tag:blogger.com,1999:blog-7785493.post906960452091738370..comments2024-01-04T04:11:55.717+02:00Comments on Dienekes’ Anthropology Blog: Denisova genome at high coverage (Meyer et al. 2012)Dienekeshttp://www.blogger.com/profile/02082684850093948970noreply@blogger.comBlogger23125tag:blogger.com,1999:blog-7785493.post-74536640401536389722013-05-23T04:20:08.598+03:002013-05-23T04:20:08.598+03:00"Apparently, there was a host of archaic homi..."Apparently, there was a host of archaic hominines out there, previously considered the evolutionary ‘dead ends’ from all over the world, whose traces can still be perceived as superimposed variability in the modern human genome. That is, up to now investigation on archaic admixture is mainly focused on the differences between modern populations, that increasingly emerge as the relicts of intense ‘archaic’ hybridization processes". <br /><br />I agree 100%. I especially note you map of ancient hybrid flows. After all we know both M and N mt-DNAs developed a long 'stem' before expanding. Surely they had spent some time breeding with the locals they had come in touch with before they began their expansion around the world. <br /><br />"But even a much lesser extend of any gradual continuation with respect to Denisova-related selective processes against hybrid incompatibility alleles would only make sense if modern populations are themselves the continuation of these same ancient hybridization processes. Apart from what this might imply for the very nature of the modern genome in general, we could at least incorporate this signature of a continuous hybridization process, that tentatively links the Altai Mountains with Oceania, in what we know about the current distribution of Denisovan admixtures. A northern route around the SE Asiatic habitat of probably very different archaic hominine populations, some of them possibly more erectus-like or even more habilis-like, such as Homo floresiensis (Argue et al., 2012), seems at present more likely than a straightforward direct southern route" <br /><br />I have spent a great deal of my time on the Internet trying to convince Maju that such is the case. If you're interested my own rather long take on the process starts here: <br /><br />http://humanevolutionontrial.blogspot.co.nz/2009/06/human-evolution-on-trial-first-point-of.htmlterrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-31334745314774468812013-05-22T12:03:27.866+03:002013-05-22T12:03:27.866+03:00In Expanding Hybrids And The Rise Of Our Genetic C...In <a href="http://rokus01.wordpress.com/2012/09/29/expanding-hybrids-and-the-rise-of-our-common-denominator/" rel="nofollow">Expanding Hybrids And The Rise Of Our Genetic Common Denominator</a> I already raised some questions about the hybrid nature of some Denisovan chromosomes and eg. their subsequent repatterning of modern descendants in Papua New Guinea. However, I found the hybridization signal especially 'modern'. Interesting that modern admixture is still excluded by new research, implying indeed the influence of a forth, still unidentified component.<br /><br /><i>Quote:</i><br /><br />Extensive contacts should at least have <i>initiated</i> a kind of fusion between the Neanderthal and Denisovan parent species into a single population where in time, due to <i>multiple</i> hybridization events, the variability of introgressed DNA would have been restored and integrated, into the Neanderthal genetic heritage and vice-versa. Hybrid repattering of admixed chromosomes probably wouldn't have raised Denisovan heterozygosity beyond the elevated levels observed in modern populations, and less given the outstanding native homozygosity of the sampled Denisovans as a starting point. Indeed, the Denisovan sample has a reduced heterozygosity compared to any of the present-day humans analyzed by Meyer et al, though they reported the relative ratios of heterozygosity as fairly constant, what could be considered problematic for the assumption of archaic Neanderthal admixture already present in the shared DNA with Denisovans. However, 29 coding CCDS genes could be identified with more than one fixed non-synonymous SNC where 'Denisova' carries the ancestral allele, while in eight of these (OR2H1, MUC17, TNFRSF10D, MUC6, MUC5B, OR4A16, OR9G1, ERCC5), the Denisovan individual appeared heterozygous for all SNCs present in the gene. In table S44 it can be verified that 37% of this heterozygosity can be found in chromosome 11, 13% in chromosomes 6 and 7, and 11% in chromosome 8, while eleven chromosomes are homozygous for all investigated genes. Though Meyer's team proposes this to be the result of duplications or repetitive regions, this heteromorph signature basically leaves the possibility of hybridization more than open. Since this results focus on the fixed non-synonymous SNC where Denisova carries the ancestral allele and modern humans the derived allele, the documented non-ancestral polymorphisms of Denisova even resemble modern-like admixtures.<br />[...]<br />Another modern-like feature of the potential Denisovan-Neanderthal hybridization is the above mentioned outstanding heterozygosity of chromosome 11, that almost screams for continuity with the hybrid signature of the same chromosome in Papuans, where Denisovan ancestry is strikingly low.Rokushttps://www.blogger.com/profile/13883125231922541439noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-47734708377569212262013-05-21T07:04:18.805+03:002013-05-21T07:04:18.805+03:00I don't know if anyone has read John Hawks'...I don't know if anyone has read John Hawks' extremely interesting latest post on the subject: <br /><br />http://johnhawks.net/weblog/reviews/denisova/biology-of-genomes-pennisi-update-2013.html<br /><br />Quote: <br /><br />"And the comparison revealed another surprise: Four percent of the Denisovan genome comes from yet another, more ancient, human—'something unknown,' Pääbo reported". <br /><br />Yet another human 'species' involved in our evolution. And: <br /><br />"With all the interbreeding, 'it's more a network than a tree,' points out Carles Lalueza-Fox, a paleogeneticist from the Institute of Evolutionary Biology in Barcelona, Spain". <br /><br />"Now, we may be learning that the Denisovan genome itself represents different ancestral groups -- not only a more ancient "something unknown" population, but substantially the local Neandertals. That kind of mixture is not the population history described by papers on the Denisova genome so far. And a third Denisovan mtDNA from one of the third molars at the site is substantially different from the other two, pointing to greater mtDNA diversity within the Denisovan population than now known from either Neandertals or living people". terrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-59121180792085974302012-09-03T15:57:56.693+03:002012-09-03T15:57:56.693+03:00There is nothing that contradicts John Hawks' ...<i>There is nothing that contradicts John Hawks' statement "Meyer and colleagues filtered out alleles found in Africa, as a way of decreasing the effect of incomplete lineage sorting compared to introgression in their comparison", to the contrary, they bolster Hawks' statement. So Hawks' criticism is valid and needs to be seriously taken into account.</i><br /><br />Of course not. The main "criticism" is simply a shortcoming the author stated themselves. So, yes, the shortcoming pointed out by the authors themselves needs to be taken seriously - even if it happens to not have any consequences. ;)eurologisthttps://www.blogger.com/profile/03440019181278830033noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-40552903999247177402012-09-03T13:10:35.703+03:002012-09-03T13:10:35.703+03:00Eurologist,
I read those pages of the supplement....Eurologist,<br /><br />I read those pages of the supplement. There is nothing that contradicts John Hawks' statement "Meyer and colleagues filtered out alleles found in Africa, as a way of decreasing the effect of incomplete lineage sorting compared to introgression in their comparison", to the contrary, they bolster Hawks' statement. So Hawks' criticism is valid and needs to be seriously taken into account.Onur Dincerhttps://www.blogger.com/profile/05041378853428912894noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-23739101258621957212012-09-03T05:26:48.429+03:002012-09-03T05:26:48.429+03:00"I think people have seriously underestimatin..."I think people have seriously underestimating the difficulty of moving overland from western India to southeast Asia compared to moving from southern Siberia". <br /><br />Yes. People look at a map and draw a straight line, then say, 'that must have been the route'. It is a very difficult route. The Movius Line passes right between the two regions so it has always been a difficult route. <br /><br />"On the other hand, Yunnan and adjacent parts of Myanmar are very much part of the steppe lands of Inner Asia". <br /><br />That's an interesting perspective. I have long suspected there must be some connection but have been unable to find a reliable natural vegetation map. <br /><br />"I have always wondered how a small band from Siberia, who are now confirmed to have been a VERY small population, would have had such a big impact in Australasia. Even with a northern route it looks unlikely". <br /><br />I think that some pre-modern archaic H. sapiens from SE Asia has contributed to the modern Papuan/Australian population, but that is not the source of the Denisova DNA. It seems to much to believe that the same human type was found right across Siberia and down into SE Asia. I think we can assume that H. erectus was at least as varied a species as is H. sapiens. In fact likely to be more geographically varied because, presumably, less mobile. <br /><br />"Well, maybe they didn't have that impact, and we are just looking at it from the wrong angle. African and West Asian pop. structure vs. Australasia and Denisova could be a better explanation". <br /><br />As I've said before, that regional population structure goes back to the H. erectus/ergaster difference. Perhaps we still have remnant genes from that difference present in the modern population.terrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-63987385465441453752012-09-02T15:52:45.312+03:002012-09-02T15:52:45.312+03:00Hawks' criticism is methodological. So his sta...<i>Hawks' criticism is methodological. So his statistical disadvantage has little relevance.</i><br /><br />Onur,<br /><br />Yes and No. No, because in the end, it is a matter of reference population resolution.<br /><br />You should read pages 36-46 of the supplement. Results are consistent with Denisovan admixture and the S-statistic.<br /><br />Without a highly-resolved Denisovan genome, you don't know which is what. Here, the authors are able to conclude that what at first glance appears Denisovan really is Neanderthal (although not to the extent I wished, given the lack of reliable Neanderthal coverage).eurologisthttps://www.blogger.com/profile/03440019181278830033noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-63756772250679368702012-09-02T10:27:48.545+03:002012-09-02T10:27:48.545+03:00@terryt
Nor if the "Denisovan" admix si...@terryt<br /><br />Nor if the "Denisovan" admix signal in Australasians and Negritos is actually shared ancestry that doesn't include African Archaic admixture nor excess Neanderthal admixture that later migrants like E Asians do have. <br /><br />I have always wondered how a small band from Siberia, who are now confirmed to have been a VERY small population, would have had such a big impact in Australasia. Even with a northern route it looks unlikely.<br /><br />Well, maybe they didn't have that impact, and we are just looking at it from the wrong angle. African and West Asian pop. structure vs. Australasia and Denisova could be a better explanation.<br />---<br />This, I think, doesn't exclude the possibility of some Erectus admixture in East Asians and Amerinds, for which there is circumstantial physical evidence but so far no genetic proof. But this is a separate issue, of course.aramthttps://www.blogger.com/profile/04486006044411081900noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-32272064843531715902012-09-02T06:54:59.169+03:002012-09-02T06:54:59.169+03:00I think people have seriously underestimating the ...I think people have seriously underestimating the difficulty of moving overland from western India to southeast Asia compared to moving from southern Siberia. There are of course the Himalayas but also the incredibly tough terrain between what is today Assam, Myanmar, and Yunnan, with 2--3,000 foot escarpments in jungles filled with big animals, snakes, malaria, etc., the river gorges virtually impossible to traverse even now. Between the Indian border today and Mandalay in Myanmar (a few hundred miles) are no less than 23 bridges over high gorges (see Where China Meets India for all the local geography and ancient history of population movements). On the other hand, Yunnan and adjacent parts of Myanmar are very much part of the steppe lands of Inner Asia. The Mongols conquered Yunnan before the China. Yunnan was arguably connected to Scythian and other Inner Asians cultures in premodern times. The point is that it was far easier for people to move from southern Siberia and Mongolia to southeast Asia than from India to southeast Asia until the advent of cross-Bay of Bengal sailing. It's no wonder that someone today from Ulaan Baator might "pass" for a native in Java, more easily than someone from Delhi. To conclude, the Denisova (as a place) to Australia journey seems much easier to me than a trip from say the Ganges basin.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-7785493.post-43265480867965415642012-09-01T12:10:05.939+03:002012-09-01T12:10:05.939+03:00From Update IV:
"Further east, heidelbergen...From Update IV: <br /><br />"Further east, heidelbergensis is less visible, and older erectus populations persist. The Denisovan population can then be seen as an eastern H. h. that had more limited opportunity to expand and/or experience gene flow, because of its remote location" <br /><br />But you've already written: <br /><br />"obviously the fact that Denisova spends the period between 750/375 to 100/50ky at a much lower population size than modern humans speaks of an isolated population with limited genetic diversity". <br /><br />That rather eliminates the possibility that the Denisova and SE Asian H. erectus populations are at all closely related. Even John Hawks admits at: <br /><br />http://johnhawks.net/weblog/reviews/denisova/denisova-high-coverage-2012.html<br /><br />that: <br /><br />"1. Maybe Denisovans didn't live in South or Southeast Asia at all". <br /><br />If we accept that possibility he sees we are left with a problem: <br /><br />"If not, that demands that we explain how Australians got their genes". <br /><br />Not really a problem if we are prepared to admit the possibility that Y-DNA C and mt-DNA N moved east through South Siberia via Altai, and then south to Australia/New Guinea.terrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-13244600702399137972012-09-01T11:24:36.604+03:002012-09-01T11:24:36.604+03:00"Based on the short segment lengths within th..."Based on the short segment lengths within the low heterozygosity, they come to the conclusion that this is not due to inbreeding, but either a generally low population number, or one that used to be very low and just recently expanded". <br /><br />But either of those options still imply quite a level of inbreeding. A 'generally low population number', for any length of time, necessarily indicates inbreeding. And a population 'that used to be very low and just recently expanded' also necessitates a period of inbreeding before the expansion. <br /><br />"Paleolithic carriers of Y-DNA haplogroup O could have expanded into Western Indonesia when it was part of a Sundland pennisula connected to mainland Asia and mainland Asia. Later waves of Asian Neolithic migrants could have diluted them again". <br /><br />I don't think the Paleolithic carriers of Y-DNA haplogroup O reached Indonesia until much later than the Upper Paleolithic. Probably only with the arrival of the Easrly neolithic. <br /><br />"How could Paleolithic hunter-gatherers with Y-DNA halogroup O so powerfully diluted prior Paleolithic hunter-gatherer populations?" <br /><br />Probably because southern China and SE Asia were but sparsely inhabited until the Neolithic expansion. That the population numbers in southern China have increased significantly only recently is indicated by the survival of the panda in the region and the reasonably recent extinction of orangutans in South China. The last survive at present only in Borneo and Sumatra, so presumably these two islands too were sparsely settled until the Neolithic expansion. terrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-47160372910154385382012-09-01T06:06:31.201+03:002012-09-01T06:06:31.201+03:00How did a population that was present in Melanesia...How did a population that was present in Melanesia leave traces in Siberia without leaving any genetic legacies in between?<br /><br />The Toba eruption may have opened SE Asia to modern human migrants by temporarily destroying jungles that had kept out more fit hominins while simultaneously decimating the Denisovan population in the middle of their geographic range where Toba's impact was greatest. This may also have provided a Denisovan-DNA free zone from which later Asian populations could emerge.<br /><br />Denisovans may have fled incoming modern humans or been slaughtered by them in circumstances where Neanderthals would have stood their ground and admixed. Neanderthals had tools comparable in efficacy to those of the first Mesolithic modern humans they encountered and similar brain size relative to body size; Homo Erectus (from whom Denisovans are likely derived at least in part) had smaller brains than modern humans and inferior tools. Thus, Denisovans may have been far more clearly outmatched. But, exile may not have been an option in ISEA because they couldn't swim long distances or make boats. Denisovan's who had undergone island dwarfism in Flores, however, might have escaped slaughter, where their non-pygmy kin did not, because they didn't seem like as much of a threat to incoming modern humans. Archaic hominins in Flores and modern humans co-existed on that small island for 25,000 years, longer in such close proximity anywhere else in the world. So even if fertile hybrids were rare, there might still have been some in Flores.<br /><br />Denisovan-modern human couplings may have been less likely to produce fertile offspring than pairing between the more closely related Neanderthals and modern humans as a result of their greater genetic distance. There could even have been just one fertile Denisovan hybrid child in all of history, perhaps in Flores where the Denisovan population was cornered, who genes were amplified by the extreme population bottle neck in the founding populations of Papua New Guinea and the Sahul which had an effective population of fewer than 100 and could have involved just 6 to 12 women. Sound improbable? What if the small extended family and a few other friends of the only fertile Denisovan-modern human hybrid child made the do or die decision to sail off into the horizon where they could see no destination that put them in Sahul (the only part of the trip to Australia and Papua New Guinea that couldn't be made by navigation to a visible destination), so that they could flee persecution because they were tied to the hybrid Denisovan child, where they were sure that no one would follow and the only reason they had to believe they would find land was faith in providence.<br /><br />First wave modern humans who were admixed with Denisovans could also have been profoundly diluted by later waves of modern humans from the Denisovan "dead zone" where they were nearly wiped out by Toba. Paleolithic carriers of Y-DNA haplogroup O could have expanded into Western Indonesia when it was part of a Sundland pennisula connected to mainland Asia and mainland Asia. Later waves of Asian Neolithic migrants could have diluted them again.<br /><br />How could Paleolithic hunter-gatherers with Y-DNA halogroup O so powerfully diluted prior Paleolithic hunter-gatherer populations? Perhaps their decisive advantage over first wave modern humans and (and perhaps also Y-DNA hg D rich populations), is that they had domesticated dogs, while the prior populations did not.andrewhttps://www.blogger.com/profile/08172964121659914379noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-18834474623487517342012-09-01T02:21:43.356+03:002012-09-01T02:21:43.356+03:00This paper brings a wealth of new data. I was part...This paper brings a wealth of new data. I was particularly fascinated by the results of the Dinka. <br /><br />They are the closest relatives of Eurasians among the African samples. According to Table S24, the French have a D-statistic of 0.6% relative to the Dinka, and 1.0-1.2% relative to the other African samples (Mandenka, Yoruba, Mbuti, San). My initial response to this result was simple; it seems like Dinka have Neanderthal ancestry. Upon further inspection, however, things do not appear that simple. <br /><br />The Nea(Europe, Africa) statistic (Table S28) was designed to find excess Neanderthal ancestry in Europeans. Here, the situation is completely reversed. <b>The estimate of Neanderthal ancestry in Europeans is highest with the Dinka reference</b>. So, what's different in this analysis? The Nea(H1,H2) statistic is limited to the parts of the genome <i>where Denisovans carry the derived allele</i>. If Dinka are more different from Denisovans at these positions than all other Africans, then this would mean that other Africans have an increased affinity with the Denisova-Neanderthal branch. Interestingly, John Hawks found a <a href="http://johnhawks.net/weblog/reviews/neandertals/neandertal_dna/1000-genomes-introgression-among-populations-2012.html" rel="nofollow">decreased Neanderthal similarity</a> in the Luhya, in comparison to Yoruba. Autosomally, Luhya fit very well a mixture of West African (similar to Yoruba) and Nilo-Saharan (<b>similar to Dinka</b>), with some Pygmy thrown in. <br /><br />This sounds as crazy to me as it does to you. Alternative explanations are welcome. <br /><br />As for the decreased Neanderthal affinities of modern Europeans (note that Paleolithic Europeans seem to have been much more Neanderthal), that could be explained with ancient African gene flow. This is one of the possibilities discussed by the authors in the paper. It would also explain why West Eurasians are the closest Eurasian relatives of Africans.Lankhttps://www.blogger.com/profile/09164328821211694856noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-23265212004773825392012-08-31T20:44:45.987+03:002012-08-31T20:44:45.987+03:00Currently, Pääbo and Matthias Meyer et al. have th...<i>Currently, Pääbo and Matthias Meyer et al. have the very well-covered Denisovan genome, while the Neanderthal one is lacking. As such, I think Hawks has a bit of a statistical disadvantage.</i><br /><br />Hawks' criticism is methodological. So his statistical disadvantage has little relevance.Onur Dincerhttps://www.blogger.com/profile/05041378853428912894noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-75674070809711436242012-08-31T18:59:15.124+03:002012-08-31T18:59:15.124+03:00... and the "interesting" alleles (e.g. ...... and the "interesting" alleles (e.g. homozygous derived in one species / ancestral in the other) are here<br />https://bioinf.eva.mpg.de/download/HighCoverageDenisovaGenome/DenHC_catalog/<br /><br />They used CircLigase to attach adaptors to single-stranded fragments BTWMOCKBAhttps://www.blogger.com/profile/05150628026789690963noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-18922654994507766672012-08-31T17:05:58.874+03:002012-08-31T17:05:58.874+03:00Onur,
Currently, Pääbo and Matthias Meyer et al. ...Onur,<br /><br />Currently, Pääbo and Matthias Meyer et al. have the very well-covered Denisovan genome, while the Neanderthal one is lacking. As such, I think Hawks has a bit of a statistical disadvantage. <br /><br />As I have mentioned numerous times in this blog, the intersection of Neanderthal and Denisovan genome, and the therefrom derived statistics of both ancient and derivative alleles is going to be crucial, IMO.eurologisthttps://www.blogger.com/profile/03440019181278830033noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-11106939732046350912012-08-31T14:25:57.407+03:002012-08-31T14:25:57.407+03:00VCF and whole genome to download
http://cdna.eva.m...VCF and whole genome to download<br />http://cdna.eva.mpg.de/denisova/Valikhanhttps://www.blogger.com/profile/13866507134402028463noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-33327007177370648052012-08-31T14:06:36.578+03:002012-08-31T14:06:36.578+03:00Dienekes
For Update II: John Hawks also covers th...Dienekes<br /><br />For Update II: John Hawks also covers this article with a detailed blog post. (Not a surprise, the topic is his main interest.) He suggests a good explanation for this data. I copy that part there, so everybody can see here without moving to the other blog. :)<br /><br />"<i>My initial reaction to this difference is that it reflects the sharing of Neandertal genes in Africa. Meyer and colleagues filtered out alleles found in Africa, as a way of decreasing the effect of incomplete lineage sorting compared to introgression in their comparison. But if Africans have some gene flow from Neandertals, eliminating alleles found in Africans will create a bias in the comparison. If (as we think) some African populations have Neandertal gene flow, that probably came from West Asia or southern Europe. So as long as the present European and Asian (and Native American) samples have undergone a history of genetic drift, or if (as mentioned in the quote) they mixed with slightly different Neandertal populations, this bias will tend to make Asians look more Neandertal and Europeans less so."</i>Slumberyhttps://www.blogger.com/profile/05139930329199925111noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-21413045783227113342012-08-31T13:40:30.860+03:002012-08-31T13:40:30.860+03:00Interestingly, we find that Denisovans share more ...<i>Interestingly, we find that Denisovans share more alleles with the three populations from eastern Asia and South America (Dai, Han, and Karitiana) than with the two European populations (French and Sardinian) (Z = 5.3). However, this does not appear to be due to Denisovan gene flow into the ancestors of present-day Asians, since the excess archaic material is more closely related to Neandertals than to Denisovans (table S27). We estimate that the proportion of Neandertal ancestry in Europe is 24% lower than in eastern Asia and South America (95% C.I. 12–36%).</i><br /><br />Dieneke, what do you think about John Hawks' criticism of the this paper's estimate of higher Neanderthal admixture in East Asians and Amerindians than in Europeans in <a href="http://johnhawks.net/weblog/reviews/denisova/denisova-high-coverage-2012.html" rel="nofollow">his overview of the paper</a>? There he writes:<br /><br />"This is a very interesting result, partially because it is the opposite of what we are finding. As <a href="http://johnhawks.net/weblog/reviews/neandertals/neandertal_dna/1000-genomes-introgression-among-populations-2012.html" rel="nofollow">I explained earlier this year</a>, we are finding Europeans to share more Neandertal alleles than Asians do. The difference in our results has been much smaller than 24%; really only an increase of less than 0.5% on the whole genome, or maybe 10% relative to the overall amount in Europe (which is on the order of 3%).<br /><br />My initial reaction to this difference is that it reflects the sharing of Neandertal genes in Africa. Meyer and colleagues filtered out alleles found in Africa, as a way of decreasing the effect of incomplete lineage sorting compared to introgression in their comparison. But if Africans have some gene flow from Neandertals, eliminating alleles found in Africans will create a bias in the comparison. If (as we think) some African populations have Neandertal gene flow, that probably came from West Asia or southern Europe. So as long as the present European and Asian (and Native American) samples have undergone a history of genetic drift, or if (as mentioned in the quote) they mixed with slightly different Neandertal populations, this bias will tend to make Asians look more Neandertal and Europeans less so."Onur Dincerhttps://www.blogger.com/profile/05041378853428912894noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-52904472969370078682012-08-31T13:18:36.204+03:002012-08-31T13:18:36.204+03:00A low heterozygosity would indicate an inbred popu...<i>A low heterozygosity would indicate an inbred population.</i><br /><br />terryt, the authors address this. Based on the short segment lengths within the low heterozygosity, they come to the conclusion that this is not due to inbreeding, but either a generally low population number, or one that used to be very low and just recently expanded.eurologisthttps://www.blogger.com/profile/03440019181278830033noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-54647523267507074022012-08-31T08:20:57.452+03:002012-08-31T08:20:57.452+03:00Would the technical breakthrough with single-stran...Would the technical breakthrough with single-stranded DNA mean that FFPE fixed DNA from tissue samples will also yield more generous coverage?MOCKBAhttps://www.blogger.com/profile/05150628026789690963noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-13521877309238862012012-08-31T06:58:19.466+03:002012-08-31T06:58:19.466+03:00The new "enhanced" D-statistic is also o...The new "enhanced" D-statistic is also of interest (restricts analysis to alleles that are not present in 35 African genomes). This seems to yet again confirm that admixture is real and not due to African sub-structure - but I still wished they had also done a basic D-statistic with the intersect of Neanderthal and Denisovan SNPs. Perhaps we just have to wait until the better-quality Neanderthal genome is in.<br /><br />Anyway, great and very promising technology.<br /><br />BTW, from the population size figure (5b) to me, the later dates make more sense. Although I previously conjectured that Denisova may be heidelbergensis-like, Fig. 5b suggest an erectus-type population history that remained fairly constant around 1-2Mya but then started declining with the spread of the more modern African/West Eurasian lineages, including heidelbergensis. Again taking the later date, Denisova would have had a population size ~tripling during the climatic optimum ~105,000-125,000 ya, followed by immediate reduction and demise with the advent of modern humans shortly thereafter (consistent with the assumption that <i>some</i> spread immediately from Arabia during favorable times).<br /><br />The later date is also consistent with a first expansion of European and Han lineages ~40,000ya.eurologisthttps://www.blogger.com/profile/03440019181278830033noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-44693779393398487742012-08-31T06:31:02.183+03:002012-08-31T06:31:02.183+03:00"The quality of this genome allows a direct e..."The quality of this genome allows a direct estimation of Denisovan heterozygosity, indicating that genetic diversity in these archaic hominins was extremely low". <br /><br />A low heterozygosity would indicate an inbred population. If such is the case it is unlikely that contemporary humans in SE Asia were at all closely related. It is quite a convincing argument that Papuans/Australians passed somewhere close by the Altai during their expansion to and beyond SE Asia. terrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.com