Peri E. Bolton

Successful implementation of evolutionary programs to rescue climatically threatened species requires identification of adaptive variation. Although many genotype–environment association methods have been successful in identifying adaptive variation, current approaches can be improved in two important aspects. First, most existing methods do not account for genotype uncertainty in widely available low-coverage whole-genome sequencing data. Researchers often restrict analysis to loci for which genotypes can be inferred reliably or call the most probable genotype, allowing the use of genotype-based methods. However, discarding data and false genotype calls increase the uncertainty in estimates of genetic variation and can introduce systematic biases. Second, most methods use phenomenological approaches, such as logistic regression, to partition estimated variation into adaptive and nonadaptive components. Consequently, current approaches may fail to account for evolutionary processes, such as migration-selection balance. Structured migration between climatically disparate locations can produce deviations from a smooth S-shaped response curve, which can be difficult to accommodate using generalized linear models. To overcome these challenges, we developed a method that accounts for genotype uncertainty in sequencing data and propagates this uncertainty to inform the parameters of an evolutionary model. A key feature of this model is that it describes mechanistically how genetic variation arises from joint interactions between local adaptation, structured migration, mutation, and drift. Our synthetic simulation tests reveal that accounting for genotype uncertainty and structured migration substantially reduces false negatives. We also applied our approach to analyze data on North American rosy-finches (3.7 million SNPs), a high-alpine, climatically threatened clade of bird species.

Evolutionary potential, the capacity to evolve in response to environmental change, is important for the persistence of threatened species. This potential is diminished by genetic drift in small populations, causing the loss of genetic diversity and reduced efficiency of selection. We introduce an approach to evaluate evolutionary potential that integrates across these components by conducting genome‐scale selection analyses of genes of ecological importance. We inferred selection in small populations of the endangered eastern massasauga rattlesnake ( Sistrurus catenatus ) by comparing summary statistics between background regions and focal adaptive gene families underlying the Major Histocompatibility Complex and venom protein phenotypes. We applied tests sensitive to selection at multiple timescales to populations that have experienced differential declines and compared results with an outbred population of the sister species, S. tergeminus . We detected signatures of selection in focal regions in the recent and distant past, suggesting balancing selection as a dominant force shaping genetic diversity underlying these traits. Recently declined S. catenatus populations exhibited weaker signals of recent selection, consistent with reduced efficiency of selection when effective population size is small. Drift has reduced genome‐wide genetic diversity both in relatively large and recently declined S. catenatus populations compared to outbred S. tergeminus , but these reductions were less pronounced in focal adaptive regions. These findings suggest that selection has buffered the loss of adaptive variation, but that small populations of these snakes may be approaching a critical loss of evolutionary potential limiting their capacity to respond to human‐induced environmental change.

Captive breeding can be a key component of species conservation strategies, but also exposes these rare species to novel environments including the pathogen landscape. The critically endangered white‐winged wood duck (WWWD) Asarcornis scutulata has experienced substantial population declines, local extirpations and fragmentation of its former range in Southeast Asia, making it one of the rarest birds in the world. As in other rare species, WWWD declines have led to the initiation of captive breeding programs, but these have been hampered by the WWWDs' high susceptibility to Mycobacterium avium , avian tuberculosis (TB). In this study we describe genome‐wide patterns of diversity to understand the WWWD's demographic and phylogeographic history, inbreeding in the wild and in captivity, and the causes of TB susceptibility. Captive birds, which originated from northeast India, are genetically differentiated from wild birds sampled in Sumatra, Indonesia, likely reflecting long‐standing phylogeographic structure. Demographic analyses revealed that long‐term (Pleistocene) population declines preceded anthropogenic declines, a pattern shared with other codistributed, forest‐dependent species. All sampled WWWD populations had extremely low genetic diversity ( π = 0.0008–0.0015) but wild‐sampled birds retained higher Major Histocompatibility Complex (MHC) diversity, reflecting important functional diversity in the wild. Genetic diversity has eroded over time in captivity and importantly, birds with higher levels of inbreeding succumb earlier to TB infections, suggesting inbreeding depression. Finally, by comparing gene expression between susceptible WWWD and resistant redhead ducks Aythya americana we identify possible mechanisms of TB susceptibility. Altogether our study provides genomically‐guided objectives for future management and a cautionary tale for ex situ conservation.

Accelerated warming at high elevations is having a disproportionate impact on alpine species. While assessments of climate vulnerability require quantifying the ecological and evolutionary components of adaptive capacity, such assessments are rare, especially in alpine systems. We leverage recent advances in population and landscape genomics to assess how variation in spatial heterogeneity and population connectivity across alpine systems influences adaptive capacity, using the North American Rosy-Finch species complex as a model system. In doing so, we clarify taxonomic relationships across the complex and identify one new ESU, the Sierra Nevada Rosy-Finch, based on its combined ecological and evolutionary distinctiveness. We then illustrate how combining genomic analyses with ecological data can improve estimates of adaptive capacity, sensitivity, and exposure and ultimately clarify climate vulnerability. Overall, our integrative analyses revealed that more isolated lineages, such as the Sierra Nevada Rosy-Finch, have lower adaptive capacity and face disproportionately high risks from climate change. This work highlights how conservation strategies that account for the multidimensional aspects of adaptive capacity can improve estimates of climate vulnerability.

Invasive species that undergo a founder event may experience a decline in genetic diversity yet still establish successful populations. A possible example is a population of the common wall lizard ( Podarcis muralis ) in Cincinnati, Ohio, USA, which was founded following an introduction in the 1950s of a small number of individuals from Europe. We used whole genome sequences of individuals from source and introduced populations to assess the origin, demographic history, population structure, and possible signatures of adaptation in this successful lizard introduction. We first confirmed that the introduced lizards in Ohio are Podarcis muralis using phylogenetic analysis. Patterns of genetic diversity indicate introduced lizards in Cincinnati went through a short‐term bottleneck with increased inbreeding but then rapidly increased in population size, thus minimising losses in genetic diversity. Comparisons of genomic variation between source and introduced populations demonstrate that populations in Cincinnati represent a subset of source genetic variation and show minimal losses of overall genetic diversity. Comparisons of mutation load between source and introduced populations reveal only small increases in load in introduced populations. Finally, tests for selection on the basis of outlier analyses detect targets for potential positive selection in multiple regions of the genome of introduced individuals, suggesting possible adaptation to a novel environment. Overall, we suggest that rapid population growth and possible adaptation have allowed the founding population of introduced lizards to evade the potential negative genetic impacts of small population size and successfully colonise a novel environment.

Disease can impact the long-term viability of threatened species. Levels of genetic variation in disease response genes could influence the magnitude of these impacts, but identifying candidate genes in endangered species is difficult. We used a multifaceted approach to identify candidate genes involved in disease response and resistance of an endangered snake, the eastern massasauga rattlesnake (Sistrurus catenatus), possibly related to an emerging infectious disease, Snake Fungal Disease (SFD). We assessed whether genes differentially expressed in an SFD disease challenge experiment showed patterns of non-neutral evolution in outlier tests of nucleotide diversity and Tajima’s D. We evaluated these patterns in two populations of S. catenatus with varying effective population sizes, and a closely-related non-endangered species, Sistrurus tergeminus. In general, we find reduced diversity in functional sites in S. catenatus relative to the outbred sister species, but not between S. catenatus populations of different sizes. Further, genetic drift in the smaller populations likely limited the number of outlier genes detected. Finally, FST outlier tests identified a small set of protein coding genes that may be linked to local adaptation in disease response. In sum, our approach identified 218 candidate genes that were differentially expressed in response to disease that contain functional variation relevant to disease resistance or defense, pending further validation for SFD specifically. Our results also demonstrate how drift complicates the detection of functional variation in rare species with small population sizes, a process that is essential for assessing adaptive variation and load.

Captive breeding can be a key component of species conservation strategies, but also exposes these rare species to novel environments including the pathogen landscape. The critically endangered white-winged wood duck (WWWD) Asarcornis scutulata has experienced substantial population declines, local extirpations and fragmentation of its former range in South-East Asia, making it one of the rarest birds in the world. Like other rare species, WWWD declines have led to the initiation of captive breeding programs, but these have been hampered by the WWWDs’ high susceptibility to Mycobacterium avium , avian tuberculosis (TB). In this study we describe genome-wide patterns of diversity to understand the WWWD’s demographic and phylogeographic history, inbreeding in the wild and in captivity, and the causes of TB susceptibility. Captive birds, which originated from northeast India, are genetically differentiated from wild birds sampled in Sumatra, Indonesia, likely reflecting long-standing phylogeographic structure. Demographic analyses revealed that long-term (Pleistocene) population declines preceded anthropogenic declines, a pattern shared with other codistributed, forest-dependent species. All sampled WWWD populations had extremely low genetic diversity but wild-sampled birds retained higher Major Histocompatibility Complex (MHC) diversity, reflecting important functional diversity in the wild. Genetic diversity has eroded over time in captivity and importantly, birds with higher levels of inbreeding succumb earlier to TB infections, suggesting inbreeding depression. Finally, by comparing gene expression between susceptible WWWD and resistant redhead ducks Aythya americana we identify possible mechanisms of TB susceptibility in WWWD. Altogether our study provides genomically-guided objectives for future management and a cautionary tale for ex-situ conservation.

Gene flow connects populations and facilitates exchanging alleles, impacting speciation and adaptation. In Panama, lekking golden-collared and white-collared manakins (Manacus vitellinus and M. candei) interbreed in a narrow hybrid zone. Males’ brilliant yellow plumage, principally controlled by the carotenoid metabolism gene BCO2, has introgressed from vitellinus into candei under sexual selection as far as the largest river in the region. Introgression is sharply limited across its lower reaches, but both color forms occur on both banks at its headwaters. Previous authors have therefore speculated that the river is a strong barrier to gene flow. In this study, we used ∼14,000 single nucleotide polymorphisms to test this hypothesis by assessing cross-river genetic differentiation and estimating gene flow. We found that, while the river clearly structured genetic variation, particularly downriver, it did not prevent extensive gene flow upriver. This result mirrors patterns observed at some of the world's largest rivers, albeit on a much smaller scale. It also implicates several alternatives to the barrier hypothesis, including that introgression is still ongoing or that selection for plumage color varies across the river—both rare phenomena to capture in nature. We recommend behavioral studies to further untangle this intriguing case of evolution in action.

In a hybrid zone between two tropical lekking birds, yellow male plumage of one species has introgressed asymmetrically replacing white plumage of another via sexual selection. Here, we present a detailed analysis of the plumage trait to uncover its physical and genetic bases and trace its evolutionary history. We determine that the carotenoid lutein underlies the yellow phenotype and describe microstructural feather features likely to enhance color appearance. These same features reduce predicted water shedding capacity of feathers, a potential liability in the tropics. Through genome-scale DNA sequencing of hybrids and each species in the genus, we identify BCO2 as the major gene responsible for the color polymorphism. The BCO2 gene tree and genome-wide allele frequency patterns suggest that carotenoid-pigmented collars initially arose in a third species and reached the hybrid zone through historical gene flow. Complex interplay between sexual selection and hybridization has thus shaped phenotypes of these species, where conspicuous sexual traits are key to male reproductive success.

The neurogenomic mechanisms mediating male–male reproductive cooperative behaviours remain unknown. We leveraged extensive transcriptomic and behavioural data on a neotropical bird species (Pipra filicauda) that performs cooperative courtship displays to understand these mechanisms. In this species, the cooperative display is modulated by testosterone, which promotes cooperation in non‐territorial birds, but suppresses cooperation in territory holders. We sought to understand the neurogenomic underpinnings of three related traits: social status, cooperative display behaviour and testosterone phenotype. To do this, we profiled gene expression in 10 brain nuclei spanning the social decision‐making network (SDMN), and two key endocrine tissues that regulate social behaviour. We associated gene expression with each bird's behavioural and endocrine profile derived from 3 years of repeated measures taken from free‐living birds in the Ecuadorian Amazon. We found distinct landscapes of constitutive gene expression were associated with social status, testosterone phenotype and cooperation, reflecting the modular organization and engagement of neuroendocrine tissues. Sex‐steroid and neuropeptide signalling appeared to be important in mediating status‐specific relationships between testosterone and cooperation, suggesting shared regulatory mechanisms with male aggressive and sexual behaviours. We also identified differentially regulated genes involved in cellular activity and synaptic potentiation, suggesting multiple mechanisms underpin these genomic states. Finally, we identified SDMN‐wide gene expression differences between territorial and floater males that could form the basis of ‘status‐specific’ neurophysiological phenotypes, potentially mediated by testosterone and growth hormone. Overall, our findings provide new, systems‐level insights into the mechanisms of cooperative behaviour and suggest that differences in neurogenomic state are the basis for individual differences in social behaviour.