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Bayesian coalescent inference of major human mitochondrial DNA haplogroup expansions in Africa.

by: QD Atkinson, RD Gray, and AJ Drummond

In: Proc Biol Sci Institute of Cognitive and Evolutionary Anthropology, University of Oxford, 64 Banbury Road, Oxford OX2 6PN, UK.: (2008 Sep 30) .

Abstract

Past population size can be estimated from modern genetic diversity using coalescent theory. Estimates of ancestral human population dynamics in sub-Saharan Africa can tell us about the timing and nature of our first steps towards colonizing the globe. Here, we combine Bayesian coalescent inference with a dataset of 224 complete human mitochondrial DNA mtDNA sequences to estimate effective population size through time for each of the four major African mtDNA haplogroups L0-L3. We find evidence of three distinct demographic histories underlying the four haplogroups. Haplogroups L0 and L1 both show slow, steady exponential growth from 156 to 213kyr ago. By contrast, haplogroups L2 and L3 show evidence of substantial growth beginning 12-20 and 61-86kyr ago, respectively. These later expansions may be associated with contemporaneous environmental and/or cultural changes. The timing of the L3 expansion-8-12kyr prior to the emergence of the first non-African mtDNA lineages-together with high L3 diversity in eastern Africa, strongly supports the proposal that the human exodus from Africa and subsequent colonization of the globe was prefaced by a major expansion within Africa, perhaps driven by some form of cultural innovation.

BibTeX record

@article{Atkinson:2008nr,
  abstract = {Past population size can be estimated from modern genetic diversity using coalescent theory. Estimates of ancestral human population dynamics in sub-Saharan Africa can tell us about the timing and nature of our first steps towards colonizing the globe. Here, we combine Bayesian coalescent inference with a dataset of 224 complete human mitochondrial DNA (mtDNA) sequences to estimate effective population size through time for each of the four major African mtDNA haplogroups (L0-L3). We find evidence of three distinct demographic histories underlying the four haplogroups. Haplogroups L0 and L1 both show slow, steady exponential growth from 156 to 213kyr ago. By contrast, haplogroups L2 and L3 show evidence of substantial growth beginning 12-20 and 61-86kyr ago, respectively. These later expansions may be associated with contemporaneous environmental and/or cultural changes. The timing of the L3 expansion-8-12kyr prior to the emergence of the first non-African mtDNA lineages-together with high L3 diversity in eastern Africa, strongly supports the proposal that the human exodus from Africa and subsequent colonization of the globe was prefaced by a major expansion within Africa, perhaps driven by some form of cultural innovation.},
  added-at = {2011-08-21T10:09:10.000+0200},
  address = {Institute of Cognitive and Evolutionary Anthropology, University of Oxford, 64 Banbury Road, Oxford OX2 6PN, UK.},
  author = {Atkinson, QD and Gray, RD and Drummond, AJ},
  bdsk-url-1 = {http://dx.doi.org/10.1098/rspb.2008.0785},
  biburl = {http://www.bibsonomy.org/bibtex/21b062e2ce3f52c1dba0e4d6492ede991/compevol},
  da = {20081001},
  date-added = {2008-11-28 10:40:25 -0800},
  date-modified = {2008-11-28 10:40:25 -0800},
  dep = {20080930},
  doi = {10.1098/rspb.2008.0785},
  edat = {2008/10/02 09:00},
  interhash = {ad61760bc16b2271de06b18e669a7ea0},
  intrahash = {1b062e2ce3f52c1dba0e4d6492ede991},
  issn = {0962-8452 (Print)},
  jid = {101245157},
  journal = {Proc Biol Sci},
  jt = {Proceedings. Biological sciences / The Royal Society},
  keywords = {from:alexei.drummond imported},
  language = {ENG},
  mhda = {2008/10/02 09:00},
  own = {NLM},
  pii = {Q322007083Q68417},
  pmid = {18826938},
  pst = {aheadofprint},
  pt = {JOURNAL ARTICLE},
  pubm = {Print-Electronic},
  so = {Proc Biol Sci. 2008 Sep 30.},
  stat = {Publisher},
  timestamp = {2011-08-21T10:09:10.000+0200},
  title = {Bayesian coalescent inference of major human mitochondrial DNA haplogroup expansions in Africa.},
  year = {2008 Sep 30}
}

Endnote record

%0 Journal Article
%1 Atkinson:2008nr
%A Atkinson, QD
%A Gray, RD
%A Drummond, AJ
%C Institute of Cognitive and Evolutionary Anthropology, University of Oxford, 64 Banbury Road, Oxford OX2 6PN, UK.
%D 2008 Sep 30
%J Proc Biol Sci
%K 
%T Bayesian coalescent inference of major human mitochondrial DNA haplogroup expansions in Africa.
%R 10.1098/rspb.2008.0785
%X Past population size can be estimated from modern genetic diversity using coalescent theory. Estimates of ancestral human population dynamics in sub-Saharan Africa can tell us about the timing and nature of our first steps towards colonizing the globe. Here, we combine Bayesian coalescent inference with a dataset of 224 complete human mitochondrial DNA (mtDNA) sequences to estimate effective population size through time for each of the four major African mtDNA haplogroups (L0-L3). We find evidence of three distinct demographic histories underlying the four haplogroups. Haplogroups L0 and L1 both show slow, steady exponential growth from 156 to 213kyr ago. By contrast, haplogroups L2 and L3 show evidence of substantial growth beginning 12-20 and 61-86kyr ago, respectively. These later expansions may be associated with contemporaneous environmental and/or cultural changes. The timing of the L3 expansion-8-12kyr prior to the emergence of the first non-African mtDNA lineages-together with high L3 diversity in eastern Africa, strongly supports the proposal that the human exodus from Africa and subsequent colonization of the globe was prefaced by a major expansion within Africa, perhaps driven by some form of cultural innovation.