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The genomic landscapes of desert birds form over multiple time scales

View ORCID ProfileKaiya Provost, Stephanie Yun Shue, Meghan Forcellati, Brian Tilston Smith
doi: https://doi.org/10.1101/2022.03.07.483329
Kaiya Provost
1Department of Ornithology, American Museum of Natural History, New York, New York, USA
2Richard Gilder Graduate School, American Museum of Natural History, New York, New York, USA
3Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, Ohio, USA
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  • ORCID record for Kaiya Provost
  • For correspondence: provost.27@osu.edu
Stephanie Yun Shue
4Bergen County Academies, Hackensack, New Jersey, USA
5Biological Sciences, University of California Berkeley, Berkeley, California, USA
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Meghan Forcellati
4Bergen County Academies, Hackensack, New Jersey, USA
6Ecology, Evolution, and Environmental Biology, Columbia University, New York, New York, USA
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Brian Tilston Smith
1Department of Ornithology, American Museum of Natural History, New York, New York, USA
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Abstract

Spatial models show that genetic differentiation between populations can be explained by factors ranging from geographic distance to environmental resistance across the landscape. However, genomes exhibit a landscape of differentiation, which could indicate that multiple spatial models better explain divergence in different portions of the genome. We test whether alternative geographic predictors of intraspecific differentiation vary across the genome in ten bird species that co-occur in Sonoran and Chihuahuan Deserts of North America. Using population-level genomic data, we characterized the genomic landscapes across species and modeled five predictors that represented historical and contemporary mechanisms. The characteristics of genomic landscapes differed across the ten species, influenced by varying levels of population structuring and admixture between deserts. General dissimilarity matrix modeling indicated that the best-fit models differed from the whole genome and partitions along the genome. Almost all of the historical and contemporary mechanisms were important in explaining genetic distance, but particularly historical and contemporary environment, while contemporary abundance, position of the barrier to gene flow, and distance explained relatively less. Individual species have significantly different patterns of genomic variation. These results illustrate that the genomic landscape of differentiation was influenced by alternative geographic factors operating on different portions of the genome.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Peer review was done on the manuscript to make major changes. Most notably, calculation of genetic distances were converted from hard-called SNPs to the ngsDist protocol that can handle genotype likelihoods. As such we are more confident in these data. All figures, text, and supplement revised.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted August 31, 2022.
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The genomic landscapes of desert birds form over multiple time scales
Kaiya Provost, Stephanie Yun Shue, Meghan Forcellati, Brian Tilston Smith
bioRxiv 2022.03.07.483329; doi: https://doi.org/10.1101/2022.03.07.483329
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The genomic landscapes of desert birds form over multiple time scales
Kaiya Provost, Stephanie Yun Shue, Meghan Forcellati, Brian Tilston Smith
bioRxiv 2022.03.07.483329; doi: https://doi.org/10.1101/2022.03.07.483329

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