Talk:Interbreeding between archaic and modern humans/Archive 1

Archive 1

Merger proposal

The following discussion is closed. Please do not modify it. Subsequent comments should be made in a new section. A summary of the conclusions reached follows.

The result of this discussion was to merge after a rename to a name not implying that neanderthals are homo sapiens. Warren Dew (talk) 23:19, 6 January 2012 (UTC)

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I'm proposing merging of Neanderthal admixture hypothesis here. "Neanderthal admixture" is kind of a specialized topic, and now that we have more than one example, it would probably make sense as a section in this page rather than a stand alone page. The other possibility would be redirecting to Multiregional origin of modern humans, but that page is too close to the suggested size limit to incorporate all of the Neanderthal admixture hypothesis page. Comments welcome. Warren Dew (talk) 16:13, 7 January 2011 (UTC)

The article is written as if there is absolute certainty that humans possess archaic admixture. The authors of the study do suggest alternative scenarios, such as ancient sub-structure, though arguing that such scenarios are less parsimonious. Furthermore, it would help their case if these findings of admixture were independently replicated by other scientists. So far it is only the Leipzig group who suggest such findings. Wapondaponda (talk) 03:27, 8 January 2011 (UTC)

I can see that as a criticism of this article, which if valid could be corrected through editing, but is that a reason against, or in favor, of a merge? The talk page of "Neanderthal admixture hypothesis" seems to indicate that most editors there now seem to regard the hypothesis as proven as well, though the recent findings haven't been reflected in the article yet. Any current or future corrections would apply to both pages proposed to be merged, so it seems to me it would be better to have them both in one article. Or - I just realized - are you objecting to the implication in this article title that archaics are Homo sapiens? That's a valid concern, and perhaps both articles should be merged into a new article entitled "Archaic human admixture with modern humans". Warren Dew (talk) 20:30, 8 January 2011 (UTC)

Not commenting the article contents, I think a merger idea is a good one, but the current article has a very incorrect (retracted) impractical name. The reasons for merger I can find up are:

• the Denisova hominins (non-Neanderthal guys) and their alleged genetic relationship to the modern Melanesian H. sapienses,
• the articles Neanderthal admixture theory and Archaic Homo sapiens admixture with modern humans are too small, and will profit from the merger effort to adapt to each other,
• Neanderthal admixture theory contains some pseudoscience (Stan Gooch speaking mysticist rubbish) that has undue weight due to lack of contextual explanations, a merger might remedy this and put Stan Gooch in a proper context.

However: the title of the current article is very incorrect by making the assumption that Denisova hominins and possibly Neanderthals were archaic H. sapienses. That violates both WP:OR and WP:NPOV. We don't know whether those should be regarded as archaic sapienses or other species. If to be merged, the current title cannot stand as it is. The title should instead be (retracted). I would prefer something shorter like Advanced Homo admixture theories or preferrably some academically attested phrase.

I also would like to add that we cannot merge until we find a proper destination, which is neither Neanderthal admixture theory nor Archaic Homo sapiens admixture with modern humans. Rursus dixit. (^mbork³!) 10:21, 21 May 2011 (UTC)

JUST MERGE ALREADY. Follow the example of science. LhunGrub (talk) 23:00, 27 August 2011 (UTC)

The discussion above is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.

Chimpanzee and human admixture

How is it possible that 4-6% percent of the human gene pool is from Neanderthals / Denisovans, yet the similarity between human and chimpanzee DNA is 95-99%? FonsScientiae (talk) 09:52, 31 July 2012 (UTC)

Maybe somebody can clarify it but I also wish all wiki mentions of shared genetics would clarify it for those trying to understand. Are they comparing specific genes or patterns in DNA? For example, we have less overall genetics in common with Orangutans than chimps but more segments in common with Orangutans. If I understand that correctly, one could argue that we are closer to Orangutans. Data can be spun and interpreted the same way businesses spin their quarterly figures. Also if I read this correctly, only a few specimens were tested and all were female. There was no mtDNA in modern humans. Doesn't rule out another specimen or contamination (which has been claimed). It does confuse to read that humans are 98%+ like chimps but some are 1-6% Neanderthal/Denisova. Throw in what people claim is mostly junk DNA (don't know if it was a joke, but a claim going around says we are 50% same as banana) and these numbers don't make sense. Not to my scientific ignorance trying to educate some sense about it anyways. I suspect the recent African origin and multiregional politics play in here too making the data subject to political spinning. Apparently there have been some groups lowering the shared DNA with chimps recently. Hopefully with time somebody can explain these things better for us and improve the articles — Preceding unsigned comment added by 166.137.88.42 (talk) 18:58, 24 October 2012 (UTC)

The short answer as to how 4-6 % of 'the human gene pool' can be from Neanderthals/Denisovans yet human and chimpanzee DNA can be 98% identical is that Neanderthal/Denisovan DNA is also 98% identical to chimpanzee DNA. It's not clear what the precise relationship of Neanderthals and Denisovans to modern humans is, but they are better thought of as closely related subspecies rather than as a separate species altogether. So, the relationship between modern humans and Neanderthals/Denisovans is more like the relationship between chimpanzees and bonobos (bonobos are basically a type of chimpanzee) than the relationship between chimpanzees and orangutans. The fact that the populations could interbreed certainly suggests this. Basically, Neanderthals and Denisovans are considered archaic primarily because they're extinct; it isn't at all clear that they were less modern in the sense of being 'more primitive'. Neanderthals for instance had the largest brains of any primate that ever lived; bigger than that of 'modern humans'. Most interesting here is the unknown 'archaic hominid' that interbred with subsaharan Africans. I'm not aware of another case where a yet undiscovered extinct species' existence was inferred from DNA evidence alone. Obviously this suggests there is a yet undiscovered extinct hominid similar to Neanderthal that lived in subsaharan Africa. It is not true by the way that there is only Neanderthal admixture in Asians and Europeans; the same admixture exists in north Africans, who are morphologically similar to Europeans (e.g. Berbers etc.). See http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047765 CannotFindAName (talk) 15:30, 27 October 2012 (UTC)

Criticism Section?

As the issue is far from being settled, a section on Criticism seems to be in order. Maybe someone more knowledgeable could help. Vilhelmo De Okcidento (talk) 16:09, 11 February 2014 (UTC)

About the introductory paragraph of "Archaic human admixture with modern humans"

Dear Sirs,

I'd like to propose, with your permission, a change in the initial paragraph of the mentioned article. The section starts with the following quote: "There have been several instances of archaic human admixture with modern humans through interbreeding of modern humans with Neanderthals, Denisovans, and/or possibly other archaic humans over the course of human history". However, the fact that the Homo Sapiens interbred with other Homo species is just a hypothesis, which has not been by any means proved. Actually, there is quite a number of experts who suggest that interbred didn't take place, since those genes in common from the Neanderthal and Denisova are simply inherited from our common ancestor. Therefore, I think it would be better to change the line I quoted to make it more neutral sounding. There is no real evidence of the fact stated there, so probably the best was to put it would be something like "A number of scholars have suggested there has been admixture of Homo Sapiens with Neanderthals...". And in the next paragraph, indicate that quite a number of scholars state there is no actual evidence.

Those who support the admixture theory have been criticized for using unreliable methods, but still keep going the same (wrong) way, ignoring any counterargument they face, apparently over-infatuated with their own hypotheses. Their conclusions should be take with a pinch of salt, in my humble opinion. Before I forget, I'd like to point out that it is not even known if Neanderthal could produce offspring with modern humans. Perhaps it would have been possible with the first Sapiens, because they were definitely more ape-like than us, therefore more resembling Neanderthals and the likes, but modern Homo Sapiens probably would not be able to produce offspring. I read this months ago, and can't seem to find the source now, sorry. I'll post it if I happen to locate it. But anyway, would you kindly consider changing the first line I mentioned before? Thank you very much for your time. Best regards.

--Chico duro (talk) 05:24, 26 March 2016 (UTC)

The great majority of experts regard admixture as a fact, so "A number of scholars" would not be accurate. A change to "Most experts believe that" would, in my view, be an improvement. The section on "Alternative hypotheses" needs revision. It has obviously been written by a sceptic, and is full of POV language. Dudley Miles (talk) 11:25, 26 March 2016 (UTC)

"The great majority of experts regard admixture as a fact" Accepting a theory as a fact is one of the greatest fallacy of 'scientists'. "Nothing can live in the acidic environment of the stomach" was a well known FACT by ALL scientist. Until it was porved to be wrong. Acceptance does not make anything a fact. Not even if the majoriy of the experts believe in it and says so. The "Most experts believe that" would be an excellent way to show that it is just a religion. Also, how was the "great majority of experts" measured? — Preceding unsigned comment added by 130.95.112.103 (talk) 07:15, 23 September 2016 (UTC)

Martin Kuhlwilm et al., Ancient gene flow from early modern humans into Eastern Neanderthals, Nature

See Main Neanderthal admixture episode was c. 100,000 years ago. Joshua Jonathan -Let's talk! 05:59, 10 January 2017 (UTC)

Well it is interesting but I do not think we should pay any attention to what appears to be a blog by an amateur who does not have access to peer-reviewed articles. Dudley Miles (talk) 12:39, 10 January 2017 (UTC)

No, we should pay attention to relevant articles in journals like Nature, as the one referred to in this blog. Joshua Jonathan -Let's talk! 14:21, 10 January 2017 (UTC)

Removed the alternative hypotheses section

...due to close paraphrasing (wholly introduced in March 2016‎), but the references (commented-out in the article) may be useful for anyone inclined to make such a section. --Cold Season (talk) 18:39, 16 June 2017 (UTC)

Neanderthal gene distribution

The claim that Neanderthal genes in Africa are only found in North Africa and at trace frequencies among the Maasai is inaccurate. Yotova et al. among other analyses have actually found Neanderthal haplotypes (ex. B006) throughout the Sahel and Horn areas, primarily among local Afroasiatic-speaking populations [1]. Soupforone (talk) 13:41, 22 July 2017 (UTC)

(1) You wrongly claim something that is NOT stated in the Wikipedia article's text (quoted below) to support your rather dubious removal of that text. Does the text below state that "Neanderthal genes in Africa are only found in North Africa" as you claim? It does not.

It has been found that North Africans have a Neanderthal admixture rate lying between that of Eurasians (highest) and Sub-Saharan Africans (lowest). It has also shown a great variation within North Africans themselves, depending primarily on the amount of Eurasian versus sub-Saharan African ancestry. However, there are indications that their Neanderthal admixture is not solely contributed by Eurasian introgression.

(2) The Maasai information (as formerly written in the Wikipedia article) is correct per the source ("we find evidence for a small but significant amount of Neanderthal admixture into the Maasai genomes"), so you're wrong here too. It has nothing to do with gene frequency either, so your rewrite is faulty.

(3) Yotova et al. does not confirm nor dispute the information about North Africans. Your removal remains dubious. Although I do see loose interpretations from your part, and even things not present in Yotova et al. from a quick read. --Cold Season (talk) 16:19, 22 July 2017 (UTC)

Ref

(1) The wikitext claimed that "it has been found that North Africans have a Neanderthal admixture rate lying between that of Eurasians (highest) and Sub-Saharan Africans (lowest)." However, what Quinto et al. actually indicate is that "We found that North African populations have a significant excess of derived alleles shared with Neandertals, when compared to sub-Saharan Africans. This excess is similar to that found in non-African humans, a fact that can be interpreted as a sign of Neandertal admixture.[...] the analysis of the Tunisian and N-TUN populations shows a higher Neandertal ancestry component than any other North African population and at least the same (or even higher) as other Eurasian populations (100–138%)" [2].
(2) I don't see what the point is here. Wall et al. indicate "recent non-African gene flow into the Maasai, with the nonAfrican alleles bringing with them low levels of Neanderthal ancestry" [3]. That is an allusion to Neanderthal gene frequencies; alleles are gene variants, and by levels they mean frequencies (ex. "The putative archaic haplotype must be at low frequency (< 5%) in the subSaharan African samples").
(3) What I actually wrote in the wikitext with regard to Yotova et al. is that "Neanderthal-associated genes, such as the haplotype B006, have been found at sizable frequencies among populations in North Africa and the Horn of Africa. The presence of such haplotypes on this northern and northeastern perimeter of Sub-Saharan Africa is attributed to genetic introgression from outside of the continent." This is based directly on their analysis, which indicates that-- "Of 1,420 sub-Saharan chromosomes, only one copy of B006 was observed in Ethiopia, and five in Burkina Faso, one among the Rimaibe and four among the Fulani and Tuareg, nomad-pastoralists known for having contacts with northern populations (supplementary table S1, Supplementary Material online). B006 only occurrence at the northern and northeastern outskirts of sub-Saharan Africa is thus likely to be a result of gene flow from a non-African source." [4]. Soupforone (talk) 04:07, 23 July 2017 (UTC)

(1) Don't make a red herring. As of now, that wikitext is correct per the source (quoted below) and your claim for removal is false. You still haven't proven your claim to support your dubious removal (as your claim is incorrect). As such I'm reinstating it.

"In the PCA analysis (Figure 2) Eurasian populations are the closest to Neandertals among modern humans, which is in agreement with previous studies [1]. Sub-Saharan Africans are, as expected, more distant to Neandertal, whereas North African individuals are placed between these two groups. North African individuals with the highest Sub-Saharan African component (as detected by ADMIXTURE) are distant from Neandertal and closer to Sub-Saharan populations. It is interesting to notice that the North African populations closer to Neandertals are populations with a large known European or Near Eastern admixture, but also the Tunisians that have an almost complete autochthonous North African genetic component."

(2) By levels, the authors mean the rate of admixture within the Maasai genome, not frequency within the Maasai population. Your rewrite is still incorrect.

(3) Yes, you have a loose interpretation (and that is one of the quotes that I had in mind when I said that you have a loose interpretation). It is not "sizable" (as that's your WP:OR claim), nor does Yotova mention any other "Neanderthal-associated gene" than B006 of dystrophin, nor does it mention a sizable frequency in the Horn of Africa. --Cold Season (talk) 11:59, 23 July 2017 (UTC)

(1) The wikitext claim attributed to Quinto et al. ("North Africans have a Neanderthal admixture rate lying between that of Eurasians (highest) and Sub-Saharan Africans (lowest)") overlooked that these scientists also stipulate that "North African populations, like all non-African humans, also carry the signature of admixture with Neandertals, and that the real geographical limit for Neandertal admixture is between sub-Saharan groups and the rest" and that "the analysis of the Tunisian and N-TUN populations shows a higher Neandertal ancestry component than any other North African population and at least the same (or even higher) as other Eurasian populations (100–138%)".[5]
(2) I did not indicate that this was the frequency within the Maasai population.
(3) Yotova et al.'s frequency map shows allele percentages in the Horn and Sahel comparable to those in most of Egypt, parts of the Arabian peninsula, Near East, East Asia and Eastern Europe, and much of Southeast Asia and Australia [6]. Soupforone (talk) 16:14, 23 July 2017 (UTC)

Alright. The mention of Tunisians makes it more complete, so that's more acceptable (over outright removal). I did not agree with the Horn of Africa, but at least the subjective and unattested "sizable" part is left out, so that's also acceptable. --Cold Season (talk) 19:15, 31 July 2017 (UTC)

Article structure

The article has come a long way since it was created in 2010 to report on a single study[7]. Obviously, this is an evolving topic, and it may be time to review how the page is organised. Topically, its scope appears to fall into three divisions: (a) Eurasians (Neanderthal admixture), (b) Oceanians (Denisovan admixture), (c) Sub-Saharan Africans (unidentified archaic hominin). It seems plausible that this list might be expanded in the future as more admixture events are discovered.

For the time being, however, the overwhelming majority of material accumulated over the past seven years concerns Neanderthal admixture, to the point where this material threatens to drown out the others. This seems like a good time to take the WP:SS approach, and reduce the Neanderthal coverage here to a summary, with detail moved to a dedicated article. --dab (𒁳) 10:10, 19 December 2017 (UTC)

I added most of the Neanderthal information here. It's weighted, but not on purpose of course. The unequal treatment reflects the academic progress that differs between each sub-topic due to--as you said it--its evolving nature. The Denisovan sub-topic is relatively very recent and less explored after all. There's really not many users that edit a lot in this specific topic area, and even less who edit every aspect of it as it progresses, so I think a whole overview is easier for the moment. As the article length doesn't seem cumbersome yet, I'm neutral to the suggestion at this time. --Cold Season (talk) 02:53, 8 January 2018 (UTC)

I completely agree, there is more material on Neanderthals because there has been the most research on this. My point is that there may in fact be enough material at this point to warrant a WP:SS subpage. It's an editorial decision, not a question of disagreement on content. I agree we can leave it as it is for now. --dab (𒁳) 12:07, 10 May 2018 (UTC)

"Admixture with"

As a point of order, people seem to be using "admixture with" synonymously with "interbreeding with" or "hybridization". But "admixture" is asymmetric, from a source population to a target population (i.e. the target population only inherits a marginal contribution from the source population) while hybridization of population A with population B is symmetric, giving you an AxB hybrid without overwhelming contribution from either A or B.

"Population A has admixture with population B" means that population B has contributed (marginally) to population A. "Archaic human admixture with modern humans" would therefore seem to imply marginal modern admixture in archaic populations, but not the inverse case. As it happens, there is evidence for both cases, i.e. early modern human admixture found in archaic populations, and archaic admixture found in modern populations, but naturally the latter case is much more prominent because modern DNA is much more readily available than ancient DNA from archaic human fossils.

My point here is that I think the title isn't technically entirely correct. It should be something like archaic–modern human hybridization or interbreeding between archaic and modern humans or similar, or, if the focus is entirely on modern humans with archaic admixture, perhaps archaic admixture in modern humans.

Find sources: Google (books · news · scholar · free images · WP refs) · FENS · JSTOR · TWL

--dab (𒁳) 12:07, 10 May 2018 (UTC)

Sure, I support a move. The title originally had some variant of "Archaic A admixture with B" which has never changed since. Archaic–modern human hybridization, Interbreeding between archaic and modern humans (my preference, as it's a clean format for splitting off possible sub-articles), or something of that sort sounds good.

Yeah, modern humans with archaic admixture is more prominently explored for now and thus the largest part of the focus in this article. But I'd rather have a generalized article, which could later be split off per interbreeding between two certain populations, than to start with an article about a specific direction of gene flow. It sound more neat in the future organizing of this topic, as it progresses.

--Cold Season (talk) 16:21, 15 May 2018 (UTC)

Small wording change suggestion

I wanted to respectfully suggest a small wording change in the sentence "The median time of the most recent common ancestor of the fifteen test subjects with the putative introgressive haplotypes was 1.2–1.3 mya." If I understand that part of the paper correct, this isn't exactly true for the subjects as whole organisms. At some places in the genome, they showed signs of a common ancestor only 10,000 years ago, which would be expected given that they are Homo sapiens and not some divergent species. It is only that in certain areas of the genome they had a most recent common ancestor from millions of years ago. That is, there was very ancient admixture with different hominin populations, but also a large amount of recent admixture with other Homo sapiens. — Preceding unsigned comment added by JohnDziak (talk • contribs) 18:20, 6 July 2018 (UTC)

I'm not sure what you mean. Like this [8]? You're free to reword it. The reference gives it as:

Strikingly, the median TMRCA for putatively introgressed haplotypes in the hunter-gatherer samples is similar to the median TMRCA for introgressed haplotypes in Europeans (1.2–1.3 Mya vs 1.1–1.2 Mya, respectively; Figure 2A), suggesting that the archaic African population diverged from anatomically modern humans in the same time frame as Neanderthals (simulations suggest that relative time of split with archaic populations can be recovered via TMRCA; Figure 3C).

--Cold Season (talk) 23:07, 6 July 2018 (UTC)

You have "The median time of the most recent common ancestor of modern humans and the putative introgressive haplotypes found in the fifteen test subjects was 1.2–1.3 mya." I suggest "Analysis of putative introgressive haplotypes in the fifteen hunter gatherer samples suggests that the archaic African population and anatomically modern humans diverged around 1.2 to 1.3 million years ago." I think this would be clearer to non-expert readers. Dudley Miles (talk) 10:24, 7 July 2018 (UTC)

This is certainly an improvement. The problem is that the most recent common ancestor of all humans today is young, likely less than 5,000 years ago. This is a result of miscegenation after 1500. The point being conveyed here, I think, is that the age of the most recent common ancestor of the two populations at the time of admixture (whenever it happened, say 50,000 years ago), was of the order of 1.2 Ma. --dab (𒁳) 12:54, 19 August 2018 (UTC)

"Indirect evidence" section

This HPV is not evidence but a loose hypothesis. In addition, what is the meaning of "[…]accepted date of the evolution of modern humans" ? So one day humans woke up and found themselves evolved? Are we celebrating some kind of evolution anniversary? Delete this section, please, and blend its reference elsewhere in the article. Cheers, Rowan Forest (talk) 14:40, 29 November 2018 (UTC)

Ping the contibutor @Virion123. --Cold Season (talk) 18:03, 30 November 2018 (UTC)

Precise date Neanderthal genome was published

Why"? I cannot fathom anybody interested in interbreeding between ancient hominins seeing that the Neanderthal genome was published on 7 May and saying, "Oh, now I understand." The same is true for it being published in Science magazine - it has a full citation if anyone cares where it was published, but the fact that it happened to have been in Science magazine does not farther our understanding of the subject. As to the suggestion that an article has to have certain information because it appears on WP:OTD is the tail wagging the dog - we should be writing these articles to communicate to the outside world, not to satisfy the whims of some intra-Wikipedia project. What makes this obscure (in the grand scheme of thing) finding so remarkable that it renders such precise publication information worth including? For some reason I don't see even the small community of genetic paleoanthropologists pausing for a moment of reflection every 7 May in remembrance of the publication of the Neanderthal genome in Science magazine. So again, why is this date and journal name so noteworthy? 01:35, 29 November 2018 (UTC)

I agree. The same applies to "Prüfer et al. (2013)". The article is also becoming too jargon ridden to be comprehensible to non-specialist readers. Few will know what a "reference-free methodology" is, (it apparently means finding introgressed segments without comparing with a reference genome, but I do not understand how you could know whether a segment is introgressed without comparing it with a reference) or what is meant by "Even though HLA-B*73 is not present in the sequenced Denisovan genome, the study noted that it was associated to the Denisovan-derived HLA-C*15:05 from the linkage disequilibrium, consistent with the estimated 98% of those modern humans who carried B*73 also carried C*15:05." I am very doubtful whether we should be reporting original journal articles, There are probably dozens published each year relevant to the article, and only some of them will find wide acceptance by experts. Dudley Miles (talk) 10:34, 29 November 2018 (UTC)

On this more general comment, I think a lot of these scientific articles end up losing the plot, getting too tied up in relating the details of each successive paper, while losing track of the general narrative of the current state of understanding/consensus. Agricolae (talk) 20:13, 29 November 2018 (UTC)

It is not necessary to remark the date of the publication of one more partial and incomplete genomic sequencing, nor the journal it was published on. That is why we append the references with such data. Rowan Forest (talk) 22:19, 29 November 2018 (UTC)

Responding to issues in general. Sure, date can be removed per seeming consensus. I would be very interested to know how this wiki article should be built without "reporting original journal articles". Sure, jargon ridden, I will give attention to that. What is the current state of understanding? It's constantly and rapidly changing, and therefore details are hard to avoid. --Cold Season (talk) 18:03, 30 November 2018 (UTC)

How to build it? By not trying to represent the most recent journal article findings immediately upon publication. There is a skewed perspective that comes from the use of primary references, the 'constantly, rapidly changing situation' you mention being one symptom of the approach. When a paper first comes out, the scientists, the publishers and the institutional media departments all have a vested self-interest in portraying a discovery as super-important, and the media can always find someone to give an immediate-response quote that rarely involves deep contemplation. Only a little bit of time will provide the perspective of how important the discovery actually is, and how it fits in to the general understanding, covering the range from paradigm-changing, contributing incremental information, trivial details, probable artifact or misinterpretation, or occasionally even purgatory (recognized as not fitting into the current understanding but nobody has figured out what to make of it yet), and it is not uncommon at all for this eventual understanding to differ from that of the initial media reports. After the initial flurry of activity, will anyone care five years later, or at least care enough to merit specific focus in an article such as this? This can be gauged by how much coverage the subject receives in scholarly reviews (from independent authors), non-introductory-level textbooks, popular books - all secondary sources. The article won't be as 'up-to-date', but then an encyclopedia article shouldn't really be trying to represent the bleeding-edge of research. Such an approach also tends to help with WP:PERSPECTIVE, letting the field, rather that the Wikipedia editors, determine the appropriate level of detail (example - I suspect a review might have a table or list of possible archaic-derived HLA genes, but not a detailed description of why Abi-Rached et al decided HLA-B*73 belongs on the list), and similarly such an approach avoids the timeline-of-discoveries presentation style that can lose the forest among all the trees. Agricolae (talk) 21:29, 30 November 2018 (UTC)

Abi-Rached et al. is one of those bits that has remained from way before I started editing, but if you find a review... feel free to revise it. From that possibility, I disagree about avoiding original journal articles and it wouldn't hold up from actual wiki policy/guidelines WP:SCIRS. --Cold Season (talk) 15:44, 1 December 2018 (UTC)

While WP:SCIRS doesn't say to avoid primary sources altogether, it does say "care should be taken to avoid recentism, focusing too much on new sources that have not yet been evaluated by the relevant community," and then goes on to give a recommendation for keeping an article in an actively researched area up-to-date: "Look for reviews published in the last five years or so, preferably in the last two or three years," not 'look for the most recent primary publications.' Agricolae (talk) 17:32, 1 December 2018 (UTC)

melanesia, oceania

Your claims in your series of edit summaries that the source does not support the information is incorrect. In addition to figure 2A in the source, I quote from the source Wolf & Akey (2018):

Analyses of introgressed Neanderthal sequence using the high-quality Altai reference genome [23] noted more regions of Neanderthal origin in Asian and American populations than European ones [32], as well as higher levels of Neanderthal ancestry in East Asian populations compared to European populations and lower levels of Neanderthal ancestry in Melanesians compared to either East Asians or Europeans [30,31] (Fig 2A).

Secondly, Sankararaman et al (2014) talks about East Asians. Your added information is not supported by this source, as Oceanians or Native Americans are not even included as one of the populations (see table 1) looked at in the article anyway! It only supports:

Third, the proportion of the genome with confidently inferred Neanderthal ancestry has a mean of 1.38% in east-Asian and 1.15% in European populations (Table 1), consistent with previous reports of more Neanderthal ancestry in east-Asian than in European populations7,17.

Wolf & Akey (2018) above references one of your cited articles even, the latter: [30] Vernot et al. (2016) [31] Sankararaman et al. (2016)

--Cold Season (talk) 05:17, 21 February 2019 (UTC)

Neanderthal Admixture in Oceanians and Native Americans

Sankararaman (2016) does appear to claim that neanderthal admixture is higher in Oceanians and Native American groups (the latter under "America" in Table 1) than in Europeans/West Eurasians (though not higher than in East Asians). See Table 1 and also Table S2 (Table S2 in the supplimentary materials) of paper "The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans" 2016. It does however seem a bit at odds with the claim of the other paper.

The caption of Table 1 reads: "We estimated the probability of Neanderthal and Denisovan ancestry for each phased genome in each population. We report the mean and SD of the proportion of confidently inferred archaic alleles (marginal probability >50%) across diploid individuals within each population. The highest point estimate of Neanderthal ancestry is in Oceania, and although this estimate is significantly higher than that in West Eurasia (Z = 3.9), consistent with previous reports [7, 8], it is not higher than that in East Asia (Z = 0.7). See also Table S2."

Skllagyook (talk) 12:58, 21 February 2019 (UTC)

They also make it a point to explore the nature of the admixture across different archaic populations and they don't draw hard conclusions about Neanderthal admixture in Oceanians (they do for Denisovan admixture though). A main thing that can be said is that Oceanians have a way lot more archaic admixture in general, both Denisovan and Neanderthal, which they acknowledge complicates inferences. Anyway, I suppose your rewrite is at least closer cited inline now. --Cold Season (talk) 15:05, 21 February 2019 (UTC)

References

Human neanderthal hybrid found in 2013

The remains of a hybrid was found in Riparo di Mezzena, Italy in 2013. Here is a source for reference -->https://www.livescience.com/28270-neanderthal-skeleton-provides-evidence-of-interbreeding-with-humans.html Should this be referenced in the article? Osh33m (talk) 15:26, 10 April 2020 (UTC)

We do reference it: Condemi et al., currently ref 51. The LiveScience source's sensationalistic headline "First Love Child of Human, Neanderthal Found" makes the original paper, reaching the much more nuanced conclusion that the data "can lend support to the hypothesis of a certain degree of continuity with AMHs or a possible interbreeding", hard to recognize. Agricolae (talk) 15:52, 10 April 2020 (UTC)

Archaic African hominins

User:Skllagyook reverted the inclusion of the findings of Arun Durvasula's and Sriram Sankararaman's 2020 article in Science Advances, "Recovering signals of ghost archaic introgression in African populations", because it's a primary source, because of WP:UNDUE and because of WP:RECENTISM. Most of this page's information is derived from similar sources (i.e. academic articles), so I don't see how that argument applies without applying to most of the text on this page. Secondary sources that summarise their article are here, here, here and here. I don't think UNDUE applies because Durvasula's and Sankararaman's findings were summarised in two sentences and some other articles are cited multiple times. As for RECENTISM, this is an area of study where interpretations are changing with the discovery of new evidence and therefore the latest research should be incorporated into the article. Quite a lot of the genetic evidence in this area is relatively recent. Why not add that the authors state that it could have occurred before OOA, rather than deleting all of it?—Britannicus (talk) 17:41, 1 June 2020 (UTC)

The article is almost wholly based on primary sources and needs rewriting mainly based on reliable secondary sources. However, I agree that at the present stage there is no reason to exclude a new study published in a peer-reviewed journal. The deleted statement would need revision, in addition to the qualification mentioned above. It starts "In 2020, scientists signalled that". Signalled is an odd and wrong word here. It could start "According to a study by Arun Durvasula et al published in 2020," Dudley Miles (talk) 18:18, 1 June 2020 (UTC)

@Britannicus: and @Dudley Miles:. I see both of your points and agree. I have reincorporated/reinstated the addition rewritten somewhat as follows:

According to a study published in 2020, there are indications that 2% to 19% (or about ≃6.6 and ≃7.0%) of the DNA of four West African populations may have come from an unknown archaic hominin which split from the ancestor of humans and Neanderthals between 360 kya to 1.02 mya. However, the study suggests that this archaic admixture is also present in Eurasians/non-Africans, and that the admixture event occurred before the Out-of-Africa migration and prior to the African/Eurasian split (thus affecting the common ancestors of both Africans and Eurasians/non-Africans). Skllagyook (talk) 18:41, 1 June 2020 (UTC)

I'm with Dudley Miles on this article needing rewriting with a focus on presenting an integrated account of the current state of knowledge based on secondary sources, rather than a timeline of the latest primary research reports, paper by paper. Agricolae (talk) 19:05, 1 June 2020 (UTC)

@Skllagyook: This same user changed some of my recent edits, and inaccurately so. Their edits misrepresent the studies presented. The study by Bergstrom et al. specifically states: "An analysis of archaic sequences in modern populations identifies ancestral genetic variation in African populations that likely predates modern humans and has been lost in most non-African populations."

It is presenting archaic admixture unique to African populations. The crux of this study was the discovery of millions of new variants which are private (exclusive) to certain populations, especially in Africa, Oceania and the Americas.

In terms of the inclusion of new studies, these are based on extensive research and published in the most highly respected journals, like Science. There's no greater importance or need for them to be only represented by "secondary sources". Primary sources are as valid, or even more valid, for inclusion. Secondary sources often contain a high amount of bias or misrepresentation of the findings of original studies, and the conclusions of those authors. Greumaich (talk) 13:08, 10 June 2020 (UTC)

@Greumaich: My understanding was/is that the study found evidence of variation (originating from an early archaic admixture/admixtures) that had been present in the common ancestors of Africans and non-Africans and partly lost in non-Africans (rather than an admixture event unique to Africans - not that the variation was not of archaic origin). Hence the statement (in the source) that Africans had "maintained" variation. I attempted to make my addition reflect this but may not have expressed it well, and now see that said addition (my addition) was unnecessary and somewhat redundant (as this was already expressed). I had no intention to "misrepresent" sources. You removed my addition, and such (your removal that is) is probably an improvement. I also noticed that you added a quote to the ref, and I have added quotes to refs in the section as well, also for clarity. Skllagyook (talk) 13:21, 10 June 2020 (UTC)

The study comments on possible sources of the archaic admixture unique to sub-Saharan Africa. Some may have been shared with the common ancestors of African and non-Africans, and some may not have been. My intention in including this was just to show other evidence for archaic introgression in Africans not found in non-Africans, which could have a source from an archaic hominin in Africa. My apologies for any lack of clarity. Greumaich (talk) 13:31, 10 June 2020 (UTC)

@Greumaich: I see. I think I understand more or less. However, I can't seem to find where in Bergstrom et al. (the study you added) it proposed that some of the variation might not have been (originally) shared by the common ancestors of Africans and non-Africans (the study seems to suggest that is was originally shared but that some or much of it was lost in non-Africans). (link here: https://science.sciencemag.org/content/367/6484/eaay5012). Unless I'm misunderstanding and you are referring to the findings of the Durvasula et al. study, where that is seemingly what is suggested (i.e., that some of the archaic admixture is shared, possibly some might not have been shared, and/or some of what may have been originally shared may have been lost in non-Africans), as the quote now present in the ref explains.

This is what I could find from the full Bergstrom et al. study (which seems to reflect the abstract):

"While there is an excess of haplotypes deriving from archaic admixture in non-Africans, many single variants present in archaic populations are also present in Africans due to their having segregated in the population ancestral to archaic and modern humans, and some of 390!these variants were subsequently lost in non-Africans due to increased genetic drift. Counting how many of the variants carried in heterozygote state in archaic individuals are segregating in balanced sets of African and non-African genomes, we find that more Vindija Neanderthal variants survive in non-Africans than in Africans (31.0% vs 26.4%). However, more Denisovan variants survive in Africans (18.9% vs 20.3%). These numbers might change if 395!larger numbers of Oceanian populations were surveyed, but they highlight how the high levels of genetic diversity in African populations mean that, despite having received much less or no Neanderthal and Denisovan admixture, they still retain a substantial, and only partly overlapping (Fig. 3E), subset of the variants which were segregating in late archaic populations" (page 16)

https://www.researchgate.net/publication/334090544_Insights_into_human_genetic_variation_and_population_history_from_929_diverse_genomes

Thank you Skllagyook (talk) 13:56, 10 June 2020 (UTC)

@Skllagyook: That last excerpt your provided is from a pre-print in June, 2019, so it is not a fully accurate version of the final, published study in Science. The published study in Science clearly specifies it is referring to archaic ancestry unique to African populations. This includes some variants from Neanderthals and Denisovans, likely in part from ancient gene flow into Africa probably before modern humans dispersed into Eurasia:

"An analysis of archaic sequences in modern populations identifies ancestral genetic variation in African populations that likely predates modern humans and has been lost in most non-African populations...We found small amounts of Neanderthal ancestry in West African genomes, most likely reflecting Eurasian admixture. Despite their very low levels or absence of archaic ancestry, African populations share many Neanderthal and Denisovan variants that are absent from Eurasia, reflecting how a larger proportion of the ancestral human variation has been maintained in Africa."

From the 2019 pre-print: "In a manner analogous to this, at fixed variants the central African Biaka have much greater affinity to Yoruba than to the Mandenka, another West African population (Fig. 2E), which would be consistent with Mandenka having some ancestry that is basal to other African ancestries."

"While there is an excess of haplotypes deriving from archaic admixture in non-Africans, many single variants present in archaic populations are also present in Africans due to their having segregated in the population ancestral to archaic and modern humans, and some of these variants were subsequently lost in non-Africans due to increased genetic drift. Counting how many of the variants carried in heterozygote state in archaic individuals are segregating in balanced sets of African and non-African genomes, we find that more Vindija Neanderthal variants survive in non-Africans than in Africans (31.0% vs 26.4%). However, more Denisovan variants survive in Africans (18.9% vs 20.3%). These numbers might change if larger numbers of Oceanian populations were surveyed, but they highlight how the high levels of genetic diversity in African populations mean that, despite having received much less or no Neanderthal and Denisovan admixture, they still retain a substantial, and only partly overlapping (Fig. 3E), subset of the variants which were segregating in late archaic populations."

The pre-print does not seem to refer to a distinct archaic African hominin per se, but does allude to it, or to Neanderthal or Denisovan DNA already segregating in Africa before the archaic-modern split, and which may have been mediated by a basal modern population like that found within the Mandenka populations. But all of this is from a pre-print, and the published study likely has more commentary on this, especially given the strong evidence from other studies in the past year about archaic admixture in Africa. Unfortuntaely, this study is still behind a pay wall. Greumaich (talk) 14:52, 10 June 2020 (UTC)

Please update with "Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph"

Please add info on this study to the article. It's currently included like so in 2020 in science:

Scientists present an extension to an algorithm to infer local genetic relationships published in October 2019, report that 3% of the Neanderthal genome was introgressed from ancient humans ~200-300kya and predict that 1% of the Denisovan genome was introgressed from an unknown highly diverged, archaic hominin ancestor of which 15% were introgressed into modern humans alive today.

You could also edit the item there.

It should also be added Neanderthal genetics and probably Denisovan#Interbreeding too.

Thank you.

--Prototyperspective (talk) 15:31, 13 September 2020 (UTC)

References