Monitoring genetic parameters is important for setting effective conservation and management strategies, particularly for small, fragmented, and isolated populations. Small populations face increased rates of genetic drift and inbreeding, which increase extinction risk especially when gene flow is limited. Here, we applied a Genotyping-in-Thousands by sequencing (GT-seq) panel to inform recovery action for the northern Idaho ground squirrel (Urocitellus brunneus), listed as threatened under the U.S. Endangered Species Act. We evaluated genetic diversity, structure, connectivity, and effective population size to address species recovery goals. We delineated 15 conservation units: (1) three evolutionarily significant units that represent long-term population structure and evolutionary history, (2) nine management units that reflect current demographic connectivity and restrictions to gene flow, and (3) three adaptive units that capture adaptive differentiation across the species range. Effective population sizes per management unit were small overall (mean 38.16, range 2.3-220.9), indicating that recovery goals have not been reached. Our results suggest that connectivity within evolutionarily significant units should be maintained through the restoration of dispersal corridors. We recommend further sampling of subpopulations that harbor unique adaptive differentiation and that are geographically isolated to refine our understanding of adaptive variation. We recommend ongoing genetic monitoring with the same GT-seq marker panel to detect dispersal, assess effective population size, monitor the effects of inbreeding, and evaluate adaptive differentiation to monitor the effects of management action and environmental change. This study provides an illustration of how genetic and genomic tools can inform management and assess recovery goals for a threatened species.

Pygmy rabbits (Brachylagus idahoensis) are closely associated with sagebrush steppe habitat across the western United States, and loss and fragmentation of this habitat has contributed to the near extirpation of the Columbia Basin population in Washington state. The Columbia Basin (WA-CB) pygmy rabbit was listed under the Endangered Species Act in 2003, and recovery efforts have included captive breeding, reintroduction, and genetic rescue with translocation of rabbits from populations across the species range. We used restriction site-associated DNA sequencing (RADseq) to determine population genetic structure across the pygmy rabbit range, test for genomic signatures of adaptive divergence among populations, assess the genetic distinctiveness of the ancestral WA-CB population, and identify loci useful for monitoring ancestry in the current admixed WA-CB population. Our dataset included 9,794 single nucleotide polymorphisms (SNPs) across 123 individuals. We identified four distinct genetic groups: (1) WA-CB, (2) Great Basin (3) northern Utah/Wyoming and (4) southern Utah. The WA-CB population showed the highest degree of genetic distinctiveness using multiple clustering, ordination, and genetic differentiation analyses. Our results highlight the long-term isolation of the WA-CB population as well as historical isolation of other peripheral populations. We identified signatures of putatively adaptive loci among populations, but no significant gene ontology associated with local adaptation. Our results provide SNP loci for monitoring demography and the consequences of genetic rescue efforts in the admixed WA-CB population.

Evolutionary theory predicts that the process of range expansion will lead to differences between core and edge populations in life-history and dispersal traits. Selection and genetic drift can influence reproductive ability, while spatial sorting by dispersal ability can increase dispersal at the edge. However, the context individuals experience (e.g., population density and mating status) also impacts dispersal behavior. We evaluated theoretical predictions for evolution of reproductive life-history and dispersal traits using the range expansion of a biological control agent, Diorhabda carinulata, or northern tamarisk beetle. We found divergence between core and edge populations in fecundity, age at first reproduction, and female body mass. We also show that density and mating status influence dispersal and that dispersal increases at the edge of the range under some conditions. We find support for most predictions about evolution during range expansion, even across a heterogeneous environment, especially when the ecological context is considered.

Madagascar’s Central Highlands are largely composed of grasslands, interspersed with patches of forest. The pre-human extent of these grasslands is a topic of vigorous debate, with conventional wisdom holding that they are anthropogenic in nature and emerging evidence supporting that grasslands were a component of the pre-human Central Highlands vegetation. Here, we shed light on the temporal dynamics of Madagascar’s vegetative composition by conducting a population genomic investigation of Goodman’s mouse lemur (Microcebus lehilahytsara; Cheirogaleidae). These small-bodied primates occur both in Madagascar’s eastern rainforests and in the Central Highlands, which makes them a valuable indicator species. Population divergences among forest-dwelling mammals can serve as a proxy for habitat fragmentation and patterns of post-divergence gene flow can reveal potential migration corridors consistent with a wooded grassland mosiac. We used RADseq data to infer phylogenetic relationships, population structure, demographic models of post-divergence gene flow, and population size change through time. These analyses offer evidence that open habitats are an ancient component of the Central Highlands, and that wide-spread forest fragmentation occurred naturally during a period of decreased precipitation near the last glacial maximum. Models of gene flow suggest that migration across the Central Highlands has been possible from the Pleistocene through the recent Holocene via riparian corridors. Notably, though our findings support the hypothesis that Central Highland grasslands predate human arrival, we also find evidence for human-mediated population declines. This highlights the extent to which species imminently threatened by human-mediated deforestation may be more vulnerable from paleoclimatic changes.

Understanding the neutral (demographic) and adaptive processes leading to the differentiation of species and populations is a critical component of evolutionary and conservation biology. In this context, recently diverged taxa represent a unique opportunity to study the process of genetic differentiation. Northern and southern Idaho ground squirrels (Urocitellus brunneus – NIDGS, and U. endemicus - SIDGS, respectively) are a recently diverged pair of sister species that have undergone dramatic declines in the last 50 years and are currently found in metapopulations across restricted spatial areas with distinct environmental pressures. Here we genotyped single-nucleotide polymorphisms (SNPs) from buccal swabs with restriction site-associated DNA sequencing (RADseq). With these data we evaluated neutral genetic structure at both the inter- and intra-specific level, and identified putatively adaptive SNPs using population structure outlier and genotype-environment association (GEA) analyses. At the interspecific level, we found a clear separation between NIDGS and SIDGS, and evidence for adaptive differentiation relating to differences in hibernation. At the intraspecific level, we identified 3 Evolutionarily Significant Units for NIDGS and 2 for SIDGS plus multiple Management and Adaptive Units. Elevation appears to be the main driver of adaptive differentiation in NIDGS, while neutral variation patterns match and extend that identified in previous studies using microsatellite markers. For SIDGS, neutral substructure generally reflected the effect of natural geographic barriers, while adaptive variation reflected differences in land cover and temperature. These results clearly highlight the roles of neutral and adaptive processes for understanding species and population differentiation, which can have important conservation implications in threatened species.

Biodiversity is under threat worldwide. Over the past decade, the field of population genomics has developed across non-model organisms, and the results of this research have begun to be applied in conservation and management of wildlife species. Genomics tools can provide precise estimates of basic features of wildlife populations, such as effective population size, inbreeding, demographic history, and population structure, that are critical for conservation efforts. Moreover, population genomics studies can identify particular genetic loci and variants responsible for inbreeding depression or adaptation to changing environments, allowing for conservation efforts to estimate the capacity of populations to evolve and adapt in response to environmental change and to manage for adaptive variation. While connections from basic research to applied wildlife conservation have been slow to develop, these connections are increasingly strengthening. Here we review the primary areas in which population genomics approaches can be applied to wildlife conservation and management, highlight examples of how they have been used, and provide recommendations for building on the progress that has been made in this field.

Maintenance of a portfolio of adaptive alleles may provide resilience of populations to natural environmental variability. We used Pacific ocean perch (POP; Sebastes alutus) to test for the maintenance of adaptive variation across overlapping generations. POP are a long-lived species characterized by widespread larval dispersal in their first year and a longevity of over 100 years. In order to understand how early marine dispersal affects POP survival and population structure, we used Restriction Site Associated DNA sequencing (RADseq) to obtain 11,146 single-nucleotide polymorphisms (SNPs) from 401 young-of-the-year (YOY) POP collected during surveys conducted in 2014 (19 stations) and 2015 (4 stations) in the eastern Gulf of Alaska. Population clustering analysis showed that the POP samples represented four distinct ancestral populations mixed throughout the sampling area. Based on prior work on larval dispersal of POP, these larvae are most likely from distinct parturition locations that are mixing during their pelagic dispersal life stage. Latent factor mixed models revealed that POP larvae face significant selection during their first year at sea, which were specific to the year of their birth. Thus each adult cohort’s genetic composition is heavily influenced by the environmental conditions experienced during their first year at sea. Long-lived species relying on broadcast spawning strategies may therefore be uniquely resilient to environmental variability by maintaining a portfolio of cohort-specific adaptive genotypes, and age truncation due to overfishing of older cohorts may have detrimental effect on the population viability.