The European Association of Zoos and Aquariums (EAZA) manages insurance populations for hundreds of species through its EAZA ex situ programs (EEPs). EEPs help safeguard against extinction in the wild and provide source populations for genetic rescue programs. However, like wild populations, populations in EEPs are at risk of genomic erosion, undermining population viability. Current population management is based on studbook...

Integrating in‐situ (wild) and ex‐situ (captive) conservation efforts can mitigate genetic diversity loss and help prevent extinction of endangered wild populations. The whooping crane ( Grus americana ) experienced severe population declines in the 18th century, culminating in a collapse to ~20 individuals by 1944. Legal protections and conservation actions have since increased the census population from a stock of 16 individ...

The Pinus mugo complex ( P. mugo Turra s. l. or P. mugo aggregate) is an important fragment of European dendroflora, which is characterized by high variability, reticulate evolution, and several hybrid zone populations in different parts of Europe. Here we tried to explore the admixture structure of four putative hybrid zones between P. mugo Turra (s. str.) and P. sylvestris L. in Slovakia, using Bayesian ancestry inference wi...

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 ba...

Invasions by fungal plant pathogens pose a significant threat to the health of agricultural ecosystems. Despite limited standing genetic variation, many invasive fungal species can adapt and spread rapidly, resulting in significant losses to crop yields. Here, we report on the population genomics of Colletotrichum truncatum , a polyphagous pathogen that can infect more than 460 plant species, and an invasive pathogen of soybea...

Cryptosporidium parvum is a globally distributed zoonotic pathogen and a major cause of diarrhoeal disease in humans and ruminants. The parasite's life cycle comprises an obligatory sexual phase, during which genetic exchanges can occur between previously isolated lineages. Here, we compare 32 whole genome sequences from human‐ and ruminant‐derived parasite isolates collected across Europe, Egypt and China. We identify three s...

The pink pigeon ( Nesoenas mayeri ) is an endemic species of Mauritius that has made a remarkable recovery after a severe population bottleneck in the 1970s to early 1990s. Prior to this bottleneck, an ex situ population was established from which captive‐bred individuals were released into free‐living subpopulations to increase population size and genetic variation. This conservation rescue led to rapid population recovery to...

Natural host populations differ in their susceptibility to infection by parasites, and these intrapopulation differences are still an incompletely understood component of host‐parasite dynamics. In this study, we used controlled infection experiments with wild‐caught guppies ( Poecilia reticulata ) and their ectoparasite Gyrodactylus turnbulli to investigate the roles of local adaptation and host genetic composition (immunogen...

The major histocompatibility complex (MHC) plays an important role in infectious disease resistance. The presence of certain MHC alleles and functionally similar groups of MHC alleles (i.e., supertypes) has been associated with resistance to particular parasite species. Farmed and domesticated fish stocks are often depleted in their MHC alleles and supertype diversity, possibly as a consequence of artificial selection for desi...

Aphids present an ideal system to study epigenetics as they can produce diverse, but genetically identical, morphs in response to environmental stimuli. Here, using whole genome bisulphite sequencing and transcriptome sequencing of the green peach aphid ( Myzus persicae ), we present the first detailed analysis of cytosine methylation in an aphid and investigate differences in the methylation and transcriptional landscapes of...

Plant immune genes, or resistance genes, are involved in a co‐evolutionary arms race with a diverse range of pathogens. In agronomically important grasses, such R genes have been extensively studied because of their role in pathogen resistance and in the breeding of resistant cultivars. In this study, we evaluate the importance of recombination, mutation and selection on the evolution of the R gene complex Rp1 of Sorghum , Tri...

Predation pressure can alter the morphology, physiology, life history, and behavior of prey; each of these in turn can change how surviving prey interact with parasites. These trait‐mediated indirect effects may change in direction or intensity during growth or, in sexually dimorphic species, between the sexes. The Trinidadian guppy, Poecilia reticulata presents a unique opportunity to examine these interactions; its behaviora...

The genotyping of highly polymorphic multigene families across many individuals used to be a particularly challenging task because of methodological limitations associated with traditional approaches. Next‐generation sequencing ( NGS ) can overcome most of these limitations, and it is increasingly being applied in population genetic studies of multigene families. Here, we critically review NGS bioinformatic approaches that hav...

Population bottlenecks can restrict variation at functional genes, reducing the ability of populations to adapt to new and changing environments. Understanding how populations generate adaptive genetic variation following bottlenecks is therefore central to evolutionary biology. Genes of the major histocompatibility complex (MHC) are ideal models for studying adaptive genetic variation due to their central role in pathogen rec...

Adaptation of guppies ( Poecilia reticulata ) to contrasting upland and lowland habitats has been extensively studied with respect to behaviour, morphology and life history traits. Yet population history has not been studied at the whole‐genome level. Although single nucleotide polymorphisms (SNPs) are the most abundant form of variation in many genomes and consequently very informative for a genome‐wide picture of standing na...

Genetic variation in many invasive species shows little or no signs of a founder event, suggesting that high genetic diversity may facilitate establishment success. The rocky‐shore, plankton‐feeding cichlid fish Cynotilapia afra is endemic to Lake Malawi, but naturally absent from many suitable sites. In the 1960s, this species was introduced to the southern areas of the lake, presumably as a result of the aquarium fish trade....

Ex situ conservation is of increasing importance to prevent the extinction of endangered animals in the wild. Despite low success rates of reintroduction programs few researchers have investigated empirically the efficacy of captive breeding regimes for the release of captive‐bred vertebrates. We used guppies ( Poecilia reticulata ) from two populations in Trinidad to compare different conservation breeding regimes. The upper...