January 20, 2010
Endangered Species: Humans Might Have Faced Extinction 1 Million Years Ago
A new approach to probe ancient regions of the genome suggests early human populations were scarce
By Carina Storrs
New genetic findings suggest that early humans living about one million years ago were extremely close to extinction.
The genetic evidence suggests that the effective population—an indicator of genetic diversity—of early human species back then, including Homo erectus, H. ergaster and archaic H. sapiens, was about 18,500 individuals (it is thought that modern humans evolved from H. erectus), says Lynn Jorde, a human geneticist at the University of Utah in Salt Lake City. That figure translates into a total population of 55,500 individuals, tops.
ANCIENT DE-POPULATIONS: Genetic study reveals that populations of ancient humans were surprisingly small.
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Mobile elements reveal small population size in the ancient ancestors of Homo sapiens
Chad D. Huff a, Jinchuan Xing a, Alan R. Rogers b, David Witherspoon a, and Lynn B. Jorde a,1
-Author Affiliations
aDepartment of Human Genetics, Eccles Institute of Human Genetics, and
bDepartment of Anthropology, University of Utah, Salt Lake City, UT 84112
Abstract
The genealogies of different genetic loci vary in depth. The deeper the genealogy, the greater the chance that it will include a rare event, such as the insertion of a mobile element. Therefore, the genealogy of a region that contains a mobile element is on average older than that of the rest of the genome. In a simple demographic model, the expected time to most recent common ancestor (TMRCA) is doubled if a rare insertion is present. We test this expectation by examining single nucleotide polymorphisms around polymorphic Alu insertions from two completely sequenced human genomes. The estimated TMRCA for regions containing a polymorphic insertion is two times larger than the genomic average (P < <10−30), as predicted. Because genealogies that contain polymorphic mobile elements are old, they are shaped largely by the forces of ancient population history and are insensitive to recent demographic events, such as bottlenecks and expansions. Remarkably, the information in just two human DNA sequences provides substantial information about ancient human population size. By comparing the likelihood of various demographic models, we estimate that the effective population size of human ancestors living before 1.2 million years ago was 18,500, and we can reject all models where the ancient effective population size was larger than 26,000. This result implies an unusually small population for a species spread across the entire Old World, particularly in light of the effective population sizes of chimpanzees (21,000) and gorillas (25,000), which each inhabit only one part of a single continent.
human effective population size human evolutionary history Alu coalescent theory population genetics
Footnotes
1To whom correspondence should be addressed. Email:lbj@odin.genetics.utah.edu.
Edited* by Wen-Hsiung Li, University of Chicago, Chicago, IL, and approved December 18, 2009 (received for review August 11, 2009)
Author contributions: C.D.H. designed research; C.D.H., J.X., A.R.R., and D.J.W. performed research; C.D.H. and J.X. contributed new reagents/analytic tools; C.D.H. and D.J.W. analyzed data; and C.D.H., J.X., A.R.R., D.J.W., and L.B.J. wrote the paper.
The authors declare no conflict of interest.
↵*This Direct Submission article had a prearranged editor.
This article contains supporting information online at www.pnas.org/cgi/content/full/0909000107/DCSupplemental.
