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According to this article, a small amount of Neanderthal DNA was introduced into the modern human gene pool. How do biologists even know what the Neanderthals' DNA look like?

The article doesn't mention how the science recognize what the Neanderthals' DNA actually is at the first place. So how do we know what the Neanderthals' DNA is if I'm guessing we never tested Neanderthals body cell samples?

If you say "From their bones/skull" but how do you know they are actually Neanderthals and not modern humans with some rare gene mutation or something else?

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Neandertal DNA has been completely sequenced multiple times now, using DNA from bone and tooth samples found in cool or cold environments. The first Neanderthal genome sequence was described in 2010:

A Draft Sequence of the Neandertal Genome

Since then, as well as higher-quality sequence, more genomes have been completed; at least 6 individuals have been sequenced (perhaps more; I've lost track a little). As well, complete genome sequences from several Denisovans -- a Homo species that were approximately contemporary with Neandertals, but a distinct species -- have been recovered.

The science of recovering ancient DNA has advanced very rapidly in the last decade, and while it isn't routine to sequence 50,000-year-old DNA it isn't as magical as it used to be. The current record for sequencing ancient DNA is 700,000 years, which is earlier than the sapiens/neandertalis split.

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    $\begingroup$ but how do they know they were not merely modern humans, deformed by diseases such as rickets, arthritis or syphilis? $\endgroup$ – Grasper Oct 25 '16 at 14:49
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    $\begingroup$ For one thing, the genomes are distinct and clearly well outside the range of the human species. For another, Neanderthal skeletons don't show signs of disease -- indeed, far from being diseased, Neanderthal skeletons are vastly more powerful and robust than puny humans. For a third, Neanderthal skeletons, of which many are known, are consistently the same as each other and consistently different from sapiens skeletons. All lines of evidence showing that they are separate species are extremely strong; taken together they are indisputable. $\endgroup$ – iayork Oct 25 '16 at 14:53
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    $\begingroup$ the mt DNA sequence differences among modern humans range from 1 to 24 substitutions, with an average of eight substitutions, whereas, the mt DNA sequence differences between modern man and the Neanderthal specimen range from 22 to 36 substitutions, placing Neanderthals, at worst, on the fringes of the modern range. $\endgroup$ – Grasper Oct 25 '16 at 14:56
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    $\begingroup$ Suggest asking a separate question, then; comments are not a good place to raise a completely new issue $\endgroup$ – iayork Oct 25 '16 at 15:09
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    $\begingroup$ Just in case anyone is taken in: Note that the comment by @Grasper above about mtDNA is copied directly (though without attribution) from the notorious "Institute for Creation Research", and as is typical from them is deliberately obfuscatory (i.e. what we call "a lie"). Genomic DNA, not mtDNA, shows that Neanderthals are a distinct species. Starting point for reality-based understanding: Strong reproductive isolation between humans and Neanderthals inferred from observed patterns of introgression. $\endgroup$ – iayork Oct 26 '16 at 10:45
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The answers here give you reference to the first draft genome. Take a look at these papers for high-quality sequences: Prufer et al., 2014 for Altai Neandertal, Meyer et al., 2012 for the Denisova individual. A third one, the Vindija Neandertal has been sequenced and the sequence is already available (though not published, yet) here. However, one thing has not been mentioned. The presence of ancient DNA can be confirmed by identifying specific damage patterns in the DNA molecules, i.e. mainly deamination. That is used to ensure that the DNA is old and does not result from contamination of present-day humans. Additionally, modern human contamination levels are estimated by two or three independent methods in the papers given above. These methods exploit the uniqueness of Neandertal mitochondria and Y-chromosomes, i.e. the fact that these variants have never been seen in present-day humans.

This answers the sequence part, but my answer focuses on the second part of your question and the issue your raise in the comment sections:

If you say "From their bones/skull" but how do you know they are actually Neanderthals and not Humans with some rare gene mutation or something else?

This can mainly be answered on two different levels. The first level is a parsimony argument: there are a lot of those skeletons (far more than the ones that have been sequenced) and it would be too unlikely they all suffered from the same disease. Additionally, skeletons of present-day humans with the diseases you mention do not at all look like Neandertal skeletons.

The second level is a bit more scientific: bones from the spanish cave Sima de los Huesos have been sequenced as well (Meyer et al. (2014) for a mitochondrial genome and Meyer et al. (2016) for nuclear sequences - not full genome!). Bones from this cave has been dated to approx 430,000 years ago which means that those bones may not even be Neandertal bones but rather Homo heidelbergensis. This makes a strong point against your suspicion as at that times modern humans did not even exist anywhere on the planet and it took another about 200,000 years until the first anatomically modern humans evolved in Africa (and then another 150,000 years until they set foot to Europe).

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The sequence of the neanderthal genome is known because it has been sequenced and could then be compared to the human reference genome. The DNA was extracted from a toe bone found in Siberia, as described in reference 1.

The sequencing was done as described in reference 2. The researchers where sure that the bones came from Neanderthals because of anthropologic differences in the built of the bones they found. They are distinct from homo sapiens bones.

References:

  1. A proximal pedal phalanx of a Paleolithic hominin from denisova cave, Altai
  2. A Draft Sequence of the Neandertal Genome
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  • $\begingroup$ but how do they know they were not merely modern humans, deformed by diseases such as rickets, arthritis or syphilis? $\endgroup$ – Grasper Oct 25 '16 at 14:49
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    $\begingroup$ You can carbon date such bones - the result is pretty clear. $\endgroup$ – Chris Oct 25 '16 at 20:03
  • $\begingroup$ I thought carbon dating is only reliable up to 5,730 years. Neandertals lived 350,000–600,000 years ago. $\endgroup$ – Grasper Oct 26 '16 at 14:29
  • $\begingroup$ @Grasper First: 5730 years is one half-life of C14, dating works for at least 10 half-lifes - with special preparations to exclude contaminations even longer. Then the neanderthal lived from about 230.000 to about 30.000 years, which is at least partly in this range. $\endgroup$ – Chris Oct 26 '16 at 14:45
  • $\begingroup$ @Grasper There are also other isotopes besides carbon that you can use to date bones and fossils; you can also use entirely different methods, such as analyzing amino acids. It's just that carbon-dating is the most common for human-age artifacts because its half-life and range tend to cover most modern and immediately prehistoric human artifacts. $\endgroup$ – TylerH Oct 26 '16 at 15:55

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