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Primate Evolutionary Genetics
2001 Journal of Heredity
doi: 10.1093/jhered/92.6.453pmid: 11948210
Primate Evolutionary Genetics
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doi: 10.1093/jhered/92.6.453pmid: 11948210
Primate Evolutionary Genetics
doi: 10.1093/jhered/92.6.454pmid: 11948211
The analysis of mitochondrial DNA (mtDNA) sequences has been a potent tool in our understanding of human evolution. However, almost all studies of human evolution based on mtDNA sequencing have focused on the control region, which constitutes less than 7% of the mitochondrial genome. The rapid development of technology for automated DNA sequencing has made it possible to study the complete mtDNA genomes in large numbers of individuals, opening the field of mitochondrial population genomics. Here we describe a suitable methodology for determining the complete human mitochondrial sequence and the global mtDNA diversity in humans. Also, we discuss the implications of the results with respect to the different hypotheses for the evolution of modern humans. « Previous | Next Article » Table of Contents This Article J Hered (2001) 92 (6): 454-461. doi: 10.1093/jhered/92.6.454 » Abstract Free Full Text (HTML) Free Full Text (PDF) Free Classifications Article Services Article metrics Alert me when cited Alert me if corrected Find similar articles Similar articles in Web of Science Similar articles in PubMed Add to my archive Download citation Request Permissions Citing Articles Load citing article information Citing articles via CrossRef Citing articles via Scopus Citing articles via Web of Science Citing articles via Google Scholar Google Scholar Articles by Ingman, M. Articles by Gyllensten, U. Search for related content PubMed PubMed citation Articles by Ingman, M. Articles by Gyllensten, U. Related Content Load related web page information Share Email this article CiteULike Delicious Facebook Google+ Mendeley Twitter What's this? Search this journal: Advanced » Current Issue September-October 2015 106 (5) Alert me to new issues The Journal About this journal Publishers' Books for Review Rights & Permissions Dispatch date of the next issue This journal is a member of the Committee on Publication Ethics (COPE) Journal of Heredity Collections We are mobile – find out more Journals Career Network Published on behalf of The American Genetic Association Impact factor: 2.088 5-Yr impact factor: 2.417 Editor-in-Chief C. Scott Baker View full editorial board For Authors Instructions to authors Online submission instructions Submit now! Data Archiving Policy This journal enables compliance with the NIH Public Access Policy Optional Open Access is Available - Visit Oxford Open Author Self Archiving Policy Alerting Services Email table of contents Email Advance Access CiteTrack XML RSS feed Corporate Services Advertising sales Reprints Supplements
doi: N/Apmid: N/A
The analysis of mitochondrial DNA (mtDNA) sequences has been a potent tool in our understanding of human evolution. However, almost all studies of human evolution based on mtDNA sequencing have focused on the control region, which constitutes less than 7% of the mitochondrial genome. The rapid development of technology for automated DNA sequencing has made it possible to study the complete mtDNA genomes in large numbers of individuals, opening the field of mitochondrial population genomics. Here we describe a suitable methodology for determining the complete human mitochondrial sequence and the global mtDNA diversity in humans. Also, we discuss the implications of the results with respect to the different hypotheses for the evolution of modern humans.
Eichler, E. E.; Johnson, M. E.; Alkan, C.; Tuzun, E.; Sahinalp, C.; Misceo, D.; Archidiacono, N.; Rocchi, M.
doi: N/Apmid: N/A
An unexpected finding of the human genome was the large fraction of the genome organized as blocks of interspersed duplicated sequence. We provide a comparative and phylogenetic analysis of a highly duplicated region of 16p12.2, which is composed of at least four different segmental duplications spanning in excess of 160 kb. We contrast the dispersal of two different segmental duplications (LCR16a and LCR16u). LCR16a, a 20 kb low-copy repeat sequence A from chromosome 16, was shown previously to contain a rapidly evolving novel hominoid gene family (morpheus) that had expanded within the last 10 million years of great ape/human evolution. We compare the dispersal of this genomic segment with a second adjacent duplication called LCR16u. The duplication contains a second putative gene family (KIAA0220/SMG1) that is represented approximately eight times within the human genome. A high degree of sequence identity (∼98%) was observed among the various copies of LCR16u. Comparative analyses with Old World monkey species show that LCR16a and LCR16u originated from two distinct ancestral loci. Within the human genome, at least 70% of the LCR16u copies were duplicated in concert with the LCR16a duplication. In contrast, only 30% of the chimpanzee loci show an association between LCR16a and LCR16u duplications. The data suggest that the two copies of genomic sequence were brought together during the chimpanzee/human divergence and were subsequently duplicated as a larger cassette specifically within the human lineage. The evolutionary history of these two chromosome-specific duplications supports a model of rapid expansion and evolutionary turnover among the genomes of man and the great apes.
E. E. Eichler, M. E. Johnson, C. Alkan, E. Tuzun, C. Sahinalp, D. Misceo, N. Archidiacono, M. Rocchi
doi: 10.1093/jhered/92.6.462pmid: 11948212
An unexpected finding of the human genome was the large fraction of the genome organized as blocks of interspersed duplicated sequence. We provide a comparative and phylogenetic analysis of a highly duplicated region of 16p12.2, which is composed of at least four different segmental duplications spanning in excess of 160 kb. We contrast the dispersal of two different segmental duplications (LCR16a and LCR16u). LCR16a, a 20 kb low-copy repeat sequence A from chromosome 16, was shown previously to contain a rapidly evolving novel hominoid gene family ( morpheus ) that had expanded within the last 10 million years of great ape/human evolution. We compare the dispersal of this genomic segment with a second adjacent duplication called LCR16u. The duplication contains a second putative gene family (KIAA0220/SMG1) that is represented approximately eight times within the human genome. A high degree of sequence identity (∼98%) was observed among the various copies of LCR16u. Comparative analyses with Old World monkey species show that LCR16a and LCR16u originated from two distinct ancestral loci. Within the human genome, at least 70% of the LCR16u copies were duplicated in concert with the LCR16a duplication. In contrast, only 30% of the chimpanzee loci show an association between LCR16a and LCR16u duplications. The data suggest that the two copies of genomic sequence were brought together during the chimpanzee/human divergence and were subsequently duplicated as a larger cassette specifically within the human lineage. The evolutionary history of these two chromosome-specific duplications supports a model of rapid expansion and evolutionary turnover among the genomes of man and the great apes. « Previous | Next Article » Table of Contents This Article J Hered (2001) 92 (6): 462-468. doi: 10.1093/jhered/92.6.462 » Abstract Free Full Text (HTML) Free Full Text (PDF) Free Classifications Article Services Article metrics Alert me when cited Alert me if corrected Find similar articles Similar articles in Web of Science Similar articles in PubMed Add to my archive Download citation Request Permissions Citing Articles Load citing article information Citing articles via CrossRef Citing articles via Scopus Citing articles via Web of Science Citing articles via Google Scholar Google Scholar Articles by Eichler, E. E. Articles by Rocchi, M. Search for related content PubMed PubMed citation Articles by Eichler, E. E. Articles by Johnson, M. E. Articles by Alkan, C. Articles by Tuzun, E. Articles by Sahinalp, C. Articles by Misceo, D. Articles by Archidiacono, N. Articles by Rocchi, M. Related Content Load related web page information Share Email this article CiteULike Delicious Facebook Google+ Mendeley Twitter What's this? Search this journal: Advanced » Current Issue September-October 2015 106 (5) Alert me to new issues The Journal About this journal Publishers' Books for Review Rights & Permissions Dispatch date of the next issue This journal is a member of the Committee on Publication Ethics (COPE) Journal of Heredity Collections We are mobile – find out more Journals Career Network Published on behalf of The American Genetic Association Impact factor: 2.088 5-Yr impact factor: 2.417 Editor-in-Chief C. Scott Baker View full editorial board For Authors Instructions to authors Online submission instructions Submit now! Data Archiving Policy This journal enables compliance with the NIH Public Access Policy Optional Open Access is Available - Visit Oxford Open Author Self Archiving Policy Alerting Services Email table of contents Email Advance Access CiteTrack XML RSS feed Corporate Services Advertising sales Reprints Supplements
Stauffer, R. L.; Walker, A.; Ryder, O. A.; Lyons-Weiler, M.; Hedges, S. Blair
doi: N/Apmid: N/A
Although the relationships of the living hominoid primates (humans and apes) are well known, the relationships of the fossil species, times of divergence of both living and fossil species, and the biogeographic history of hominoids are not well established. Divergence times of living species, estimated from molecular clocks, have the potential to constrain hypotheses of the relationships of fossil species. In this study, new DNA sequences from nine protein-coding nuclear genes in great apes are added to existing datasets to increase the precision of molecular time estimates bearing on the evolutionary history of apes and humans. The divergence of Old World monkeys and hominoids at the Oligocene-Miocene boundary (approximately 23 million years ago) provides the best primate calibration point and yields a time and 95% confidence interval of 5.4 ± 1.1 million years ago (36 nuclear genes) for the human-chimpanzee divergence. Older splitting events are estimated as 6.4 ± 1.5 million years ago (gorilla, 31 genes), 11.3 ± 1.3 million years ago (orangutan, 33 genes), and 14.9 ± 2.0 million years ago (gibbon, 27 genes). Based on these molecular constraints, we find that several proposed phylogenies of fossil hominoid taxa are unlikely to be correct.
R. L. Stauffer, A. Walker, O. A. Ryder, M. Lyons-Weiler, S. Blair Hedges
doi: 10.1093/jhered/92.6.469pmid: 11948213
Although the relationships of the living hominoid primates (humans and apes) are well known, the relationships of the fossil species, times of divergence of both living and fossil species, and the biogeographic history of hominoids are not well established. Divergence times of living species, estimated from molecular clocks, have the potential to constrain hypotheses of the relationships of fossil species. In this study, new DNA sequences from nine protein-coding nuclear genes in great apes are added to existing datasets to increase the precision of molecular time estimates bearing on the evolutionary history of apes and humans. The divergence of Old World monkeys and hominoids at the Oligocene-Miocene boundary (approximately 23 million years ago) provides the best primate calibration point and yields a time and 95% confidence interval of 5.4 ± 1.1 million years ago (36 nuclear genes) for the human-chimpanzee divergence. Older splitting events are estimated as 6.4 ± 1.5 million years ago (gorilla, 31 genes), 11.3 ± 1.3 million years ago (orangutan, 33 genes), and 14.9 ± 2.0 million years ago (gibbon, 27 genes). Based on these molecular constraints, we find that several proposed phylogenies of fossil hominoid taxa are unlikely to be correct. « Previous | Next Article » Table of Contents This Article J Hered (2001) 92 (6): 469-474. doi: 10.1093/jhered/92.6.469 » Abstract Free Full Text (HTML) Free Full Text (PDF) Free Classifications Article Services Article metrics Alert me when cited Alert me if corrected Find similar articles Similar articles in Web of Science Similar articles in PubMed Add to my archive Download citation Request Permissions Citing Articles Load citing article information Citing articles via CrossRef Citing articles via Scopus Citing articles via Web of Science Citing articles via Google Scholar Google Scholar Articles by Stauffer, R. L. Articles by Hedges, S. B. Search for related content PubMed PubMed citation Articles by Stauffer, R. L. Articles by Walker, A. Articles by Ryder, O. A. Articles by Lyons-Weiler, M. Articles by Hedges, S. B. Related Content Load related web page information Share Email this article CiteULike Delicious Facebook Google+ Mendeley Twitter What's this? Search this journal: Advanced » Current Issue September-October 2015 106 (5) Alert me to new issues The Journal About this journal Publishers' Books for Review Rights & Permissions Dispatch date of the next issue This journal is a member of the Committee on Publication Ethics (COPE) Journal of Heredity Collections We are mobile – find out more Journals Career Network Published on behalf of The American Genetic Association Impact factor: 2.088 5-Yr impact factor: 2.417 Editor-in-Chief C. Scott Baker View full editorial board For Authors Instructions to authors Online submission instructions Submit now! Data Archiving Policy This journal enables compliance with the NIH Public Access Policy Optional Open Access is Available - Visit Oxford Open Author Self Archiving Policy Alerting Services Email table of contents Email Advance Access CiteTrack XML RSS feed Corporate Services Advertising sales Reprints Supplements
Jensen-Seaman, M. I.; Deinard, A. S.; Kidd, K. K.
doi: N/Apmid: N/A
In order to fully understand human evolutionary history through the use of molecular data, it is essential to include our closest relatives as a comparison. We provide here estimates of nucleotide diversity and effective population size of modern African ape species using data from several independent noncoding nuclear loci, and use these estimates to make predictions about the nature of the ancestral population that eventually gave rise to the living species of African apes, including humans. Chimpanzees, bonobos, and gorillas possess two to three times more nucleotide diversity than modern humans. We hypothesize that the last common ancestor (LCA) of these species had an effective population size more similar to modern apes than modern humans. In addition, estimated dates for the divergence of the Homo, Pan, and Gorilla lineages suggest that the LCA may have had stronger geographic structuring to its mtDNA than its nuclear DNA, perhaps indicative of strong female philopatry or a dispersal system analogous to gorillas, where females disperse only short distances from their natal group. Synthesizing different classes of data, and the inferences drawn from them, allows us to predict some of the genetic and demographic properties of the LCA of humans, chimpanzees, and gorillas.
M. I. Jensen-Seaman, A. S. Deinard, K. K. Kidd
doi: 10.1093/jhered/92.6.475pmid: 11948214
In order to fully understand human evolutionary history through the use of molecular data, it is essential to include our closest relatives as a comparison. We provide here estimates of nucleotide diversity and effective population size of modern African ape species using data from several independent noncoding nuclear loci, and use these estimates to make predictions about the nature of the ancestral population that eventually gave rise to the living species of African apes, including humans. Chimpanzees, bonobos, and gorillas possess two to three times more nucleotide diversity than modern humans. We hypothesize that the last common ancestor (LCA) of these species had an effective population size more similar to modern apes than modern humans. In addition, estimated dates for the divergence of the Homo, Pan , and Gorilla lineages suggest that the LCA may have had stronger geographic structuring to its mtDNA than its nuclear DNA, perhaps indicative of strong female philopatry or a dispersal system analogous to gorillas, where females disperse only short distances from their natal group. Synthesizing different classes of data, and the inferences drawn from them, allows us to predict some of the genetic and demographic properties of the LCA of humans, chimpanzees, and gorillas. « Previous | Next Article » Table of Contents This Article J Hered (2001) 92 (6): 475-480. doi: 10.1093/jhered/92.6.475 » Abstract Free Full Text (HTML) Free Full Text (PDF) Free Classifications Article Services Article metrics Alert me when cited Alert me if corrected Find similar articles Similar articles in Web of Science Similar articles in PubMed Add to my archive Download citation Request Permissions Citing Articles Load citing article information Citing articles via CrossRef Citing articles via Scopus Citing articles via Web of Science Citing articles via Google Scholar Google Scholar Articles by Jensen-Seaman, M. I. Articles by Kidd, K. K. Search for related content PubMed PubMed citation Articles by Jensen-Seaman, M. I. Articles by Deinard, A. S. Articles by Kidd, K. K. Related Content Load related web page information Share Email this article CiteULike Delicious Facebook Google+ Mendeley Twitter What's this? Search this journal: Advanced » Current Issue September-October 2015 106 (5) Alert me to new issues The Journal About this journal Publishers' Books for Review Rights & Permissions Dispatch date of the next issue This journal is a member of the Committee on Publication Ethics (COPE) Journal of Heredity Collections We are mobile – find out more Journals Career Network Published on behalf of The American Genetic Association Impact factor: 2.088 5-Yr impact factor: 2.417 Editor-in-Chief C. Scott Baker View full editorial board For Authors Instructions to authors Online submission instructions Submit now! Data Archiving Policy This journal enables compliance with the NIH Public Access Policy Optional Open Access is Available - Visit Oxford Open Author Self Archiving Policy Alerting Services Email table of contents Email Advance Access CiteTrack XML RSS feed Corporate Services Advertising sales Reprints Supplements
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