berry (Aristotelia chilensis [Molina] Stuntz): implications for its conservation and use - Matías Cona; Alexandra Chávez; Pedro León-Lobos; Juan Carlos Marín; Patricio Hinrichsen (Conservation Genetics, 2023)

Large effective size as determinant of population persistence in Anostraca (Crustacea: Branchiopoda) - Lucía Sainz-Escudero; Marta Vila; Silvia Perea; Mario García-París (Conservation Genetics, 2023)
The fairy shrimp Branchinectella media , because of its passive dispersal capacity and scarce and irregularly distributed habitats (temporary saline aquatic systems), is an intriguing organism from a population genomics and conservation perspective. Stochasticity of dispersal events and the irregular distribution of its habitat might lead to low levels of population connectivity and genetic diversity, and consequently, populations with limited persistence through time. Indeed, by using genomic data (SNPs), we found a strong genetic structure among some of the geographically isolated Iberian populations of B. media. Interestingly, we also obtained high estimates of effective population sizes. Lack of suitable habitat between populations (absence of a “stepping stone” network) and strong genetic differentiation suggest limited dispersal success in B. media . However, the high effective population sizes observed ensure persistence of B. media populations against genetic stochasticity (genetic drift). These results indicate that rescue-effect might not be essential for population persistence if they maintain high effective population sizes able to hold adequate levels of genetic diversity. Should high population sizes be reported in other low dispersing Anostraca, one might be optimistic with regard to their conservation status and fate, provided that their natural habitats remain undisturbed.

Unexpected and spatially structured genetic diversity of the relict population of the endangered corsican land snail Tyrrhenaria ceratina - Louise Camus; Pedro Poli; Michel-Jean Delaugerre; Stéphane Dréano; Xavier Cucherat; Christine Natali; Annie Guiller (Conservation Genetics, 2023)

Population genetics and phylogeography of Paramisgurnus dabryanus (Cypriniformes: Cobitidae) in six river basins of China - Honglu Chen; YuanKui Zhu; Shaokui Yi; Qingfei Zhang; Weimin Wang (Conservation Genetics, 2023)

Environmental, morphological, and molecular data reveal a new species of freshwater mussel, Strophitus howellsi, endemic to the Edwards Plateau in Texas - Chase H. Smith; Alexander H. Kiser; Nathan A. Johnson; Charles R. Randklev (Conservation Genetics, 2023)

Population genomic evidence that stream networks structure genetic diversity in the narrowly endemic patch-nosed salamander (Urspelerpes brucei) - Todd W. Pierson; Carlos D. Camp; Jessica A. Wooten (Conservation Genetics, 2023)

Strong decreases in genetic diversity despite high gene flow for a solitary bee - Sevan Suni; Melissa Hernandez (Conservation Genetics, 2023)
Many organisms live in landscapes that include fragments of natural habitat interspersed with agricultural or urban areas. In such areas, dispersal across human-dominated landscapes may be important for the maintenance of genetic diversity within habitat fragments. Understanding the extent to which dispersal occurs across fragmented habitat and how genetic diversity changes over time is particularly important for bee populations. Population sizes of many bee species are declining, which can have profound negative impacts on both agricultural pollination and the fitness of wild plants. We quantified dispersal across 100 km of mixed landscapes in southern Costa Rica for the solitary bee species Euglossa championi , and we quantified changes in genetic diversity over an eleven-year period. Our SNP-based analysis revealed high dispersal across the geographic area and no evidence that deforestation restricted dispersal. However, we found strong decreases in genetic diversity over time. Expected heterozygosity decreased by 28% over eleven years, regardless of the amount of forest that surrounded sites. Our results suggest that while high dispersal over deforested landscapes may render E. championi less susceptible to land use change than species that show restricted dispersal, the strong decrease in genetic diversity within sites over time suggests this species may warrant conservation monitoring.

Genetic diversity and structure of Eurasian otters on Kinmen Island - Nian-Hong Jang-Liaw; Yu-Chun Tan; Chia-Jui Chang; Chung-Hao Juan; Hsuan-Yi Hou; Li-Wai Chung; Huan-Song Cao; Daisuke Waku; Shih-Wei Chang; Ling-Ling Lee (Conservation Genetics, 2023)

Uncovering inbreeding, small populations, and strong genetic isolation in an Australian threatened frog, Litoria littlejohni - Sarah E. Stock; Kaya Klop-Toker; Samantha Wallace; Oliver Kelly; Alex Callen; Rebecca Seeto; Stephen V. Mahony; Matt W. Hayward; Michael J. Mahony (Conservation Genetics, 2023)
The status of many amphibian populations remains unclear due to undetected declines driven by disease and difficulties in obtaining accurate population estimates. Here, we used genome complexity reduction-based sequencing technology to study the poorly understood Littlejohn’s treefrog , Litoria littlejohni across its fragmented distribution in eastern Australia. We detected five identifiable genetic clusters, with moderate to strong genetic isolation. At a regional scale, population isolation was likely driven by population crashes, resulting in small populations impacted by founder effects. Moderate genetic isolation was detected among populations on the Woronora Plateau despite short distances between population clusters. Evidence of recent declines was apparent in three populations that had very small effective population size, reduced genetic diversity and high inbreeding values. The rates of inbreeding detected in these populations combined with their small size leave these populations at elevated risk of extinction. The Cordeaux Cluster was identified as the most robust population as it was the largest and most genetically diverse. This study exemplifies the value of employing genetic methods to study rare, cryptic species. Despite low recapture rates using traditional capture-recapture demographic methods, we were able to derive population estimates, describe patterns of gene flow, and demonstrate the need for urgent conservation management.

Highly accurate species identification of Eastern Pacific rockfishes (Sebastes spp.) with high-throughput DNA sequencing - Diana S. Baetscher; Hayley M. Nuetzel; John Carlos Garza (Conservation Genetics, 2023)

Translocations restore a population of a threatened rock-wallaby and bolster its genetic diversity - Kristen Nilsson; David Pearson; Mike Paxman; Anthony Desmond; Jason Kennington; Margaret Byrne; Kym Ottewell (Conservation Genetics, 2023)

Correction to: Using genetic analysis to estimate population size, sex ratio, and social organization in an Asian elephant population in conflict with humans in Alur, southern India - Subhankar Chakraborty; D. Boominathan; Ajay A. Desai; T. N. C. Vidya (Conservation Genetics, 2023)

Landscape genomics reveals signals of climate adaptation and a cryptic lineage in Arthropodium fimbriatum - Rebecca Jordan; Meridy Price; Peter A. Harrison; Suzanne M. Prober; René E. Vaillancourt; Dorothy Steane (Conservation Genetics, 2023)
Habitat loss and fragmentation are critical threats to biodiversity. Consequent decreases in population size and connectivity can impact genetic diversity and, thus, future adaptability and resilience to environmental change. Understanding landscape patterns of genetic diversity, including patterns of adaptive variation, can assist in developing conservation strategies that maximise population persistence and adaptability in the face of environmental change. Using a reduced-representation genomic approach, we investigated genetic diversity, structure, and adaptive variation across an aridity gradient in the woodland forb Arthropodium fimbriatum . Moderate levels of genetic diversity ( H S = 0.14–0.23) were found in all 13 sampled provenances. Inbreeding varied among provenances ( F IS = 0.08–0.42) but was not associated with estimated population size. Four genetic clusters were identified, including one highly differentiated cluster. Higher pairwise F ST (0.23–0.42) between the three provenances of this cluster and the remaining 10 provenances (pairwise F ST between 10 provenances 0.02–0.32) suggested two highly divergent lineages or potentially a cryptic species. After excluding the three highly differentiated populations, outlier and genotype-environment association analysis identified 275 putatively adaptive loci suggesting genomic signatures of climate adaptation in A. fimbriatum is primarily associated with changes in aridity. Combined, these results suggest that all provenances have conservation value, contributing to the maintenance of genetic diversity and adaptive variation in this species. The uncovering of a potential cryptic taxon highlights the power of genomics approaches in conservation genetics and the importance of understanding the role of landscape variation shaping genetic variation to effectively define conservation management units in an era of rapid biodiversity decline.

The persistence of the critically endangered Asiatic cheetah relies upon urgent connectivity protection: a landscape genetics perspective - Leili Khalatbari; Raquel Godinho; Hamed Abolghasemi; Ehsan Hakimi; Taher Ghadirian; Houman Jowkar; Urs Breitenmoser; José Carlos Brito (Conservation Genetics, 2023)
Decreasing genetic diversity, gene flow rates and population connectivity can increase inbreeding rates and extinction risks. Asiatic cheetah is a critically endangered mammal with large home range that suffered from extreme range reduction and population decline. Their population is now fragmented into two subpopulations. We used genetic markers to estimate genetic diversity, relatedness, minimum effective population size and gene flow, and to assess population structure. Putative corridors connecting subpopulations were inferred using connectivity models based on topography, land cover and human footprints resistance variables. Individual pairwise genetic relatedness was compared with resistance values obtained from these models and with Euclidean distances between samples to assess the most important factors shaping the current genetic structure. The estimated effective population size was extremely low ( N e = 11 to 17). Both Northern and Southern Subpopulations exhibited low genetic diversity and high relatedness. Several signatures of gene flow and movement of individuals between subpopulations were observed suggesting that inferred corridors potentially connecting subpopulations are functional. However, no traces of gene flow were observed for the latest generations, maybe due to a decrease of functional connectivity in recent years. The resistance model including all variables was best related to genetic relatedness, whereas population differentiation is mostly driven by isolation by distance. The very low estimated effective population size, decreased genetic diversity, and high relatedness of Asiatic cheetah suggests that population reinforcement, removing obstacles to connectivity and boosting prey population conservation in stepping stones are urgently needed to prevent the imminent extinction of iconic biodiversity.

The detailed population genetic structure of the rare endangered latid fish akame Lates japonicus with extremely low genetic diversity revealed from single-nucleotide polymorphisms - Takuya Naito; Kouji Nakayama; Hirohiko Takeshima; Yasuyuki Hashiguchi; Tetsuya Akita; Yo Y. Yamasaki; Tappei Mishina; Naohiko Takeshita; Atsushi J. Nagano; Hiroshi Takahashi (Conservation Genetics, 2023)

DNA-based species identification of shark fins traded in thai markets - Wanlada Klangnurak; Sirachai Arunrugstichai; Petch Manopawitr; Tassapon Krajangdara (Conservation Genetics, 2023)

Recent reduction of genetic diversity in markless form of the red-spotted masu salmon Oncorhynchus masou ishikawae in the Ono River, Kyushu, Japan - Shigeru Kitanishi; Takuya Kondou; Hiroshi Takahashi; Naohiko Takeshita; Shingo Nagata; Kaneaki Edo (Conservation Genetics, 2023)

Effects of subpopulation extinction on effective size (Ne) of metapopulations - Sara Kurland; Nils Ryman; Ola Hössjer; Linda Laikre (Conservation Genetics, 2023)
Population extinction is ubiquitous in all taxa. Such extirpations can reduce intraspecific diversity, but the extent to which genetic diversity of surviving populations are affected remains largely unclear. A key concept in this context is the effective population size ( N e ), which quantifies the rate at which genetic diversity within populations is lost. N e was developed for single, isolated populations while many natural populations are instead connected to other populations via gene flow. Recent analytical approaches and software permit modelling of N e of interconnected populations (metapopulations). Here, we apply such tools to investigate how extinction of subpopulations affects N e of the metapopulation ( N eMeta ) and of separate surviving subpopulations ( N eRx ) under different rates and patterns of genetic exchange between subpopulations. We assess extinction effects before and at migration-drift equilibrium. We find that the effect of extinction on N eMeta increases with reduced connectivity, suggesting that stepping stone models of migration are more impacted than island-migration models when the same number of subpopulations are lost. Furthermore, in stepping stone models, after extinction and before a new equilibrium has been reached, N eRx can vary drastically among surviving subpopulations and depends on their initial spatial position relative to extinct ones. Our results demonstrate that extinctions can have far more complex effects on the retention of intraspecific diversity than typically recognized. Metapopulation dynamics need heightened consideration in sustainable management and conservation, e.g., in monitoring genetic diversity, and are relevant to a wide range of species in the ongoing extinction crisis.

Conservation genomics of an exploited, popular aquarium trade species: the giant Caribbean sea anemone Condylactis gigantea (Anthozoa: Actiniidae) - Nancy E. Sheridan; Seifu Seyoum; William C. Sharp; Benjamin M. Titus; Marymegan Daly; Christina L. Richards; Aaron W. Schrey (Conservation Genetics, 2023)

Shifting range in a stingless bee leads to pre-mating reproductive interference between species - Grace Paul; Louisa Bartels; Francisco Garcia Bulle Bueno; Genevieve Law; Tim Heard; Nadine Chapman; Gabriele Buchmann; Julianne Lim; Rosalyn Gloag (Conservation Genetics, 2023)
Human-induced shifts in species’ ranges can increase contact between closely related species and lead to reproductive interference. In Australia, climate change and trade in stingless bee colonies is increasing the range overlap of two cryptic species: Tetragonula carbonaria and T. hockingsi . To investigate reproductive interactions between these species, we validated a diagnostic-PCR test based on the mitochondrial gene COI to ID field specimens to species. We then assessed the likelihood of reproductive interference in four ways. First, we imaged the male genitalia of each species and found no evidence of reproductive character displacement. Second, we assessed species composition of mating aggregations in an area of sympatry (Southeast Queensland) and confirmed that some males join the mating aggregations of interspecific colonies. Third, we translocated T. hockingsi colonies into the southern range of T. carbonaria (Sydney) and tracked their ability to requeen. These translocated colonies attracted mating aggregations comprised almost entirely of interspecific males, but never formed hybrid colonies; instead, queens either mated with their brothers, or the colony failed to requeen at all. Finally, we presented T. carbonaria males with either conspecific or interspecific virgin queens and found that males attempted to mate only with their own species’ queens. In all, we conclude that reproductive barriers between these species are complete with respect to “short-range” mating cues, but not for “long-range” mate attraction cues. Our study highlights that hive movements can increase some forms of pre-mating reproductive interference between managed bee species, even where the species do not actually mate or hybridize.

To all the gar I loved before: range-wide population genetic structure in Alligator gar - Sandra E. Bohn; Brian R. Kreiser; Damon Williford; Joel Anderson; William Karel (Conservation Genetics, 2023)

Conservation genetics of the tropical gar (Atractosteus tropicus, Lepisosteidae) - Maura Palacios Mejia; Lenin Arias-Rodriguez; Martha Arciniega; Victoria Rodríguez; José Enrique Barraza Sandoval; Néstor Herrera; Dora Carolina Marroquín Mora; Juan B. Ulloa Rojas; Gabriel Márquez Couturier; Gary Voelker; Michael Tobler (Conservation Genetics, 2023)

A 37 K SNP array for the management and conservation of Golden Eagles (Aquila chrysaetos) - Megan E. Judkins; Gary W. Roemer; Brian A. Millsap; Joseph G. Barnes; Bryan E. Bedrosian; Stephen L. Clarke; Robert Domenech; Garth Herring; Myles Lamont; Brian W. Smith; Dale W. Stahlecker; Matthew J. Stuber; et al. (Conservation Genetics, 2023)

Fine-scale functional connectivity of two syntopic pond-breeding amphibians with contrasting life-history traits: an integrative assessment of direct and indirect estimates of dispersal - Helena Martínez-Gil; Gregorio Sánchez-Montes; Pedro Montes-Gavilán; Gorka Ugarte; Íñigo Martínez-Solano (Conservation Genetics, 2023)
Assessing patterns of functional connectivity among amphibian demes is crucial to unravel their population dynamics and prevent their isolation and eventual extinction. Integrative studies based on direct (capture-mark-recapture) and indirect (genetic) estimates of dispersal provide robust, biologically realistic inferences on population structure and connectivity, with applications for conservation efforts. We focused on two pond-breeding amphibians with contrasting life-history traits: the short-lived, semi-arboreal Hyla molleri and the long-lived, fossorial Pelobates cultripes . We PIT-tagged 2150 individuals of both species in two ponds (Laguna and Gravera, separated by 700 m) and monitored them from 2009 to 2021 to document the frequency and spatial extent of dispersal events. In addition, we genotyped individuals from these and two additional breeding populations at a maximum distance of 5 km with 15–16 microsatellites to characterize fine-scale patterns of genetic structure. We detected dispersal events connecting Laguna and Gravera in both species, albeit at low frequencies (4.8% and 7.7% of recaptured individuals of H. molleri and P. cultripes, respectively). However, both species were capable of covering long distances, with individual accumulated displacements up to 3.5 km ( Hyla ) and 1.8 km ( Pelobates ). Breeding populations > 2 km apart were genetically differentiated, indicating lower connectivity at this spatial scale. Estimates of pairwise migration rates differed between species and were asymmetrical, with different ponds representing “source” populations contributing more migrants to other populations in each species. We discuss the role of differences in life history traits and ecological preferences in shaping population dynamics in the two species and highlight management implications of our results.

Conservation genomics reveals low connectivity among populations of threatened roseate terns (Sterna dougallii) in the Atlantic Basin - Paige A. Byerly; R. Terry Chesser; Robert C. Fleischer; Nancy McInerney; Natalia A. S. Przelomska; Paul L. Leberg (Conservation Genetics, 2023)

Landscape genetics identifies barriers to Natterjack toad metapopulation dispersal - Marina I. Reyne; Kara Dicks; Jason Flanagan; Paul Nolan; Joshua P. Twining; Aurélie Aubry; Mark Emmerson; Ferdia Marnell; Sarah Helyar; Neil Reid (Conservation Genetics, 2023)
Habitat fragmentation and loss reduce population size and connectivity, which imperils populations. Functional connectivity is key for species persistence in human-modified landscapes. To inform species conservation management, we investigated spatial genetic structure, gene flow and inferred dispersal between twelve breeding sites of the Natterjack toad ( Bufo calamita ); regionally Red-Listed as Endangered in Ireland. Spatial genetic structure was determined using both Bayesian and non-Bayesian clustering analysis of 13 polymorphic microsatellite loci genotyping 247 individuals. We tested the influence of geographic distance, climate, habitat, geographical features, and anthropogenic pressure on pairwise genetic distances between breeding sites using Isolation-by-distance and Isolation-by-resistance based on least-cost path and circuit theory models of functional connectivity. There was clear spatial structuring with genetic distances increasing with geographic distance. Gene flow was best explained by Isolation-by-resistance models with coniferous forestry plantations, bog, marsh, moor and heath, scrub, anthropogenic presence (Human Influence Index) and rivers (riparian density) identified as habitats with high resistance to gene flow while metapopulation connectivity was enhanced by coastal habitats (beaches, sand dunes and salt marshes) and coastal grassland. Despite substantial declines in census numbers over the past 15 years and its regional status as Endangered, the Natterjack toad population in Ireland retains high genetic diversity. If declines continue, maintaining habitat connectivity to prevent genetic erosion by management of coastal grasslands, pond construction and assisted migration through translocation will be increasingly important.

Genetic differences among the Interior Highlands walleye (Sander vitreus) with mitochondrial and nuclear markers indicate the need for updated stocking practices - Leah K. Berkman; Chelsea L. Titus; Dustin R. Thomas; Brook L. Fluker; Paul Cieslewicz; Dave Knuth; Jeffrey B. Koppelman; Lori S. Eggert (Conservation Genetics, 2023)

Inferring inter-colony movement within metapopulations of yellow-footed rock-wallabies using estimates of kinship - Deane A. Smith; Mark R. Lethbridge; Benjamin L. Allen; Rose L. Andrew (Conservation Genetics, 2023)
Understanding the exchange of individuals between wildlife populations, particularly those with naturally fragmented habitats, is important for the effective management of these species. This is of particular consequence when the species is of conservation concern, and isolated populations may be lost due to pressures from predation or competition, or catastrophic events such as wildfire. Here we demonstrate the use kinship and population structure analysis to show potential recent movement between colonies in metapopulations of yellow-footed rock-wallaby ( Petrogale xanthopus Gray 1854) at two sites in the Grey Range of Queensland, and at four sites in the Gawler Ranges of South Australia. These colonies are also compared to a single colony from the Flinders Ranges, a connected landscape of rock-wallaby habitat. Using reduced representation next-generation sequencing, we acquired and filtered a set of ~ 17,000 single-nucleotide polymorphisms to examine population genetic variation, structure and relationships within populations, and also identify putative migrants. Initial STRUCTURE analysis re-confirmed each population should be considered separately. Tests of population genetic variation identify several colonies appearing to be experiencing genetic erosion, also with low calculated effective population sizes (N e = 4.5–36.6). Pairwise comparisons of individual relatedness (relatedness coeffiecients; r ) implied several contemporary movement events between colonies within both the Gawler and Grey Ranges ( r > 0.125), which was then affirmed with tests for putative first generation migrants. These results are of particular note in South Australia, where threat abatement (management of key predators and competitors) may facilitate dispersion. Additionally, in Queensland, colonies are separated by anthropogenic barriers: predator exclusion fencing designed to exclude dingoes ( Canis familiaris ) from grazing land, which may hinder dispersal. This work highlights the usefulness of population genetics to inform management outcomes in wildlife, in this case, highlighting the need for threatened species management at the landscape level.

Examining the spatiotemporal variation of genetic diversity and genetic rarity in the natural plant recolonization of human-altered areas - Pedro J. Garrote; Antonio R. Castilla; F. Xavier Picó; Jose M. Fedriani (Conservation Genetics, 2023)
The spatiotemporal genetic variation at early plant life stages may substantially affect the natural recolonization of human-altered areas, which is crucial to understand plant and habitat conservation. In animal-dispersed plants, dispersers’ behavior may critically drive the distribution of genetic variation. Here, we examine how genetic rarity is spatially and temporally structured in seedlings of a keystone pioneer palm ( Chamaerops humilis ) and how the variation of genetic rarity could ultimately affect plant recruitment. We intensively monitored the seed rain mediated by two medium-sized carnivores during two consecutive seasons in a Mediterranean human-altered area. We genotyped 143 out of 309 detected seedlings using 12 microsatellite markers. We found that seedlings emerging from carnivore-dispersed seeds showed moderate to high levels of genetic diversity and no evidence of inbreeding. We found inflated kinship among seedlings that emerged from seeds within a single carnivore fecal sample, but a dilution of such FSGS at larger spatial scales (e.g. latrine). Seedlings showed a significant genetic sub-structure and the sibling relationships varied depending on the spatial scale. Rare genotypes arrived slightly later throughout the dispersal season and tended to be spatially isolated. However, genetic rarity was not a significant predictor by itself which indicates that, at least, its influence on seedling survival was smaller than other spatiotemporal factors. Our results suggest strong C. humilis resilience to genetic bottlenecks due to human disturbances. We highlight the study of plant-animal interactions from a genetic perspective since it provides crucial information for plant conservation and the recovery of genetic plant resilience.

Whole genome re-sequencing uncovers significant population structure and low genetic diversity in the endangered clouded apollo (Parnasssius mnemosyne) in Sweden - Venkat Talla; Veronika Mrazek; Jacob Höglund; Niclas Backström (Conservation Genetics, 2023)
The clouded apollo ( Parnassius mnemosyne ) used to have a wide distribution in Fennoscandia. Recent population declines have, however, led to regional extinctions and in Sweden it is currently one of the most endangered butterflies, confined to three geographically separated metapopulations: Blekinge, Roslagen and Västernorrland. Especially the Blekinge population has declined dramatically and few imagines have been observed during recent census efforts (< 10 in some localities). The clouded apollo is subject to a species action plan which includes both habitat restorations and captive breeding to produce individuals for release and reintroductions. Here, we apply whole-genome resequencing of clouded apollo individuals collected in the three natural populations and the captive population in Sweden and apply population genomic approaches to get a better understanding of the genetic structure and levels of genetic diversity in the species. We find that the clouded apollo populations in the different geographic regions have similar, but comparatively low levels of genetic diversity and we find evidence for significant genetic differentiation between the northernmost population and the populations in southern Sweden. Additional analysis, including previously available mitochondrial data, unveil that a bi-directional re-colonization of Fennoscandia after the latest glacial maximum most likely is the explanation for the considerable differentiation between some Swedish populations. Finally, we find evidence for population sub-structure in one of the Swedish populations. The results provide insights into the genetic consequences of population size declines and fragmentation in general and provide important information for direct conservation actions for the clouded apollo in Sweden in particular.

Genomic evidence for three distinct species in the Erebia manto complex in Central Europe (Lepidoptera, Nymphalidae) - Amanda Jospin; Yannick Chittaro; Daniel Bolt; David Demergès; Kevin Gurcel; Jürgen Hensle; Andreas Sanchez; Christophe Praz; Kay Lucek (Conservation Genetics, 2023)
A problem to implement conservation strategies is that in many cases recognized taxa are in fact complexes of several cryptic species. Failure to properly delineate species may lead to misplaced priorities or to inadequate conservation measures. One such species complex is the yellow-spotted ringlet Erebia manto , which comprises several phenotypically distinct lineages, whose degree of genomic isolation has so far not been assessed. Some of these lineages are geographically restricted and thus possibly represent distinct units with conservation priorities. Using several thousand nuclear genomic markers, we evaluated to which degree the bubastis lineage from the Alps and the vogesiaca lineage from the Vosges, are genetically isolated from the widespread manto lineage. Our results suggest that both lineages are genetically as strongly differentiated from manto as other taxonomically well separated sibling species in this genus from each other, supporting a delineation of bubastis and vogesiaca as independent species. Given the restricted and isolated range of vogesiaca as well as the disjunct distribution of bubastis, our findings have significant implication for future conservation efforts on these formerly cryptic species and highlight the need to investigate the genomic identity within species complexes.

Genome-wide assessment of population genetic and demographic history in Magnolia odoratissima based on SLAF-seq - Tao Zhang; Jing Meng; Fengmao Yang; Xue Li; Xuanpeng Yin; Jing Zhang; Shuilian He (Conservation Genetics, 2023)

Correction: Conservation genetics of Phlox hirsuta, a serpentine endemic - James I. Cohen; Lauren R. Griffen (Conservation Genetics, 2023)

Conservation genomics reveals fine-scale population structuring and recent declines in the Critically Endangered Australian Kuranda Treefrog - Lorenzo V. Bertola; Megan Higgie; Kyall R. Zenger; Conrad J. Hoskin (Conservation Genetics, 2023)
The Kuranda Treefrog occurs in tropical north-east Australia and is listed as Critically Endangered due to its small distribution and population size, with observed declines due to drought and human-associated impacts to habitat. Field surveys identified marked population declines in the mid-2000s, culminating in very low abundance at most sites in 2005 and 2006, followed by limited recovery. Here, samples from before (2001–2004) and after (2007–2009) this decline were analysed using 7132 neutral genome-wide SNPs to assess genetic connectivity among breeding sites, genetic erosion, and effective population size. We found a high level of genetic connectivity among breeding sites, but also structuring between the population at the eastern end of the distribution (Jumrum Creek) versus all other sites. Despite finding no detectable sign of genetic erosion between the two times periods, we observed a marked decrease in effective population size (Ne), from 1720 individuals pre-decline to 818 post-decline. This mirrors the decline detected in the field census data, but the magnitude of the decline suggested by the genetic data is greater. We conclude that the current effective population size for the Kuranda Treefrog remains around 800 adults, split equally between Jumrum Creek and all other sites combined. The Jumrum Creek habitat requires formal protection. Connectivity among all other sites must be maintained and improved through continued replanting of rainforest, and it is imperative that impacts to stream flow and water quality are carefully managed to maintain or increase population sizes and prevent genetic erosion.

Genetic diversity and connectivity of moose (Alces americanus americanus) in eastern North America - Elias Rosenblatt; Katherina Gieder; Therese Donovan; James Murdoch; Timothy P.L. Smith; Michael P. Heaton; Theodore S. Kalbfleisch; Brenda M. Murdoch; Suraj Bhattarai; Emory Pacht; Emma Verbist; Veronica Basnayake; et al. (Conservation Genetics, 2023)
Genetic diversity is critical to a population’s ability to overcome gradual environment change. Large-bodied wildlife existing in regions with relatively high human population density are vulnerable to isolation-induced genetic drift, population bottlenecks, and loss of genetic diversity. Moose ( Alces americanus americanus ) in eastern North America have a complex history of drastic population changes. Current and potential threats to moose populations in this region could be exacerbated by loss of genetic diversity and connectivity among subpopulations. Existing genetic diversity, gene flow, and population clustering and fragmentation of eastern North American moose are not well quantified, while physical and anthropogenic barriers to population connectivity already exist. Here, single nucleotide polymorphism (SNP) genotyping of 507 moose spanning five northeastern U.S. states and one southeastern Canadian province indicated low diversity, with a high proportion of the genomes sharing identity-by-state, with no consistent evidence of non-random mating. Gene flow estimates indicated bidirectionality between all pairs of sampled areas, with magnitudes reflecting clustering and differentiation patterns. A Discriminant Analysis of Principal Components analysis indicated that these genotypic data were best described with four clusters and indicated connectivity across the Saint Lawrence River and Seaway, a potential physical barrier to gene flow. Tests for genetic differentiation indicated restricted gene flow between populations across the Saint Lawrence River and Seaway, and between many sampled areas facing expanding human activity. These results document current genetic variation and connectivity of moose populations in eastern North America, highlight potential challenges to current population connectivity, and identify areas for future research and conservation.

Genetic diversity goals and targets have improved, but remain insufficient for clear implementation of the post-2020 global biodiversity framework - Sean Hoban; Michael W. Bruford; Jessica M. da Silva; W. Chris Funk; Richard Frankham; Michael J. Gill; Catherine E. Grueber; Myriam Heuertz; Margaret E. Hunter; Francine Kershaw; Robert C. Lacy; Caroline Lees; et al. (Conservation Genetics, 2023)
Genetic diversity among and within populations of all species is necessary for people and nature to survive and thrive in a changing world. Over the past three years, commitments for conserving genetic diversity have become more ambitious and specific under the Convention on Biological Diversity’s (CBD) draft post-2020 global biodiversity framework (GBF). This Perspective article comments on how goals and targets of the GBF have evolved, the improvements that are still needed, lessons learned from this process, and connections between goals and targets and the actions and reporting that will be needed to maintain, protect, manage and monitor genetic diversity. It is possible and necessary that the GBF strives to maintain genetic diversity within and among populations of all species, to restore genetic connectivity, and to develop national genetic conservation strategies, and to report on these using proposed, feasible indicators.

Genomic evidence uncovers inbreeding and supports translocations in rescuing the genetic diversity of a landlocked seal population - Tarja Sundell; Juhana I. Kammonen; Ella Mustanoja; Vincent Biard; Mervi Kunnasranta; Marja Niemi; Milaja Nykänen; Tommi Nyman; Jukka U. Palo; Mia Valtonen; Lars Paulin; Jukka Jernvall; et al. (Conservation Genetics, 2023)
Fragmentation of isolated populations increases the risk of inbreeding and loss of genetic diversity. The endemic Saimaa ringed seal ( Pusa hispida saimensis ) is one of the most endangered pinnipeds in the world with a population of only ~ 400 individuals. The current genetic diversity of this subspecies, isolated in Lake Saimaa in Finland for ca. 1000 generations, is alarmingly low. We performed whole-genome sequencing on Saimaa ringed seals (N = 30) and analyzed the level of homozygosity and genetic composition across the individual genomes. Our results show that the Saimaa ringed seal population has a high number of runs of homozygosity (RoH) compared with the neighboring Baltic ringed seal ( Pusa hispida botnica ) reference population ( p < 0.001). There is also a tendency for stillborn seal pups to have more pronounced RoH. Since the population is divided into semi-isolated subpopulations within the Lake Saimaa exposing the population to deleterious genomic effects, our results support augmented gene flow as a genetic conservation action. Based on our results suggesting inbreeding depression in the population, we recommend Pihlajavesi as a potential source and Southern Saimaa as a potential recipient subpopulation for translocating individuals. The Saimaa ringed seal is a recognized subspecies and therefore translocations should be considered only within the lake to avoid an unpredictable risk of disease, the introduction of deleterious alleles, and severe ecological issues for the population.

Genomic divergence of hatchery- and natural-origin Chinook salmon (Oncorhynchus tshawytscha) in two supplemented populations - Michael J. Ford; Ewann A. Berntson; Paul Moran; Garrett J. McKinney (Conservation Genetics, 2023)

Effects of genomic homozygosity on total fitness in an invertebrate: lethal equivalent estimates for Drosophila melanogaster - Richard Frankham (Conservation Genetics, 2023)

Ex situ versus in situ Eurasian lynx populations: implications for successful breeding and genetic rescue - Jarmila Krojerová-Prokešová; Barbora Gajdárová; Tobias Erik Reiners; Petra Bolechová; Oddmund Kleven; Petr Koubek; Carsten Nowak; Jānis Ozoliņš; Branislav Tám; Inna Voloshina; Peter Vallo (Conservation Genetics, 2023)

Isolated on sky islands: genetic diversity and population structure of an endangered mountain lizard - Renée Hartley; Nick Clemann; Zak Atkins; Ben C. Scheele; David B. Lindenmayer; Michael D. Amor (Conservation Genetics, 2023)

Conservation genetics of Phlox hirsuta, a serpentine endemic - James I. Cohen; Lauren R. Griffen (Conservation Genetics, 2023)

The potential and shortcomings of mitochondrial DNA analysis for cheetah conservation management - René Meißner; Sven Winter; Uta Westerhüs; Alexander Sliwa; Carola Greve; Lena Godsall Bottriell; Paul Bottriell; Carlos Rodríguez Fernandes; Paul Vercammen; Luke T. B. Hunter; Alexei V. Abramov; Leili Khalatbari; et al. (Conservation Genetics, 2023)
There are only about 7,100 adolescent and adult cheetahs ( Acinonyx jubatus ) remaining in the wild. With the majority occurring outside protected areas, their numbers are rapidly declining. Evidence-based conservation measures are essential for the survival of this species. Genetic data is routinely used to inform conservation strategies, e.g., by establishing conservation units (CU). A commonly used marker in conservation genetics is mitochondrial DNA (mtDNA). Here, we investigated the cheetah’s phylogeography using a large-scale mtDNA data set to refine subspecies distributions and better assign individuals to CUs. Our dataset mostly consisted of historic samples to cover the cheetah’s whole range as the species has been extinct in most of its former distribution. While our genetic data largely agree with geography-based subspecies assignments, several geographic regions show conflicting mtDNA signals. Our analyses support previous findings that evolutionary forces such as incomplete lineage sorting or mitochondrial capture likely confound the mitochondrial phylogeography of this species, especially in East and, to some extent, in Northeast Africa. We caution that subspecies assignments solely based on mtDNA should be treated carefully and argue for an additional standardized nuclear single nucleotide polymorphism (SNP) marker set for subspecies identification and monitoring. However, the detection of the A. j. soemmeringii specific haplogroup by a newly designed Amplification-Refractory Mutation System (ARMS) can already provide support for conservation measures.

High genetic variation of Trifolium alpestre at the northern margin: but for how long? - Aigi Ilves; Karin Kaljund; Erkki Sild; Zuzana Münzbergová (Conservation Genetics, 2023)

Genetic restoration of black rhinoceroses in South Africa: conservation implications - Debbie Stanbridge; M. Justin O’Riain; Cathy Dreyer; Nikki le Roex (Conservation Genetics, 2023)

Historic DNA uncovers genetic effects of climate change and landscape alteration in two wild bee species - Sandara N. R. Brasil; Evan P. Kelemen; Sandra M. Rehan (Conservation Genetics, 2023)

Genetic dynamics of a 11-year ex situ managed Itasenpara bitterling population - Yuji Yamazaki; Koki Ikeya (Conservation Genetics, 2023)

The genetic structure and connectivity in two sympatric rodent species with different life histories are similarly affected by land use disturbances - Roberto Biello; Andrea Brunelli; Giulia Sozio; Katja Havenstein; Alessio Mortelliti; Valerio Ketmaier; Sibelle Torres Vilaça; Giorgio Bertorelle (Conservation Genetics, 2023)
The negative impact of habitat fragmentation due to human activities may be different in different species that co-exist in the same area, with consequences on the development of environmental protection plans. Here we aim at understanding the effects produced by different natural and anthropic landscape features on gene flow patterns in two sympatric species with different specializations, one generalist and one specialist, sampled in the same locations. We collected and genotyped 194 wood mice (generalist species) and 199 bank voles (specialist species) from 15 woodlands in a fragmented landscape characterized by different potential barriers to dispersal. Genetic variation and structure were analyzed in the two species, respectively. Effective migration surfaces, isolation-by-resistance (IBR) analysis, and regression with randomization were used to investigate isolation-by-distance (IBD) and the relative importance of land cover elements on gene flow. We observed similar patterns of heterozygosity and IBD for both species, but the bank vole showed higher genetic differences among geographic areas. The IBR analysis suggests that (i) connectivity is reduced in both species by urban areas but more strongly in the specialist bank vole; (ii) cultivated areas act as dispersal corridors in both species; (iii) woodlands appear to be an important factor in increasing connectivity in the bank vole, and less so in the wood mouse. The difference in dispersal abilities between a generalist and specialist species was reflected in the difference in genetic structure, despite extensive habitat changes due to human activities. The negative effects of fragmentation due to the process of urbanization were, at least partially, mitigated by another human product, i.e., cultivated terrains subdivided by hedgerows, and this was true for both species.

Capturing conservation in the post-genomics era: a book review of “Conservation and the Genomics of Populations.” - Stephanie J. Galla; Cinnamon S. Mittan-Moreau; Soraia Barbosa (Conservation Genetics, 2023)

Not all is black and white: phylogeography and population genetics of the endemic blackbuck (Antilope cervicapra) - Ananya Jana; K. Praveen Karanth (Conservation Genetics, 2023)

High genetic diversity in American chestnut (Castanea dentata) despite a century of decline - Sophia S. Stoltz; Brian C. Husband (Conservation Genetics, 2023)

Reproductive biology and population structure of the endangered shrub Grevillea bedggoodiana (Proteaceae) - Stanislaw Wawrzyczek; Gareth D. Holmes; Susan E. Hoebee (Conservation Genetics, 2023)
Narrowly endemic species are particularly vulnerable to catastrophic events. Compared to widespread species, they may also be less capable of adapting to shifts in environmental pressures as a result of specialisation on a narrow range of local condition and limited ability to disperse. However, life-history traits, such as preferential outcrossing and high fecundity can maintain genetic diversity and evolutionary potential, and boost species resilience. The endangered Grevillea bedggoodiana (Enfield Grevillea) is an understorey shrub restricted to an area of ca. 150 km 2 in south-eastern Australia with a legacy of large-scale anthropogenic disturbance. Prior to this study little was known about its biology and population structure. Here, its breeding system was assessed through a controlled pollination experiment at one of its central populations, and eight populations were sampled for genetic analysis with microsatellite markers. The species was found to be preferentially outcrossing, with no evidence of pollination limitation. In most populations, allelic richness, observed heterozygosity and gene diversity were high (Ar: 3.8–6.3; H o : 0.45–0.65, H e : 0.60 − 0.75). However, the inbreeding coefficients were significant in at least four populations, ranging from F i -0.061 to 0.259 despite high outcrossing rates. Estimated reproductive rates varied among sampled populations but were independent of gene diversity and inbreeding. Despite its small geographic range, the species’ populations showed moderate differentiation (AMOVA: F ST = 0.123), which was largely attributable to isolation by distance. We interpret these results as suggesting that G. bedggoodiana is reproductively healthy and has maintained high levels of genetic diversity despite recent disturbance.

Phylogeography and population genetics of a headwater-stream adapted crayfish, Cambarus pristinus (Decapoda: Cambaridae), from the Cumberland Plateau in Tennessee - Brooke Grubb; John W. Johansen; Rebecca E. Blanton (Conservation Genetics, 2022)

Bidirectional hybridisation and introgression between introduced European brown hare, Lepus europaeus and the endemic Irish hare, L. timidus hibernicus - Neil Reid; Maria F. Hughes; Rosaleen A. Hynes; W. Ian Montgomery; Paulo A. Prodöhl (Conservation Genetics, 2022)
Introduced non-native species can threaten native species through interspecific hybridisation and genetic introgression. We assessed the prevalence of hybridisation and introgression between introduced European brown hare, Lepus europaeus , and the endemic Irish hare, L. timidus hibernicus . Roadkill hares ( n = 56) were sequenced for a 379bp section of the mitochondrial DNA D-loop and a 474bp segment of the nuclear transferrin ( Tf ) gene. A species-specific indel in the transferrin gene was present in L.t. hibernicus and absent in L. europaeus . Excluding three hares from which molecular data could not be recovered, 28 hares (53%) were native L.t. hibernicus , 7 (13%) were non-native L. europaeus and 18 (34%) were hybrids; of which 5 (28%) were first generation (F1) involving bidirectional crosses with mismatched nuclear and mtDNA (3 ♂ europaeus x ♀ hibernicus and 2 ♂ hibernicus x ♀ europaeus ). Mixed nuclear transferrin sequences suggested 13 (72%) of hybrids were at least 2nd generation (F2) with 9 (69%) possessing L.t. hibernicus and 4 (31%) L. europaeus mtDNA (the latter indicative of hybrid backcrossing with the non-native). The prevalence of hybridisation at similar mountain-brown hare contact zones throughout Europe is notably lower (4–16%) and typically unidirectional (♂ europaeus x ♀ timidus ). A high prevalence of bidirectional hybridisation and introgression (in association with projected climate change) may favour the introduced species over the native. Genetic surveillance and population monitoring are needed to further explore the potential conservation implications of European brown hare in Ireland.

Population structure of threatened caribou in western Canada inferred from genome-wide SNP data - Maria Cavedon; Jocelyn Poissant; Bridgett vonHoldt; Anita Michalak; Troy Hegel; Elizabeth Heppenheimer; Dave Hervieux; Lalenia Neufeld; Jean L. Polfus; Helen Schwantje; Robin Steenweg; Marco Musiani (Conservation Genetics, 2022)

Strong bidirectional gene flow between fish lineages separated for over 100,000 years - Maiko L. Lutz; Paul Sunnucks; David G. Chapple; Dean Gilligan; Mark Lintermans; Alexandra Pavlova (Conservation Genetics, 2022)
Restoring levels of genetic diversity in small and declining populations is increasingly being considered in biodiversity conservation. Evidence-based genetic management requires assessment of risks and benefits of crossing populations. Because risks are challenging to assess experimentally, e.g. through multi-generational crosses, decision-support approaches utilize proxy risk factors such as time since separation of lineages. However, the paucity of empirical datasets on fitness consequences of longer separation times tends to favour crossing lineages with conservatively short separations, restricting wildlife managers’ options. Here, we assessed the genetic outcomes of interbreeding in the wild between lineages of a threatened Australian freshwater fish (Macquarie perch) separated by an estimated 119,000–385,000 years of evolution in distinct environments. Fish belonging to the Murray-Darling Basin (MDB) lineage escaped from Cataract Dam—into which they were translocated in ~ 1915—into the Cataract River, where they interbred with the local Hawkesbury-Nepean Basin (HNB) lineage. Analyses of reduced-representation genomic data revealed no evidence of genetic incompatibilities during interbreeding of the two lineages in the Cataract River: assignment to genotypic clusters indicated a spectrum of hybrid types including second generation hybrids and backcrosses to both parental lineages. Thus, no adverse effects were detected from genetic mixing of populations separated by > 100,000 years. We are not advocating purposely crossing the two lineages for management purposes under present cost–benefit considerations, because there are currently sufficient intra-lineage source populations to beneficially mix. Instead, this study presents a useful calibration point: two morphologically different lineages evolved in different habitats for 119,000–385,000 years can successfully interbreed.

DNA-typing surveillance of the bushmeat in Côte d'Ivoire: a multi-faceted tool for wildlife trade management in West Africa - Koffi Jules Gossé; Sery Gonedelé-Bi; Fabienne Justy; Anne-Lise Chaber; Bamba Kramoko; Philippe Gaubert (Conservation Genetics, 2022)

Genetic structure and diversity of amphidromous sculpin in Shiretoko, a mountainous peninsula in Japan - Yuh Aoki; Souta Nakajima; Futoshi Nakamura (Conservation Genetics, 2022)

Conservation genetics of three Rafflesia species in Java Island, Indonesia using SNP markers obtained from MIG-seq - Yayan Wahyu Candra Kusuma; Ayumi Matsuo; Yoshihisa Suyama; Stefan Wanke; Yuji Isagi (Conservation Genetics, 2022)

A range-wide analysis of population structure and genomic variation within the critically endangered spiny daisy (Acanthocladium dockeri) - Elodie Brooks; Amy L Slender; Suong Cu; Martin F Breed; James CR Stangoulis (Conservation Genetics, 2022)
Understanding population structure and genetic diversity is important for designing effective conservation strategies. As a critically endangered shrub, the six remaining extant populations of spiny daisy ( Acanthocladium dockeri ) are restricted to country roadsides in the mid-north of South Australia, where the species faces many ongoing abiotic and biotic threats to survival. Currently the spiny daisy is managed by selecting individuals from the extant populations and translocating them to establish insurance populations. However, there is little information available on the genetic differentiation between populations and diversity within source populations, which are essential components of planning translocations. To help fill this knowledge gap, we analysed population structure within and among all six of its known wild populations using 7,742 SNPs generated by a genotyping-by-sequencing approach. Results indicated that each population was strongly differentiated, had low levels of genetic diversity, and there was no evidence of inter-population gene flow. Individuals within each population were generally closely related, however, the Melrose population consisted entirely of clones. Our results suggest genetic rescue should be applied to wild spiny daisy populations to increase genetic diversity that will subsequently lead to greater intra-population fitness and adaptability. As a starting point, we suggest focussing on improving seed viability via inter-population crosses such as through hand pollination experiments to experimentally assess their sexual compatibility with the hope of increasing spiny daisy sexual reproduction and long-term reproductive fitness.

G﻿lobal phylogeography of ridley sea turtles (Lepidochelys spp.): evolution, demography, connectivity, and conservation - Sibelle Torres Vilaça; Anelise Torres Hahn; Eugenia Naro-Maciel; F. Alberto Abreu-Grobois; Brian W. Bowen; Jaqueline C. Castilhos; Claudio Ciofi; Nancy N. FitzSimmons; Michael P. Jensen; Angela Formia; Colin J. Limpus; Chiara Natali; et al. (Conservation Genetics, 2022)
Globally distributed marine taxa are well suited for investigations of biogeographic impacts on genetic diversity, connectivity, and population demography. The sea turtle genus Lepidochelys includes the wide-ranging and abundant olive ridley ( L. olivacea ), and the geographically restricted and ‘Critically Endangered’ Kemp’s ridley ( L. kempii ). To investigate their historical biogeography, we analyzed a large dataset of mitochondrial DNA (mtDNA) sequences from olive (n = 943) and Kemp’s (n = 287) ridleys, and genotyped 15 nuclear microsatellite loci in a global sample of olive ridleys (n = 285). We found that the ridley species split ~ 7.5 million years ago, before the Panama Isthmus closure. The most ancient mitochondrial olive ridley lineage, located in the Indian Ocean, was dated to ~ 2.2 Mya. Both mitochondrial and nuclear markers revealed significant structure for olive ridleys between Atlantic (ATL), East Pacific (EP), and Indo-West Pacific (IWP) areas. However, the divergence of mtDNA clades was very recent (< 1 Mya) with low within- clade diversity, supporting a recurrent extinction-recolonization model for these ocean regions. All data showed that ATL and IWP groups were more closely related than those in the EP, with mtDNA data supporting recent recolonization of the ATL from the IWP. Individual olive ridley dispersal between the ATL, EP, and IN/IWP could be interpreted as more male- than female-biased, and genetic diversity was lowest in the Atlantic Ocean. All populations showed signs of recent expansion, and estimated time frames were concordant with their recent colonization history. Investigating species abundance and distribution changes over time is central to evolutionary biology, and this study provides a historical biogeographic context for marine vertebrate conservation and management.

Cores, edges and beyond: insights into the phylogeography of frigatebirds with a focus on ultraperipheral and endemic populations - Filipa M. S. Martins; Raquel Godinho; Luís Palma (Conservation Genetics, 2022)

Demographic history of two endangered Atlantic eel species, Anguilla anguilla and Anguilla rostrata - Xiu Feng; Shenglin Liu; Michael M. Hansen (Conservation Genetics, 2022)

Rediscovery of a native freshwater shrimp, Neocaridina denticulata, and expansion of an invasive species in and around Lake Biwa, Japan: genetic and morphological approach - Keisuke Onuki; Yusuke Fuke (Conservation Genetics, 2022)

Assessing tiger corridor functionality with landscape genetics and modelling across Terai-Arc landscape, India - Suvankar Biswas; Supriya Bhatt; Debanjan Sarkar; Gautam Talukdar; Bivash Pandav; Samrat Mondol (Conservation Genetics, 2022)

Relative impact of pollen and seed dispersal on population viability of a neotropical tree species - Israel Flor Silva de Araújo; Elaine Cristina Fernandes; Felipe Neves da Silva; Patricia Sanae Sujii (Conservation Genetics, 2022)

Islands in the desert: assessing fine scale population genomic variation of a group of imperiled desert fishes - D. Cooper Campbell; D. T. Camak; K. R. Piller (Conservation Genetics, 2022)

A phylogeographic assessment of the greater kudu (Tragelaphus strepsiceros) across South Africa - R. Jacobs; W. G. Coetzer; J. P. Grobler (Conservation Genetics, 2022)

A decade of genetic monitoring reveals increased inbreeding for the Endangered western leopard toad, Sclerophrys pantherina - Kirstin Stephens; Krystal A. Tolley; Jessica M. da Silva (Conservation Genetics, 2022)

Population genetic structure and demographic history of Rhodeus atremius suigensis, an endangered bitterling in Japan - Kouichi Kawamura; Takuya Miyake; Carl Smith (Conservation Genetics, 2022)

Evaluation of proposed genetic goals and targets for the Convention on Biological Diversity - Richard Frankham (Conservation Genetics, 2022)
In the current negotiations regarding revision of the Convention on Biological Diversity (CBD) proposals have been made to strengthen the genetic goals, indicators, and targets for wild species in natural habitats by specifying “tolerable” losses of genetic diversity. However, they have not been subjected to evaluations of their continued use over 100 years, a common conservation time frame. I evaluated six scenarios (3, 5 or 10% loss of genetic diversity [heterozygosity] over 8 or 32 years) proposed as targets for revision of genetic indicators in CBD by predicting their consequences on genetic diversity, inbreeding, fitness, and evolutionary potential when applied at the same rate for 100 years. All proposals lead to substantial genetic harm to species when continued for 100 years that will compromise species persistence, especially in the context of environmental change. Consequently, none of the proposals are suitable for inclusion in the CBD. However, alternative indicators are proposed that would reflect improvements in the genetic status of populations and species, namely (1) the number of species and their populations being maintained at sizes sufficient to retain evolutionary potential in perpetuity, and (2) the number of species for which population genetic connectivity has been improved.

Estimation of the census (Nc) and effective (Ne) population size of a wild mandrill (Mandrillus sphinx) horde in the Lopé National Park, Gabon using a non-invasive genetic approach - Amour GuibingaMickala; Anna Weber; Stephan Ntie; Prakhar Gahlot; David Lehmann; Patrick Mickala; Katherine Abernethy; Nicola Anthony (Conservation Genetics, 2022)

Population genetics reveals bidirectional fish movement across the Continental Divide via an interbasin water transfer - Audrey C. Harris; Sara J. Oyler-McCance; Jennifer A. Fike; Matthew P. Fairchild; Christopher M. Kennedy; Harry J. Crockett; Dana L. Winkelman; Yoichiro Kanno (Conservation Genetics, 2022)

Genetic diversity and spatial genetic structure support the specialist-generalist variation hypothesis in two sympatric woodpecker species - Gilberto Pasinelli (Conservation Genetics, 2022)
Species are often arranged along a continuum from “specialists” to “generalists”. Specialists typically use fewer resources, occur in more patchily distributed habitats and have overall smaller population sizes than generalists. Accordingly, the specialist-generalist variation hypothesis (SGVH) proposes that populations of habitat specialists have lower genetic diversity and are genetically more differentiated due to reduced gene flow compared to populations of generalists. Here, expectations of the SGVH were tested by examining genetic diversity, spatial genetic structure and contemporary gene flow in two sympatric woodpecker species differing in habitat specialization. Compared to the generalist great spotted woodpecker ( Dendrocopos major ), lower genetic diversity was found in the specialist middle spotted woodpecker ( Dendrocoptes medius ). Evidence for recent bottlenecks was revealed in some populations of the middle spotted woodpecker, but in none of the great spotted woodpecker. Substantial spatial genetic structure and a significant correlation between genetic and geographic distances were found in the middle spotted woodpecker, but only weak spatial genetic structure and no significant correlation between genetic and geographic distances in the great spotted woodpecker. Finally, estimated levels of contemporary gene flow did not differ between the two species. Results are consistent with all but one expectations of the SGVH. This study adds to the relatively few investigations addressing the SGVH in terrestrial vertebrates.

Genetic differentiation of a critically endangered population of the limpet Patella candei candei d’Orbigny, 1840, in the Canary Islands - Javier Quinteiro; Gustavo González-Lorenzo; Dailo Hernández-Reyes; Lara Quinteiro; Rogelio Herrera-Pérez; Juán Martínez-Barrio; José Antonio González; Manuel Rey-Méndez; Nieves González-Henríquez (Conservation Genetics, 2022)
The adoption of measures to protect the viability of threatened populations should be supported by empirical data identifying appropriate conservation units and management strategies. The global population of the majorera limpet, P. candei candei d’Orbigny, 1840, is restricted to the Macaronesian islands in the NE Atlantic, including near-to-extinct and healthy populations in Fuerteventura and Selvagens, respectively. The taxonomic position, genetic diversity and intra- and interspecific relationships of these populations are unclear, which is hindering the implementation of a recovery plan for the overexploited majorera limpet on Fuerteventura. In this study, ddRAD-based genome scanning was used to overcome the limitations of mitochondrial DNA-based analysis. As a result, P. candei candei was genetically differentiated from the closely related P. candei crenata for the first time. Moreover, genetic differentiation was detected between P. candei candei samples from Selvagens and Fuerteventura, indicating that translocations from the healthy Selvagens source population are inadvisable. In conclusion, the majorera limpet requires population-specific management focused on the preservation of exceptional genetic diversity with which to face future environmental challenges.

Global distribution of cryptic native, introduced and hybrid lineages in the widespread estuarine amphipod Ampithoe valida - Katherine E. Harper; Lauren A. Scheinberg; Katharyn E. Boyer; Erik E. Sotka (Conservation Genetics, 2022)

Genomics facilitates evaluation and monitoring of McCloud River Redband Trout (Oncorhynchus mykiss stonei) - Ensieh Habibi; Michael R. Miller; Daphne Gille; Leigh Sanders; Jeff Rodzen; Grace M. Aurniger; Molly Stephens; Amanda J. Finger (Conservation Genetics, 2022)
The McCloud River Redband Trout (MRRT; Oncorhynchus mykiss stonei ) is a unique subspecies of rainbow trout that inhabits the isolated Upper McCloud River of Northern California. A major threat to MRRT is introgressive hybridization with non-native rainbow trout from historical stocking and contemporary unauthorized introductions. To help address this concern, we collected RAD-sequencing data on 308 total individuals from MRRT and other California O. mykiss populations and examined population structure using Principal Component and admixture analyses. Our results are consistent with previous studies; we found that populations of MRRT in Sheepheaven, Swamp, Edson, and Moosehead creeks are nonintrogressed. Additionally, we saw no evidence of introgression in Dry Creek, and suggest further investigation to determine if it can be considered a core MRRT conservation population. Sheepheaven Creek was previously thought to be the sole historical lineage of MRRT, but our analysis identified three: Sheepheaven, Edson, and Dry creeks, all of which should be preserved. Finally, we discovered diagnostic and polymorphic SNP markers for monitoring introgression and genetic diversity in MRRT. Collectively, our results provide a valuable resource for the conservation and management of MRRT.

Landscape genetics of an endangered salt marsh endemic: Identifying population continuity and barriers to dispersal - Mark J. Statham; Cody M. Aylward; Laureen Barthman-Thompson; Elizabeth M. Kierepka; Benjamin N. Sacks (Conservation Genetics, 2022)
Preserving the genetic diversity of endangered species is fundamental to their conservation and requires an understanding of genetic structure. In turn, identification of landscape features that impede gene flow can facilitate management to mitigate such obstacles and help with identifying isolated populations. We conducted a landscape genetic study of the endangered salt marsh harvest mouse ( Reithrodontomys raviventris ), a species endemic to the coastal marshes of the San Francisco Estuary of California. We collected and genotyped > 500 samples from across the marshes of Suisun Bay which contain the largest remaining tracts of habitat for the species. Cluster analyses and a population tree identified three geographically discrete populations. Next, we conducted landscape genetic analyses at two scales (the entire study area and across the Northern Marshes) where we tested 65 univariate models of landscape features and used the best supported to test multivariable analyses. Our analysis of the entire study area indicated that open water and elevation (> 2 m) constrained gene flow. Analysis of the Northern Marshes, where low elevation marsh habitat is more continuous, indicated that geographic distance was the only significant predictor of genetic distance at this scale. The identification of a large, connected population across Northern Marshes achieves a number of recovery targets for this stronghold of the species. The identification of landscape features that act as barriers to dispersal enables the identification of isolated and vulnerable populations more broadly across the species range, thus aiding conservation prioritization.

Genetic diversity and structure of an endangered medicinal plant species (Pilocarpus microphyllus) in eastern Amazon: implications for conservation - Waleria Pereira Monteiro; Jeronymo Dalapicolla; Carolina Silva Carvalho; Jamille Costa Veiga; Santelmo Vasconcelos; Silvio Junio Ramos; Markus Gastauer; Rodolfo Jaffé; Cecílio Frois Caldeira (Conservation Genetics, 2022)

Speciation with gene flow in a narrow endemic West Virginia cave salamander (Gyrinophilus subterraneus) - Evan H. Campbell Grant; Kevin P. Mulder; Adrianne B. Brand; Douglas B. Chambers; Addison H. Wynn; Grace Capshaw; Matthew L. Niemiller; John G. Phillips; Jeremy F. Jacobs; Shawn R. Kuchta; Rayna C. Bell (Conservation Genetics, 2022)

Genomic population structure of Grass Pickerel (Esox americanus vermiculatus) in Canada: management guidance for an at-risk fish at its northern range limit - Nathan K. Lujan; Julia E. Colm; Jason T. Weir; Fielding A. Montgomery; Brice P. Noonan; Nathan R. Lovejoy; Nicholas E. Mandrak (Conservation Genetics, 2022)

Parentage assignment reveals multiple paternity in the critically-endangered Guatemalan beaded lizard (Heloderma charlesbogerti) - Brenna A. Levine; Robert. L. Hill; Joseph R. Mendelson; Warren Booth (Conservation Genetics, 2022)

Assessing the genetic consequences of habitat fragmentation on the federally threatened cheat mountain salamander (Plethodon nettingi): a comparative, multi-locus approach - Lauren Rowan; Brian Arbogast; Stephanie Jill Kamel (Conservation Genetics, 2022)

Population genomics study for the conservation management of the endangered shrub Abeliophyllum distichum - Jung-Hoon Lee; Homervergel G. Ong; Bo-Yun Kim; Yong-In Kim; Eui-Kwon Jung; Myong Gi Chung; Young-Dong Kim (Conservation Genetics, 2022)
Natural monuments are IUCN Category III protected areas that play an important role in biodiversity conservation as they provide species refuge and allow species migration. Despite their status, natural monuments are often confined to cultural and fragmented landscapes due to anthropogenic land-use demands. In this population genomic study, we surveyed 11 populations of the endemic shrub Abeliophyllum distichum Nakai (Oleaceae), including five natural monument habitats, covering its range-wide distribution in South Korea. Using 2,254 SNPs as markers, our results showed a mean expected heterozygosity ( He ) of 0.319, with populations in the central distribution showing significantly higher He than those at the periphery. There was no significant heterozygote deficiency and inbreeding among studied populations overall ( F IS = −0.098), except for a single natural monument population (GS-NM147). Population structure and differentiation was moderate to high ( F ST = 0.196), while recent gene flow between populations appeared weak, which can be attributed to the fragmented distribution and the outcrossing mating system of the heterostylous plant. Based on these findings, we provide suggestions for the population conservation and management of this endangered species.

Transcriptome annotation reveals minimal immunogenetic diversity among Wyoming toads, Anaxyrus baxteri - Kara B. Carlson; Dustin J. Wcisel; Hayley D. Ackerman; Jessica Romanet; Emily F. Christiansen; Jennifer N. Niemuth; Christina Williams; Matthew Breen; Michael K. Stoskopf; Alex Dornburg; Jeffrey A. Yoder (Conservation Genetics, 2022)

Investigations on origin and status of a Faxonius crayfish population in the upper James River Basin, Virginia - Paul R Cabe; Morgan D. T. Frost; Bradleigh E. Navalsky; Zachary J. Loughman (Conservation Genetics, 2022)

Inbreeding is associated with shorter early-life telomere length in a wild passerine - Michael Le Pepke; Alina K. Niskanen; Thomas Kvalnes; Winnie Boner; Bernt-Erik Sæther; Thor Harald Ringsby; Henrik Jensen (Conservation Genetics, 2022)
Inbreeding can have negative effects on survival and reproduction, which may be of conservation concern in small and isolated populations. However, the physiological mechanisms underlying inbreeding depression are not well-known. The length of telomeres, the DNA sequences protecting chromosome ends, has been associated with health or fitness in several species. We investigated effects of inbreeding on early-life telomere length in two small island populations of wild house sparrows ( Passer domesticus ) known to be affected by inbreeding depression. Using genomic measures of inbreeding we found that inbred nestling house sparrows ( n = 371) have significantly shorter telomeres. Using pedigree-based estimates of inbreeding we found a tendency for inbred nestling house sparrows to have shorter telomeres ( n = 1195). This negative effect of inbreeding on telomere length may have been complemented by a heterosis effect resulting in longer telomeres in individuals that were less inbred than the population average. Furthermore, we found some evidence of stronger effects of inbreeding on telomere length in males than females. Thus, telomere length may reveal subtle costs of inbreeding in the wild and demonstrate a route by which inbreeding negatively impacts the physiological state of an organism already at early life-history stages.

Population genetics of three at-risk tiger beetles Habroscelimorpha dorsalis dorsalis, H. d. media, and Ellipsoptera puritana - David C. Kazyak; Aaron W. Aunins; Shannon L. White; Michael S. Eackles; C. Barry Knisley (Conservation Genetics, 2022)

Genome-wide SNPs detect fine-scale genetic structure in threatened populations of squirrel glider Petaurus norfolcensis - Monica L. Knipler; Mark Dowton; John Clulow; Ninon Meyer; Katarina M. Mikac (Conservation Genetics, 2022)
Australian arboreal mammals are experiencing significant population declines, particularly due to land clearing and resulting habitat fragmentation. The squirrel glider, Petaurus norfolcensis , is a threatened species in New South Wales, with a stronghold population in the Lake Macquarie Local Government Area (LGA) where fragmentation due to urbanization is an ongoing problem for the species conservation. Here we report on the use of squirrel glider mitochondrial (385 bp cytochrome b gene, 70 individuals) and nuclear DNA (6,834 SNPs, 87 individuals) markers to assess their population genetic structure and connectivity across 14 locations sampled in the Lake Macquarie LGA. The mitochondrial DNA sequences detected evidence of a historical genetic bottleneck, while the genome-wide SNPs detected significant population structure in the Lake Macquarie squirrel glider populations at scales as fine as one kilometer. There was no evidence of inbreeding within patches, however there were clear effects of habitat fragmentation and biogeographical barriers on gene flow. A least cost path analysis identified thin linear corridors that have high priority for conservation. These areas should be protected to avoid further isolation of squirrel glider populations and the loss of genetic diversity through genetic drift.

Genetic variation in lowland and mountain populations of Tofieldia calyculata and their ability to survive within low levels of genetic diversity - Tomáš Vlasta; Zuzana Münzbergová (Conservation Genetics, 2022)

A genomic perspective on the conservation status of the endangered Nashville crayfish (Faxonius shoupi) - Carla Hurt; Parker Hildreth; Carl Williams (Conservation Genetics, 2022)

Selection and localised genetic structure in the threatened Manauense Harlequin Frog (Bufonidae: Atelopus manauensis) - Rafael Filgueira Jorge; Albertina Pimentel Lima; Adam James Stow (Conservation Genetics, 2022)

Landscape genetic connectivity in European wildcat (Felis silvestris silvestris): a matter of food, shelters and demographic status of populations - Elodie Portanier; François Léger; Laurence Henry; Thibault Gayet; Guillaume Queney; Sandrine Ruette; Sébastien Devillard (Conservation Genetics, 2022)

Population structure and genetic diversity of the threatened pygmy newt Triturus pygmaeus in a network of natural and artificial ponds - Eva M. Albert; Vicente García-Navas (Conservation Genetics, 2022)
Pond physical characteristics (connectivity, hydroperiod) have shown to be highly relevant in explaining species presence, reproductive success, and survival in breeding-pond amphibians. However, few studies have addressed the influence that these factors may have on the genetic variability of pond populations. We examined genetic variation at 11 microsatellite loci in Iberian endemic, the pygmy newt ( Triturus pygmaeus ), from 58 breeding ponds in the Doñana National Park (Andalusia), including both temporary ponds and artificially deepened ponds that remain wet during the whole year. Temporary ponds are located in the North part of the region where the surrounding habitat-wet meadows-facilitates the connectivity among populations, whereas the deepest ponds (‘zacallones’) are located in the southern edge embedded in a matrix of unsuitable habitat (thickets and dry underbrush). We investigated genetic diversity and structure within and among ponds. Our results show that both regions (Doñana-North and Doñana-South) are well-differentiated and form two main clusters. We found higher genetic diversity within ponds from the North region, which also exhibited a higher degree of genetic admixture in comparison with populations from the southern edge. Although we found an isolation-by-distance pattern within each cluster, it arose due to the effect of a few isolated ponds located on the edge of each zone, suggesting the existence of substantial gene flow between ponds in the core area. According to our findings, landscape’s permeability to movement (pond connectivity) may constitute a more important factor than hydroperiod length in determining the genetic diversity and viability of pygmy newt populations in this area. Although Doñana populations show a good state, more peripheral and isolated populations present a more worrisome condition as a result of fragmentation and thus, require conservation efforts. Our study provides key insights that could help guide management practices of this threatened and poorly-studied salamander.

The Balkan chamois, an archipelago or a peninsula? Insights from nuclear and mitochondrial DNA - Andrea Rezić; Laura Iacolina; Elena Bužan; Toni Safner; Ferdinand Bego; Dragan Gačić; Vladimir Maletić; Georgi Markov; Dragana Milošević; Haritakis Papaioannou; Nikica Šprem (Conservation Genetics, 2022)

Strong population genetic structure and cryptic diversity in the Florida bonneted bat (Eumops floridanus) - James D. Austin; Jeffery A. Gore; John S. Hargrove; Elizabeth C. Braun de Torrez; Celine M. Carneiro; Frank N. Ridgley; Samantha M. Wisely (Conservation Genetics, 2022)

Population genetics, demographic and evolutionary history of the Dudley’s lousewort (Pedicularis dudleyi), a rare redwood forest specialist - Tracy M. Misiewicz; Christopher Hauser; Benjamin E. Carter (Conservation Genetics, 2022)

Genetic recruitment patterns are patchy and spatiotemporally unpredictable in a deep-water snapper (Lutjanus vivanus) sampled in fished and protected areas of western Puerto Rico - Stuart C. Willis; Christopher M. Hollenbeck; Jonathan B. Puritz; David S. Portnoy (Conservation Genetics, 2022)

Restoring marble trout genes in the Soča River (Slovenia) - Patrick Berrebi; Dušan Jesenšek; Martin Laporte; Alain J. Crivelli (Conservation Genetics, 2022)

Exploring the effect of 195 years-old locks on species movement: landscape genetics of painted turtles in the Rideau Canal, Canada - Audrey Turcotte; Gabriel Blouin-Demers; Dany Garant (Conservation Genetics, 2022)

Conservation genomics of an Australian cycad Cycas calcicola, and the Absence of Key Genotypes in Botanic Gardens - James A. R. Clugston; Markus Ruhsam; Gregory J. Kenicer; Murray Henwood; Richard Milne; Nathalie S. Nagalingum (Conservation Genetics, 2022)