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Population genomic analysis uncovers African and European admixture in Drosophila melanogaster populations from the southeastern United States and Caribbean Islands

Joyce Y. Kao, Asif Zubair, Matthew P. Salomon, Sergey V. Nuzhdin, Daniel Campo
doi: https://doi.org/10.1101/009092
Joyce Y. Kao
Section of Molecular and Computational Biology, Department of Biology, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089
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Asif Zubair
Section of Molecular and Computational Biology, Department of Biology, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089
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Matthew P. Salomon
Section of Molecular and Computational Biology, Department of Biology, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089
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Sergey V. Nuzhdin
Section of Molecular and Computational Biology, Department of Biology, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089
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Daniel Campo
Section of Molecular and Computational Biology, Department of Biology, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089
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Abstract

Genome sequences from North American Drosophila melanogaster populations have become available to the scientific community. Deciphering the underlying population structure of these resources is crucial to make the most of these population genomic resources. Accepted models of North American colonization generally purport that several hundred years ago, flies from Africa and Europe were transported to the east coast United States and the Caribbean Islands respectively and thus current east coast US and Caribbean populations are an admixture of African and European ancestry. Theses models have been constructed based on phenotypes and limited genetic data. In our study, we have sequenced individual whole genomes of flies from populations in the southeast US and Caribbean Islands and examined these populations in conjunction with population sequences from Winters, CA, (USA); Raleigh, NC (USA); Cameroon (Africa); and Montpellier (France) to uncover the underlying population structure of North American populations. We find that west coast US populations are most like European populations likely reflecting a rapid westward expansion upon first settlements into North America. We also find genomic evidence of African and European admixture in east coast US and Caribbean populations, with a clinal pattern of decreasing proportions of African ancestry with higher latitude further supporting the proposed demographic model of Caribbean flies being established by African ancestors. Our genomic analysis of Caribbean flies is the first study that exposes the source of previously reported novel African alleles found in east coast US populations.

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Posted September 13, 2014.
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Population genomic analysis uncovers African and European admixture in Drosophila melanogaster populations from the southeastern United States and Caribbean Islands
Joyce Y. Kao, Asif Zubair, Matthew P. Salomon, Sergey V. Nuzhdin, Daniel Campo
bioRxiv 009092; doi: https://doi.org/10.1101/009092
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Population genomic analysis uncovers African and European admixture in Drosophila melanogaster populations from the southeastern United States and Caribbean Islands
Joyce Y. Kao, Asif Zubair, Matthew P. Salomon, Sergey V. Nuzhdin, Daniel Campo
bioRxiv 009092; doi: https://doi.org/10.1101/009092

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