NEW YORK (GenomeWeb News) – Men may have outnumbered women during the human migration out of Africa, according to a new paper appearing in yesterday’s advance online version of Nature Genetics.
Researchers from Harvard Medical School, the Broad Institute, and the National Human Genome Research Institute assessed more than 130,000 SNPs and a billion bases of sequence data representing individuals of West African, European, and East Asian descent. Together, the X chromosome and autosomal chromosome data suggest that the effective female population size was unexpectedly low when humans migrated from Africa to other parts of the world some 60,000 years ago.
“We have shown that there was a period of accelerated genetic drift on chromosome X associated with the human dispersal out of Africa, which was qualitatively different from what occurred during the subsequent human dispersals into Northern Europe and East Asia,” senior author David Reich, a geneticist affiliated with Harvard Medical School and the Broad Institute, and his colleagues wrote.
The researchers speculated that the observed chromosome X bottleneck may have resulted from either a dearth of females in the migration from Africa to other parts of the world or high selective pressure on the X chromosome outside of Africa.
Genetic evidence suggests human populations populated the globe by spreading outward from Africa thousands of years ago. In an effort to learn more about this human dispersal — as well as the relative histories of male and female populations — Reich and his colleagues assessed genomic data representing both autosomal and X chromosomes.
Their analysis relied on two large datasets: one containing SNP data that allowed them to understand allele frequency at the population level and another containing sequence data that provided hints about individual DNA sequence histories.
“[A]llele frequency differences between two populations are affected only by the history after the populations split,” the authors explained, “whereas sequence diversity within and between populations is also affected by the history of the ancestral population.”
For the former dataset, researchers focused on roughly 130,000 SNPs that differed over two chromosomes in HapMap samples representing 120 unrelated West Africans from Ibadan, Nigeria, 120 unrelated Americans from Utah, and 180 unrelated East Asians — 90 Han Chinese individuals from Beijing and 90 Japanese individuals from Tokyo.
To flesh out this data with information about the X chromosome, the researchers turned to shotgun sequence data from public databases, identifying 1,087 X chromosome SNPs from sequence data representing four West African individuals. They then genotyped 77 Yoruban, 82 European-American, and 122 Han Chinese and Japanese individuals at these SNPs.
Based on these analyses, the researchers found that the relationship between the amount of genetic drift in autosomal and X chromosome regions were similar between European and East Asian populations.
In contrast, the autosomal-to-X chromosome genetic drift was unexpectedly low when comparing either East Asian or European populations with West African populations. Subsequent analyses supported the notion that there was stronger genetic drift on the X chromosome after human populations left Africa than there was on autosomes.
“These results point to a period of accelerated drift on chromosome X that largely occurred after the split of West Africans and non-Africans, but before the separation of North Europeans and East Asians,” Reich and his co-workers wrote.
The team also evaluated a billion base pairs of sequence data representing more than a dozen people — five individuals of Northern European ancestry, four of East Asian ancestry, and five of West African ancestry — in order to determine the sequence diversity on the X chromosomes compared to the autosomal chromosomes.
After calculating within- and between-population sequence diversity from the data, gleaned from public databases, the researchers again found evidence for genetic drift on the X chromosomes of ancestral populations from Northern Europe and East Asia.
The researchers examined several possibilities for this phenomenon, including changes in selection pressures or selection. They concluded that it’s possible but unlikely that X chromosome alleles came under new and widespread selective pressures after the split between West-African and non-African populations. The more likely explanation: a long distance, primarily male migration out of Africa.
Lead author Alon Keinan, a post-doctoral researcher in Reich’s lab, said in a statement that such findings would be “in line with what anthropologists have taught us about hunter-gatherer populations, in which short distance migration is primarily by women and long distance migration primarily by men.”
That, in turn, has implications for understanding human history, interpreting modern genetic data, and even designing experiments the authors argued.
“Chromosome Y and mitochondrial DNA are usually analyzed to study sex-biased demographic events,” they wrote. “However, these loci provide limited resolution about ancient demographic processes ... By contrast, chromosome X and the autosomes encompass thousands of independent genetic loci, each of which probes more ancient times than the mtDNA and the Y chromosome.”