The Pecos pupfish, Cyprinodon pecosensis , is an imperilled freshwater fish found in arid regions of Texas and New Mexico (USA). The species faces multiple challenges to persistence including reductions in suitable habitat, water shortages, as well as hybridization and competition with an introduced congener (sheepshead minnow, C. variegatus ). As part of the current management strategy, refuge populations, seeded with non‐int...

The Leon Springs pupfish, Cyprinodon bovinus , is federally listed as endangered and currently confined to spring-fed pools on the Diamond Y Spring Preserve in Pecos County, Texas, USA. A refuge population is maintained by U.S. Fish and Wildlife Service in Dexter, New Mexico, USA because of ongoing threats from hybridization with the introduced congener, the sheepshead minnow, C. variegatus. To inform continued conservation an...

Whole‐genome sequencing (WGS) has greatly expanded researchers' ability to study structural variants (SVs), that is, the variation in the presence, number, orientation or position of a DNA sequence. This has paved the way to study the eco‐evolutionary dynamics of SVs across the tree of life and within a population genomics framework. In this review, we provide the necessary fundamentals to help researchers generate and analyse...

A major goal of speciation research is identifying loci that underpin barriers to gene flow. Population genomics takes a ‘bottom‐up’ approach, scanning the genome for molecular signatures of processes that drive or maintain divergence. However, interpreting the ‘genomic landscape’ of speciation is complicated, because genome scans conflate multiple processes, most of which are not informative about gene flow. However, studying...

Inferring genealogical relationships of wild populations is useful because it gives direct estimates of mating patterns and variance in reproductive success. Inference can be improved by including information about parentage shared between siblings, or by modelling phenotypes or population data related to mating. However, we currently lack a framework to infer parent–offspring relationships, sibships and population parameters...

Marine protected areas (MPAs) are widely implemented tools for long‐term ocean conservation and resource management. Assessments of MPA performance have largely focused on specific ecosystems individually and have rarely evaluated performance across multiple ecosystems either in an individual MPA or across an MPA network. We evaluated the conservation performance of 59 MPAs in California's large MPA network, which encompasses...

Antarctic krill ( Euphausia superba ) are a key component of the Antarctic ecosystem linking primary and some secondary production to higher trophic levels including fish, penguins, seals, and whales. Understanding their response to environmental stimuli therefore provides insights into the trophic ecology of Antarctic systems. This laboratory study quantified the influence of penguin guano, a presumptive predator cue, chlorop...

The presence of cryptic species can hinder effective conservation planning and implementation, as has been the case for speciose groups of freshwater fishes that are difficult to differentiate due to conserved morphologies. The West Texas shiner Notropis megalops and the Texas shiner Notropis amabilis are a cryptic pair of leuciscids (minnows) that co‐occur in spring‐fed tributaries of the Rio Grande in Texas and Mexico. Both...

The future survival of coral reefs in the Anthropocene depends on the capacity of corals to adapt as oceans warm and extreme weather events become more frequent. Targeted interventions designed to assist evolutionary processes in corals require a comprehensive understanding of the distribution and structure of standing variation, however, efforts to map genomic variation in corals have so far focussed almost exclusively on SNP...