About

Rachael Bay is an Associate Professor in the Department of Evolution and Ecology at UC Davis. Her research focuses on the interactions between human-induced environmental changes and evolutionary processes. She studies how animals respond to environmental changes caused by humans and investigates how evolution might mitigate some of the negative impacts of these changes. Her work employs a combination of ecological and physiological experiments along with large-scale genomic and environmental data to understand patterns of evolution associated with anthropogenic impacts across a wide range of non-model animals. Her research aims to inform conservation management decisions by providing a forward-looking understanding of evolutionary responses to environmental change.

Research topics

• Computational biology
• Evolutionary biology
• Biology
• Genetics
• Ecology

Selected publications

• Long-term increases in wing length occur independently of changes in climate and climate-driven shifts in body size

  Proceedings of the Royal Society B Biological Sciences · 2025-01-01 · 10 citations

  articleOpen access

  Recent widespread reductions in body size across species have been linked to increasing temperatures; simultaneous increases in wing length relative to body size have been broadly observed but remain unexplained. Size and shape may change independently of one another, or these morphological shifts may be linked, with body size mediating or directly driving the degree to which shape changes. Using hierarchical Bayesian models and a morphological time series of 27 366 specimens from five North American migratory passerine bird species, we tested the roles that climate and body size have played in shifting wing length allometry over four decades. We found that colder temperatures and reduced precipitation during the first year of life were associated with increases in wing length relative to body size but did not explain long-term increases in wing length. We found no conclusive evidence that the slope of the relationship between body size and wing length changed among adult birds in response to any climatic variable or through time, suggesting that body size does not mediate shifts in relative wing length. Together, these findings suggest that long-term increases in wing length are not a compensatory adaptation mediated by size reductions, but rather are driven by non-climatic factors.

  PublisherOA PDFDOI

• Developmental and Transcriptomic Responses in Sea Urchin Larvae to an Urban‐Associated Pollutant

  Ecology and Evolution · 2025-09-01 · 2 citations

  articleOpen accessSenior author

  ABSTRACT Urban environments provide a unique opportunity to investigate the impacts of novel stressors on organismal performance. Marine intertidal zones exist at the transition from sea to land, where they are exposed to a unique suite of stressors, including those associated with wastewater outflow, sewage effluent, and coastline development. Although studies have shown that compounds found in wastewater, including endocrine disrupting chemicals ( EDCs ), can affect the survival and development of marine organisms, the mechanisms for those effects are relatively unknown. Our study investigates the developmental and transcriptomic responses to a common EDC , nonylphenol, using the Pacific purple sea urchin ( Strongylocentrotus purpuratus ) as a model system. Beginning exposure prior to fertilization, we found that nonylphenol impacts only materialize 24 h postfertilization when the embryonic transcriptome begins to be expressed, and these impacts vary significantly by mate pair. In addition, survival was lowest at the lowest concentration of nonylphenol. Transcriptomic patterns also varied by chemical concentration and developmental stage, with ribosomal genes differentially expressed among different treatments at both early and later larval stages. We also found a strong parental effect: survival, morphology, developmental abnormalities, and gene expression vary among mate pairs despite all of the adult urchins coming from the same population. This potentially suggests standing within‐population variation, which may impact evolutionary responses to anthropogenic stress. Overall, our study finds that nonylphenol affects survival, morphology, and gene expression at early life history stages, and that more work needs to be done to understand intraspecific variation in those effects.

  PublisherOA PDFDOI

• Telomere Length Differences Indicate Climate Change‐Induced Stress and Population Decline in a Migratory Bird

  Molecular Ecology · 2025-01-03 · 4 citations

  articleOpen access

  Genomic projections of (mal)adaptation under future climate change, known as genomic offset, faces limited application due to challenges in validating model predictions. Individuals inhabiting regions with high genomic offset are expected to experience increased levels of physiological stress as a result of climate change, but documenting such stress can be challenging in systems where experimental manipulations are not possible. One increasingly common method for documenting physiological costs associated with stress in individuals is to measure the relative length of telomeres-the repetitive regions on the caps of chromosomes that are known to shorten at faster rates in more adverse conditions. Here we combine models of genomic offsets with measures of telomere shortening in a migratory bird, the yellow warbler (Setophaga petechia), and find a strong correlation between genomic offset, telomere length and population decline. While further research is needed to fully understand these links, our results support the idea that birds in regions where climate change is happening faster are experiencing more stress and that such negative effects may help explain the observed population declines.

  PublisherOA PDFDOI

• Genetic, phenotypic, and environmental drivers of local adaptation and climate change–induced maladaptation in a migratory songbird

  Proceedings of the National Academy of Sciences · 2025-09-29 · 1 citations

  articleOpen access

  Understanding processes driving local adaptation in wild species is a key goal in evolutionary biology, but linking genotype to phenotype to environmental drivers of natural selection remains challenging. Even more rare are empirical examples of what happens when genotype and phenotype fail to keep pace with environmental change. Here, we explore these connections by conducting an integrative study on the breeding range of the yellow warbler ( Setophaga petechia ). Using genome-wide association studies (GWAS), we first identify loci associated with variation in bill morphology and individual quality. We then employ gene–environment association (GEA) analyses and find that precipitation is a key environmental driver of putative selection on bill shape. Finally, we test whether contemporary individuals whose bill shapes deviate from the historical relationship with precipitation experience increased stress (measured by telomere length) as a result of maladaptation. We also use historical DNA to test whether local populations have shifted their ranges over the past century, confirming that the observed changes are not due to range shifts. Our results align with predictions from GWAS and GEA analyses, indicating that birds with shallower bills in increasingly arid regions suffer higher stress (i.e., shorter telomeres) because of maladaptation. Overall, this study links genetic, phenotypic, and environmental data with stress biomarkers to improve understanding of the process of local adaptation and the consequence of failing to keep pace with changing climate conditions.

  PublisherOA PDFDOI

• Parallel polygenic urban adaptation despite high gene flow in a coastal marine invertebrate

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-10-04

  preprintOpen accessSenior author

  Abstract Urbanization results in novel environments, offering a unique opportunity to investigate natural selection on small spatiotemporal scales. Using whole genomes from Pacific purple sea urchins ( Strongylocentrotus purpuratus) across three coastal cities spanning >2000km, we investigated genomic signals for adaptation to urban environments. We found genetic variants differentiating urban and nonurban sites within each city region, despite high gene flow and little evidence for differentiation across latitudinal gradients. While these SNP-level candidates for selection were largely non-overlapping, polygenic approaches uncover a distinct parallel signal of urban adaptation across the sampled range. Our results suggest that adaptation over small scale urbanization gradients is possible even in high gene flow systems and the polygenic architecture of adaptation is, at least in part, parallel. More broadly, our work highlights the importance of polygenic methods in ecological genomics in expanding our understanding of how evolutionary forces operate in natural systems.

  PublisherOA PDFDOI

• Chromatin accessibility and heat stress gene expression in the reef-building coral, <i>Acropora millepora</i>

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-08-27

  preprintOpen accessSenior author

  Abstract Understanding how organisms regulate gene expression to maintain homeostasis in the face of environmental changes is critical, particularly considering increasing climate stressors. While DNA methylation has dominated the literature on epigenetic control of gene expression in ecological systems, alternative epigenetic layers may provide additional insight into mechanisms of gene expression regulation. This study investigates the role of chromatin accessibility in influencing gene expression in the reef-building coral Acropora millepora , especially in response to thermal stress. We find that highly accessible regions of chromatin, or open chromatin, are predominantly located in distal intergenic regions, promoters, and introns. Genes with open promoters exhibit increased expression and reduced variability, suggesting that chromatin accessibility may influence gene expression plasticity. The baseline state of promoter accessibility is weakly correlated with the expression response to heat stress, suggesting chromatin state can influence organismal response to environmental stress. This study contributes new insights into regulatory mechanisms important for responding to acute environmental stressors. This work also establishes a foundation to investigate the interactions between chromatin accessibility, additional epigenetic layers, and how the dynamics of these interacting epigenetic layers contribute to adaptive molecular and cellular responses, which will be critical for understanding organismal resilience to ongoing environmental change.

  PublisherOA PDFDOI

• The Effects of Latitudinal Gradients, Climatic Anomalies, and Size‐Selective Harvesting on the Adaptive Potential of an Intertidal Gastropod

  Evolutionary Applications · 2025-09-01

  articleOpen accessSenior author

  ABSTRACT Coastal organisms live in a dynamic environment where a myriad of environmental stressors, including climate change, ocean acidification, and human harvesting, act on variable spatio‐temporal scales. Each of these stressors may impose unique selective forces on a population, shaping a species' adaptive potential and its ability to persist under future climatic conditions. Genomic investigations of adaptive responses to environmental and anthropogenic disturbances remain rare, especially in marine systems. Here, we use whole genome sequencing data from the owl limpet, Lottia gigantea , and outlier detection methods to pinpoint signals of selection (1) across long‐standing environmental gradients spanning the species' distribution, (2) at the poleward edge of the species' range where it experienced a recent expansion, and (3) between sites vulnerable to or protected from human size‐selective harvesting within California. Loci associated with environmental gradients across the entire range show the strongest differentiation at the southern end of the species' range, potentially driven by adaptation to sea surface temperature and pH. Additional ad‐hoc outlier analyses revealed a distinct set of loci potentially under selection in the expanded range, with different functional roles than the range‐wide outliers. Despite demographic models suggesting that protection from harvesting has a positive impact on the abundance of large individuals, we did not find strong signals of selection or changes in genetic diversity between sites differing in harvesting vulnerability. Our findings suggest that range‐wide environmental selective signals established over longer time scales are distinct from those imposed by climatic anomalies at finer spatio‐temporal scales. We found that climatic variation has a stronger selective imprint than human harvesting, and thus conservation interventions should consider prioritizing the maintenance of climate‐related adaptive potential. Understanding how climatic trends and anomalies interact with anthropogenic pressures will allow us to make more informed decisions to sustain the evolutionary capacity of L. gigantea and other key coastal species.

  PublisherDOI

• Genetic and morphological shifts associated with climate change in a migratory bird

  BMC Biology · 2025-01-07 · 9 citations

  articleOpen accessSenior author

  BACKGROUND: Rapid morphological change is emerging as a consequence of climate change in many systems. It is intuitive to hypothesize that temporal morphological trends are driven by the same selective pressures that have established well-known ecogeographic patterns over spatial environmental gradients (e.g., Bergman's and Allen's rules). However, mechanistic understanding of contemporary morphological shifts is lacking. RESULTS: We combine morphological data and whole genome sequencing from a four-decade dataset in the migratory bird hermit thrush (Catharus guttatus) to test whether morphological shifts over time are accompanied by genetic change. Using genome-wide association, we identify alleles associated with body size, bill length, and wing length. Shifts in morphology and concordant shifts in morphology-associated alleles over time would support a genetic basis for the observed changes in morphology over recent decades, potentially an adaptive response to climate change. In our data, bill size decreases were paralleled by genetic shifts in bill size-associated alleles. On the other hand, alleles associated with body size showed no shift in frequency over time. CONCLUSIONS: Together, our results show mixed support for evolutionary explanations of morphological response to climate change. Temporal shifts in alleles associated with bill size support the hypothesis that selection is driving temporal morphological trends. The lack of evidence for genetic shifts in body size alleles could be explained by a large role of plasticity or technical limitations associated with the likely polygenic architecture of body size, or both. Disentangling the mechanisms responsible for observed morphological response to changing environments will be vital for predicting future organismal and population responses to climate change.

  PublisherOA PDFDOI

• Transcriptomic responses of gecarcinid land crabs to acute and prolonged desiccation stress

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-07-05 · 2 citations

  preprintOpen accessSenior author

  Abstract Decapod crabs have repeatedly and convergently colonized land. Because of their aquatic ancestry, desiccation is their greatest physiological challenge, yet the genetic basis of their responses to desiccation are unknown. For this study, we sought to identify osmoregulatory genes that were differentially expressed in their antennal glands and posterior gills in response to desiccation stress. We dehydrated and tracked gene expression across three confamilial species displaying increasing degrees of terrestrial adaptation: Tuerkayana celeste , T. magna , and Gecarcoidea natalis . We observed acute dramatic upregulation in the posterior gills of T. celeste and G. natalis and a more muted response in T. magna ; however some genes with known osmoregulatory functions were downregulated throughout the trial. We also found that some modules of orthologous genes with correlated expression were associated with greater degrees of terrestriality whereas others reflected shared ancestry, suggesting that different parts of the transcriptome are under varying degrees of terrestrial selective pressure. Finally, while differentially expressed genes were likely to be conserved across the three species, genes from expanded gene families and species-specific genes may also play a role in how land crabs adapt to the unique selective challenges that accompany a terrestrial life.

  PublisherDOI

• TELOMERE LENGTH DIFFERENCES INDICATE CLIMATE CHANGE-INDUCED STRESS AND POPULATION DECLINE IN A MIGRATORY BIRD

  2024-07-16

  preprintOpen access

  Genomic projections of (mal)adaptation under future climate change, known as genomic offset, faces limited application due to challenges in validating model predictions. Individuals inhabiting regions with high genomic offset are expected to experience increased levels of physiological stress as a result of climate change, but documenting such stress can be challenging in systems where experimental manipulations are not possible. One increasingly common method for documenting physiological costs associated with stress in individuals is to measure the relative length of telomeres – the repetitive regions on the caps of chromosomes that are known to shorten at faster rates in more adverse conditions. Here we combine models of genomic offsets with measures of telomere shortening in a migratory bird, the yellow warbler (Setophaga petechia), and find a strong correlation between genomic offset, telomere length, and population decline. While further research is needed to fully understand these links, our results support the idea that birds in regions where climate change is happening faster are experiencing more stress and that such negative effects may help explain the observed population declines.

  PublisherOA PDFDOI

Recent grants

• RoL:FELS:EAGER: Linking physiology, morphology, and genomics to investigate adaption to rapid environmental change

  NSF · $312k · 2018–2023

• NSF Postdoctoral Fellowship in Biology FY 2015

  NSF · $138k · 2015–2017

• Evolutionary and ecological dynamics of a contemporary climate-driven range expansion

  NSF · $1.1M · 2020–2025

Frequent coauthors

• Kristen Ruegg

  Colorado State University

  29 shared

• Stephen R. Palumbi

  Pacific University

  27 shared

• Eric C. Anderson

  Colorado State University

  21 shared

• Noah H. Rose

  21 shared

• Thomas B. Smith

  University of California, Los Angeles

  19 shared

• Eben H. Paxton

  Pacific Island Ecosystems Research Center

  16 shared

• Luke Thomas

  East Carolina University

  12 shared

• Megan K. Morikawa

  Navistar International (United States)

  10 shared

Awards & honors

• 2023 Annual Award and Citation Ceremony
• 2022 Rachael Bay Lab Wins Top Safety Award
• 2021 UC Davis Ecologist Awarded Packard Fellowship (2021)