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Human Evolution Study Suggests Multiple Early Lineages in Africa

NEW YORK – Investigators at McGill University; the University of California, Davis; and other centers in the US and South Africa have used genetic data from present-day populations in southern, eastern, and western Africa to retrace human origins on the continent. Based on the results, they came up with a new model that involves mixing between closely related ancestral populations with similar physical features.

"We are presenting something that people had never even tested before," co-senior author Brenna Henn, a researcher at UC Davis, said in a statement. "This moves anthropological science significantly forward."

As they reported in Nature on Wednesday, the researchers brought together published whole-genome sequencing data for 290 individuals from populations in Eurasia or southern, eastern, and western Africa, including agriculturalist groups and recent descendants of hunter-gatherers in Ethiopia and Sierra Leone.

Together with fossil data, Neanderthal genome sequence data, and new shallow whole-genome sequences for 44 individuals from a genetically diverse Indigenous Nama (Khoe-San) population in southern Africa, they analyzed genetic diversity patterns to compare competing Homo evolutionary and migration models in Africa.

"By including geographically and genetically diverse populations across Africa, we infer demographic models that explain more features of genetic diversity in more populations than previously reported," the authors wrote.

The team's demographic analyses, which relied on linkage disequilibrium and diversity-based statistic data, led to a new model that argued against prevailing human evolution models centered on a single ancestral human population that met and mixed with archaic hominins in Africa.

"Previous, more complicated models proposed contributions from archaic hominins, but this model indicates otherwise," co-author Tim Weaver, an anthropology researcher at UC Davis, said in a statement.

Instead, the results led to a "reticulated" population history model involving multiple, genetically similar Homo genus groups that continued interbreeding for hundreds of thousands of years. The lineage that led to existing humans appeared to have split off from this ancestral human melange some 120,000 to 135,000 years ago, followed by further migration that continued to bring the so-called "stem" groups together over time.

"Such weakly structured stem models explain patterns of polymorphisms that had previously been attributed to contributions from archaic hominins in Africa," Henn and co-senior author Simon Gravel, a human geneticist at McGill University, and their colleagues reported.

"In contrast to models with archaic introgression," they explained, "we predict that fossil remains from coexisting ancestral populations should be genetically and morphologically similar, and that only an inferred [1 percent to 4 percent] of genetic differentiation among contemporary human populations can be attributed to genetic drift between stem populations."

The team also delved into population migration and structure patterns following the early human divergence from related groups, including migrations out of eastern Africa and "back-to-Africa" migrations by groups that had previously moved out of the continent, which left their mark on agricultural populations in Ethiopia.

Together, "best-fit models presented here include reticulation and migration between early human populations, rather than archaic hominin admixture from long-isolated branches," the authors wrote, noting that "recent expansion and African multi-regionalism feature in our best-fit models."

Even so, they cautioned that "[w]e cannot rule out the possibility that more complex models involving additional stems, more complex population structure, or hybrid models including both weak structure and archaic hominin admixture, may better explain the data."