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Population Genomics of Sub-Saharan Drosophila melanogaster: African Diversity and Non-African Admixture

Drosophila melanogaster has played a pivotal role in the development of modern population genetics. However, many basic questions regarding the demographic and adaptive history of this species remain unresolved. We report the genome sequencing of 139 wild-derived strains of D. melanogaster, represen...

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Autores principales: Pool, John E., Corbett-Detig, Russell B., Sugino, Ryuichi P., Stevens, Kristian A., Cardeno, Charis M., Crepeau, Marc W., Duchen, Pablo, Emerson, J. J., Saelao, Perot, Begun, David J., Langley, Charles H.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3527209/
https://www.ncbi.nlm.nih.gov/pubmed/23284287
http://dx.doi.org/10.1371/journal.pgen.1003080
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author Pool, John E.
Corbett-Detig, Russell B.
Sugino, Ryuichi P.
Stevens, Kristian A.
Cardeno, Charis M.
Crepeau, Marc W.
Duchen, Pablo
Emerson, J. J.
Saelao, Perot
Begun, David J.
Langley, Charles H.
author_facet Pool, John E.
Corbett-Detig, Russell B.
Sugino, Ryuichi P.
Stevens, Kristian A.
Cardeno, Charis M.
Crepeau, Marc W.
Duchen, Pablo
Emerson, J. J.
Saelao, Perot
Begun, David J.
Langley, Charles H.
author_sort Pool, John E.
collection PubMed
description Drosophila melanogaster has played a pivotal role in the development of modern population genetics. However, many basic questions regarding the demographic and adaptive history of this species remain unresolved. We report the genome sequencing of 139 wild-derived strains of D. melanogaster, representing 22 population samples from the sub-Saharan ancestral range of this species, along with one European population. Most genomes were sequenced above 25X depth from haploid embryos. Results indicated a pervasive influence of non-African admixture in many African populations, motivating the development and application of a novel admixture detection method. Admixture proportions varied among populations, with greater admixture in urban locations. Admixture levels also varied across the genome, with localized peaks and valleys suggestive of a non-neutral introgression process. Genomes from the same location differed starkly in ancestry, suggesting that isolation mechanisms may exist within African populations. After removing putatively admixed genomic segments, the greatest genetic diversity was observed in southern Africa (e.g. Zambia), while diversity in other populations was largely consistent with a geographic expansion from this potentially ancestral region. The European population showed different levels of diversity reduction on each chromosome arm, and some African populations displayed chromosome arm-specific diversity reductions. Inversions in the European sample were associated with strong elevations in diversity across chromosome arms. Genomic scans were conducted to identify loci that may represent targets of positive selection within an African population, between African populations, and between European and African populations. A disproportionate number of candidate selective sweep regions were located near genes with varied roles in gene regulation. Outliers for Europe-Africa F(ST) were found to be enriched in genomic regions of locally elevated cosmopolitan admixture, possibly reflecting a role for some of these loci in driving the introgression of non-African alleles into African populations.
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spelling pubmed-35272092013-01-02 Population Genomics of Sub-Saharan Drosophila melanogaster: African Diversity and Non-African Admixture Pool, John E. Corbett-Detig, Russell B. Sugino, Ryuichi P. Stevens, Kristian A. Cardeno, Charis M. Crepeau, Marc W. Duchen, Pablo Emerson, J. J. Saelao, Perot Begun, David J. Langley, Charles H. PLoS Genet Research Article Drosophila melanogaster has played a pivotal role in the development of modern population genetics. However, many basic questions regarding the demographic and adaptive history of this species remain unresolved. We report the genome sequencing of 139 wild-derived strains of D. melanogaster, representing 22 population samples from the sub-Saharan ancestral range of this species, along with one European population. Most genomes were sequenced above 25X depth from haploid embryos. Results indicated a pervasive influence of non-African admixture in many African populations, motivating the development and application of a novel admixture detection method. Admixture proportions varied among populations, with greater admixture in urban locations. Admixture levels also varied across the genome, with localized peaks and valleys suggestive of a non-neutral introgression process. Genomes from the same location differed starkly in ancestry, suggesting that isolation mechanisms may exist within African populations. After removing putatively admixed genomic segments, the greatest genetic diversity was observed in southern Africa (e.g. Zambia), while diversity in other populations was largely consistent with a geographic expansion from this potentially ancestral region. The European population showed different levels of diversity reduction on each chromosome arm, and some African populations displayed chromosome arm-specific diversity reductions. Inversions in the European sample were associated with strong elevations in diversity across chromosome arms. Genomic scans were conducted to identify loci that may represent targets of positive selection within an African population, between African populations, and between European and African populations. A disproportionate number of candidate selective sweep regions were located near genes with varied roles in gene regulation. Outliers for Europe-Africa F(ST) were found to be enriched in genomic regions of locally elevated cosmopolitan admixture, possibly reflecting a role for some of these loci in driving the introgression of non-African alleles into African populations. Public Library of Science 2012-12-20 /pmc/articles/PMC3527209/ /pubmed/23284287 http://dx.doi.org/10.1371/journal.pgen.1003080 Text en © 2012 Pool et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Pool, John E.
Corbett-Detig, Russell B.
Sugino, Ryuichi P.
Stevens, Kristian A.
Cardeno, Charis M.
Crepeau, Marc W.
Duchen, Pablo
Emerson, J. J.
Saelao, Perot
Begun, David J.
Langley, Charles H.
Population Genomics of Sub-Saharan Drosophila melanogaster: African Diversity and Non-African Admixture
title Population Genomics of Sub-Saharan Drosophila melanogaster: African Diversity and Non-African Admixture
title_full Population Genomics of Sub-Saharan Drosophila melanogaster: African Diversity and Non-African Admixture
title_fullStr Population Genomics of Sub-Saharan Drosophila melanogaster: African Diversity and Non-African Admixture
title_full_unstemmed Population Genomics of Sub-Saharan Drosophila melanogaster: African Diversity and Non-African Admixture
title_short Population Genomics of Sub-Saharan Drosophila melanogaster: African Diversity and Non-African Admixture
title_sort population genomics of sub-saharan drosophila melanogaster: african diversity and non-african admixture
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3527209/
https://www.ncbi.nlm.nih.gov/pubmed/23284287
http://dx.doi.org/10.1371/journal.pgen.1003080
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