tag:blogger.com,1999:blog-7785493.post1126683188669641199..comments2024-01-04T04:11:55.717+02:00Comments on Dienekes’ Anthropology Blog: Imperfection of the Molecular Clock of Hominid Mitochondria (Loogväli et al. 2009)Dienekeshttp://www.blogger.com/profile/02082684850093948970noreply@blogger.comBlogger9125tag:blogger.com,1999:blog-7785493.post-20412439950630356432010-01-02T11:19:45.447+02:002010-01-02T11:19:45.447+02:00the existence of a single parent species for Neand...<i>the existence of a single parent species for Neanderthals and Sapiens after 900 Kya is not justified on archaeological grounds.</i><br /><br />Maju,<br /><br />Of course the problem is that there are few remains in those regions to start with. Still, <i>heidelbergensis</i> had about half a million years to enter North Africa, during varied climatic periods. During some such phases, it would have been able to cross into more southern regions through the central Sahara and also via the Nile valley. <br /><br />I wouldn't propose that such hypothetical intruders were the progenitors of AMHs. But at least until Neanderthal genetic comparisons have become more refined, we can't exclude some (perhaps even significant) mixing, either. If the Neanderthal studies turn out to be sufficiently reliable, it may be possible to identify "blocks" of material that were shared ~400,000 years ago, if there are any.<br /><br />Oh, and many thanks for all your other insightful comments with regard to this paper.eurologisthttps://www.blogger.com/profile/03440019181278830033noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-38168013621413502522010-01-01T20:00:18.947+02:002010-01-01T20:00:18.947+02:00I thank you for your aid and of course you'll ...I thank you for your aid and of course you'll be able to see my results also before I submit them to GenBank. My reasoning was this: the paper in object says that K1c1* (my daughter), mutations 9093-11377, was born from a K1c 3100 YBP. My K1a1b1 (11914) was born 22500 YBP… For this I had thought that a K1 had survived for a long time… but K1c1 was born from a previous K1c and K1a1b1 from previous subclades. Then the dates of the paper are misleading. We must presuppose that the subhaplogroups a, b, c were born from K1 at about the same time, and my reasoning then was wrong. In Y we are now discovering some SNPs that differentiate, for instance, R-P312 before the subclades. For mtDNA we haven’t the same, except perhaps heteroplasmy, but anyway after so much time any trace is deleted. But like in Y, probably not all subclades accumulate during the time the same number of mutations, and this is a problem to explain.<br />For the Y there is something not convincing in the calculation of the TMRCA. I wrote this to Nordtvedt:<br />“Ken, I know better my R1b1b2.<br />DYS426 is a very slow mutating marker.<br />R1b1* had 12<br />R1b1b2 (L23-) had 11<br />R1b1b2/L23+ (mine) had and has 12<br />R1b1b2/L51+ had and has 13<br />All subclades have 12<br />From R1b1* to R1b1b2a1b may have passed 40,000 years and not a few thousands. Probably they have passed less than 40,000, but certainly not about 6,000 as Vizachero pretends and hopes.<br /> In the meanwhile faster mutating markers have changed many times around the modal and perhaps now are the same of the origin, except someone: see DYS385: R1b1b2 14-11, R1a1 11-14 etc.<br />This is my thought (and my hope if you want)”.Gioiellohttps://www.blogger.com/profile/00999270356447668208noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-71792560447605684912009-12-30T10:22:03.828+02:002009-12-30T10:22:03.828+02:00What I have supported about the YDNA, i.e. the ca...What I have supported about the YDNA, i.e. the calculation of Nordtvedt, Klyosov etc. (I don’t take in consideration Vizachero) is wrong, because it doesn’t take in consideration the mutations happened around the modal, it is also worth for mtDNA. The youngest clades, like that of my daughter K1c1*, have less mutations than my K1a1b1, because they arose from an old K1 purified during the time from deleterious mutations. Then everything has been said about the extinction and the non continuity of European ancient mtDNA from Paleolithic to Neolithic is wrong, because only a few clades from that time have survived, were purified and expanded.Gioiellohttps://www.blogger.com/profile/00999270356447668208noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-31500464395465297182009-12-30T08:30:22.755+02:002009-12-30T08:30:22.755+02:00... they will survive if there is very little sele...<i>... they will survive if there is very little selection</i>.<br /><br />No because you also have to consider drift. Drift probably annihilates more mutations than selection, even some favorable ones. <br /><br /><i>As Dienekes wrote, 'as populations expand, even slightly deleterious alleles (and even non-deleterious ones) have a higher chance of surviving in a population'. And selection automatically reduces the number of mutations even if the selection is not actually acting on those mutations</i>.<br /><br />The greater the population the weaker both the drift and the selection. In fact weak selection is not too different from drift, just that the adaptative alleles have slightly better chances of survival. But chances are not any guarantees, just slightly better odds. <br /><br /><i>I don't think you're justified in that belief. I can sort of concede your chimp/human split could be correct. But then that still wouldn't place the Neanderthal/modern human split as long ago as you would like</i>.<br /><br />There are other people who think that way: the existence of a single parent species for Neanderthals and Sapiens after 900 Kya is not justified on archaeological grounds. <br /><br />The correction for the Pan-Homo split may not justify that extension from the viewpoint of the molecular clock complicated and controversial theory but that means little in comparison. Specially as the various hominid branches could well have also suffered from various accelerations and decelerations as population figures changed in all that time, something not considered here or anywhere that I know of. <br /><br /><i>If there have been several periods of what the authors call 'purifying selection' in various populations even the possibility of comparative dating between different haplogroups dissappears. It would also make precise dating of any OoA movement impossible</i>.<br /><br />These may be wise words.Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-57982364452298941182009-12-30T03:45:39.402+02:002009-12-30T03:45:39.402+02:00"However that does not mean these mutations w..."However that does not mean these mutations will necesarily survive or will become frequent enough as to be noticeable in the usual samples". <br /><br />I think the argument here is that they will survive if there is very little selection. As Dienekes wrote, 'as populations expand, even slightly deleterious alleles (and even non-deleterious ones) have a higher chance of surviving in a population'. And selection automatically reduces the number of mutations even if the selection is not actually acting on those mutations. <br /><br />"I don't believe in an universal 'Homo heidelbergensis' but in different Erectus-derived lineages for the two last human species: H. heidelbergensis in Europe for Neanderthal and H. rhodesiensis in Africa for H. sapiens" <br /><br />I don't think you're justified in that belief. I can sort of concede your chimp/human split could be correct. But then that still wouldn't place the Neanderthal/modern human split as long ago as you would like. <br /><br />"I'd like to know what do people think of the fact that the two apparent signatures of expansion in this study (fig. 2) are dated by the authors to (1) c. 55 Kya and (2) c. 15 Kya, suggesting that the OoA expansion happened much later than their own age estimates for mtDNA M and N (77 Kya and 68 Kya respectively) and also quite some time before Neolithic (with a decrease of the expansion signature in fact after 10 Kya, i.e. after Neolithic)". <br /><br />For a start I strongly suspect that their narrowing their idea to just the two postulated expansions followed by selection is a considerable underestimate, especially if we look at the combined haplogroups, and bound to lead to inconsistencies. If there have been several periods of what the authors call 'purifying selection' in various populations even the possibility of comparative dating between different haplogroups dissappears. It would also make precise dating of any OoA movement impossible.terrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-64951230674364815272009-12-30T02:22:16.872+02:002009-12-30T02:22:16.872+02:00And finally (and sorry for posting so fragmentaril...And finally (and sorry for posting so fragmentarily), has anybody opinions on table S1, with age estimates for some R sublineages that are clearly older than their age estimate for their ancestor N (R30 and R31 yield ages of 75 and 78 Kya respectively)?<br /><br />Other oddly old age estimates are in that table are U8 (56 Kya - i.e. long before the colonization of West Eurasia) and H1 (31 Kya - much older than the ages of other H subclades).Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-79365280372234877672009-12-30T01:56:08.914+02:002009-12-30T01:56:08.914+02:00Also I'd like to know what do people think of ...Also I'd like to know what do people think of the fact that the two apparent signatures of expansion in this study (fig. 2) are dated by the authors to (1) c. 55 Kya and (2) c. 15 Kya, suggesting that the OoA expansion happened much later than their own age estimates for mtDNA M and N (77 Kya and 68 Kya respectively) and also quite some time before Neolithic (with a decrease of the expansion signature in fact after 10 Kya, i.e. after Neolithic). <br /><br />I make little sense of this and makes again be extremely wary of pure molecular clock estimates without proper hard data to confirm these ages. <br /><br />Finally, has anyone read the briefly mentioned <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=Search&doptcmdl=Citation&defaultField=Title%20Word&term=Endicott%5Bauthor%5D%20AND%20Evaluating%20the%20mitochondrial%20timescale%20of%20human%20evolution." rel="nofollow">Endicott et al. 2009</a>, which argued that mtDNA H and U are as old as 75 Kya?Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-51105901053683557902009-12-30T01:33:02.414+02:002009-12-30T01:33:02.414+02:00Correction: double ages sound good for the Sapiens...Correction: double ages sound good for the Sapiens-Neanderthal divergence but for the Pan-Homo one the difference is not as extreme but rather 23-54% older. I discussed the Pan-Homo divergence issue <a href="http://leherensuge.blogspot.com/2008/04/new-paper-ofn-chimpanzee-and-bonobo.html" rel="nofollow">here</a>.Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-81822403704600774182009-12-30T01:19:01.504+02:002009-12-30T01:19:01.504+02:00I'm still reading it but so far I have two opi...I'm still reading it but so far I have two opinions:<br /><br />1. It is only normal to expect that the number of mutations should grow as population grows (more people = more novel mutations necesarily). However that does not mean these mutations will necesarily survive or will become frequent enough as to be noticeable in the usual samples. <br /><br />2. Notice (fig. 3) that the central referential ages for Sapiens-Neanderthal and Homo-Pan divergences are in the shortest imaginable ranges (440 Ky and 6.5 My respectively) and are not something I can admit. I have already argued that the Pan-Homo divergence must be older (at least 8 My maybe as much as 10 My) and also that the Neanderthal-Sapiens divergence must be of c. 900 Ky. (I don't believe in an universal "Homo heidelbergensis" but in different Erectus-derived lineages for the two last human species: H. heidelbergensis in Europe for Neanderthal and H. rhodesiensis in Africa for H. sapiens). <br /><br />Hence, and taking the Neanderthal reference as safer, I'd argue that all the age estimates of this paper (assuming that everything else is correct) should be doubled in age (i.e. twice older).Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.com