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Recent research suggests that bird populations are declining at alarming rates across the United States. Over the last century, local, national, and international efforts to limit declines in bird populations have resulted in state and federal laws that now protect most of California’s 650 bird species. To comply with these protections, transportation infrastructure projects often face strict mitigation requirements, which can be expensive and cause delays. Understanding a project’s effects on specific bird populations can refine mitigation requirements and optimize infrastructure planning.The tools for identifying separate populations within species and understanding protected birds’ seasonal movement have been limited until recently. New genetic and genomic tools now provide a method for understanding population differentiation, which is vital to a wide array of conservation goals including estimating population declines, identifying potential for adaptation to stressors, measuring connectivity between populations, and estimating inbreeding. Because infrastructure projects can directly impact genetic diversity and connectivity, a toolkit to assess population structure and the distribution of genetic variation could aid in predicting and mitigating the impacts of such projects. As a test case, researchers at the University of California, Davis, sequenced entire genomes for 40 individual Anna’s hummingbirds (Calypte anna) from across California to identify breeding populations and develop a genetic toolkit to assign individuals to those populations. The presence of this species at bridge construction sites has resulted in construction delays in part because little information exists on the status of different populations within the species.This research brief summarizes findings and implications from the project.View the NCST Project Webpage

Recent studies have highlighted alarming rates of declines in bird populations across the country. The State of California is home to over 650 resident and migrant avian species. Legislation for protecting these species has existed for over a century now, yet tools for identifying populations and understanding seasonal movement remain limited. Recently, genetic and genomic tools have provided a method for understanding population structure, allowing for more informed delineation of management units. The goal of this project was to create a genetic toolkit for identifying breeding populations and assigning individuals to those populations. Ultimately, such tools could be used to assess population-level impacts when there are conflicts with birds at infrastructure construction sites. As a test case, we sequenced entire genomes for 40 individual Anna’s hummingbirds (Calypte anna) from across the state. Based on this initial data, we found low levels of differentiation between sampled locations, suggesting that C. anna in California are not subdivided into different population units. However, there was a weak signal of geography suggesting there may be localized genetic differences in a small proportion of the genome. Follow-up work will focus on a broader sampling across the state of California to clarify any possible population subdivision or geographical patterns of differentiation.View the NCST Project Webpage

In animals, introgression between species is often perceived as the breakdown of reproductive isolating mechanisms, but gene flow between incipient species can also represent source for potentially beneficial alleles. Recently, genome-wide datasets have revealed clusters of differentiated loci (‘genomic islands of divergence’) that are thought to play a role in reproductive isolation and therefore have reduced gene flow. We use simulations to further examine the evolutionary forces that shape and maintain genomic islands of divergence between two subspecies of the migratory songbird, Swainson's thrush (Catharus ustulatus), which have come into secondary contact since the last glacial maximum. We find that, contrary to expectation, gene flow is high within islands and is highly asymmetric. In addition, patterns of nucleotide diversity at highly differentiated loci suggest selection was more frequent in a single ecotype. We propose a mechanism whereby beneficial alleles spread via selective sweeps following a post-glacial demographic expansion in one subspecies and move preferentially across the hybrid zone. We find no evidence that genomic islands are the result of divergent selection or reproductive isolation, rather our results suggest that differentiated loci both within and outside islands could provide opportunities for adaptive introgression across porous species boundaries.

In animals, introgression between species is often perceived as the breakdown of reproductive isolating mechanisms, but gene flow between incipient species can also represent source for potentially beneficial alleles. Recently, genome-wide datasets have revealed clusters of differentiated loci (‘genomic islands of divergence’) that are thought to play a role in reproductive isolation and therefore have reduced gene flow. We use simulations to further examine the evolutionary forces that shape and maintain genomic islands of divergence between two subspecies of the migratory songbird, Swainson's thrush (Catharus ustulatus), which have come into secondary contact since the last glacial maximum. We find that, contrary to expectation, gene flow is high within islands and is highly asymmetric. In addition, patterns of nucleotide diversity at highly differentiated loci suggest selection was more frequent in a single ecotype. We propose a mechanism whereby beneficial alleles spread via selective sweeps following a post-glacial demographic expansion in one subspecies and move preferentially across the hybrid zone. We find no evidence that genomic islands are the result of divergent selection or reproductive isolation, rather our results suggest that differentiated loci both within and outside islands could provide opportunities for adaptive introgression across porous species boundaries.