Earliest Humans Had Sex With Neanderthals

The eartliest known homo sapiens had sex with Neanderthals and another close relative, the recently discovered Denisovans, according to genetic research
at the Stanford University School of Medicine.

Although modern humans, Neanderthals and Denisovans share a common ancestor in Africa, the groups split into separate, distinct populations approximately 400,000 years ago. The Neanderthal lineage migrated northwestward into West Asia and Europe, and the Denisovan lineage moved northeastward into East Asia. The ancestors of modern man stayed in Africa until 65,000 years or so ago, when they expanded into Eurasia and then encountered the other human-like groups. In some cases, the rendezvous were amorous in nature.

Last year, a partial genome sequence of Neanderthals, who died out approximately 30,000 years ago, revealed that these trysts left as much as 4 percent Neanderthal DNA in the genetic blueprint of some present-day humans. Last December, the genome of another human cousin, the extinct Denisovans, made clear that up to 6 percent of some people's genomes are Denisovan in origin.

Now, a team of researchers led by Peter Parham, PhD, professor of structural biology and of microbiology and immunology, has found that these matings had a positive effect on modern human fitness. "The cross breeding wasn't just a random event that happened, it gave something useful to the gene pool of the modern human," said Parham.

The useful gift was the introduction of new variants of immune system genes called the HLA class I genes, which are critical for our body's ability to recognize and destroy pathogens. HLA genes are some of the most variable and adaptable genes in our genome, in part because the rapid evolution of viruses demands flexibility on the part of our immune system.

"The HLA gene system, with its diversity of variants, is like a magnifying glass," said researcher Laurent Abi-Rached, explaining that it provides a lot more detail about the history of populations than typical gene families. 

Prior to the sequencing of the Neanderthal and Denisovan genomes, Parham and his group had suspected that at least one HLA variant came from archaic humans. They determined that the variant known as HLA-B*73 is rare in present-day African populations but occurs with significant frequency in West Asian populations. The ethnic distribution of HLA-B*73 and its similarity across populations suggested that it came from a relatively recent co-mingling of modern human and archaic human DNA, which most likely would have happened outside of Africa. Parham's team wanted to discern which archaic humans were the source of the HLA-B*73 gene type. In the last year they have found the answer in the genome sequence of a recently discovered human relative, the Denisovans, whose existence first came to light in 2008 with the discovery of an unfamiliar finger bone and tooth in a cave in Siberia.

By comparing the HLA genes of the archaic humans with modern humans, the researchers were able to show that the HLA-B*73 allele likely came from cross breeding with Denisovans. Little is known about what the Denisovans looked like (the finger bone and the tooth are the only known fossils), but the genome sequence extracted from the finger bone gives insight into where they overlapped with modern humans. Gene flow from the Denisovans into modern humans has left the highest frequency of the HLA-B*73 allele in populations in West Asia, the most likely site for the fortuitous mating to have taken place.

Even in West Asian populations, the HLA-B*73 variant never represents more than 5 percent of all known variants of that gene. However, other human HLA types that arose from ancient matings are found in much greater frequencies. "Certain traits coming from these archaic humans have become the dominant form," said Parham. For example, another HLA gene type, called HLA-A*11, is absent from African populations, but represents up to 64 percent of variants in East Asia and Oceania, with the greatest frequency in people from Papua New Guinea. "The likely interpretation was that these HLA class variants provided an advantage to modern human and so rose to high frequencies," Parham said.

A similar scenario is seen in some HLA gene types found in the Neanderthal genome, which was also sequenced from DNA extracted from ancient bones. These gene variants are common in European and Asian populations but rare in African populations. "We are finding frequencies in Asia and Europe that are far greater than whole genome estimates of archaic DNA in modern human genomes, which is 1 to 6 percent," said Parham. Within one class of HLA gene, the researchers estimate that Europeans owe half of their variants to interbreeding with Neanderthals and Denisovans, Asians owe up to 80 percent and Papua New Guineans, up to 95 percent.

"This is not the pattern seen genome-wide," said Abi-Rached. "The HLA system is unique in its diversity and the strength of natural selection acting on it, but it's possible that other gene systems, particularly the ones under similar pressure for variation, could show a similar pattern."

Stanford University School of Medicine departments of Structural Biology and of Microbiology and Immunology

Lousy Sex
Lousy Sex
Creating Self in an Infectious World
by Gerald N. Callahan

"For millenia, evolution has been shaping human genes for a single purpose - reproduction. Those who didn't measure up didn't reproduce. Evolution is a harsh mistress. Genes that helped animals make more of themselves survived.

"At the moment of conception each of us is given that legacy - helices full of genes as old as life itself. Genes that brought fish from the dark into the light, genes that made lizards strong, genes that allowed apes to stand up, genes that crushed others and forged a living from their remains, genes that will write poetry and explore constellations, genes that will stare and the stars and wonder, and genes to make us care about all of it, A genomeful of genes."

This collection of essays blending personal history with scientific discoveries and philosophical musings challenges our conventional definitions of self, evolution, and mortality.

In the concluding section of the book, titled "This Is Not The End," Callahan confronts the existential question facing a fast-growing segment of the human population -- seniors past the age of reproduction no longer contributing to the gene pool: what's our purpose? He suggests that language, the ability to share knowledge from beyong the grave, was a evolutionary game-changer. "Once we spoke, we took a first stpe toward immortality and a non-Dariwnian way of evolving," he writes, "There had never been anything quite like language, and those who spoke it spread. Along with that spread there was abruptly a selective advantage to longer-lived humans."

And then there's the question of our mortality, which preachers and teachers have convinced us is our lot in life. "In truth, we've been lied tom," Callahan says. "Death is not an essential element of life. Very long-lived and even large immortal beings do just fine on this Earth. That means that what stands between us and immortality isn't some unbreakable law of nature. We grow old and die because of nothing more than our profligate past and our genetic heritage. At the beginning of the twent-first century. we can change our genes almost as easily as we change our jeans. If we wish to reach for the golden ring of old age, perhaps even immortality, all we need to do is figure out which of our genes are killing us."

Darwin's Sacred Cause
Darwin's Sacred Cause
Race, Slavery and the Quest for Human Origins
by Adrian Desmond

Celebrated for his famous theory of evolution tracing all of life back to a common ancestor, Charles Darwin held an overlooked passion that fired his belief in life’s unity.

The thesis of this book is that Darwin's commitment to the abolition of slavery – his “sacred cause” – led him from a recognition of the shared racial roots of black and white people to the ‘common descent’ of all organisms. This belief in the brotherhood of races – whether animals, plants or people – was the seed that grew into his revolutionary theory.

Darwin's five-year voyage aboard the HMS Beagle not only fired his scientific curiosity, but also stoked a moral fervor in "a squeamish, humanitarian young gentleman from Cambridge." The prevalence of slavery in the ports they visited, and Darwin's exposure to it on the Beagle has been underestimated., the authors contend. He concluded the voyage "world-weary and wiser," having seen slavery for what it was - "a global empire of evil requiring a global remedy."