Low-coverage whole genome sequencing for highly accurate population assignment: Mapping migratory connectivity in the American Redstart (Setophaga ruticilla)

Matthew G DeSaix¹, Eric C Anderson^{1

2

3}, Christen M Bossu¹, Christine E Rayne¹, Teia M Schweizer³, Nicholas J Bayly⁴, Darshan S Narang⁵, Julie C Hagelin⁶, H Lisle Gibbs^{7

8}, James F Saracco⁹, Thomas W Sherry^{10

11}, Michael S Webster^{12

13}, Thomas B Smith^{14

15}, Peter P Marra^{16

17}, Kristen C Ruegg¹

Affiliations

¹ Department of Biology, Colorado State University, Fort Collins, Colorado, USA.
² Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Santa Cruz, California, USA.
³ Department of Fisheries, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, Colorado, USA.
⁴ SELVA Investigación para la conservación en el Neotropico, DG42A #20-37, Bogotá, Colombia.
⁵ Trinidad and Tobago Field Naturalists' Club, Port of Spain, Trinidad and Tobago.
⁶ Threatened, Endangered and Diversity Program, Alaska Department of Fish and Game, Fairbanks, Alaska, USA.
⁷ Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio, USA.
⁸ Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, Ohio, USA.
⁹ The Institute for Bird Populations, Petaluma, California, USA.
¹⁰ Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, Louisiana, USA.
¹¹ Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA.
¹² Cornell Lab of Ornithology, Ithaca, New York, USA.
¹³ Department of Neurobiology and Behavior, Cornell University, Ithaca, New York, USA.
¹⁴ Center for Tropical Research, Institute of the Environment & Sustainability, University of California Los Angeles, Los Angeles, California, USA.
¹⁵ Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA.
¹⁶ Department of Biology, Georgetown University, Washington, District of Columbia, USA.
¹⁷ McCourt School of Public Policy, Georgetown University, Washington, District of Columbia, USA.

PMID: 37706673
DOI: 10.1111/mec.17137

Low-coverage whole genome sequencing for highly accurate population assignment: Mapping migratory connectivity in the American Redstart (Setophaga ruticilla)

Matthew G DeSaix et al. Mol Ecol. 2023 Oct.

. 2023 Oct;32(20):5528-5540.

doi: 10.1111/mec.17137. Epub 2023 Sep 14.

Authors

Affiliations

¹ Department of Biology, Colorado State University, Fort Collins, Colorado, USA.
² Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Santa Cruz, California, USA.
³ Department of Fisheries, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, Colorado, USA.
⁴ SELVA Investigación para la conservación en el Neotropico, DG42A #20-37, Bogotá, Colombia.
⁵ Trinidad and Tobago Field Naturalists' Club, Port of Spain, Trinidad and Tobago.
⁶ Threatened, Endangered and Diversity Program, Alaska Department of Fish and Game, Fairbanks, Alaska, USA.
⁷ Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio, USA.
⁸ Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, Ohio, USA.
⁹ The Institute for Bird Populations, Petaluma, California, USA.
¹⁰ Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, Louisiana, USA.
¹¹ Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA.
¹² Cornell Lab of Ornithology, Ithaca, New York, USA.
¹³ Department of Neurobiology and Behavior, Cornell University, Ithaca, New York, USA.
¹⁴ Center for Tropical Research, Institute of the Environment & Sustainability, University of California Los Angeles, Los Angeles, California, USA.
¹⁵ Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA.
¹⁶ Department of Biology, Georgetown University, Washington, District of Columbia, USA.
¹⁷ McCourt School of Public Policy, Georgetown University, Washington, District of Columbia, USA.

PMID: 37706673
DOI: 10.1111/mec.17137

Abstract

Understanding the geographic linkages among populations across the annual cycle is an essential component for understanding the ecology and evolution of migratory species and for facilitating their effective conservation. While genetic markers have been widely applied to describe migratory connections, the rapid development of new sequencing methods, such as low-coverage whole genome sequencing (lcWGS), provides new opportunities for improved estimates of migratory connectivity. Here, we use lcWGS to identify fine-scale population structure in a widespread songbird, the American Redstart (Setophaga ruticilla), and accurately assign individuals to genetically distinct breeding populations. Assignment of individuals from the nonbreeding range reveals population-specific patterns of varying migratory connectivity. By combining migratory connectivity results with demographic analysis of population abundance and trends, we consider full annual cycle conservation strategies for preserving numbers of individuals and genetic diversity. Notably, we highlight the importance of the Northern Temperate-Greater Antilles migratory population as containing the largest proportion of individuals in the species. Finally, we highlight valuable considerations for other population assignment studies aimed at using lcWGS. Our results have broad implications for improving our understanding of the ecology and evolution of migratory species through conservation genomics approaches.

Keywords: assignment bias; conservation genomics; effective sample size; migration; population genetics; songbird.

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References

REFERENCES

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Low-coverage whole genome sequencing for highly accurate population assignment: Mapping migratory connectivity in the American Redstart (Setophaga ruticilla)

Affiliations

Low-coverage whole genome sequencing for highly accurate population assignment: Mapping migratory connectivity in the American Redstart (Setophaga ruticilla)

Authors

Affiliations

Abstract

References

REFERENCES

Publication types

MeSH terms

LinkOut - more resources

Full Text Sources