Biology subjects

Bolton, P. E.

Publications and source records attributed to Bolton, P. E..

5 recordsLinked to original sources

bioRxiv2026

Loss of Adaptive Capacity Drives Climate Vulnerability Across Taxonomic Scales in an Alpine Specialist Species Complex

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.

evolutionary biology↗

bioRxiv2026

Identifying adaptive variation in spatially structured populations using low-coverage whole-genome sequencing data

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 non-adaptive 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-shape 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.

genomics↗

bioRxiv2025

Inbreeding depression and tuberculosis susceptibility in the critically endangered white-winged wood duck Asarcornis scutulata

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 WWWDs 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.

evolutionary biology↗

bioRxiv2022

Neurogenomic landscape of social status-dependent cooperative display behavior

The neurogenomic mechanisms mediating male-male reproductive cooperative behaviors are unknown. We leveraged extensive transcriptomic and behavioral data on a neotropical bird (Pipra filicauda) that perform cooperative courtship displays to understand these mechanisms. Cooperative display is modulated by testosterone, it promotes cooperation in non-territorial birds, but suppresses cooperation in territory holders. We sought to understand the neurogenomic underpinnings of these three related traits: social status, cooperative behavior, 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 behavior. We associated gene expression with each birds behavioral and endocrine profile derived from three 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 signaling appeared to be important in mediating status-specific relationships between testosterone and cooperation, suggesting shared regulatory mechanisms with male aggressive and sexual behaviors. 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 behavior and suggest that differences in neurogenomic state are the basis for individual differences in social behavior.

evolutionary biology↗

bioRxiv2022

Evolution of the Growth Hormone Gene Duplication in Passerine Birds

Birds of the order Passeriformes represent the most speciose radiation of land vertebrates, yet the cause or causes of their elevated species richness have not been satisfactorily explained. One potential key adaptation is their sole lineage-specific gene, a duplicate copy of growth hormone (GH), present in all major lineages of passerines, but in no other group of birds. Growth hormone genes plausibly influence extreme life history traits that passerines exhibit, including the shortest embryo-to-fledging developmental period of any avian order. To unravel the implications of this GH duplication, we investigated the molecular evolution of the ancestral avian GH gene (GH or GH1) and the novel passerine GH paralog (GH2), using 497 gene sequences extracted from 342 genomes. Passerine GH1 and GH2 are reciprocally monophyletic, consistent with a single duplication event from a microchromosome onto a macrochromosome in a common ancestor of extant passerines. Additional chromosomal rearrangements have changed the syntenic and potential regulatory context of these genes. Both passerine GH1 and GH2 paralogs display substantially higher rates of nonsynonymous codon change than non-passerine avian GH, suggesting positive selection following duplication. A site involved in signal peptide cleavage is under selection in both paralogs. Other sites under positive selection differ between the two paralogs, but many are clustered in one region of a 3D model of the protein. Both paralogs retain key functional features and are actively but differentially expressed in two major passerine suborders. These phenomena suggest that growth hormone genes may be evolving novel adaptive roles in passerine birds.

molecular biology↗