Did Homo Sapiens Arise As A Hybrid?

In addition to being highly model dependent and unsupported by ancient DNA data, and hence somewhat speculative, this is really a less revolutionary proposal than it seems. 

Modern humans still arise in Africa (including a hypothetical admixture event that gives rise to the new species ca. 290,000 years ago). Basically, it is just proposing that in addition to the Neanderthal admixture shared by all non-Africans, and the Denisovan admixture that took place in the first generation of modern humans to reach Asia, there was an 20% admixture event from Homo erectus involving all modern humans associated with the emergence of the new species.

In their model, the 80% source, probably Homo heidelbergensis is also ancestral to Neanderthals and Denisovans, evolves from from Homo erectus about 1,500,000 years ago and suffers a severe bottleneck period, while the 20% Homo erectus ancestry was exclusive to Homo sapiens and was probably initially a larger percentage as a result of an admixture event in Africa about 290,000 years ago. The Homo erectus ancestry percentage was reduced in percentage over time due to its inferior selective fitness in most parts of the Homo erectus genome that have an impact on phenotypes (i.e. that have any actual discernible effect).

The evolutionary path leading to the rise of modern humans is full of twists and turns, and the latest surprise reveals that our species likely sprung forth from two ancient intermingling populations. A new study has confirmed that these groups first diverged from each other around 1.5 million years ago and later merged back together 300,000 years ago, initiating a genetic mixing event that culminated with the birth of modern humans.

The study, published in Nature Genetics, completely rewrites the story of humans. Scientists have long believed that Homo sapiens first appeared in Africa somewhere between 200,000 years and 300,000 years ago, having descended from a single ancestral lineage. The idea of genetic admixture flips the script, however, showing that human origins are much more complex than previously thought.

The researchers . . . tapped into modern human DNA from the 1000 Genomes Project, an international catalog filled with human genomes from a variety of populations. The research team created a computational algorithm called cobraa, which was designed to represent the event of an ancestral population splitting and rejoining. . . . 

With this method, they were able to produce a structured model that displayed two ancestral populations breaking apart in ancient times. In the years after this divergence, one of the populations experienced major fluctuations in size.

“Immediately after the two ancestral populations split, we see a severe bottleneck in one of them — suggesting it shrank to a very small size before slowly growing over a period of one million years,” said co-author Aylwyn Scally from the University of Cambridge’s Department of Genetics, in a statement. “This population would later contribute about 80 percent of the genetic material of modern humans and also seems to have been the ancestral population from which Neanderthals and Denisovans diverged.”

The second population, meanwhile, contributed 20 percent to the genetic makeup of modern humans. The researchers found that many of the genes this group passed along to humans were not located near regions of the genome corresponding to gene functions; this could reflect a concept called purifying selection, which is the process of natural selection filtering out harmful mutations. However, the researchers believe that some of the genes from the second population may have still been integral to brain development in modern humans.  . . .

An element of mystery still surrounds the identity of these ancestral populations. The researchers point to Homo erectus and Homo heidelbergensis as potential answers since they were present in Africa around the time of the genetic admixture, but further research is needed to match genetic ancestors with fossil groups.

Nature Genetics. A structured coalescent model reveals deep ancestral structure shared by all modern humans

From Discover Magazine. The abstract of the open access paper states:

Understanding the history of admixture events and population size changes leading to modern humans is central to human evolutionary genetics. Here we introduce a coalescence-based hidden Markov model, cobraa, that explicitly represents an ancestral population split and rejoin, and demonstrate its application on simulated and real data across multiple species. 

Using cobraa, we present evidence for an extended period of structure in the history of all modern humans, in which two ancestral populations that diverged ~1.5 million years ago came together in an admixture event ~300 thousand years ago, in a ratio of ~80:20%. Immediately after their divergence, we detect a strong bottleneck in the major ancestral population. 

We inferred regions of the present-day genome derived from each ancestral population, finding that material from the minority correlates strongly with distance to coding sequence, suggesting it was deleterious against the majority background. Moreover, we found a strong correlation between regions of majority ancestry and human–Neanderthal or human–Denisovan divergence, suggesting the majority population was also ancestral to those archaic humans.