Genetics and Human Migration

Scientific American has a terrific article about the use of genetics to trace human migration patters across the globe:

Almost all our DNA—99.9 percent of the three billion “letters,” or nucleotides, that make up the human genome—is the same from person to person. But interwoven in that last 0.1 percent are telltale differences. A comparison among, say, East Africans and Native Americans can yield vital clues to human ancestry and to the inexorable progression of colonizations from continent to continent. Until recent years, DNA passed down only from fathers to sons or from mothers to their children has served as the equivalent of fossilized footprints for geneticists. The newest research lets scientists adjust their focus, widening the field of view beyond a few isolated stretches of DNA to inspect hundreds of thousands of nucleotides scattered throughout the whole genome.

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The fast, relatively predictable rate of “neutral” mitochondrial mutations—ones that are neither beneficial nor harmful—lets the organelles operate as molecular clocks. Counting the differences in the number of mutations (ticks of the clock) between two groups, or lineages, allows a researcher to construct a genetic tree that tracks back to a common ancestor—Mitochondrial Eve or another woman who founded a new lineage. Comparison of the ages of the lineages from different regions permits the building of a timeline of human migrations.

Since 1987 the data bank on human diversity has broadened to encompass the Y chromosome—the sex chromosome passed down only by males to their sons. The male-transmitted DNA carries many more nucleotides than mitochondrial DNA does (tens of millions, as opposed to just 16,000), enhancing investigators’ ability to distinguish one population from another. Analyzing mitochondrial and Y chromosome DNA from human populations has turned up hundreds of genetic markers (DNA sites having identifiable mutations specific to particular lineages).

The route humans took from Africa to the Americas over the course of tens of thousands of years can now be tracked on the map as if the travelers were moving, albeit extremely slowly, on a series of interconnected superhighways. Alphanumeric route signs, such as I-95, can be recast as alphanumeric genetic markers. In the case of the Y chromosome, for instance, cross the Bab el Mandeb on highway (genetic marker) M168, which becomes M89 when heading north through the Arabian Peninsula. Make a right at M9 and set out toward Mesopotamia and beyond. Once reaching an area north of the Hindu Kush, turn left onto M45. In Siberia, go right and follow M242 until it eventually traverses the land bridge to Alaska. Pick up M3 and proceed to South America.

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During this decade, researchers have made dramatic discoveries by simultaneously comparing a multitude of variable, or polymorphic, sites interspersed throughout the genome’s three billion nucleotides. The first whole-genome studies earlier in this decade looked at differences among populations in short repetitive stretches of DNA known as microsatellites. More recently, the scope afforded by whole-genome scans has widened further. In February two papers, one in Science, the other in Nature, reported the largest surveys to date of human diversity. Both examined more than 500,000 single nucleotide polymorphisms (SNPs)—swaps of one nucleotide for another at a particular spot in the DNA—from the Human Genome Diversity Panel. These cell lines were drawn from about 1,000 individuals from 51 populations worldwide and are maintained by the Center for the Study of Human Polymorphisms in Paris.

The two research teams analyzed the wealth of data in various ways. They compared SNPs directly among distinct populations. They also looked at haplotypes, blocks of DNA containing numerous SNPs that are inherited intact through many generations. The group that wrote the Nature paper also explored a new technique for surveying human variation by comparing repetitions or deletions of DNA stretches of up to 1,000,000 nucleotides long (copy number variations) throughout a person’s genome, consistent with the larger trend to mine the genome for ever more markers of variation. “Any one piece of the genome will have a history that doesn’t necessarily reflect the ancestry of the genome as a whole,” says Noah A. Rosenberg of the University of Michigan at Ann Arbor and lead author of the Nature paper. But looking at many areas at once, he explains, can overcome that problem: “With thousands of markers, it’s possible to determine the overall story of human migrations.”

Looking at hundreds of thousands of SNPs allowed the researchers to resolve the identities of individual populations—and to see how genetically close relations spread far and wide. Native South American ancestry was tracked back to Siberians and some other Asians. The Han people, China’s principle ethnic group, has distinct northern and southern populations. Bedouins are related to groups from Europe and Pakistan as well as the Middle East.

The findings, which jibed with previous research from anthropology, archaeology, linguistics and biology (including previous mitochondrial and Y DNA studies), also provided a broader statistical foundation for the out-of-Africa hypothesis, supporting the idea that a small population of humans moved out of the continent, then grew in size in a new home until another subgroup of “founders” broke off and moved away—a process that repeated itself until the entire world was settled. These wayfarers edged out archaic human populations—Homo neanderthalensis and Homo erectus—with little or no interbreeding when they met. The new DNA work indicates that each time a smaller group split off, it carried only a subset of the genetic diversity originally present in the African population. So as distance (and time) removed from Africa lengthens, diversity diminishes, providing a means to follow population movements. Native Americans, sojourners on the last major continental migrations, have much less variety in their genomes than Africans do.

Read it all here.