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My questions arose from an online course video at 3:11-19

The professor mentioned that the Neanderthals were inbred with their cousins breeding together but the Denisovans were very diverse , with 70% Neanderthal's DNA, there was found mixing between Denisovans and an even earlier mysterious species. The followings are my questions:

  1. Did he mean that most of Neanderthals were prone to inbreeding? Why?

  2. I'm not sure if that was exectly what he meant by 70% Neanderthal's DNA could exist in a Denisovan. If that were true, why not just called it Neanderthal if only 30% is not Neanderthal?

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You should be very careful trying to conclude something from what is known about Neandertal genetics.

To answer question 1: NO! This is probably not what he meant. To date, we have only two high-quality full genomes of archaich humans, one being the (Neandertal from Denisova cave, called Altai Neandertal (Prüfer et al., 2014)) and one being the (Denisovan from Denisova cave (Meyer et. al., 2012)). From this sample (which is exactly one Neandertal) you cannot draw conclusion for the whole population. It seems, however, that this Neandertal individual from the Altai Mountains was indeed inbreed (high runs of homozygosity in the genome) - it does, however, not even tell us in what way her parents were related. Prüfer et al. (2014) write

We conclude that the parents of this Neandertal individual were either half-siblings who had a mother in common, double first cousins, an uncle and a niece, an aunt and a nephew, a grandfather and a granddaughter, or a grandmother and a grandson.

You cannot say more. You also cannot say if this was due to preference in mate choice, or caused by the fact that this group was very isolated, or that this population had an extreme small effective population size (note that it is debated whether the last two effects are actually equivalent).
To make a long story short: based on the available data it is not wise to draw general conlcusions about Neandertal mating behaviour. Altai is the only example where direct inbreeding could be shown, all other genetic data from Neandertals suggest that genetic diversity was just low.

To answer question 2: I do not really know what this means, 70% Neandertal DNA in Densiovans. I can just generally tell you something about Densiovan-Neandertal differences. The Densiovan might be the only (at least mammal) species that was defined based on genetic information alone. Alle that was found were a few teeth and a pinky bone. People thought this was another Neandertal. After sequencing the DNA from that bones to high coverage (vaguely, a measure of qualtiy), one found that the DNA falls both outside the variation of modern humans - showing that this was not a Homo sapiens, but interestingly it also clearly falls outside the variation of known Neandertal sequences - showing that this was not a Neandertal. It also became clear that Densiovans are more closely related to Neandertals than to modern humans (you might now ask yourself how this is possible with just one genome. In fact, there are more genetic data availabe: low coverage genomes, exome sequences, mtDNA and all of them show the same thing: Neandertals and Densiovans are different but more closely related to each other than to modern humans). Overall, Denisovans also seem to have had rather low genetic diversity (which by the way is also a characteristic of modern humans).
Long story short: There seem to have been admixture events between Denisovans and Neandertals but I do not know how to relate this to the 70%. Prüfer et al. (2014) detected about 0.5% contribution from Neandertals in Denisovans.

One last comment about this mysterious species (nobody says it but most people think of Homo erectus): again, Prüfer et al. (2014) found some interesting patterns of derived allele sharing between present-day Africans, Denisovans and Neandertals (this should be equal for African-Denisovan and African-Neandertal comparisons, but present-day Africans share about 7% more derived alleles with Neandertals than with Densiovans - even 13-16% in alleles fixed in present-day Africans). This is either ancient population structure (however, with very deep lineages) or, as suggested in the paper, due to gene flow from a (genetically) unknown archaic hominin into Denisovans.

I hope this clears things up a bit. Feel free to ask in the comment and I will edit the post as it might be a bit unstructured.

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  • $\begingroup$ Can you explain about what you mentioned --"Overall, Denisovans also seem to have had rather low genetic diversity (which by the way is also a characteristic of modern humans)"-- As what you said ,It seems both species have rather low genetic diversity, but with whom we are comparing ? Does that mean there is a mistake in the video ,which mentioned -- the Denisovans were very diverse--?And also being against the quote from the link you give --several gene flow events occurred among Neanderthals, Denisovans and early modern humans--? $\endgroup$ – Snake Jun 19 '16 at 11:20
  • $\begingroup$ I compare genetic diversity between 'relevant' species that have a comparable evolutionary history and are closely related, i.e great apes: chimpanzees have about 3-4 times more genetic diversity than present-day modern humans (and other apes even more). I have not seen the whole video, so I am careful calling it a mistake. In the Meyer (2012) paper cited above you will find evidence that the genetic diversity in Denisovans was by far lower than that in present-day modern humans. And yes, there seem to have been multiple gene flow events. $\endgroup$ – AlexDeLarge Jun 19 '16 at 15:42
  • $\begingroup$ Thanks for your reply ,but I still not understand :Why couldn't "multiple gene flow events" relate to "high genetic diversity'' ? Aren't they equivalent ? To quote-- present-day Africans share about 7% more derived alleles with Neanderthals than with Densiovans--(I conclusively say that it means we are more relative to Neanderthals than Denisovans ) and-- It also became clear that Densiovans are more closely related to Neanderthals than to modern humans --Can I say that Neanderthals were tend to interbreed so their genetic diversity were higher than both modern humans and Denisovans? $\endgroup$ – Snake Jun 20 '16 at 1:46
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    $\begingroup$ You are mixing up some concepts there. 1. Gene flow does not automatically cause genetic diversity. If you have gene flow between hypothetical identical populations, the diversity stays constant. Neandertals and Denisovans were closely related - gene flow obviously did not lead to excess diversity in any of them as both populations lacked high levels of diversity. 2. The 7% shared derived alleles do not mean that Neandertals and humans are more closely related than humans and Denisovans - they just share some haplotypes. In fact, humans are equally related to Neandertals and Denisovans. $\endgroup$ – AlexDeLarge Jun 20 '16 at 9:10
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    $\begingroup$ (continue) 3. You cannot say that Neandertals tend to interbreed (see my answer. The high quality genome available just happens to come from an inbreed individual. You will find inbred individuals in almost any population, also in present-day modern humans. You must not generalise this to the whole population.) 4. Inbreeding does not cause genetic diversity. In contrast, inbreeding decreases genetic diversity as closely related individuals share alleles by descent so you will have a lot of homozygous sites in inbreed individuals (homzygosity is proxy for genetic diversity). $\endgroup$ – AlexDeLarge Jun 20 '16 at 9:14

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