tag:blogger.com,1999:blog-7785493.post4029780338881405368..comments2024-01-04T04:11:55.717+02:00Comments on Dienekes’ Anthropology Blog: Paternal and maternal demographic histories (Lippold et al. 2014)Dienekeshttp://www.blogger.com/profile/02082684850093948970noreply@blogger.comBlogger55125tag:blogger.com,1999:blog-7785493.post-85962138364381145782014-02-19T04:42:48.121+02:002014-02-19T04:42:48.121+02:00"Plus he mistakenly assumed that I follow the..."Plus he mistakenly assumed that I follow the alphabetical order of haplogroup names". <br /><br />I doubt that is the case, although I'm sure he has not a clue as to what reasoning you do actually use to follow the order of haplogroup names. Nor do I for that matter. terrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-55096680434717000992014-02-18T20:01:03.968+02:002014-02-18T20:01:03.968+02:00@Ebizur
"Ebizur has raised a valid point her...@Ebizur<br /><br />"Ebizur has raised a valid point here, and you cannot glibbly dismiss it without appearing to use different criteria for different haplogroups."<br /><br />No he hasn't. If we are talking about a general principle and the terminology we use, it doesn't matter what haplogroups we're talking about. Plus he mistakenly assumed that I follow the alphabetical order of haplogroup names.German Dziebelhttps://www.blogger.com/profile/10703679732205862495noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-26984736275803969612014-02-18T03:31:00.009+02:002014-02-18T03:31:00.009+02:00"Let's not switch gears".
Ebizur ..."Let's not switch gears". <br /><br />Ebizur has raised a valid point here, and you cannot glibbly dismiss it without appearing to use different criteria for different haplogroups. terrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-63294746803187485732014-02-17T05:36:51.280+02:002014-02-17T05:36:51.280+02:00@Ebizur
"I suppose you must also believe tha...@Ebizur<br /><br />"I suppose you must also believe that Y-DNA haplogroup N is "hierarchically above" O3 or R1."<br /><br />Let's not switch gears. Although elephants' trunks do look like snakes, I'm not willing to discuss snakes at this point.<br /><br />"haplogroup N is superordinate to haplogroup M or L3, is nonsensical and incorrect; you cannot make such a statement about two haplogroups that belong to separate lines of descent."<br /><br />Oh yes I can. Although in the current rendition of the tree M and L3 are not 'daughter' haplogroups to N, N is an "aunt" to them. And aunts and nieces belong to different generations. It's true that some aunts are younger than nieces but it's rare and the analogy is irrelevant for present purposes.German Dziebelhttps://www.blogger.com/profile/10703679732205862495noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-36884710891011153732014-02-16T03:39:20.024+02:002014-02-16T03:39:20.024+02:00German Dziebel wrote,
"A small correction: N...German Dziebel wrote,<br /><br />"A small correction: N is hierarchically above M and L3. There're no sequences that are M'L3*. The rest of my original statement stays the same."<br /><br />I suppose you must also believe that Y-DNA haplogroup N is "hierarchically above" O3 or R1. It is meaningless to compare across different lines of descent in that manner; the phylogeny is not constructed in such a way that the letters or numbers (or the number of letters or numbers) in an alphanumeric appellation for a haplogroup has any regular, measurable chronological significance.<br /><br />You may say, for example, that mtDNA haplogroup M is superordinate to mtDNA haplogroup D, haplogroup D is superordinate to haplogroup D5, or haplogroup U is subordinate to haplogroup R (or, one order further removed, haplogroup N). Saying that haplogroup D5b is subordinate to haplogroup R, or that haplogroup N is superordinate to haplogroup M or L3, is nonsensical and incorrect; you cannot make such a statement about two haplogroups that belong to separate lines of descent.<br /><br />(By the way, in reality, the MRCA of all extant haplogroup N Y-chromosomes is much more recent than the MRCA of all O3 Y-chromosomes or the MRCA of all R1 Y-chromosomes.)Ebizurhttps://www.blogger.com/profile/16925110639823856429noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-40028075343880750212014-02-14T04:07:24.626+02:002014-02-14T04:07:24.626+02:00@Ebizur
"No, it does not mean that N is hier...@Ebizur<br /><br />"No, it does not mean that N is hierarchically above M'L3. They are coordinate clades; neither is superordinate nor subordinate to the other."<br /><br />A small correction: N is hierarchically above M and L3. There're no sequences that are M'L3*. The rest of my original statement stays the same.German Dziebelhttps://www.blogger.com/profile/10703679732205862495noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-32444435529023898252014-02-13T00:00:32.791+02:002014-02-13T00:00:32.791+02:00German Dziebel wrote,
"It's the mother M...German Dziebel wrote,<br /><br />"It's the mother M'L3 superhaplogroup that's a sister to haplogroup N. It means N is hierarchically above M'L3. This is the most important thing. I'm glad we got there."<br /><br /><b>No, it does not mean that N is hierarchically above M'L3.</b> They are coordinate clades; neither is superordinate nor subordinate to the other.Ebizurhttps://www.blogger.com/profile/16925110639823856429noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-47452339574768782322014-02-11T04:58:15.918+02:002014-02-11T04:58:15.918+02:00@Ebizur
"What you have written here makes no...@Ebizur<br /><br />"What you have written here makes no sense at all. According to the present paper's phylogeny, M'L3 is a single haplogroup, and this haplogroup is a sister clade to Haplogroup N. N'M'L3 is also described as a single haplogroup, which is the ancestor of both Haplogroup N and Haplogroup M'L3, and a sister clade to Haplogroup L2a'b'c. Why is that so hard for you and Rokus to comprehend?"<br /><br />I think we are talking about the same thing. I didn't realize you were referring to M'L3 as the mother of M and L3. If M and L3 are sister lineages within a single haplogroup, it means they are descendants of the "mother" M'L3 superhaplogroup. It's the mother M'L3 superhaplogroup that's a sister to haplogroup N. It means N is hierarchically above M'L3. This is the most important thing. I'm glad we got there.<br /><br />"You are free to argue why you think any particular published phylogeny is inaccurate, but you are not free to misrepresent others' work."<br /><br />I didn't. I was referring to what you wrote, which I misunderstood.German Dziebelhttps://www.blogger.com/profile/10703679732205862495noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-67790951949373696552014-02-11T04:44:06.198+02:002014-02-11T04:44:06.198+02:00"the full mtDNA phylogeny as provided in Supp..."the full mtDNA phylogeny as provided in Supplementary Figure 14. Do you agree with this?" <br /><br />There are huge conflicts in the M phylogeny as compared to Phylotree. I have long believed the M tree is capable of greater definition however. It remains to be seen how it is all resolved. And the tree omits many important basal branches and so I think we cannot yet assume the new tree is 100% accurate. <br /><br />"Hence the point of divergence for L3+ and M may eg. be imagined being after C10873T and C9540T, halfway N and nearest to L3e1c/L3eia3. However you may object to this interpretation, this configuration simply follows from the figure. Does this possible outcome still look like a sister grouping to you?". <br /><br />You may have something but more peple need to do more work shuffling the haplogroups around. terrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-60559747626714750072014-02-10T18:52:35.393+02:002014-02-10T18:52:35.393+02:00'According to the present paper's phylogen...<i>'According to the present paper's phylogeny, M'L3 is a single haplogroup, and this haplogroup is a sister clade to Haplogroup N. N'M'L3 is also described as a single haplogroup, which is the ancestor of both Haplogroup N and Haplogroup M'L3, and a sister clade to Haplogroup L2a'b'c. Why is that so hard for you and Rokus to comprehend?'</i><br /><br /><i>'[...] please refrain from misrepresenting the phylogeny as it has been presented by any particular author(s).'</i><br /><br />Lippold's investigation on the paternal and maternal demographic histories of humans results in the full mtDNA phylogeny as provided in Supplementary Figure 14. Do you agree with this?<br /><br />Well, no matter what you infer about sister clades, stems and trunks: here mtDNA L and mtDNA M emerge as members of a single subclade of mtDNA N. You don't have to agree with this, but this is what all people with eyes can see on the figure.<br /><br />The problem seems to be that you (and others) have difficulties to take Lippold's new phylogeny as is. The authors don't comment on it, so why should you attempt to see the new phylogeny using older insights and shuffle existing branch orders - while actually current stem definitions have to be redefined entirely?<br /><br />Sure, N has several stem mutations in the <i>current phylogeny</i> that are not shared by most M and L3+ subclades. Hence, you think that N can't be ancestral to L3 and M per definition. Your refusal to consider that current definitions should be changed accordingy and your shuffling of branches instead may be interpreted as misrepresenting the impact of the new phylogeny. <br /><br />My proposals are not misrepresenting figure 14 in mtDNA N being ancestral to L3+ and M, only free of the need to please current dogmas - that explicitly are not part of the new phylogeny.<br /><br />Literally, if you don't want to misrepresent the tree in figure 14, you should be prepared to consider the defining mutations of mtDNA N to be potentially all 'ancestral' and those of L3+ and M all derived. Are you ready for this?<br /><br />N is defined by the following mutations: G8701A, C9540T, G10398A, C10873T, and A15301G!<br />. All the sequences before the N* point have C10873T and C9540T. Ancestral or derived? Since N is older than M and L3 this mutation must be ancestral downstream L2.<br />. A15301G! is most probably simply not a backmutation in N, but a mutation in U5a2b4 and the subclade for L3+ and M.<br />. N's defining G8701A mutation exists in L3e1c as well (found in South Africa and Oman) and currently has 'backmutations' in N21, R0a2e, U5b3e. If indeed <i>not ancestral in N</i>, this may also be interpreted thus that N21, R0a2e, U5b3e are actually more basal within N since they lack the derived mutation.<br />. N's defining G10398A mutation exists in L3e1a3 as well (found in Chad and Syria), backmutations in N8, S3, Y, N1a'e'I, P4, R11, R12'21, R0a2k1. If indeed <i>not ancestral in N</i>, this may also be interpreted thus that N8, S3, Y, N1a'e'I, P4, R11, R12'21, R0a2k1 are actually more basal within N since they lack the derived mutation.<br /><br />Hence the point of divergence for L3+ and M may eg. be imagined being after C10873T and C9540T, halfway N and nearest to L3e1c/L3eia3. However you may object to this interpretation, this configuration simply follows from the figure. Does this possible outcome still look like a sister grouping to you?<br /><br />Interesting is that, despite L3e's current west-African connotation, Majo already came to the conclusion that branches of the L3e1 lineage maybe coalesced much more to the east very long ago.<br /><br />Rokushttps://www.blogger.com/profile/13883125231922541439noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-59201678942932384772014-02-10T07:30:46.270+02:002014-02-10T07:30:46.270+02:00"Please acquire a copy of the docs before com..."Please acquire a copy of the docs before commenting". <br /><br />I have and have now commented on what I see. I still agree with Ebizur and see he was correct in his interpretation. <br /><br />"Please be careful here. N does not show a simple east-west dichotomy; N(xR) does so (Eastern A'N9 vs. Western W'X'N1)". <br /><br />True. We have to explain that dichotomy. Unless we're going to claim R's presence through South Asia prevented any other basal N haplogroups establishing a presence there. <br /><br />"Then again, X is sort of ambiguous, since it is found in both the extreme east (America) and the extreme west (Europe, Southwest Asia, North Africa)". <br /><br />And may have survived in between the eastern and western branches. However it looks most likely to have spread from the west. A is also actually ambiguous as well, and even more likely to represent a survival somewhere between east and west. <br /><br />"This study actually has fairly good coverage of South Asian M haplogroups (better than their coverage of South Asian R, at least)". <br /><br />Their ommission of South Asian R is unfortunate. <br /><br />"most of South Asian haplogroup M appears to have invaded South Asia from East Asia via southern East Asia/Southeast Asia well after the diversification and dispersal of haplogroup R from South Asia". <br /><br />I have long accepted the M distribution reflects a major spread from the hill region between northeast India and southwest China. Maju has posted some information on Burmese haplogroups and notes two new M clades from there. <br /><br />"Western Eurasian/African M1 and South Asian M2 seem to have a different history from the main body of South Asian M, and may reflect more closely the path of early members of haplogroup M after separating from their L3 relatives'. <br /><br />Which suggests to me that M's original route east was via South Asia, but members of the haplogroup later re-entered from the east. <br /><br />"Of the second branches, R9'F is Eastern and R1 is North-Central. The next branch, R2'JT, is South-Central > Western. The next branch, R5, is South-Central. Thus, R0HV'B'P most likely has originated somewhere around the center of the southern part of Asia, i.e. in the region that is generally known as 'South Asia' or somewhere between Iran and Bangladesh" <br /><br />To me the South Asian Rs look to be either eastern or western in origin, not indigenous. R0 is definitely 'SW Asian' rather than 'South Asian', as is R2'JT and probably R1. R5 is the only unambiguously South Asia haplogroup represented in the study, and may have entered from the northwest as we can be sure members of the above R haplogroups as well as representatives of several N did. As may have R30 and R31. <br /><br />"most of South Asian haplogroup M appears to have invaded South Asia from East Asia via southern East Asia/Southeast Asia well after the diversification and dispersal of haplogroup R from South Asia". <br /><br />But we have the obviously indigenous M haplogroups presnt in South Asia before any likely eastward movement from East/SE Asia. Besides which the other three South Asian R haplogroups such as R7, R8, R6 look very likely to have expanded from along the eastern coast of South Asia rather than be ancient indigenous to Greater India. Other R haplogroups present in South Asia are definitely eastern in origin. <br /><br />"As for the R half of haplogroup N, this study has placed U as the most basal subclade of R" <br /><br />And that is extremely revealing. U looks to have formed at the southern margin of the steppe, which tends to indicate R too may have a split distribution. The pattern of R's distribution may suggest R's original route east was also through Central Asia rather than through South Asia. terrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-37533121804432466042014-02-09T10:13:34.964+02:002014-02-09T10:13:34.964+02:00TerryT,
"First, figure 14 doesn't show t...TerryT,<br /><br /><i>"First, figure 14 doesn't show two branches, it shows M and L3 as derived from N".</i><br /><br /><i>I am unable to see the supplementary material for some reason</i> <br /><br /><i>In fact the figure seems to show (as near as I can judge through comments here)</i> <br /><br />Not 'in fact', in your fantasies. Please acquire a copy of the docs before commenting.<br /><br /><i>"this is mere semantics that has all appearance to obfuscate some current misunderstandings on the origin".</i> <br /><br /><i>Not so. I agree with Ebizur.</i><br /><br />You agree to obfuscate. Without a copy. So now what? Rokushttps://www.blogger.com/profile/13883125231922541439noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-63489993187016712812014-02-09T06:00:58.595+02:002014-02-09T06:00:58.595+02:00German Dziebel wrote,
"There's a problem...German Dziebel wrote,<br /><br />"There's a problem here. M and L3 are sister clades. But, if this is so, M'L3 cannot be a sister clade to N without N becoming a sister clade to M and L3. So N or NUR must be a common ancestor to M'L3 and in turn a sister clade to L2a'b'c."<br /><br />What you have written here makes no sense at all. According to the present paper's phylogeny, M'L3 is a single haplogroup, and this haplogroup is a sister clade to Haplogroup N. N'M'L3 is also described as a single haplogroup, which is the ancestor of both Haplogroup N and Haplogroup M'L3, and a sister clade to Haplogroup L2a'b'c. Why is that so hard for you and Rokus to comprehend?<br /><br />I understand that you have some doubts about the rooting of the human mtDNA phylogeny. I am sympathetic in that regard, but please refrain from misrepresenting the phylogeny <i>as it has been presented by any particular author(s).</i> You are free to argue why you think any particular published phylogeny is inaccurate, but you are not free to misrepresent others' work.Ebizurhttps://www.blogger.com/profile/16925110639823856429noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-74915464836823594012014-02-09T05:45:40.272+02:002014-02-09T05:45:40.272+02:00terryt wrote,
"I've managed to see the s...terryt wrote,<br /><br />"I've managed to see the supplementary figures, and I see what German is on about. M is not simply a branch within L3. But, unfortunately for him, neither is L3 a branch within M. L3'M splits in two: an African branch and a Eurasian branch. Likewise we have a simple split between N and L3'M. That gives no idea as to direction of movement but the ancestral form is L2, a definitely African haplogroup."<br /><br />Yes, just as I have already stated...twice.<br /><br />terryt wrote,<br /><br />"Interestingly N still shows a simple east/west split, which is difficult to explain without extinction. And U is still part of R but an early split from it. The authors include just one 'South Asian' R haplogroup unfortunately, and so we can't determine if South Asian R entered from the east or the west."<br /><br />Please be careful here. N does not show a simple east-west dichotomy; N(xR) does so (Eastern A'N9 vs. Western W'X'N1). Then again, X is sort of ambiguous, since it is found in both the extreme east (America) and the extreme west (Europe, Southwest Asia, North Africa).<br /><br />As for the R half of haplogroup N, this study has placed U as the most basal subclade of R, sharing a most recent common ancestor with the rest of R at about 62,000 YBP, only about 5,000 years after the split of R from N(xR). The next haplogroups to split from the main body of R are R9'F and R1 at about 60,000 YBP. The next to split off is R2'JT at about 57,000 YBP. This is followed almost immediately by the derivation of R5. The rest of R trifurcates into P, B (including R11 as a sister clade of the B5 branch), and R0'HV at about 55,000 YBP. One of these clades (P) is Australasian, one (B) is East Asian (with a southerly tendency), and one (R0'HV) is Western Eurasian (but with an apparent origin in southwestern Asia between the Mediterranean and Pakistan). <br /><br />In other words, unlike N(xR), haplogroup R in the present study's phylogeny does not exhibit a simple east-west dichotomy. The first branch, U, is Western. Of the second branches, R9'F is Eastern and R1 is North-Central. The next branch, R2'JT, is South-Central > Western. The next branch, R5, is South-Central. Thus, R0HV'B'P most likely has originated somewhere around the center of the southern part of Asia, <i>i.e.</i> in the region that is generally known as "South Asia" or somewhere between Iran and Bangladesh.<br /><br />terryt wrote, "They have also ignored the numerous South Asian M haplogroups. Their tree is by no means complete although they do indicate an interesting sequence of M's divergence. We will have to wait and see if Phylotree adopts any of their suggestions."<br /><br />This study actually has fairly good coverage of South Asian M haplogroups (better than their coverage of South Asian R, at least). They find that all the South Asian M haplogroups except M2 (<i>i.e.</i> M5, M3, M4, M18, M30, and M65) plus the Cambodian M24 form a monophyletic sister clade to East Asian M11, separating from M11 at about 44,000 YBP. (South Asian M2 is instead positioned as a sister clade of Northeast Asian D, sharing a MRCA with D at approximately 53,000 YBP.) All the South Asian M(xM2) clades (including Cambodian M24) coalesce to a MRCA at approximately 37,000 YBP. The nearest outgroup to the {M11 + M3'4'5'18'24'30'65} group is Cambodian M51.<br /><br />In other words, most of South Asian haplogroup M appears to have invaded South Asia from East Asia via southern East Asia/Southeast Asia well after the diversification and dispersal of haplogroup R from South Asia. Haplogroup R (or at least the R5'R0HV'B'P subclade) probably represents the genetic legacy of the real aborigines of South Asia. Western Eurasian/African M1 and South Asian M2 seem to have a different history from the main body of South Asian M, and may reflect more closely the path of early members of haplogroup M after separating from their L3 relatives.Ebizurhttps://www.blogger.com/profile/16925110639823856429noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-53160018801765546772014-02-09T05:22:00.447+02:002014-02-09T05:22:00.447+02:00"There's a problem here. M and L3 are sis..."There's a problem here. M and L3 are sister clades. But, if this is so, M'L3 cannot be a sister clade to N without N becoming a sister clade to M and L3. So N or NUR must be a common ancestor to M'L3 and in turn a sister clade to L2a'b'c" <br /><br />I've just thought of a way to explain it in a way you can perhaps understand things. Yes, M and L3 are sisters. Their mother is M'L3. M'L3 is sister to N. Therefore M'L3 and N are cousins. Their grandmother is ML3NUR. And that means their great grandmother is L2Ml3NUR, or something like L2'3'4'6 in the 'old' nomenclature, although the position of L4 and L6 remains problematical at this stage. terrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-48053681204543310662014-02-09T03:42:21.250+02:002014-02-09T03:42:21.250+02:00"There's a problem here. M and L3 are sis..."There's a problem here. M and L3 are sister clades. But, if this is so, M'L3 cannot be a sister clade to N without N becoming a sister clade to M and L3". <br /><br />You seem to be confused about divergence here. I thought it was simple: M and L3 are sister clades to each other, and their ancestral clade, L3'M, is sister clade to N. Yes, N is sister clade to L3'M, but not to L3 and M individually. How come you see a problem? <br /><br />"So N or NUR must be a common ancestor to M'L3 and in turn a sister clade to L2a'b'c". <br /><br />Neither N nor NUR are ancestor to M'L3 (we may as well forget the UR part of NUR as U and R both descend from N). The ancestor of both N and L3'M is L3'M'N. Agreed that L3'M'N is sister clade to L2a'b'c. But L3, M, N, L2a, L2b, and L2c are not all sister clades with each other. We have a progressive divergence. terrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-53108501483722298662014-02-08T07:08:14.036+02:002014-02-08T07:08:14.036+02:00@Rokus
"I already illustrated the arbitrarit...@Rokus<br /><br />"I already illustrated the arbitrarity of the current phylogeny referring to MA-1's purported A16399G mutation, while 16399G is ancestral in primates, Denisova, Sima and the Insert of chr.11. This 'mutation' is recurrent in L3, L4, M and P and defines U5a1 - the latter situation would thus require an intermediate flip in U to sustain the current phylogeny. Relevant to and in favor of the 'new phylogeny' is the A15301G! backmutation in N that is actually ancestral now we can compare rCRS with the genomes of Sima/Denisova, what means 'more basal' than M and L3. N, L3 and M are currently all defined by A769G, while this 'mutation' is actually ancestral as well - what may be important to redefine the phylogeny of other L-clades as well."<br /><br />Yes, that's the most important point. Although technically the new phylogeny didn't explicitly make NUR ancestral to L3'M, it's still fundamentally a problematic phylogeny because ancestral and derived states have not all been determined.<br /><br />@Ebizur<br /><br />"M'L3 is not descended from N; M'L3 and N are sister clades, both descended from a common ancestor, and that common ancestor is a sister clade of L2a'b'c."<br /><br />There's a problem here. M and L3 are sister clades. But, if this is so, M'L3 cannot be a sister clade to N without N becoming a sister clade to M and L3. So N or NUR must be a common ancestor to M'L3 and in turn a sister clade to L2a'b'c.German Dziebelhttps://www.blogger.com/profile/10703679732205862495noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-57475982419252820482014-02-08T05:06:51.640+02:002014-02-08T05:06:51.640+02:00I've managed to see the supplementary figures,...I've managed to see the supplementary figures, and I see what German is on about. M is not simply a branch within L3. But, unfortunately for him, neither is L3 a branch within M. L3'M splits in two: an African branch and a Eurasian branch. Likewise we have a simple split between N and L3'M. That gives no idea as to direction of movement but the ancestral form is L2, a definitely African haplogroup. <br /><br />Interestingly N still shows a simple east/west split, which is difficult to explain without extinction. And U is still part of R but an early split from it. The authors include just one 'South Asian' R haplogroup unfortunately, and so we can't determine if South Asian R entered from the east or the west. They have also ignored the numerous South Asian M haplogroups. Their tree is by no means complete although they do indicate an interesting sequence of M's divergence. We will have to wait and see if Phylotree adopts any of their suggestions. terrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-12167264065836247782014-02-07T04:37:05.353+02:002014-02-07T04:37:05.353+02:00"this is mere semantics that has all appearan..."this is mere semantics that has all appearance to obfuscate some current misunderstandings on the origin". <br /><br />Not so. I agree with Ebizur. <br /><br />"Supplementary Figure 14 has L2a'b'c as a sister clade to N'M'L3 (the most recent common ancestor of N, M, and L3), with the two sister clades, L2a'b'c and N'M'L3, sharing a most recent common ancestor approximately 105,000 years before present. L2a'b'c yields L2a and L2b'c approximately 81,000 years before present" <br /><br />So far that fits the 'old' tree': <br /><br />http://www.phylotree.org/tree/subtree_L.htm<br /><br />According to that tree basal L2 shares a number of mutations with basal L3'4'6 before the two separate, presumably because they became isolated from each other in some way. With L2 undergoing a further series of mutations until expanding as L2a and L2b'c, completely independent of any L3'4'6 haplogroup's expansion. Similarly basal L3'4'6 undergoes a couple of mutations before forming L6 and L3'4. The problem I have is will someone tell me where N fits into this diversity? <br /><br />"whereas N'M'L3 yields N and M'L3 approximately 76,000 years before present". <br /><br />That is where the 'new' tree is different from the 'old' tree. N forms a sister clade to L3'M sometime about the stage L4 and L6 branch off L3'M. <br /><br />"figure 14 doesn't show two branches, it shows M and L3 as derived from N". <br /><br />In fact the figure seems to show (as near as I can judge through comments here) that L3'M and N, like L2 and L3'4'6, are 'sisters'. One doesn't 'descend' from the other. To sum up: <br /><br />"M'L3 is not descended from N; M'L3 and N are sister clades, both descended from a common ancestor, and that common ancestor is a sister clade of L2a'b'c". terrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-54806824399836458822014-02-06T20:40:54.528+02:002014-02-06T20:40:54.528+02:00'I should not need to explicate how to read a ...<i>'I should not need to explicate how to read a phylogenetic tree.'</i><br /><br /><i>'M'L3 is not descended from N; M'L3 and N are sister clades, both descended from a common ancestor, and that common ancestor is a sister clade of L2a'b'c.'</i><br /><br />Reading a phylogenetic tree is not the same as interpreting the phylogenetic tree. Earlier you said <i>'this tree has N and M'L3 as two coordinate branches of a stem that ultimately derives from the same trunk as L2'</i>, what may be an elaborate way to express that current groupings carry the load of tens of thousands of years of divergence and hence can't be attributed any ancestral status per definition. It isn't my intention to deny you the pleasure of this precaution, though this is mere semantics that has all appearance to obfuscate some current misunderstandings on the origin. Especially since <i>L3</i> 'sensu stricto' was always explicitly understoood as the very trunk of mtDNA N, M and L+ (ie. Out of Africa). According to the defining mutations of L3, that were fully shared by N and M, the opposite applied here in the sense that mtDNA and mtDNA M were always understood as mtDNA L3 'sensu lato'. Now, with this study, we may agree this isn't the case, not even implicitly by renaming the trunk. <br />Instead, reading the tree 'as is' it doesn't elaborate on the renaming of trunks as you do, what indeed may foster similar suggestions the other way round (ie. Into Africa). However, the ancestor of mtDNA N is still N back in time when it ceased to be L2 'sensu stricto', but at least we may agree that mtDNA N is not mtDNA L2 'sensu lato': per definition it never was. This may conflict with the divergence of L3 and M from a point in time where only a few defining mutations of <i>current</i> N were in place, such as the A15301G! backmutation in N that is actually ancestral and even conflicts with L2 being an ancestral grouping. As I already say, Lippold et al. don't elaborate on these issues. In a way all branches are sisters and at the same distance to e.g. the Neanderthal outgroup. However, this is not the way how people think nor how any phylogenetic tree is represented.<br />Rokushttps://www.blogger.com/profile/13883125231922541439noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-81471364593560445152014-02-06T14:45:29.004+02:002014-02-06T14:45:29.004+02:00However, please note that this study's Y-DNA p...<i>However, please note that this study's Y-DNA phylogeny is also somewhat different from the currently "standard" tree of ISOGG; it does not recognize a CF node, but rather places C as a basal branch of DE (i.e. {C + {D + E}}) or as a basal branch of CDEF (i.e. {C + {DE + F}}).</i><br /><br />I trust their new mtDNA tree better than their y-DNA trees - especially since those are dependent on the mutation rate. And yes, I know -I can't wrap my mind around that. eurologisthttps://www.blogger.com/profile/03440019181278830033noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-57879262760751711302014-02-06T10:15:26.768+02:002014-02-06T10:15:26.768+02:00Rokus wrote,
"First, figure 14 doesn't s...Rokus wrote,<br /><br />"First, figure 14 doesn't show two branches, it shows M and L3 as derived from N. This means, with your proposal there won't be any L2M1 or L2M2, only L2NM1 and L2NM2."<br /><br />Are we both looking at the present study's Supplementary Figure 14?<br /><br />I should not need to explicate how to read a phylogenetic tree.<br /><br />I repeat: Supplementary Figure 14 has L2a'b'c as a sister clade to N'M'L3 (the most recent common ancestor of N, M, and L3), with the two sister clades, L2a'b'c and N'M'L3, sharing a most recent common ancestor approximately 105,000 years before present. L2a'b'c yields L2a and L2b'c approximately 81,000 years before present, whereas N'M'L3 yields N and M'L3 approximately 76,000 years before present. M'L3 yields M and L3 approximately 71,000 YBP, whereas N yields R and N(xR) approximately 66,500 YBP. <b>M'L3 is not descended from N; M'L3 and N are <i>sister clades</i>, both descended from a common ancestor, and that common ancestor is a sister clade of L2a'b'c.</b>Ebizurhttps://www.blogger.com/profile/16925110639823856429noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-11446955254959756652014-02-06T05:21:03.121+02:002014-02-06T05:21:03.121+02:00"First, figure 14 doesn't show two branch..."First, figure 14 doesn't show two branches, it shows M and L3 as derived from N". <br /><br />I am unable to see the supplementary material for some reason and so I have to rely on your collective contributions. <br /><br />"In other words, L2 was not really designed as ancestral to L3" <br /><br />I don't think L2 has ever actually been considered 'as ancestral to L3'. Rather 'sister to L3'4'6'. Have either L4 or L6 been considered in the figure? Both have been found outside Africa, but not too far removed. Perhaps N was part of that exit but managed to move further than either L4 or L6. <br /><br />"Actually, this tree has N and M'L3 as two coordinate branches of a stem that ultimately derives from the same trunk as L2". <br /><br />Possibly L2 remains sister haplogroup to N and M'L3. And L2 is certainly African, and so we still have no reason to claim L3 as having originated outside that continent. <br /><br />"There is now an L3MNUR group, which is upstream of L3M and NUR". <br /><br />Does the paper change the phylogeny that went: N-R-U? In other words do we now have three new separate basal haplogroups within N before the other N and R haplogroups form? terrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-57469603008478638422014-02-06T00:14:57.575+02:002014-02-06T00:14:57.575+02:00'Actually, this tree has N and M'L3 as two...<i>'Actually, this tree has N and M'L3 as two coordinate branches of a stem that ultimately derives from the same trunk as L2.'</i><br />First, figure 14 doesn't show two branches, it shows M and L3 as derived from N. This means, with your proposal there won't be any L2M1 or L2M2, only L2NM1 and L2NM2.<br />Second, of L2's defining mutations only C16311T may be presented as 'inherited by L3'. In other words, L2 was not really designed as ancestral to L3, very unlike the defining mutations of L3 that were (erroneously) designed as inherited by N and M. Indeed, only this single mutation separates a common L2'N clade from the 'more ancestral' African lineages L0 and L1. I figure that to make a really good mtDNA match with YDNA, Lippold et al. could as well have proposed an Eurasian L2-clade that backmigrated to Africa, analogous with the E clade of CFDE. Why did they scare away from this result, if C16311T was also found in the very divergent mtDNA of Lake Mungo 3?Rokushttps://www.blogger.com/profile/13883125231922541439noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-61015251683583580842014-02-04T13:02:46.676+02:002014-02-04T13:02:46.676+02:00Rokus wrote,
"Wrong figure. Lippold's in...Rokus wrote,<br /><br />"Wrong figure. Lippold's investigation on the paternal and maternal demographic histories of humans results in the full mtDNA phylogeny as provided in Supplementary Figure 14. Here mtDNA L and mtDNA M emerge as a single subclade of mtDNA N."<br /><br />Actually, this tree has N and M'L3 as two coordinate branches of a stem that ultimately derives from the same trunk as L2. In other words, according to this phylogeny, former L3 would be better named as M1 (or L2m1) with former M being renamed M2 (or L2m2). This African-Asian linkage in the mtDNA phylogeny seems to be paralleled in the Y-DNA phylogeny by haplogroup DE-YAP.<br /><br />However, please note that this study's Y-DNA phylogeny is also somewhat different from the currently "standard" tree of ISOGG; it does not recognize a CF node, but rather places C as a basal branch of DE (<i>i.e.</i> {C + {D + E}}) or as a basal branch of CDEF (<i>i.e.</i> {C + {DE + F}}).Ebizurhttps://www.blogger.com/profile/16925110639823856429noreply@blogger.com