Razib Khan One-stop-shopping for all of my content

June 30, 2017

Basal humans in our evolutionary closet

Filed under: Basal Humans,Neanderthal — Razib Khan @ 12:19 am

The ancient genome from South Africa was of not because it confirmed what many had long suspected: the deep structure of modern humans in Africa goes back quite a bit further than we had been assuming. A few years ago I co-wrote an op-ed for USA Today where I initially wrote that the Khoisan divergence from other humans was around ~200,000 years ago. For various reasons I let a “fact-checker” change that to ~150,000 years ago. But as I told my co-author Alex Berezow people had access to whole genomes just leaning toward an older date than in the current literature.

Now we know that the date of divergence may be closer to ~300,000 years. Both because of the ancient DNA, and the Moroccan fossils which make it obvious that morphology associated with our own lineage was already beyond incipient before 300,000 years ago.

The past was more complicated than we think. Ancient DNA has made us toss many of our preconceptions out. For example, several years ago researchers concluded that the Out of Africa populations exhibited a different structure than we had thought. Populations of the Near East and Europe had ancestry from a group that was basal to all other non-Africans. That is, if you have a family tree then Oceanians, East Asians, Amerindians, Siberians, and European hunter-gatherers would be on one branch. On the other branch would be “Basal Eurasians” (BEu), named due to their basal position on the tree in comparison to all other non-Africans. Ancient DNA has not uncovered any population which is mostly BEu. Early Holocene Near Eastern populations, the various first farmers, invariably seem to show mixture between BEu and a West Eurasian element similar to what gave rise to the Mesolithic hunter-gatherers of Europe.

It seems possible we may never find “pure” BEu samples. We know that 10,000-15,000 years ago in Europe there was a massive expansion of a population of hunter-gatherers with stronger affinities to modern Middle Easterners than in the past. Perhaps this was part of a broader expansion of this group of hunter-gatherers across vast swaths of Western Eurasia, and in the process they absorbed the BEu populations until there were no pure populations left?

These questions were triggered by novel results which couldn’t be accommodated by current accepted models. This reminds me of a paper from over a year ago which presented some puzzling results which make much more sense now, Ancient gene flow from early modern humans into Eastern Neanderthals. The authors compared the Altai Neanderthal genome, the Denisovan genome, and those of modern humans (as well as a European Neanderthal). The stylized phylogenetic tree is one which the Neanderthal-Denisovan clade spits off from African proto-modern humans ~600,000 years ago. Then around ~400,000 years ago you see the divergence between Neanderthals and Denisovans. This gives us rough expectations as to the nature of the genetic variation in these populations, as they shared quite distinct periods of evolutionary history together and apart.

What the authors found is that a small minority of the Altai Neanderthal genome exhibited much stronger affinities to modern African populations than to the Denisovan. On the order of ~5%. Looking at the length of the haplotypes they estimated that the admixture occurred ~100,000 year ago. Curiously, at least at the time, this modern human population was basal to all modern humans. The authors estimate that the divergence from modern lineages occurred about ~200,000 year ago based on what was understood about modern human differentiation at the time.

At the time that was pushing it, though not unreasonably so. Now that number is probably comfortably defensible. One important point to note is that the modern human admixture was from a group equally related to all Africans. This implied that this group separated before the division of the Bantu and the Yoruba. So if you accept the most recent genomics then this group may date to closer to 260,000 years before the present. And in fact if the fossil record is correct they might have separated as early 350,000 years before the present. Additionally, the group which published the South African genome study posited another group, Basal Africans (BA), who diverged far earlier than the Khoisan from most African (and also non-African) groups.

Maximal Neanderthal range

The Neanderthals are a well studied group. We know what their range was. One can spit all sorts of speculative scenarios, from wide range proto-modern humans pushing deep in Eurasia during the Eemian interglacial 130,000 years ago. Or, it may have been through contact in the Near East and expansion of a somewhat admixed Neanderthal population north and east over time. Who knows? At least until there’s more ancient DNA….

October 18, 2012

The original Africans are Neandertals (in part)

Filed under: Anthroplogy,Neanderthal — Razib Khan @ 1:10 am

In antiquity what we term Tunisia and Tripolitania were part of “African province.” Just as “Asia” originally referred to the margins of what we now term Asia (regions of Anatolia), so “Africa” originally denoted a subset of the northwest fringe of the continent which became Africa. In biogeography this segment of the continent is actually not part of Africa (it is part of the Palearctic ecozone). And yet the vicissitudes of early modern cartography are such that continent had to be bounded by water on as many sides as possible, and today we clumsily make recourse to the term “Sub-Saharan Africa” to distinguish that region from the northern littoral, which is really part of the Mediterranean world.

This context is somewhat relevant when we evaluate a new PLoS ONE paper, North African Populations Carry the Signature of Admixture with Neandertals. This paper makes little sense unless you’ve read an earlier one, Genomic Ancestry of North Africans Supports Back-to-Africa Migrations. In that paper authors make the case that a majority of the ancestry of modern Maghrebis seems to date back to before the Neolithic, from a late ...

July 19, 2011

What did red-haired Neanderthals look like?

So asks a commenter below in relation to the question above. First, why would one even presume that they were red-haired, see my 2007 post, or the paper in Science: A Melanocortin 1 Receptor Allele Suggests Varying Pigmentation Among Neanderthals. In humans loss of pigmentation can usually be thought of as loss of function on genes. That’s probably one reason that there are several different genetic architectures for light skin, but only one for very dark skin. There might be only one way for an engine to operate as designed, but there are many different ways you can tweak a part and render it broken.


The reason that scientists have posited that Neanderthals were red-haired is that they examined the region around a melanocortin receptor gene which serves as something of a master regulator in terms of melanin production. Their sample was of two Neanderthals, one from Italy and one from Spain, and both exhibited signs of loss of function within this region. An N = 2 is small, but one must recall the fact that they are independent draws as they were sampled from different regions. Also, since then from what I ...

May 6, 2010

Breaking: there’s a little bit of Neandertal in all of us

Filed under: Anthroplogy,Evolution,Human Evolution,Neandertal,Neanderthal — Razib Khan @ 10:00 am

We’re all a bit of a Neanderthal:

As a result, between 1pc [percent] and 4pc of the DNA of non-African people alive today is Neanderthal, according to the research. The discovery emerged from the first attempt to map the complete Neanderthal genetic code, or genome. It more or less settles a long-standing academic debate over interbreeding between separate branches of the human family tree. Evidence in the past has pointed both ways, for and against modern humans and Neanderthals mixing their genes.

Prof Svante Paabo, of the Institute for Evolutionary Anthropology in Leipzig, Germany, said: “Those of us who live outside Africa carry a little Neanderthal DNA in us.”

eva-green-picture-1I will have a thorough write-up when I get a hold of the paper, which should be soon. As I said, this is a story of genomics, not just genetics. 1-4% is not trivial. The Daily Telegraph has more:

They were surprised to find that Neanderthals were more closely related to modern humans from outside Africa than to Africans.

Even more mysteriously, the relationship extended to people from eastern Asia and the western Pacific – even though no Neanderthal remains have been found outside Europe and western Asia.

The most likely explanation is that Neanderthals and Homo sapiens interbred before early modern humans struck out east, taking traces of Neanderthal with them in their genes.

Professor Svante Paabo, director of evolutionary genetics at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, who led the international project, said: “Since we see this pattern in all people outside Africa, not just the region where Neanderthals existed, we speculate that this happened in some population of modern humans that then became the ancestors of all present-day non-Africans.

“The most plausible region is in the Middle East, where the first modern humans appeared before 100,000 years ago and where there were Neanderthals until at least 60,000 years ago.

“Modern humans that came out of Africa to colonise the rest of the world had to pass through that region.”

Several genes were discovered that differed between Neanderthals and Homo sapiens and may have played important roles in the evolution of modern humans.

They included genes involved in mental functions, metabolism, and development of the skull, collar bone and rib cage.

Image Credit: United Press International

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