Environmental change reshapes species’ distributions and abundances globally, yet the numerous ways genetic variation, life-history, and climate change influence population dynamics remain poorly understood. Using 316 whole-genomes from 21 subspecies of resident and migrant song sparrows (Melospiza melodia) across western North America, we tested whether population growth was predicted by genomic offset—the mismatch between a population’s current climate-adapted genomic composition and that predicted as optimal under future or spatially distinct climates. Genomic offset explained 59% of the variation in population growth from 2001-11 to 2012-22. While genomic offsets were similar in migrant and resident populations, residents declined, especially where thermal and/or hydric stress increased, whereas migrants increased where climatic limits on population growth were ameliorated. Our results support that genomic offset can predict the dynamics of locally adapted species, highlight the potential utility of such models in conservation, and suggest seasonal migration may mitigate maladaptation to environmental change in mobile animals.

Many North American game animals experienced severe population declines during the 19th century due to market hunting. However, estimates of the timing and magnitude of these declines often relies on anecdotal evidence, which makes it difficult to understand the lasting impacts of hunting pressures versus climate or landscape changes on the genetic diversity of contemporary populations. Historical reports suggest the California quail (Callipepla californica) suffered more significant hunting pressure in the late 19th century relative to either Gambel’s (Callipepla gambelii) or mountain quail (Oreortyx pictus). Genomic data can help illuminate the extent to which historical exploitation molded the genetic health of modern quail populations. We compared whole genome sequences from these three quail species to evaluate whether reported differences in hunting pressure affected contemporary patterns of genetic diversity. Contrary to our expectations, California quail did not exhibit any evidence for population declines until the late 20th century, long after the era of market hunting ended. California quail also exhibited the highest levels of genetic diversity across most analyses with evidence for population expansion over the past 500,000 years. In contrast, Gambel’s quail appears to have suffered a recent bottleneck in association with a major drought that impacted the desert southwest during the mid-20th century. Gambel’s quail also exhibited increased realized genetic load for mild and moderately deleterious genetic variants. Together, our results demonstrate that market hunting had little lasting impact on the genetic diversity of these quail species, whereas landscape and climate changes have led to fluctuations in effective population size (Ne) and the buildup of genetic load.

Museum specimens offer a unique and powerful tool for understanding the impact of anthropogenic change on populations over time. Morphological traits can be impacted by many different environmental variables that are difficult to separate from one another as potential driving factors. Comparative analyses among similar species jointly experiencing change in the same environmental variables can help pinpoint the selective pressures driving temporal morphological change. We assessed temporal change in bill size, tarsus length, and body size between six species of songbirds from the San Francisco Bay Area over the past 150 years. Proxies for body size (wing and tarsus length) exhibited idiosyncratic temporal changes among species. In contrast, we found a significant increase in bill surface area across all but one species. Quantile regression analyses on bill size variation additionally revealed that temporal increases over the past century have been driven by increases in the largest bill sizes in some species, but increases in the smallest bills over time in others. The climate variables best explaining temporal change in bill size also differed among species with some species responding more to changing summer variables (e.g. maximum annual temperature) and others in response to a changing winter climate. These results together suggest that different sympatric, resident bird species may be experiencing temporal morphological change in response to selective pressures experienced at different seasons. Our finding provides support for the season of critical thermal stress hypothesis that suggests variation in functional traits will be shaped by the season that imposes the greatest selective force on a population. Overall, this study has important implications for future research on the role of bills in thermoregulation and for conservation efforts based on the adaptive capacity of birds to respond to climate change.