Analysis of Chimpanzee History Based on Genome Sequence Alignments
Population geneticists often study small numbers of carefully chosen loci, but it has become possible to obtain orders of magnitude for more data from overlaps of genome sequences. Here, we generate tens of millions of base pairs of multiple sequence alignments from combinations of three western chi...
Autores principales: | , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
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Public Library of Science
2008
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2278377/ https://www.ncbi.nlm.nih.gov/pubmed/18421364 http://dx.doi.org/10.1371/journal.pgen.1000057 |
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author | Caswell, Jennifer L. Mallick, Swapan Richter, Daniel J. Neubauer, Julie Schirmer, Christine Gnerre, Sante Reich, David |
author_facet | Caswell, Jennifer L. Mallick, Swapan Richter, Daniel J. Neubauer, Julie Schirmer, Christine Gnerre, Sante Reich, David |
author_sort | Caswell, Jennifer L. |
collection | PubMed |
description | Population geneticists often study small numbers of carefully chosen loci, but it has become possible to obtain orders of magnitude for more data from overlaps of genome sequences. Here, we generate tens of millions of base pairs of multiple sequence alignments from combinations of three western chimpanzees, three central chimpanzees, an eastern chimpanzee, a bonobo, a human, an orangutan, and a macaque. Analysis provides a more precise understanding of demographic history than was previously available. We show that bonobos and common chimpanzees were separated ∼1,290,000 years ago, western and other common chimpanzees ∼510,000 years ago, and eastern and central chimpanzees at least 50,000 years ago. We infer that the central chimpanzee population size increased by at least a factor of 4 since its separation from western chimpanzees, while the western chimpanzee effective population size decreased. Surprisingly, in about one percent of the genome, the genetic relationships between humans, chimpanzees, and bonobos appear to be different from the species relationships. We used PCR-based resequencing to confirm 11 regions where chimpanzees and bonobos are not most closely related. Study of such loci should provide information about the period of time 5–7 million years ago when the ancestors of humans separated from those of the chimpanzees. |
format | Text |
id | pubmed-2278377 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-22783772008-04-18 Analysis of Chimpanzee History Based on Genome Sequence Alignments Caswell, Jennifer L. Mallick, Swapan Richter, Daniel J. Neubauer, Julie Schirmer, Christine Gnerre, Sante Reich, David PLoS Genet Research Article Population geneticists often study small numbers of carefully chosen loci, but it has become possible to obtain orders of magnitude for more data from overlaps of genome sequences. Here, we generate tens of millions of base pairs of multiple sequence alignments from combinations of three western chimpanzees, three central chimpanzees, an eastern chimpanzee, a bonobo, a human, an orangutan, and a macaque. Analysis provides a more precise understanding of demographic history than was previously available. We show that bonobos and common chimpanzees were separated ∼1,290,000 years ago, western and other common chimpanzees ∼510,000 years ago, and eastern and central chimpanzees at least 50,000 years ago. We infer that the central chimpanzee population size increased by at least a factor of 4 since its separation from western chimpanzees, while the western chimpanzee effective population size decreased. Surprisingly, in about one percent of the genome, the genetic relationships between humans, chimpanzees, and bonobos appear to be different from the species relationships. We used PCR-based resequencing to confirm 11 regions where chimpanzees and bonobos are not most closely related. Study of such loci should provide information about the period of time 5–7 million years ago when the ancestors of humans separated from those of the chimpanzees. Public Library of Science 2008-04-18 /pmc/articles/PMC2278377/ /pubmed/18421364 http://dx.doi.org/10.1371/journal.pgen.1000057 Text en Caswell 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 Caswell, Jennifer L. Mallick, Swapan Richter, Daniel J. Neubauer, Julie Schirmer, Christine Gnerre, Sante Reich, David Analysis of Chimpanzee History Based on Genome Sequence Alignments |
title | Analysis of Chimpanzee History Based on Genome Sequence Alignments |
title_full | Analysis of Chimpanzee History Based on Genome Sequence Alignments |
title_fullStr | Analysis of Chimpanzee History Based on Genome Sequence Alignments |
title_full_unstemmed | Analysis of Chimpanzee History Based on Genome Sequence Alignments |
title_short | Analysis of Chimpanzee History Based on Genome Sequence Alignments |
title_sort | analysis of chimpanzee history based on genome sequence alignments |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2278377/ https://www.ncbi.nlm.nih.gov/pubmed/18421364 http://dx.doi.org/10.1371/journal.pgen.1000057 |
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