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Tag Archives: David Reich

Genetic distance between humans, neanderthals & other primates

25 Saturday May 2019

Posted by pumpkinperson in Uncategorized

≈ 92 Comments

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anatomically modern humans, David Reich, Denisovans, genetic distance, genus, Neanderthals, race, species, taxonomy

About a year ago I wrote:

The following chart (created by some scientist(s) led by David Reich) shows the genetic divergence between hominin samples as a fraction of the human-chimp difference.  So for example, all the human groups have just over a 0.12 genetic divergence with Neanderthals, meaning that the genetic difference between humans and Neanderthals is only 12% as great as the genetic difference between humans and Chimps (source: supplement of Genetic history of an archaic hominin group from Denisova Cave in Siberia.)

distance4

The purpose of the chart is to estimate how long ago the different populations diverged from a common ancestor.  So since the fossil record tells us that Neanderthals and chimps diverged about 6.5 million years, then humans and Neanderthals should have diverged roughly 0.8 million years ago (12% of 6.5 million) assuming genetic divergence maps to chronological divergence in a linear way.

I transformed the genetic distance matrix into a dendrogram, which looks at all the distances and creates the most parsimonious family tree:

Dendogram showing genetic relationship between 8 groups. From left to right: chimps, san, Yoruba, French, Papuan, East Asian, Denisovan, Neanderthals

What’s cool about dendrograms is they let you determine the number of categories and subcategories in a very objective way.

Of course dendrograms are only as good as the data you put into them, and I don’t endorse basing taxonomy simply on genetic relatedness, but if I did, here’s how I’d interpret the above tree:

The first major split is between chimps & everyone else. This is consistent with two well recognized genera of hominins : Pan (i.e. chimps) and Homo (humans and near-humans).

Now within the Homo genus, we see another major split in the tree. Anatomically Modern Humans (AMH) vs Archaic Humans. Thus we can divide the homo genus into at least two major species.

Within the Archaic Humans we can further subdivide into major races: Denisovans and Neanderthals.

Now within our own species, AMH, the dendrogram shows three major races: Capoids, Congoids and Non-Africans.

I’m not saying I agree with this taxonomy since it was only based on genetic distance (much of which is junk DNA) but what’s great about using dendrograms is almost everyone looking at them will assign groups to the same categories and subcategories, even if they don’t use the same words (race, species, genus) to describe them. It’s wholly objective.

But what is needed is a dendrogram based on polygenic scores of actual phenotypes. That way people who have the same phenotypes caused by the same genomic architecture could be grouped together.

Unlike the above dendrogram, which groups based on how recently we share a common ancestor, we need to group based on how much of the common ancestor we share.

[update may 26, 2019: an earlier version of this article misspelled dendrogram]

[2nd update may 26, 2019: an earlier version of this article contained bragging that has since been removed]

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The evolution of behavioral modernity

10 Friday May 2019

Posted by pumpkinperson in Uncategorized

≈ 292 Comments

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David Reich, Richard Klein

Commenter Nehemiah writes:

It is implausible that the Bushmen populations (which once occupied a much larger range than today) lived in total isolation from non-Bushmen populations. Presumably the mutation or mutations that facilitated the emergence of grammar appeared or came together in one population first. This development was so valuable that the relevant genes had a high chance of being preserved and spreading to fixation if even a small amount of interbreeding occurred with a neighboring population. Thus, even if Bushmen (and Pygmies, BTW) split off between 200kya and 300kya, that would not have prevented the spread of an especially valuable mutation from any one human population to all the rest. I argue that a limited vocabulary already existed in all sapiens populations (and probably some non-Sapiens populations as well), but the appearance of the “grammar gene(s)” made vocabulary immensely more useful so that it was now worthwhile to coin many more words, and the more intelligent band members could master the use and comprehension of this expanding vocabulary much better than the less intelligent. The grammar mutation should have spread relatively rapidly from any human population to all the rest. If we backcrossed with Neanderthals and Denisovans, I cannot imagine that there was not also gene flow to (and from) Bushmen (and Pygmies) as well. Further, I know of no reason to presume that grammar did not first emerge in Bushmen and spread to non-Bushmen rather than vice versa. We simply do not know.

Neanderthals possessed our FOXP2 gene and a hyoid bone that facilitate speech, but the larynx was still in a more anterior position, as in an infant of our species, which restricted the number of vowel sounds that could be formed, and therefore the number of words that could be created. I argue that if Neanderthal has possessed grammatical language at an earlier date, there would have been evolutionary selection for a larynx positioned so that a larger number of words could be formed. Thus, I also argue that grammar evolved sometime after Neanderthals split from the lineage that led to sapiens, and our sudden and rapid colonization of the world in the last 70ky suggests that the grammatically structured use of vocabular evolved shortly before we exploded suddenly over the world’s surface, since the appearance of grammatical language is the most likely advantage that allowed us to expand rapidly and to quickly displace our rivals who were longer established and better adapted to the local environment.

The notion that a small number of genetic mutation(s) gave rise to behavioral modernity and the upper Paleothic revolution is associated with paleontologist Richard Klein:

But geneticist David Reich is having none of it:

Expanding our analysis to the whole genome, we could not find any location–apart from mitochondrial DNA and the Y chromosome, where all people living today share a common ancestor less than 320,000 years ago. This is a far longer time scale than the one required by Klein’s hypothesis. If Klein was right, it would be expected that there would be places in the genome, beyond mitochondrial DNA and the Y chromosome, where almost everyone shares a common ancestor within the last hundred thousand years. But these do not in fact seem to exist.

Our results do not completely rule out the hypothesis of a single critical genetic change. There is a small fraction of the genome that contains complicated sequences that are difficult to study and that was not included in our survey. But the key change, if it exists, is running out of places to hide….

From Who are we and how we got here by David Reich, pg 18

But while Reich largely rejects the idea of a single (or small number) of genetic mutations giving rise to behavior modernity, he seems open to the possibility that “…coordinated natural selection on combinations of many mutations simultaneously–did enable new cognitive capacities…”

See also: The importance of brain shape

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