Publications

Erica S Nielsen, Samuel Walkes, Jacqueline L Sones, Phillip B Fenberg, David a Paz-Garcı́a, Brenda B Cameron, Richard K Grosberg, Eric Sanford, Rachael a Bay (2024). Pushed waves, trailing edges, and extreme events: Eco-evolutionary dynamics of a geographic range shift in the owl limpet, Lottia gigantea. Global Change Biology.

Leslie Guerrero, Rachael Bay (2024). Patterns of methylation and transcriptional plasticity during thermal acclimation in a reef-building coral. Evolutionary applications.

Whitney LE Tsai, Merly Escalona, Kimball L Garrett, Ryan S Terrill, Ruta Sahasrabudhe, Oanh Nguyen, Eric Beraut, William Seligmann, Colin W Fairbairn, Ryan J Harrigan, Others (2024). A highly contiguous genome assembly for the Yellow Warbler (Setophaga petechia). Journal of Heredity.

Nicole E Adams, Ruta R Bandivadekar, CJ Battey, Michael W Clark, Kevin Epperly, Kristen Ruegg, Lisa a Tell, Rachael a Bay (2023). Widespread gene flow following range expansion in Anna's Hummingbird. Molecular Ecology.

Sheela P Turbek, Christen Bossu, Christine Rayne, Cristian Gruppi, Barbara E Kus, Mary Whitfield, Thomas B Smith, Eben H Paxton, Rachael a Bay, Kristen C Ruegg (2023). Historical DNA reveals climate adaptation in an endangered songbird. Nature Climate Change.

Lauren M Schiebelhut, Richard K Grosberg, John J Stachowicz, Rachael a Bay (2023). Genomic responses to parallel temperature gradients in the eelgrass Zostera marina in adjacent bays. Molecular Ecology.

Kelly Barr, Christen M Bossu, Rachael a Bay, Eric C Anderson, Jim Belthoff, Lynne a Trulio, Debra Chromczak, Colleen L Wisinski, Thomas B Smith, Kristen C Ruegg (2023). Genetic and environmental drivers of migratory behavior in western burrowing owls and implications for conservation and management. Evolutionary Applications.

Emily J Howells, Line K Bay, Rachael a Bay (2022). Identifying, Monitoring, and Managing Adaptive Genetic Variation in Reef-Building Corals under Rapid Climate Warming. Coral Reef Conservation and Restoration in the Omics Age.

Allison H Alvarado, Christen M Bossu, Ryan J Harrigan, Rachael a Bay, Allison RP Nelson, Thomas B Smith, Kristen C Ruegg (2022). Genotype--environment associations across spatial scales reveal the importance of putative adaptive genetic variation in divergence. Evolutionary Applications.

Kristen C Ruegg, Michaela Brinkmeyer, Christen M Bossu, Rachael a Bay, Eric C Anderson, Clint W Boal, Russell D Dawson, Amber Eschenbauch, Christopher JW McClure, Karl E Miller, Others (2021). The American Kestrel (Falco sparverius) genoscape: Implications for monitoring, management, and subspecies boundaries. The Auk.

Kelly Barr, Annabel C Beichman, Pooneh Kalhori, Jasmine Rajbhandary, Rachael a Bay, Kristen Ruegg, Thomas B Smith (2021). Persistent panmixia despite extreme habitat loss and population decline in the threatened tricolored blackbird (Agelaius tricolor). Evolutionary applications.

Kristen Ruegg, Eric C Anderson, Marius Somveille, Rachael a Bay, Mary Whitfield, Eben H Paxton, Thomas B Smith (2021). Linking climate niches across seasons to assess population vulnerability in a migratory bird. Global Change Biology.

Noah H Rose, Rachael a Bay, Megan K Morikawa, Luke Thomas, Elizabeth a Sheets, Stephen R Palumbi (2021). Genomic analysis of distinct bleaching tolerances among cryptic coral species. Proceedings of the Royal Society B.

Rachael a Bay, Daniel S Karp, James F Saracco, William RL Anderegg, Luke O Frishkoff, David Wiedenfeld, Thomas B Smith, Kristen Ruegg (2021). Genetic variation reveals individual-level climate tracking across the annual cycle of a migratory bird. Ecology Letters.

Marius Somveille, Rachael a Bay, Thomas B Smith, Peter P Marra, Kristen C Ruegg (2021). A general theory of avian migratory connectivity. Ecology Letters.

Thibaut Capblancq, Matthew C Fitzpatrick, Rachael a Bay, Moises Exposito-Alonso, Stephen R Keller (2020). Genomic prediction of (mal) adaptation across current and future climatic landscapes. Annual Review of Ecology, Evolution, and Systematics.

Rachael a Bay, Leslie Guerrero (2020). Can genomes predict coral bleaching?. Science.

Rachael A Bay (2019). An example preprint / working paper.

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Tania Chavarria-Pizarro, Juan Pablo Gomez, Judit Ungvari-Martin, Rachael Bay, Michael M Miyamoto, Rebecca Kimball (2019). Strong phenotypic divergence in spite of low genetic structure in the endemic Mangrove Warbler subspecies (Setophaga petechia xanthotera) of Costa Rica. Ecology and evolution.

Rachael a Bay, Eric B Taylor, Dolph Schluter (2019). Parallel introgression and selection on introduced alleles in a native species. Molecular Ecology.

Andrea Contina, Rachael a Bay, Vinh Le Underwood, Thomas B Smith, Jeffrey F Kelly, Eli S Bridge, Kristen C Ruegg (2019). Characterization of SNP markers for the Painted Bunting (Passerina ciris) and their relevance in population differentiation and genome evolution studies. Conservation Genetics Resources.

Noah H Rose, Rachael a Bay, Megan K Morikawa, Stephen R Palumbi (2018). Polygenic evolution drives species divergence and climate adaptation in corals. Evolution.

Luke Thomas, Noah H Rose, Rachael a Bay, Elora H López, Megan K Morikawa, Lupita Ruiz-Jones, Stephen R Palumbi (2018). Mechanisms of Thermal Tolerance in Reef-Building Corals across a Fine-Grained Environmental Mosaic: Lessons from Ofu, American Samoa. Frontiers in Marine Science.

Rachael a Bay, Ryan J Harrigan, Vinh Le Underwood, H Lisle Gibbs, Thomas B Smith, Kristen Ruegg (2018). Genomic signals of selection predict climate-driven population declines in a migratory bird. Science.

Kristen Ruegg, Rachael a Bay, Eric C Anderson, James F Saracco, Ryan J Harrigan, Mary Whitfield, Eben H Paxton, Thomas B Smith (2018). Ecological genomics predicts climate vulnerability in an endangered southwestern songbird. Ecology letters.

R Cunning, RA Bay, P Gillette, AC Baker, N Traylor-Knowles (2018). Comparative analysis of the Pocillopora damicornis genome highlights role of immune system in coral evolution. Scientific Reports.

Rachael a Bay, Stephen R Palumbi (2017). Transcriptome predictors of coral survival and growth in a highly variable environment. Ecology and evolution.

Rachael a Bay, Noah Rose, Rowan Barrett, Louis Bernatchez, Cameron K Ghalambor, Jesse R Lasky, Rachel B Brem, Stephen R Palumbi, Peter Ralph (2017). Predicting responses to contemporary environmental change using evolutionary response architectures. The American Naturalist.

Rachael a Bay, Kristen Ruegg (2017). Genomic islands of divergence or opportunities for introgression?. Proceedings of the Royal Society B: Biological Sciences.

Rachael a Bay, Matthew E Arnegard, Gina L Conte, Jacob Best, Nicole L Bedford, Shaugnessy R McCann, Matthew E Dubin, Yingguang Frank Chan, Felicity C Jones, David M Kingsley, Others (2017). Genetic Coupling of Female Mate Choice with Polygenic Ecological Divergence Facilitates Stickleback Speciation. Current Biology.

Rachael A Bay, Robert Ford (2015). An example journal article. Journal of Source Themes, 1(1).

Rachael a Bay, Stephen R Palumbi (2015). Rapid acclimation ability mediated by transcriptome changes in reef-building corals. Genome biology and evolution.

Rachael a Bay, Stephen R Palumbi (2014). Multilocus Adaptation Associated with Heat Resistance in Reef-Building Corals. Current Biology.

Stephen R Palumbi, Daniel J Barshis, Nikki Traylor-Knowles, Rachael a Bay (2014). Mechanisms of reef coral resistance to future climate change. Science.

Rachael a Bay, Uma Ramakrishnan, Elizabeth a Hadly (2014). A call for tiger management using “reserves” of genetic diversity. Journal of Heredity.

Rachael A Bay, Robert Ford (2013). An example conference paper. In ICW.

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Rachael a Bay, Joseph P Bielawski (2013). Inference of functional divergence among proteins when the evolutionary process is non-stationary. Journal of molecular evolution.

Rachael a Bay, Joseph P Bielawski (2011). Recombination detection under evolutionary scenarios relevant to functional divergence. Journal of Molecular Evolution.