Paleogenetics and human history

[HMS_Beagle]

One of the neatest new sciences that has arisen in the last decade is Paleogenetics. DNA degrades quite rapidly so recovering useable sequences beyond a few thousand years in age has been quite problematic. New advances in DNA sequencing however have now allowed the recovery of DNA snippets going back hundreds of thousands of years. The current record is the recovered DNA from a Pleistocene horse approx. 700,000 years old.

This has huge ramifications for our understanding of human origins history since we can now sequence the DNA of our extinct sister species. Last year a major milestone was accomplished with the sequencing of a complete Neanderthal genome. Research published last week now shows non-African humans got some critical genes, particularly those involved in skin and hair development, from interbreeding with Neanderthals.

The genomic landscape of Neanderthal ancestry in present-day humans
Sankararaman et al
Nature, doi:10.1038/nature12961 29 January 2014

Abstract: Genomic studies have shown that Neanderthals interbred with modern humans, and that non-Africans today are the products of this mixture. The antiquity of Neanderthal gene flow into modern humans means that genomic regions that derive from Neanderthals in any one human today are usually less than a hundred kilobases in size. However, Neanderthal haplotypes are also distinctive enough that several studies have been able to detect Neanderthal ancestry at specific loci. We systematically infer Neanderthal haplotypes in the genomes of 1,004 present-day humans. Regions that harbour a high frequency of Neanderthal alleles are enriched for genes affecting keratin filaments, suggesting that Neanderthal alleles may have helped modern humans to adapt to non-African environments. We identify multiple Neanderthal-derived alleles that confer risk for disease, suggesting that Neanderthal alleles continue to shape human biology. An unexpected finding is that regions with reduced Neanderthal ancestry are enriched in genes, implying selection to remove genetic material derived from Neanderthals. Genes that are more highly expressed in testes than in any other tissue are especially reduced in Neanderthal ancestry, and there is an approximately fivefold reduction of Neanderthal ancestry on the X chromosome, which is known from studies of diverse species to be especially dense in male hybrid sterility genes. These results suggest that part of the explanation for genomic regions of reduced Neanderthal ancestry is Neanderthal alleles that caused decreased fertility in males when moved to a modern human genetic background.

link

For reference, humans and Neanderthals last shared a common ancestor around 600,000 years ago. The interbreeding is though to have taken place between 45,000 and 60,000 years ago. Neanderthals went extinct about 30,000 years ago.

Next on the list to be sequenced and analyzed are Homo floresiensis who lived as recently as 12,000 years ago in Indonesia and the mysterious Denisonans who lived about 40,000 years ago in Siberia. The results should give new insight into the tangled bush of human evolution.

Interesting stuff!

[phank]

This seems puzzling to me. It's generally considered the case that if two populations establish breeding isolation, they are different species. Given enough time (and 600,000 years should be enough), mutations occurring in both populations and not being shared should result in sufficient divergence so that fertile interbreeding is unlikely. If fertile interbreeding is still occurring, would it be reasonable to suspect that these two populations have never quite fully diverged? Clearly, according to this genetic evidence, genes were still being exchanged between these populations.

[HMS_Beagle]

This seems puzzling to me. It's generally considered the case that if two populations establish breeding isolation, they are different species. Given enough time (and 600,000 years should be enough), mutations occurring in both populations and not being shared should result in sufficient divergence so that fertile interbreeding is unlikely.

On what do you base the claim that 600K years should be enough time to produce non-interfertility? Lions and tigers can still produce fertile offspring and they diverged some 3.7 million years ago.

If fertile interbreeding is still occurring, would it be reasonable to suspect that these two populations have never quite fully diverged? Clearly, according to this genetic evidence, genes were still being exchanged between these populations.

What do you mean by "fully diverged"? The genetic evidence suggests the two species first split around 600K years ago then remained more or less genetically isolated until a wave of Homo sapiens out of Africa moved into Europe around 100K years ago. (Aside: None of the above dates are firmly establish, most are +/- 20% at least).

[phank]

On what do you base the claim that 600K years should be enough time to produce non-interfertility? Lions and tigers can still produce fertile offspring and they diverged some 3.7 million years ago.

If they were still interbreeding successfully, on what basis can we say they were in fact separate species, rather than subspecies? The relationship seems to have remained close enough during this time to regard the speciation as still being in progress.

What do you mean by "fully diverged"? The genetic evidence suggests the two species first split around 600K years ago then remained more or less genetically isolated until a wave of Homo sapiens out of Africa moved into Europe around 100K years ago. (Aside: None of the above dates are firmly establish, most are +/- 20% at least).

So you are saying the two populations (not yet two species) started to split about 600K years ago, but probably did not remain fully genetically isolated? The impression I get from this is that Neandertals began to split from ??? around 600K years ago, and the ??? were still genetically quite close to the homo sapiens who happened by 500K years later. I'm sort of seeing three populations closely enough related to all interbreed successfully when they came in contact. So the idea of species here is (not atypically) pretty hazy.

So I'm struggling with an image of a clade tree in which there are multiple proto-branches, all in the process of diverging but none fully genetically isolated. Very similar populations separated more by distance than by genetics. And what went extinct wasn't so much a species, as a usually-isolated population running into local hard times.

And isn't there a school of thought that holds that the Neandertals didn't die off, but rather interbred with a much larger population and were assimilated? I should read a book or two...

[HMS_Beagle]

If they were still interbreeding successfully, on what basis can we say they were in fact separate species, rather than subspecies?

Are tigers a subspecies of lions? "Can't interbreed" isn't a defining requirement for separate species.

The relationship seems to have remained close enough during this time to regard the speciation as still being in progress.

The only place I've heard the idea that Homo sapiens and Neanderthals are the same species is from AIG, not from any real paleontologist or anthropologist. You're not a disciple of Ken Ham are you?

So you are saying the two populations (not yet two species) started to split about 600K years ago, but probably did not remain fully genetically isolated? The impression I get from this is that Neandertals began to split from ??? around 600K years ago, and the ??? were still genetically quite close to the homo sapiens who happened by 500K years later. I'm sort of seeing three populations closely enough related to all interbreed successfully when they came in contact. So the idea of species here is (not atypically) pretty hazy.

Yes, our specific ancestry isn't a clean lineage tree but is a big messy bush. That's what the paleogenetics hopes to sort out, when and for how long genetic sharing took place between the various hominids.

I should read a book or two...

As should we all.

[phank]

Are tigers a subspecies of lions? "Can't interbreed" isn't a defining requirement for separate species.

There is no particular specific definition. By convention, "do not interbreed in nature" is considered generally close enough, while CAN not interbreed isn't. And apparently these populations chose to interbreed. That's why I ask.

The only place I've heard the idea that Homo sapiens and Neanderthals are the same species is from AIG, not from any real paleontologist or anthropologist. You're not a disciple of Ken Ham are you?

I'm trying to avoid binary thinking here. If they had a common ancestor ("they" being several populations of closely related groups), AND these populations were still exchanging genes, THEN ordinarily it's considered that the branching event has not run all the way to full voluntary breeding isolation. If 600,000 years is not sufficiently long for this point to be reached for these populations, then they were not entirely distinct species, only mostly distinct.

Yes, our specific ancestry isn't a clean lineage tree but is a big messy bush. That's what the paleogenetics hopes to sort out, when and for how long genetic sharing took place between the various hominids.



As should we all.

This makes sense. The original description sounded like Neandertals broke off from ???, lived in genetic isolation for 600,000 years, at which point another group happened along that either also broke off from ???, or maybe broke off from Neandertals, or maybe all three broke off from something else, but in any case, never having encountered one another before, the Cro Magnons and Neandertals just happened to interbreed successfully and with some regularity. Interesting...

[Ucchedavāda]

And isn't there a school of thought that holds that the Neandertals didn't die off, but rather interbred with a much larger population and were assimilated? I should read a book or two...

From what I recall, the studies (e.g. Green et al. 2010) only suggest that about 4% of modern European DNA is derived from interbreeding with Neanderthals, corresponding to a very low rate of successful matings between the two groups, and much less than what you would have expected if the Neanderthals were subsumed into humans populations.

[phank]

From what I recall, the studies (e.g. Green et al. 2010) only suggest that about 4% of modern European DNA is derived from interbreeding with Neanderthals, corresponding to a very low rate of successful matings between the two groups, and much less than what you would have expected if the Neanderthals were subsumed into humans populations.

I notice that the Neandertal genome has now been completely sequenced, so there is a solid basis of comparison. And that the overlap (that is, Neandertal "content") tends to vary quite widely, being considerably more extensive in far East Asia populations. Whatever that means historically.

[shunyadragon]

I notice that the Neandertal genome has now been completely sequenced, so there is a solid basis of comparison. And that the overlap (that is, Neandertal "content") tends to vary quite widely, being considerably more extensive in far East Asia populations. Whatever that means historically.

Agreed