Archaic Introgression And Natural Selection in yhe Evolution Of Modern Humans: A Study of Genetic Variation at the Loci Containing the Immune Genes OAS1 and STAT2

Persistent Link:
http://hdl.handle.net/10150/216971
Title:
Archaic Introgression And Natural Selection in yhe Evolution Of Modern Humans: A Study of Genetic Variation at the Loci Containing the Immune Genes OAS1 and STAT2
Author:
Mendez, Fernando Luis
Issue Date:
2011
Publisher:
The University of Arizona.
Rights:
Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author.
Embargo:
Embargo: Release after 01/10/2013
Abstract:
Human populations evolved throughout the Old World for over 1 million years. However, anatomical characteristics of modern humans are thought to have evolved only in Africa in the last 200 thousand years. To this day, the extent to which archaic human populations contributed to the modern human gene pool is largely unknown. This work explores the evidence of genetic contribution from archaic populations at two loci in chromosome 12. Two different archaic humans, Neandertal and Denisova, living respectively in West Eurasia and in East Asia, have been indicated as potential contributors to anatomically modern human populations outside of Africa. This research shows the presence in non-Africans of two distinct introgressive alleles from archaic populations at the immune genes OAS1 and STAT2. In addition to the detection of patterns of genetic variation previously proposed as indicators of genetic introgression from archaic populations, it was possible to use the sequence of archaic individuals to infer a recent common ancestry between the introgressive modern allele and the archaic sequences. The analysis of genetic variation at the genomic region containing the gene STAT2 shows the presence of introgressive Neandertal-like and Denisova-like haplotypes. The elevated frequency in Melanesian populations of the haplotype introgressive from Neandertals suggests that this haplotype has been adaptive in Melanesians (APPENDIX B). A haplotype of the gene OAS1, nearly restricted to Melanesian populations, provides evidence of introgression from a population with genetic affinities to Denisova. The introgressive haplotype carries non-synonymous variants predicted to have functional significance and a block of very deep divergence with the remaining modern sequences (APPENDIX A). A second haplotype, observed mostly in Eurasian populations, shows evidence of having introgressed recently from Neandertals. The Neandertal-like haplotype also contains a block with very deep divergence with the remaining modern sequences (APPENDIX C). Blocks of very deep divergence within introgressive haplotypes suggest an important role of ancient population structure in the evolution of humans.
Type:
text; Electronic Dissertation
Keywords:
denisova; human; introgression; neandertal; Ecology & Evolutionary Biology; admixture; archaic
Degree Name:
Ph.D.
Degree Level:
doctoral
Degree Program:
Graduate College; Ecology & Evolutionary Biology
Degree Grantor:
University of Arizona
Advisor:
Hammer, Michael F.

Full metadata record

DC FieldValue Language
dc.language.isoenen_US
dc.titleArchaic Introgression And Natural Selection in yhe Evolution Of Modern Humans: A Study of Genetic Variation at the Loci Containing the Immune Genes OAS1 and STAT2en_US
dc.creatorMendez, Fernando Luisen_US
dc.contributor.authorMendez, Fernando Luisen_US
dc.date.issued2011-
dc.publisherThe University of Arizona.en_US
dc.rightsCopyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author.en_US
dc.description.releaseEmbargo: Release after 01/10/2013en_US
dc.description.abstractHuman populations evolved throughout the Old World for over 1 million years. However, anatomical characteristics of modern humans are thought to have evolved only in Africa in the last 200 thousand years. To this day, the extent to which archaic human populations contributed to the modern human gene pool is largely unknown. This work explores the evidence of genetic contribution from archaic populations at two loci in chromosome 12. Two different archaic humans, Neandertal and Denisova, living respectively in West Eurasia and in East Asia, have been indicated as potential contributors to anatomically modern human populations outside of Africa. This research shows the presence in non-Africans of two distinct introgressive alleles from archaic populations at the immune genes OAS1 and STAT2. In addition to the detection of patterns of genetic variation previously proposed as indicators of genetic introgression from archaic populations, it was possible to use the sequence of archaic individuals to infer a recent common ancestry between the introgressive modern allele and the archaic sequences. The analysis of genetic variation at the genomic region containing the gene STAT2 shows the presence of introgressive Neandertal-like and Denisova-like haplotypes. The elevated frequency in Melanesian populations of the haplotype introgressive from Neandertals suggests that this haplotype has been adaptive in Melanesians (APPENDIX B). A haplotype of the gene OAS1, nearly restricted to Melanesian populations, provides evidence of introgression from a population with genetic affinities to Denisova. The introgressive haplotype carries non-synonymous variants predicted to have functional significance and a block of very deep divergence with the remaining modern sequences (APPENDIX A). A second haplotype, observed mostly in Eurasian populations, shows evidence of having introgressed recently from Neandertals. The Neandertal-like haplotype also contains a block with very deep divergence with the remaining modern sequences (APPENDIX C). Blocks of very deep divergence within introgressive haplotypes suggest an important role of ancient population structure in the evolution of humans.en_US
dc.typetexten_US
dc.typeElectronic Dissertationen_US
dc.subjectdenisovaen_US
dc.subjecthumanen_US
dc.subjectintrogressionen_US
dc.subjectneandertalen_US
dc.subjectEcology & Evolutionary Biologyen_US
dc.subjectadmixtureen_US
dc.subjectarchaicen_US
thesis.degree.namePh.D.en_US
thesis.degree.leveldoctoralen_US
thesis.degree.disciplineGraduate Collegeen_US
thesis.degree.disciplineEcology & Evolutionary Biologyen_US
thesis.degree.grantorUniversity of Arizonaen_US
dc.contributor.advisorHammer, Michael F.en_US
dc.contributor.committeememberNachman, Michael W.en_US
dc.contributor.committeememberWatkins, Joseph C.en_US
dc.contributor.committeememberWorobey, Michaelen_US
dc.contributor.committeememberHammer, Michael F.en_US
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