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Genomic architecture controls spatial structuring in Amazonian birds

View ORCID ProfileGregory Thom, View ORCID ProfileLucas Rocha Moreira, View ORCID ProfileRomina Batista, Marcelo Gehara, Alexandre Aleixo, Brian Tilston Smith
doi: https://doi.org/10.1101/2021.12.01.470789
Gregory Thom
1Department of Ornithology, American Museum of Natural History, New York, United States
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  • For correspondence: gthomesilva@amnh.org
Lucas Rocha Moreira
2Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
3Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Romina Batista
4Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
5Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
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Marcelo Gehara
6Department of Earth and Environmental Sciences, Rutgers University, Newark, United States
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Alexandre Aleixo
7Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
8Instituto Tecnológico Vale, Belém, Brazil
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Brian Tilston Smith
1Department of Ornithology, American Museum of Natural History, New York, United States
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Abstract

Large rivers are ubiquitously invoked to explain the distributional limits and speciation of the Amazon Basin’s mega-diversity. However, inferences on the spatial and temporal origins of Amazonian species have narrowly focused on evolutionary neutral models, ignoring the potential role of natural selection and intrinsic genomic processes known to produce heterogeneity in differentiation across the genome. To test how these factors may influence evolutionary inferences across multiple taxa, we sequenced whole genomes of populations for three bird species that co-occur in southeastern Amazonian and exhibit different life histories linked to their propensity to maintain gene flow across the landscape. We found that phylogenetic relationships within species and demographic parameters varied across the genome in predictable ways. Genetic diversity was positively associated with recombination rate and negatively associated with the species tree topology weight. Gene flow was less pervasive in regions of low recombination, making these windows more suitable for commonly used phylogenetic methods that assume a bifurcating-branching model. To corroborate that these associations were attributable to selection, we modeled the signature of adaptive alleles across the genome taking demographic history into account, and found that on average 31.6 % of the genome showed high probability for patterns consistent with selective sweeps and linked selection directly affecting the estimation of evolutionary parameters. By implementing a comparative genomic approach we were able to disentangle the effects of intrinsic genomic characteristics and selection from the neutral processes and show how speciation hypotheses are sensitive to genomic architecture.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/GregoryThom/Genomic-architecture-Amazonian-birds

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 December 02, 2021.
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Genomic architecture controls spatial structuring in Amazonian birds
Gregory Thom, Lucas Rocha Moreira, Romina Batista, Marcelo Gehara, Alexandre Aleixo, Brian Tilston Smith
bioRxiv 2021.12.01.470789; doi: https://doi.org/10.1101/2021.12.01.470789
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Genomic architecture controls spatial structuring in Amazonian birds
Gregory Thom, Lucas Rocha Moreira, Romina Batista, Marcelo Gehara, Alexandre Aleixo, Brian Tilston Smith
bioRxiv 2021.12.01.470789; doi: https://doi.org/10.1101/2021.12.01.470789

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