tag:blogger.com,1999:blog-7785493.post7318656521950010055..comments2024-01-04T04:11:55.717+02:00Comments on Dienekes’ Anthropology Blog: Refined structure in haplogroup K-M526 (Karafet et al. 2014)Dienekeshttp://www.blogger.com/profile/02082684850093948970noreply@blogger.comBlogger72125tag:blogger.com,1999:blog-7785493.post-39984144821364751432014-09-09T04:33:33.148+03:002014-09-09T04:33:33.148+03:00Terry - sorry for the late reply.
I've seen r...Terry - sorry for the late reply.<br /><br />I've seen researchers acknowledge the possibility of recurring mutation (and therefore parallel evolution) only in cases where the geographical separation just absolutely demands it and mainly with regard to human female lineage. But that's unfortunate because extreme cases are not the only ones where a recurring mutations is possible and the probabilities are unknown and so the history has to be unsure.<br /><br />Compare your case of the Polynesian and Madagascar split to a case like mtDNA haplogroup X, where "recurrence appears most plausible:<br /><br />"In a parsimony tree, this Iranian mtDNA would share a common ancestor with the Native American clade (fig. 2). Yet, the nonsynonymous substitution at np 12397 converting threonine to alanine cannot be regarded a conservative marker, as it has also been observed in two different phylogenetic contexts—in haplogroups J1 and L3e—among 794 complete mtDNA sequences (Finnilä et al. 2001; Maca-Meyer et al. 2001; Herrnstadt et al. 2002). Therefore, the scenario that the threonine to alanine change in the haplogroup X background is indeed due to recurrence appears most plausible."<br /><br />Maere Reidla et al, Origin and Diffusion of mtDNA Haplogroup X (2004)<br /><br />In the same paper, "distinct geographical distribution" was actually used against reversion as a possible alternative explanation of temporal relationship, despite good evidence in the other direction:<br />"“Moreover, haplogroup X is subdivided into two major subhaplogroups, designated “X1” and “X2.” Subhaplogroup X1, represented by a single Druze mtDNA in figure 1, differs from the root of haplogroup X by eight coding and three control region transitions and lacks the two transitions (195 and 1719) that characterize X2. These two nucleotides are rather mutable (Finnilä et al. 2001; Herrnstadt et al. 2002); thus, it cannot be completely ruled out that X1 is indeed a subset of X2 that reverted at both nucleotide positions. However, this possibility appears very unlikely, especially when one considers the time depth and the distinct geographic distribution of X1"<br /><br />LivoniaGhttps://www.blogger.com/profile/05589404219598229067noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-38666627470519781172014-08-17T06:12:56.662+03:002014-08-17T06:12:56.662+03:00"The point is that the male carrying the new ..."The point is that the male carrying the new mutation -- the founder -- would already be part of a group -- the parent haplogroup"<br /><br />Yes. A member of a tribe. <br /><br />"So that population would now consist of two nodes on the tree -- the parent and the new mutation. But the mutation is neutral, so none of them know that" <br /><br />They don't need to know anything about haplogroups. Most living today know nothing of the subject. But members of the tribe would know the father/son relationships. <br /><br />"Therefore there is no reason for them to separate". <br /><br />It's extremely doubtful that they would separate. <br /><br />"Unless there is strong drift, the two nodes should stay together. And travel together. So why do we find clean breaks between these nodes later on in their history?" <br /><br />We see the explanation in the recent mt-DNA tree: <br /><br />http://dienekes.blogspot.co.nz/2014/08/new-estimates-of-human-mtdna-node-dates.html<br /><br />What is obvious from that paper is that Polynesian B4a1a1a left Taiwan accompanied by a number of related haplogroups including its parent haplogroup. Polynesian-specific B4a1a1a3 and Madagascar-specific B4a1a1a2 had already formed and were already quite diverse. Along the route to those two extremes other haplogroups dropped out leaving the two apparently isolated in their particular regions. <br /><br />"The tree would look exactly the same if all those node mutations happened in Las Vegas or Antarctica 200 years ago". <br /><br />True but the geographic distribution in either case would look completely different. <br /><br />"With parent and offspring nodes, we can assume some kind of proximity, but the tree does not tell you where on earth either were located". <br /><br />But the geographic distributions of the related haplogroups go a considerable way to telling us where the origins of the various branches lie. <br /><br />"The tree itself and the process that forms it contains NO information about the actual time or location of any haplogroup. That has to be inferred from external info -- current location, conjectured rate of mutation and of course ancient DNA". <br /><br />Exactly We actually have far more information on current distribution and so that makes the greatest contribution to our understanding. <br /><br />"And obviously if there was any parallel occurrence of the same mutation, the tree would diverge from what actually happened, unless it showed two branches for the same mutation". <br /><br />Only if the two mutations happened within a line that had already been defined by exactly the same pre-existing mutations. The chance of that occurring are very remote. terrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-14839250785362185792014-08-16T19:57:01.240+03:002014-08-16T19:57:01.240+03:00I wrote:
"If the parent group ends up in a fa...I wrote:<br />"If the parent group ends up in a far-away place from that single individual’s offspring, we might picture how that could happen. How did they separate so cleanly from the parent group?" <br />terryt wrote: “In the Paleolithic it is extremely unlikely a single individual moved far from its origin without being accompanied by a number of relations. The only time we would get a huge movement would be into an as yet unoccupied region.”<br /><br />my reply:<br />The point is that the male carrying the new mutation -- the founder -- would already be part of a group -- the parent haplogroup. So that population would now consist of two nodes on the tree -- the parent and the new mutation. But the mutation is neutral, so none of them know that.<br /><br />Therefore there is no reason for them to separate. Unless there is strong drift, the two nodes should stay together. And travel together. So why do we find clean breaks between these nodes later on in their history?<br /> I wrote: "But this kind of phylogenetic tree tells you only the order of descent, NOT where and when. That kind of information is not contained in the data used to make the tree. It’s an extra conjecture away from what the tree is able to say". <br />terryt wrote: “The phylogenetic tree tells us where a particular haplogroup's closest relations are found. From that we can get a very good idea of where it originated. Of course a haplogroup could expand greatly but be later replaced by the later expansion of another haplogroup. We can often see where that has happened.”<br /><br />The tree would look exactly the same if all those node mutations happened in Las Vegas or Antarctica 200 years ago. All you are seeing in the tree is lines of descent. There is no actual time or place represented in this tree. Only the order of appearance in relation to one another.<br /><br /><br />With parent and offspring nodes, we can assume some kind of proximity, but the tree does not tell you where on earth either were located.<br /><br />The tree itself and the process that forms it contains NO information about the actual time or location of any haplogroup. That has to be inferred from external info -- current location, conjectured rate of mutation and of course ancient DNA. <br /><br />And obviously if there was any parallel occurrence of the same mutation, the tree would diverge from what actually happened, unless it showed two branches for the same mutation.LivoniaGhttps://www.blogger.com/profile/05589404219598229067noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-20190072204887694522014-08-15T03:49:15.484+03:002014-08-15T03:49:15.484+03:00"If the parent group ends up in a far-away pl..."If the parent group ends up in a far-away place from that single individual’s offspring, we might picture how that could happen. How did they separate so cleanly from the parent group?" <br /><br />In the Paleolithic it is extremely unlikely a single individual moved far from its origin without being accompanied by a number of relations. The only time we would get a huge movement would be into an as yet unoccupied region. <br /><br />"But this kind of phylogenetic tree tells you only the order of descent, NOT where and when. That kind of information is not contained in the data used to make the tree. It’s an extra conjecture away from what the tree is able to say". <br /><br />The phylogenetic tree tells us where a particular haplogroup's closest relations are found. From that we can get a very good idea of where it originated. Of course a haplogroup could expand greatly but be later replaced by the later expansion of another haplogroup. We can often see where that has happened. terrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-74113684225365271382014-08-13T05:26:12.203+03:002014-08-13T05:26:12.203+03:00I wrote: "The clover study is mainly of note ...I wrote: "The clover study is mainly of note because it points to different measures of likelihood that a particular mutation will recur because of a matter of differential biochemistry in the DNA (or RNA). In other words, some single mutations may be mechanically more likely than others, and therefore more predictable". <br /><br />terryt replied:<br />“Well no. In the case of the clover mutations they have only lasted because they have been selected for in independent lines. Yes, it shows that the same mutation can occur multiple times but in this case it has not occurred within the same genetic landscape.” My reply: Terry, the research focuses on two closely related variants. The defined observational difference between them are two mutations. The researchers believe they are seeing recurring mutations, not recessives. BOTH mutations arise in both environments. One is selected in one environment. The other is selected in the second environment. The mutations would of course precede any selection. <br /><br />I wrote:<br />"Terry, please understand that this phylogenetic tree is not based on the whole Y-chromosome". <br /><br />terryt replied:<br />“That doesn't really matter. Under your scheme it would be impossible to construct any sort of Y-DNA phylogeny.” <br />My reply: As with any kind of inference from historical evidence, there’s always uncertainty. The best we can do is admit the uncertainties and figure where they may be and how they might offer alternative explanations. The one thing not to do is to pretend they are not there.<br /> <br />The tree in the article is pretty impressive. But this kind of phylogenetic tree tells you only the order of descent, NOT where and when. That kind of information is not contained in the data used to make the tree. It’s an extra conjecture away from what the tree is able to say.<br /><br />terryt wrote:<br />“The chance of the same mutation occurring in two branches of a haplogroup with the same identified mutations is very remote considering the number of mutations possible.”<br /><br />My reply: Yes, that’s the crux of it. Whether EACH of these mutations on the tree is a once in 70,000 years occurrence. Or could some have recurred. I don’t think we know how to measure that. But we do know that some mutations recur. It appears to be a matter of bio-chemical structure. This IS a problem with phylogenetic tree on a grander than scale than human Y-chromosome, as the other paper I mentioned points out. So it’s not totally outside the realm of possibility regarding this tree.<br /><br />I wrote:<br />"It means that, for example, the haplogroup labelled R1a may have arisen more than once in a parent group R(1)" <br /><br />terryt wrote:<br />“So with regard to one of my earlier comments where would you like R1a (and K) to have originated?” My reply: No opinions and no preferences.<br /><br />But simply as a matter of its historical implications, remember that in theory each of these nodes represents a single individual -- one founder in a pre-existing parent haplogroup of men.<br /><br />If the parent group ends up in a far-away place from that single individual’s offspring, we might picture how that could happen. How did they separate so cleanly from the parent group? Especially since none of them would be aware of the mutation.<br /><br />And if the offspring end up in two very different far away places from each other, we might wonder if there was more than one founder.LivoniaGhttps://www.blogger.com/profile/05589404219598229067noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-22302314122852329542014-08-11T07:30:51.388+03:002014-08-11T07:30:51.388+03:00"The clover study is mainly of note because i..."The clover study is mainly of note because it points to different measures of likelihood that a particular mutation will recur because of a matter of differential biochemistry in the DNA (or RNA). In other words, some single mutations may be mechanically more likely than others, and therefore more predictable". <br /><br />Well no. In the case of the clover mutations they have only lasted because they have been selected for in independent lines. Yes, it shows that the same mutation can occur multiple times but in this case it has not occurred within the same genetic landscape. <br /><br />"Terry, please understand that this phylogenetic tree is not based on the whole Y-chromosome". <br /><br />That doesn't really matter. Under your scheme it would be impossible to construct any sort of Y-DNA phylogeny. As it stands the phylogenies are based on mutations within a defined series of previous mutations. Perhaps I should have been more specific. and said, 'The Y-chromosome is subject to a high mutation rate therefore the chance of Y-chromosomes with a particular set of identified mutations being present in two geographically separated populations is pretty low. Y-chromosomes with an identical set of identified mutations are extremely unlikely except in father/son relationships...' The chance of the same mutation occurring in two branches of a haplogroup with the same identified mutations is very remote considering the number of mutations possible. <br /><br />"It means that, for example, the haplogroup labelled R1a may have arisen more than once in a parent group R(1)" <br /><br />So with regard to one of my earlier comments where would you like R1a (and K) to have originated? terrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-43214280151685471522014-08-10T02:33:21.132+03:002014-08-10T02:33:21.132+03:00terry t wrote: “The Y-chromosome is subject to a h...terry t wrote: “The Y-chromosome is subject to a high mutation rate therefore the chance of identical Y-chromosomes being present in two geographically separated populations is pretty low. Identical Y-chromosomes are extremely unlikely except in father/son relationships...” <br /><br />my reply:<br />Terry, please understand that this phylogenetic tree is not based on the whole Y-chromosome. The nodes you see are a SINGLE MUTATION on the Y chromosome. The parent branch of the tree represents a single shared mutation. The split at the node represents differentiating mutations.<br /><br />In this kind of phylogenetic tree, lineage mainly follows a series of single mutations from ancestor to descendants.<br /><br />Parallel evolution (or convergent evolution) would mean that single mutation that creates the new node happened more than once, but this kind of tree would not show it. <br /><br /> terry t wrote:<br />“Besides which any difficulties you see with Y-DNA K are surely just as valid for any other Y-DNA phylogeny.” <br /><br />my reply:<br />Yes. It means that, for example, the haplogroup labelled R1a may have arisen more than once in a parent group R(1). Two different populations that arose at different times and places, but with a common descent as far as the parent haplogroup. <br />terry t wrote: “But the mutations would only be seen as a 'tree' if a reasonable number of descendants survive.” my reply:<br />Technically, the tree needs only one descendant to survive and reproduce. But remember that some nodes are reconstructed but unattested. The tree assumes they had to have occurred for the sequence of descent to have happened. terry t wrote: “The genes involved in cyanogenesis involve selection and I don't think any evidence indicates particular mutations on the Y-chromosome are considered a product of selection.”<br /><br />It’s not selection but persistence. The clover study is mainly of note because it points to different measures of likelihood that a particular mutation will recur because of a matter of differential biochemistry in the DNA (or RNA). In other words, some single mutations may be mechanically more likely than others, and therefore more predictable.<br /><br />See, eg, http://www.nature.com/nrg/journal/v14/n11/full/nrg3483.html Whether this applies to the mutations that are used in this phylogenetic tree is a much more complicated matter than whether or not parallel evolution might have occurred. <br /><br />A different question is the historical meaning of the tree. The moment these kinds of tree go beyond sequence of descent and are applied to chronology and geography, the problems begin. LivoniaGhttps://www.blogger.com/profile/05589404219598229067noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-45784517592988311862014-08-07T08:24:06.041+03:002014-08-07T08:24:06.041+03:00"The two lines of descent would be in homogen..."The two lines of descent would be in homogeny with this mutation -- they would be identical". <br /><br />The Y-chromosome is subject to a high mutation rate therefore the chance of identical Y-chromosomes being present in two geographically separated populations is pretty low. Identical Y-chromosomes are extremely unlikely except in father/son relationships or perhaps as far as grandson. At a more distant relationship more mutations would appear. Besides which any difficulties you see with Y-DNA K are surely just as valid for any other Y-DNA phylogeny. <br /><br />"As a matter of how the tree works, relevant mutations on this tree would create new branches". <br /><br />But the mutations would only bee seen as a 'tree' if a reasonable number of descendants survive. <br /><br />"I actually expect that this matter of parallel evolution in specifically human Y-haplotype trees has already been addressed somewhere in the literature. It’s real. It’s not a quibble or diversion. It’s a scientific question". <br /><br />Any reference? <br /><br />"Relationships of DNA sequence haplotypes at the cyanogenesis loci and flanking genomic regions suggest independent evolution of gene deletions within species. This study thus provides evidence for the parallel evolution of adaptive biochemical polymorphisms through recurrent gene deletions in multiple species". <br /><br />The genes involved in cyanogenesis involve selection and I don't think any evidence indicates particular mutations on the Y-chromosome are considered a product of selection. And don't forget that the remainder of the genome in the various clover lines would be quite different from each other. It is just the 'adaptive biochemical polymorphisms through recurrent gene deletions' that are the same in the various lines. terrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-28078357843515404122014-08-02T20:25:44.360+03:002014-08-02T20:25:44.360+03:00I wrote:
"Because if a defining mutation can...I wrote:<br />"Because if a defining mutation can happen twice, then the first time could have arisen a thousand miles from and a thousand years before the second time". <br />terryt replied “Yes, but by then other mutations will have occurred and the recurring ones become reasonably obvious.”<br /><br />Terry, if you look at this again, I think you’ll see it doesn’t work. <br /><br />The two lines of descent would be in homogeny with this mutation -- they would be identical. As a matter of how the tree works, relevant mutations on this tree would create new branches. Mutations outside the branches of the tree would be on a different tree of decent.<br /><br />Telling the difference between the two duplicated branches would need to be a matter of direct observation. But given the ages of these mutations, that would be difficult or impossible. Remember that a good part of this Y-haplotype tree is reconstructed, not observed. I’m not saying I have any problem with that, but it does mean this tree as is would not “see” parallel evolution.<br /><br />And based on the average rate of mutation we see on the tree, there’s no reason to think recurring mutations would occur often enough to be detectible, much less obvious.<br /><br />terryt also replied:<br />“I have observed that in general those who question haploid phylogenies are those who have a pre-existing belief that cannot be made to fit the phylogeny. Consequently rather than studying the phylogeny as to what it can reveal they dismiss it outright. And I have every confidence in these authors' work after all those years.”<br /><br />Terry, this is something different. I actually expect that this matter of parallel evolution in specifically human Y-haplotype trees has already been addressed somewhere in the literature. It’s real. It’s not a quibble or diversion. It’s a scientific question.<br /><br />And the fact of parallel evolution could affect whether a phylogenetic tree reflects the historical events or distorts them. <br /><br />BTW: interesting paper with a twist on parallel evolution in clover just out: Olsen, Kooyers and Small. Adaptive gains through repeated gene loss: parallel evolution of cyanogenesis polymorphisms in the genus Trifolium (Fabaceae). Philosophical Transactions of the Royal Society B, 2014 DOI: 10.1098/rstb.2013.0347LivoniaGhttps://www.blogger.com/profile/05589404219598229067noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-52200406047090923522014-07-30T06:36:09.716+03:002014-07-30T06:36:09.716+03:00"Because if a defining mutation can happen tw..."Because if a defining mutation can happen twice, then the first time could have arisen a thousand miles from and thousands of years before the second time". <br /><br />Yes, but by then other mutations will have occurred and the recurring ones become reasonably obvious. There are some disagreements concerning the various trees but actually a fairly wide consensus has been reached. I have observed that in general those who question haploid phylogenies are those who have a pre-existing belief that cannot be made to fit the phylogeny. Consequently rather than studying the phylogeny as to what it can reveal they dismiss it outright. And I have every confidence in these authors' work after all those years. terrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-89018996258598112002014-07-27T21:09:30.696+03:002014-07-27T21:09:30.696+03:00Can a Y haplogroup defining mutation happen only o...Can a Y haplogroup defining mutation happen only once? Is there only one branch per mutation?<br /><br />Because if a defining mutation can happen twice, then the first time could have arisen a thousand miles from and thousands of years before the second time. And there would be two of the same haplogroup out there, easily confused as being the same descent.<br /><br />You would have two groups showing the same haplogroup but being only indirectly related to one another. There would be two different lineages, for example, for R1a.<br />Any detection of R1a would not tell you which lineage you were looking at.<br /><br />The phylogenetic tree we see in the diagram in this paper is based on nodes that begin new branches that represent defining mutations. <br /><br />What if any of those mutation happened twice and survived?<br /><br />Only as an example of how this would work, the branch P is defined by mutation P295. P originates at that point/node in the phylogenetic tree, branching from a parent branch K (P331).<br /><br />At some point in time, in parent branch K (P331), mutation P295 occurs, beginning a new branch.<br /><br />At some later point in time, in parent branch K (P331)mutation P295 occurs again, at some other geographic location.<br /><br />These two P haplogroups would show the same Y haplotype, but they would not be the same branch. They would only be indirectly related to one another.<br /><br />You would have two populations showing Y haplotype P. They could easily be confused as a single branch. But in fact they would represent two completely different genetic histories.<br /><br />BTW, this does happen in microbe populations. Some mutations, being highly probable, occur again and again. When cultures contain these mutations, there is sometimes no way to tell whether the mutation spread to or originated in a particular culture.LivoniaGhttps://www.blogger.com/profile/05589404219598229067noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-77593447950965270072014-06-21T07:01:05.588+03:002014-06-21T07:01:05.588+03:00@ Dr Rob:
I see what you're getting at now. ...@ Dr Rob: <br /><br />I see what you're getting at now. <br /><br />"the structured distribution of derived subgroups suggests an initial rapid dispersal into .virgin territory' with little subsequent gene flow between 'demes'" <br /><br />There was certainly 'subsequent gene flow' and the expansion certainly was not strictly into 'virgin territory' (people already lived in the region) but the expanding group must have formed a coherent population to be able to expand so rapidly. The comparison to Roma may be very apt. The apparent likelihood of a coherent population points strongly to one (or more) accompanying mt-DNA lines. Although some M haplogroups look to have expanded west from SE Asia to some extent, and Y-DNA C1 also looks to have been involved, the only real possibility is mt-DNA R. <br /><br />I have long noticed there is a significant gap between South Chinese (N21 and N22) and Australian (N13, N14, O and S) mt-DNA. That gap is filled with mt-DNA R haplogroups(B4'5, R9, R14, R21, R22 and R23). As a result I have concluded that mt-DNA originated, and expanded from, that region. The distribution of South Asian mt-DNA R haplogroups can easily be interpreted as indicating an entry along India's east coast and subsequent expansion up the Godavari and Ganges River systems. Perhaps we can regard as supporting evidence the MA-1 haplogroups Y-DNA R and mt-DNA U.terrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-27575379879000771462014-06-20T13:37:28.091+03:002014-06-20T13:37:28.091+03:00This comment has been removed by the author.Robhttps://www.blogger.com/profile/07166839601638241857noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-70436021252441901122014-06-17T14:50:07.379+03:002014-06-17T14:50:07.379+03:00@ Terry
"with little subsequent gene flow be...@ Terry<br /><br />"with little subsequent gene flow between 'demes' (ie genetically defined 'regions')". <br /><br />On the contrary it looks as though there was (perhaps later) substantial gene flow between populations. At present the haplogroups do not define phenotype."<br /><br />That was the author's statement; not mine. Of course, there was probable *later* gene flowRobhttps://www.blogger.com/profile/07166839601638241857noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-67986067388853336572014-06-17T05:34:00.818+03:002014-06-17T05:34:00.818+03:00Further thoughts on:
"Such a genetic distan...Further thoughts on: <br /><br />"Such a genetic distance makes three thousand years for a haplogroup rapidly expanding from SE Asia to Central Asia (P-P27: 27,200 ka => MA-1, 24,000 ka) quite impossible". <br /><br />The Romani, or Gypsies, made it all the way from northern India to the far west of Europe in much less than 3000 years. Something like 400 years: <br /><br />http://en.wikipedia.org/wiki/Romani_people<br /><br />It might be possible to argue that these people had a superior method of transport than did the Y-DNA K people, but to me that argument doesn't really stand up to any sort of scrutiny. <br /><br />"Moreover, the structured distribution of derived subgroups suggests an initial rapid dispersal into .virgin territory' with little subsequent gene flow between 'demes' (ie genetically defined 'regions')". <br /><br />Surely it is undeniable that the Y-DNA K people mixed with others they met along the way. Most admixture analyses show a widespread 'Papuan' element which can best be explained by the Y-DNA K expansion from a Papuan SE Asian region. As to what happened to the Denisovan element: Papuans have no more than 6% Denisova. Most Eurasians have no more than 2-3% Papuan. Six per cent of two or three per cent is an extremely small amount. <br /><br />"the puerile debate about the supposed SE Asian origin of ancestral Hg K" <br /><br />'Puerile'? Are you not interested in our remote ancestry? Creationist perhaps? terrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-79642331673902908542014-06-16T23:14:48.489+03:002014-06-16T23:14:48.489+03:00"Such a genetic distance makes three thousand...<i>"Such a genetic distance makes three thousand years for a haplogroup rapidly expanding from SE Asia to Central Asia (P-P27: 27,200 ka => MA-1, 24,000 ka) quite impossible". </i><br /><br /><i>I don't see a problem. Especially when we turn our minds back to the old idea of a great southern coastal migration. It was supposed to have carried a whole major human population from Africa all the way to Australia in an instant. So what has changed minds now? </i><br /><br />Only the context changed: Out of Africa could always be cited to quell any serious discussion with a lot of nonsense, and nobody cares - or dares - to disagree. The comfort of such a mindset can't be taken as a valid argument against a serious attempt to deal with real data.Rokushttps://www.blogger.com/profile/13883125231922541439noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-82608477413391135822014-06-16T06:37:28.600+03:002014-06-16T06:37:28.600+03:00"Such a genetic distance makes three thousand..."Such a genetic distance makes three thousand years for a haplogroup rapidly expanding from SE Asia to Central Asia (P-P27: 27,200 ka => MA-1, 24,000 ka) quite impossible". <br /><br />I don't see a problem. Especially when we turn our minds back to the old idea of a great southern coastal migration. It was supposed to have carried a whole major human population from Africa all the way to Australia in an instant. So what has changed minds now? <br /><br />"Moreover, the structured distribution of derived subgroups suggests an initial rapid dispersal into .virgin territory" <br /><br />I don't think the authors at all propose an expansion into virgin territory, although its quite possible the expansion was aided by exploitation of a so-far unexploited habitat. It is surely obvious the ancestors of the K expansion must have arrived in SE Asia from somewhere. The phylogeny suggests strongly that the route was via South Asia. <br /><br />"with little subsequent gene flow between 'demes' (ie genetically defined 'regions')". <br /><br />On the contrary it looks as though there was (perhaps later) substantial gene flow between populations. At present the haplogroups do not define phenotype. terrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-53351477112912535892014-06-15T13:09:11.187+03:002014-06-15T13:09:11.187+03:00"Such a genetic distance makes three thousand...<i>"Such a genetic distance makes three thousand years for a haplogroup rapidly expanding from SE Asia to Central Asia (P-P27: 27,200 ka => MA-1, 24,000 ka) quite impossible. Moreover, this timing is not supported by archeological evidence. Dispersal of P-P295 P27- between 51,200 ka and 45,000 ka, thus applying a 30% correction to the dates of Karafet (2008), would solve this problem."</i><br /><br />Rokus,<br /><br />I largely agree.eurologisthttps://www.blogger.com/profile/03440019181278830033noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-25595394172910485992014-06-15T12:04:26.718+03:002014-06-15T12:04:26.718+03:00This comment has been removed by the author.Robhttps://www.blogger.com/profile/07166839601638241857noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-26071775857663816992014-06-15T08:27:55.659+03:002014-06-15T08:27:55.659+03:00"Raghavan (2014)'s supplement Figure SI 5..."Raghavan (2014)'s supplement Figure SI 5a reveals MA-1 as an extinct branch - otherwise already on its way on the branch leading to R1+R2 sharing 19 derived base paires and just having 5 ancestral positions". <br /><br />I was fairly sure it was something like that. Thanks for the clarification. <br /><br />"Such a genetic distance makes three thousand years for a haplogroup rapidly expanding from SE Asia to Central Asia (P-P27: 27,200 ka => MA-1, 24,000 ka) quite impossible". <br /><br />Do youi really think so? Don't forget it would have been expanding through a region already occupied to a large extent. It wouldn't necessarily have had to carry a particular mt-DNA along with it. <br /><br />"Dispersal of P-P295 P27- between 51,200 ka and 45,000 ka, thus applying a 30% correction to the dates of Karafet (2008), would solve this problem". <br /><br />Possibly. I'm more than a little inclined to agree with Maju on 'molecular-clockology' anyway. terrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-9153646157807700632014-06-14T17:07:20.957+03:002014-06-14T17:07:20.957+03:00"MA-1's R1 was dated 24,000 ka."
Is...<i>"MA-1's R1 was dated 24,000 ka."</i><br /><br /><i>Is MA-1 actually R1, or just R*? If the latter it would fit the first list of dates you provided. Three thousand years for a haplogroup rapidly expanding from SE Asia to Central Asia is not impossible.</i><br /><br />How careless of me. Raghavan (2014)'s supplement Figure SI 5a reveals MA-1 as an extinct branch - otherwise already on its way on the branch leading to R1+R2 sharing 19 derived base paires and just having 5 ancestral positions. Moreover, having 35 "private" mutations against 18 listed R1* mutations MA-1 is confirmed ancestral for, and even counting the 17 R1* mutations that resulted in no-calls, MA-1 is quite comparable to R1*. <br /><br />Such a genetic distance makes three thousand years for a haplogroup rapidly expanding from SE Asia to Central Asia (P-P27: 27,200 ka => MA-1, 24,000 ka) quite impossible. Moreover, this timing is not supported by archeological evidence. Dispersal of P-P295 P27- between 51,200 ka and 45,000 ka, thus applying a 30% correction to the dates of Karafet (2008), would solve this problem.Rokushttps://www.blogger.com/profile/13883125231922541439noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-54819624649194340092014-06-14T12:16:05.736+03:002014-06-14T12:16:05.736+03:00Chad,
Good points, and I agree.Chad,<br /><br />Good points, and I agree.eurologisthttps://www.blogger.com/profile/03440019181278830033noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-64235917046152725812014-06-13T14:54:05.722+03:002014-06-13T14:54:05.722+03:00This comment has been removed by the author.Robhttps://www.blogger.com/profile/07166839601638241857noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-58661950272336544132014-06-13T08:41:22.499+03:002014-06-13T08:41:22.499+03:00"I still can't deny that I'd happily ..."I still can't deny that I'd happily replace every other human being on earth with a cat". <br /><br />Who was it said, 'the more I see of humans the more I admire dogs'? But, living in New Zealand, I definitely wouldn't want to replace humans with cats. Introduced mammals, and not just predators, have devastated the native wildlife. <br /><br />"So ignoring the arguments about the details of the sequence 'Out of Africa' has been replaced by a sequence of 'Out of X' events?" <br /><br />What has become more and more obvious is that we have backwards and forwards, to and fro, etc. Surely it has become impossible to believe that 'modern humans' originated in a single region and spread throughout the world from that region. terrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-55797335847637074572014-06-13T05:52:13.589+03:002014-06-13T05:52:13.589+03:00@ Daniel Szelkey:
"90+% of aeta have N"...@ Daniel Szelkey: <br /><br />"90+% of aeta have N" <br /><br />I've just followed that commnet up and see the Aeta have 40% mt-DNA P, actually an R-derived haplogroup rather than N. But anyway, that supports the notion that humans arrived in the Philippines from the south and after they'd reached Australia. P is almost certainly an Australian haplogroup. Four of the seven basal haplogroups are exclusively Australian (P5, P6, P7 and P9), two are shared between Australia and New Guinea with the earlier branches in Austraklia (P3 and P4) leaving just one not particularly Australian although a small level of P1 has been found there. <br /><br />I read somewhere (sorry, I forget where) that both Q1 and P1'2'8'10 moved back to 'Eastern Indonesia' from New Guinea/Australia before both expanded from that region once more. P8 and P10 both reached the Philippines and presumably that is the 'N' haplogroup you refer to. But its association with Y-DNA K2b need date no earlier than its voyaging to the Philippines. And certainly not as early as its original arrival in Australia. <br /><br />I'm presuming the remaining 50% Aeta mt-DNA 'N' is actually B, most of which is probably no earlier than the Austronesian expansion, even in the Philippines. terrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.com