Biology subjects

Bay, R. A.

Publications and source records attributed to Bay, R. A..

4 recordsLinked to original sources

bioRxiv2026

Spatial inference of ancestor locations suggests northern refugia for canopy-forming kelps in the Northeast Pacific

O_LIPockets of the formerly glaciated Pacific coastline of North America likely remained ice-free throughout the Last Glacial Maximum (LGM). These areas may have served as refugia for terrestrial species, but less is known about their role in the persistence of coastal marine species. C_LIO_LIWe examined genetic diversity from >1,000 newly and previously sequenced whole genomes of canopy-forming kelps of the genera Nereocystis and Macrocystis, and built simple ecological niche models. We then reconstructed ancestral recombination graphs and modelled the geographic locations of genetic ancestors through time. C_LIO_LIWe detected high genetic diversity in both species in north-central British Columbia, in a region where suitable LGM habitat is plausible. Ancestor locations spatially converged backward in time toward this region, with multiple refugia inferred between northern Vancouver Island and southern Haida Gwaii. An expanded set of global samples for Macrocystis confirmed pre-LGM divergence with California but hinted at the possibility of subsequent gene flow. C_LIO_LIKelp forests survived in northern refugia and have continuously occupied portions of the northern Pacific coastline since the LGM. One implication of these results is their support for the Kelp Highway Hypothesis of the peopling of the Americas by a coastal route. C_LI

evolutionary biology↗

bioRxiv2025

Chromatin accessibility and heat stress gene expression in the reef-building coral, Acropora millepora

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.

genomics↗

bioRxiv2024

A highly contiguous genome assembly for the Yellow Warbler (Setophaga petechia)

The Yellow Warbler (Setophaga petechia) is a small songbird in the New World Warbler family (Parulidae) that exhibits phenotypic and ecological differences across a widespread distribution and is important to Californias riparian habitat conservation. Here, we present a high-quality de novo genome assembly of a vouchered female Yellow Warbler from southern California. Using HiFi long-read and Omni-C proximity sequencing technologies, we generated a 1.22 Gb assembly including 687 scaffolds with a contig N50 of 6.80 Mb, scaffold N50 of 21.18 Mb, and a BUSCO completeness score of 96.0%. This highly contiguous genome assembly provides an essential resource for understanding the history of gene flow, divergence, and local adaptation and can inform conservation management of this charismatic bird species.

evolutionary biology↗

bioRxiv2020

Genetic variation reveals individual-level climate tracking across the full annual cycle of a migratory bird

For migratory species, seasonal movements complicate local climate adaptation, as it is unclear whether individuals track climate niches across the annual cycle. In the migratory songbird yellow warbler (Setophaga petechia), we find a correlation between individual-level wintering and breeding precipitation but not temperature. Birds wintering in the driest regions of the Neotropics breed in the driest regions of North America. Individuals from drier regions also possess distinct morphologies and population responses to varying rainfall. We find a positive association between bill size and breeding season precipitation which, given documented climate-associated genomic variation, might reflect adaptation to local precipitation regimes. Relative abundance in the breeding range is linked to interannual fluctuations in precipitation, but the directionality of this response varies across geography. Together, our results suggest that variation in climate optima may exist across the breeding range of yellow warblers and provide a mechanism for selection across the annual cycle.

evolutionary biology↗