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Thread: The Origin of Y-DNA DE?2012 days old

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    Default The Origin of Y-DNA DE?

    The debate about the origins of haplogroup DE have come down to Africa or Asia. In my opinion I believe DE arose before the migration out of Africa along with CF. With DE diversifying in Asia and moving on to Europe then later become extinct. While in Africa DE remained dominate for quite some time until begin replaced it’s descendants especially E1b1a. Also E being the most diverse of all major clades could put it at a much older age than it is currently given according to the study below.

    Source:New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree.



    Haplogroup E is now defined by 18 mutations (SRY4064, M96, P29, P150, P152, P154, P155, P156, P162, P168, P169, P170, P171, P172, P173, P174, P175, and P176) (Supplemental Fig. 5). There are a total of 83 polymorphic sites that mark lineages within this clade, compared with a total of 30 internal mutations in 2002. This makes haplogroup E by far the most mutationally diverse of all major Y chromosome clades. These polymorphisms define 56 distinct haplogroups, which can be found at high frequencies in Africa, at moderate frequencies in the Middle East and southern Europe, and with occasional occurrence in Central and South Asia (Hammer et al. 1998; Underhill et al. 2001; Cruciani et al. 2002; Jobling and Tyler-Smith 2003; Semino et al. 2004; Sims et al. 2007).
    This other study is more evidence for the origin of DE in Africa.

    Source:Use of Y Chromosome and Mitochondrial DNA Population Structure in Tracing Human Migrations

    Phylogenetic resolution of the Y chromosome tree displaying possible explanation of DE in both Africa and Asia.



    With the exception of African-specific haplogroups A and B, all other Y chromosome haplogroups descend from one ancestral node of the tree termed CDEF, which is defined by mutations M168 and M294 (Figure 8). This previously unresolved trifurcation of this node into haplogroups C, DE, and F comprises the majority of African- and all non- African-affiliated chromosomes (Figure 8a). There are three possible solutions to this tripartite structure as presented in Figure 8b–d. Using the principle of phylogeographicparsimony, which minimizes the number of inferred migrations and the fact that the deepest clades (A and B) occur solely in Africans, an African origin of haplogroup CDEF-M168, M294 node was proposed (39, 116) and supported in a survey of over 12,000 Asian men (50). Although the initial proposal (38) of an Asian origin of haplogroup DE was first neutralized by the recognition of the haplogroup D-M174 (115) and further eroded by the detection ofDE∗ chromosomes in Nigeria (120), the previous inability to resolve the earlier tripartite structure left an element of uncertainty because the Asian origin of haplogroup DE could be resurrected using the same principle of parsimony [e.g., consider the parallel example of catarrhine evolution (99)] if the trifurcation were resolved in favor of a common ancestor of haplogroups DE and F (Figure 8b). Such an ancestral node would imply that DE is a subset of Eurasian variation and therefore the African YAP (Ychromosome Alu polymorphism) chromosomes could be considered as due to a backmigration from Asia. Second, if haplogroups C and F were to share a common recent ancestor apart from the DE clade (Figure 8d), the distribution of Y chromosome haplogroup D in Asia could be explained by an evolutionary history separate from that of the other two clades. Haplogroup D is particularly enigmatic because of its widely separated disjunctive distribution in Asia suggestive of an ancient (perhaps independent) range expansion to Asia followed by fragmentation and considerable isolation. The absence of haplogroup D in Oceania and its relic peripheral distribution in Asia is in contrast to that observed for haplogroup C and F chromosomes. We resolved this discrepancy by using improved phylogenetic resolution in the Y chromosomemosome phylogeny. This was achieved by leveraging knowledge contained in some of the phylogenetically consistent Y chromosome SNPs reported by Hinds et al. (42) (Figure 7b). By experimentally haplogrouping the same 33 males that were used to ascertain these Y chromosome polymorphisms, it was possible to infer that 22 of the SNPs were derived in all haplogroup E chromosomes and 24 in all F chromosomes (125) when the individuals in the ascertainment panel were subjected to phylogenetic analysis. Since haplogroup E and F chromosomes were present in the ascertainment panel but haplogroupCandDrepresentatives were not, the possibility existed that some of these 46 SNPs might be positioned upstream of either the E or F node in the phylogeny. A total of 18 of these were designed as successful PCR- (polymerase chain reaction) based assays and genotyped by DHPLC (denaturing high-performance liquid chromatography) (113) in samples belonging to haplogroups A, B, C-M216, D-M174, E-M96, and F-M89. The results of these haplogrouping experiments indicated that one (Table 1) of the 18 SNPs evaluated shared derived alleles in haplogroups C and F while being at an ancestral state in the other haplogroups. These results hold up the phylogenetic senario shown in Figure 8d, which is consistent with two independent founder types, D and CF, evolving outside Africa, and thus weakens the other two possible interpretations discussed above. However, the common ancestry of C and F founder types is supported by a short branch, defined by a single mutation, implying the diversification of CF from DE was shortly followed by the split of C from F. Although extinction events within Africa offset by haplogroup survival of descendents in Asia cannot be empirically demonstrated, both the refutation of the option shown in Figure 8b and the apparent absence of deep-rooted haplogroups for either CF or D chromosomes in Africa bolsters the model that haplogroup CF and DE molecular ancestors first evolved inside Africa and subsequently contributed as Y chromosome founders to pioneering migrations that successfully colonized Asia. While not proof, the DE and CF bifurcation (Figure 8d ) is consistent with independent colonization impulses possibly occurring in a short time interval. Although haplogroupsDandEshare common ancestry, a geographic gap exists between the frequent occurrence of haplogroup E in Africa and the relic distribution of D in Asia, suggestive of long-term isolation and extinction of descendents in the geographic intermediary zone to Asia. Although it is difficult to distinguish the influence of positive selection from demographic expansion, this anomaly in distribution could also be explained, in part, by negative selection affecting haplogroup D carriers. A slightly deleterious mutation may become fixed in some peripheral populations after its increase in frequency while surfing the wave of population advancement (26, 55). A possible candidate locus to be considered in the Y chromosome is copy-number variation in the aZFc gene as a possible haplogroupassociated risk factor regarding male fertility (47). Although such partial deletions of<2MB that occur across the spectrum of Y chromosome haplogroups (79, 80) are indicative of parallel mutations, this feature is significantly common in some Y chromosome haplogroup backgrounds (4, 127), especially those that were successful in recent demographic expansions such as haplogroup N (81, 86) in northern Asia. Individuals with haplogroup D affiliation have been reported to have such partial deletions in association with lower sperm concentrations in Japan (58). This partial deletion may in some measure explain the absence of haplogroup D in India, a zone implicated in the southern coastal migratory route, whereas haplogroup D is fixed in some tribal populations of the Andaman Islands (106). However, not all haplogroup D carriers have been reported to have such partial deletions (22). Nonetheless, the question remains to what extent, if any, susceptibility to a potential reproductive liability has influenced the phylogeography of D and other haplogroups in the Y chromosome and mtDNA phylogenies. Imbalance of the proportions of nonsynonymous mutations among and within the old and young clades of the mtDNA tree (53) further suggests that the outcome of some puzzling phenomena in uniparental haplogroup distributions might be the result of intertwining factors such as drift, selection, founder effect, and migration.
    Do you think the African origin of DE is correct? Poll added as well.
    Last edited by Zero; 2012-05-17 at 12:00.

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    Okay .. yeah those Hammer and Zegura dates are old. Looking at the dates: CT gets 70,000 years old, CF 68,900 (64,600 - 69,900), and DE gets 65,000 (59,100 - 68,300) years, respectively. This shere time frame is congruent with them being African since the time frame given for "Out of Africa", the main trek out of the the continent responsible for populating the rest of the globe, is 60-70kya or 60,000 - 70,000 (60 to 70 thousand) years ago. Migration(s) out prior went extinct and posterior (later) ones resulted in mere admixture, and aren't germain anyway, since these ones don't occur after that time frame.

    So if they were non-African they were barely out of the continent, which brings me to my next opinion, which is that in a way, this wouldn't matter anyway as the continents weren't seperated and aren't to this day, but just geographic regions that got different names, nothing else magical to them.

    Aside from those two points, isn't Hap D rare in Asia (exceot far South Asia) and found in areas where Negrito populations reside and also eminating from there? Not only that, but as far as I'm aware, they keep finding DE* (asterisk meaning not derived) in Nigeria, which would make this a cased closed in the way of parsimony. What if this is really African and Asian because the folks who made the Haplogroup were residing in an Island in between the two lands? What if they were conceiving each with one foot in one continent Africa, and the other in the other land Asia, and also 9 months later gave birth there right at that same position? Sorry, couldn't resist.

    But it is an extremely archaic Haplogroup to where it seriously wouldn't matter (that half African half Asian little scenario) were that the case.

    Also, note that E is not far behind the other three. E gets like 52.5 kya (52,500 thousand years ago). Also, aren't CT & CF like hypothetical Haps (Haplogroups) that have never been found (how this happens is existing Haplogroups can certainly have common distant ancestor Haplogroups that have not been found and possibly died off, hence the existence rather than non-existence of the hypothetical group)? Added with their hyper-ancientness, wouldn't this make analing that they might be Asian especially pointless?

    ---------- Post added 2012-05-17 at 07:11 ----------

    Ok edit: going back to DE*, I think descendents of the haplogroup have been found in Asia.
    Last edited by EclectYummination; 2012-05-17 at 13:13.
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    The above rule, if true, would mean it was true for each rule (as by it's own words it specifies "every rule"), thus becoming the exception to itself, thus further solidifying its own truth / validity / veracity.

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    ^Ainu people and Tibetans are predominantly D too.

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    Speaking of Tibetans, I believe they were the group they found DE* in. A group of its descendents still harboring some or at least one carrying the original DE*? Ugh, I'll go look it up, I suppose.

    ---------- Post added 2012-05-17 at 08:11 ----------

    Yeah, it's Tibetian. Anyway, I won't say that for Tibetians, but a lot of the photos representing the Ainu sure show hair not all that straight for East Asians.

    [imglink]http://upload.wikimedia.org/wikipedia/commons/thumb/a/a4/AinuManStilflied.JPG/495px-AinuManStilflied.JPG[/imglink]

    East Asians, and even East Indians have hair that is some of the straightest in the world. Very straight hair is found going from there up through the Bering Straight in Inuit (Eskimo) and Native American descendents, who have extremely straight (non-frizzy) hair as well. Just an observation.

    Descendents of South Asians in far East Asia? Then again, it's so old, it wouldn't even matter though. It could be found in Siberia / North Eurasia and still wouldn't matter.
    Last edited by EclectYummination; 2012-05-17 at 14:12.
    Curious rule here: There is an exception to every rule.

    The above rule, if true, would mean it was true for each rule (as by it's own words it specifies "every rule"), thus becoming the exception to itself, thus further solidifying its own truth / validity / veracity.

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    ^
    The Andamanese carry basal D* and C and more importantly, basal and divergent M lineages. They have the nappiest of nappy hair, and the closest to "black" skin you'll ever see. So I'm not getting the theory. It's all environmental.

    Within this lineage, the Andamanese (Onges and Jarawas) belong almost exclusively to the subtype designated Haplotype D, which is also common in Tibet and Japan, but absent on the Indian mainland.[13] However, this is a subclade of the D haplogroup which has not been seen outside of the Andamans, marking the insularity of these tribes.[14] The only other group that is known to predominantly belong to haplogroup D are the Ainu aboriginal people of Japan.

    http://en.wikipedia.org/wiki/Andamanese#Genetic_legacy




    That being said,

    In a study of over 8000 men worldwide including 1247 Nigerians, Haplogroup DE* was observed in only 5 Nigerian males (5/1247). However, the study's authors caution that "the apparently paraphyletic status of this haplogroup, and hence the conclusions of nested cladistic analysis, are also likely to be illusory" and that "the only genealogically meaningful definition of the age of a clade is the time to its most recent common ancestor, but only if DE* is paraphyletic does it also become automatically older than D or E in this sense."[6] More recently, one example of DE* was found amongst the Nalu in Guinea Bissau (1/17). The DE* sequence of this individual differs by one mutation from the DE* sequence of the Nigerian individuals. This indicates common ancestry, though the phylogenetic relationship between the two lineages was not determined in this particular study.[7] A 2008 study detected DE* in two individuals from Tibet (2/594).

    ^
    http://en.wikipedia.org/wiki/Haplogr...)#Distribution

    This is most likely an early migration of Wet Saharans into Asia. I'm going with Africa
    Last edited by pgbk87; 2012-05-17 at 15:33.
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    Quote Originally Posted by pgbk87 View Post
    This is most likely an early migration of Wet Saharans into Asia. I'm going with Africa
    The Sahara wasn't green around 75-55 kya. In fact, it was more arid than it's today. The world was characterized by hyper-aridity during the MIS 4 phase, which possibly explains why early OOA populations underwent a strong genetic bottleneck around this period.

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    Quote Originally Posted by Bandar Qasim View Post
    The Sahara wasn't green around 75-55 kya. In fact, it was more arid than it's today. The world was characterized by hyper-aridity during the MIS 4 phase, which possibly explains why early OOA populations underwent a strong genetic bottleneck around this period.
    Thanks for the info. What is your stance on the origin of DE*? I don't think I've asked you about that, only E* & E1b1*
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    Quote Originally Posted by pgbk87 View Post
    Thanks for the info. What is your stance on the origin of DE*? I don't think I've asked you about that, only E* & E1b1*
    I'm indifferent about it at the moment, it all seems too vague for now, but I'm leaning towards an East African origin rather than a West African or Asian one. IMO, those collected DE* samples should be given new sub-clades. Worst case scenario would be if those African ones are simply pre-E and the Syrian and Tibetan ones pre-D, making the origin of DE even more elusive.

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    Quote Originally Posted by EclectYummination View Post
    Okay .. yeah those Hammer and Zegura dates are old. Looking at the dates: CT gets 70,000 years old, CF 68,900 (64,600 - 69,900), and DE gets 65,000 (59,100 - 68,300) years, respectively. This shere time frame is congruent with them being African since the time frame given for "Out of Africa", the main trek out of the the continent responsible for populating the rest of the globe, is 60-70kya or 60,000 - 70,000 (60 to 70 thousand) years ago. Migration(s) out prior went extinct and posterior (later) ones resulted in mere admixture, and aren't germain anyway, since these ones don't occur after that time frame.

    So if they were non-African they were barely out of the continent, which brings me to my next opinion, which is that in a way, this wouldn't matter anyway as the continents weren't seperated and aren't to this day, but just geographic regions that got different names, nothing else magical to them.

    Aside from those two points, isn't Hap D rare in Asia (exceot far South Asia) and found in areas where Negrito populations reside and also eminating from there? Not only that, but as far as I'm aware, they keep finding DE* (asterisk meaning not derived) in Nigeria, which would make this a cased closed in the way of parsimony. What if this is really African and Asian because the folks who made the Haplogroup were residing in an Island in between the two lands? What if they were conceiving each with one foot in one continent Africa, and the other in the other land Asia, and also 9 months later gave birth there right at that same position? Sorry, couldn't resist.

    But it is an extremely archaic Haplogroup to where it seriously wouldn't matter (that half African half Asian little scenario) were that the case.

    Also, note that E is not far behind the other three. E gets like 52.5 kya (52,500 thousand years ago). Also, aren't CT & CF like hypothetical Haps (Haplogroups) that have never been found (how this happens is existing Haplogroups can certainly have common distant ancestor Haplogroups that have not been found and possibly died off, hence the existence rather than non-existence of the hypothetical group)? Added with their hyper-ancientness, wouldn't this make analing that they might be Asian especially pointless?

    ---------- Post added 2012-05-17 at 07:11 ----------

    Ok edit: going back to DE*, I think descendents of the haplogroup have been found in Asia.
    Quote Originally Posted by pgbk87 View Post
    ^
    The Andamanese carry basal D* and C and more importantly, basal and divergent M lineages. They have the nappiest of nappy hair, and the closest to "black" skin you'll ever see. So I'm not getting the theory. It's all environmental.

    Within this lineage, the Andamanese (Onges and Jarawas) belong almost exclusively to the subtype designated Haplotype D, which is also common in Tibet and Japan, but absent on the Indian mainland.[13] However, this is a subclade of the D haplogroup which has not been seen outside of the Andamans, marking the insularity of these tribes.[14] The only other group that is known to predominantly belong to haplogroup D are the Ainu aboriginal people of Japan.

    http://en.wikipedia.org/wiki/Andamanese#Genetic_legacy




    That being said,

    In a study of over 8000 men worldwide including 1247 Nigerians, Haplogroup DE* was observed in only 5 Nigerian males (5/1247). However, the study's authors caution that "the apparently paraphyletic status of this haplogroup, and hence the conclusions of nested cladistic analysis, are also likely to be illusory" and that "the only genealogically meaningful definition of the age of a clade is the time to its most recent common ancestor, but only if DE* is paraphyletic does it also become automatically older than D or E in this sense."[6] More recently, one example of DE* was found amongst the Nalu in Guinea Bissau (1/17). The DE* sequence of this individual differs by one mutation from the DE* sequence of the Nigerian individuals. This indicates common ancestry, though the phylogenetic relationship between the two lineages was not determined in this particular study.[7] A 2008 study detected DE* in two individuals from Tibet (2/594).

    ^
    http://en.wikipedia.org/wiki/Haplogr...)#Distribution

    This is most likely an early migration of Wet Saharans into Asia. I'm going with Africa
    These are the exact reasons I don’t believe DE could have begun in Asia. If DE is indeed 70,000 years old or over it means it could have very well left with first migration out of African. The early travelers most likely followed the southern coastline of Asia between 60,000 to 50,000 years ago. So western Austronesians and Daic populations must be the descendants of that first wave as showed by frequencies of D in the study below. If DE did begin in Asia it would be much more wide spread, since it only found in these anarchic populations we can safely assume it's origins are in Africa.

    Source:Paternal genetic affinity between western Austronesians and Daic populations.

    Y-SNP haplogroup frequencies of the newly studied samples (%)



    Our results show that the Daic populations are closer to the Western Austronesian populations in paternal lineages than any other ethnic groups in East Asia are. The STR diversity of the Y chromosome haplogroup O1a-M119, the major haplogroup among the Daic and Western Austronesian populations, shows that Taiwan and ISEA, two groups of Western Austronesian, derived from the Daic independently of each other. Therefore, it is most likely that the ISEA populations mainly originated in the region around the Tonkin Gulf, the homeland of the Daic, and migrated to Indonesia through the Vietnam corridor. In contrast, the Taiwan aborigines migrated from mainland China directly. Our results indicate that a super-phylum, which includes Taiwan aborigines, Daic, and Malayo-Polynesians, is genetically educible.
    Quote Originally Posted by Bandar Qasim View Post
    I'm indifferent about it at the moment, it all seems too vague for now, but I'm leaning towards an East African origin rather than a West African or Asian one. IMO, those collected DE* samples should be given new sub-clades. Worst case scenario would be if those African ones are simply pre-E and the Syrian and Tibetan ones pre-D, making the origin of DE even more elusive.
    Wasn't it your hypothesis that West Africans could have come from Proto-Nilotic people? Do you know why they stayed A and B while West Africans are nearly all E?
    Last edited by Zero; 2012-05-17 at 22:39.

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    Quote Originally Posted by Zero View Post
    Wasn't it your hypothesis that West Africans could have come from Proto-Nilotic people? Do you know why they stayed A and B while West Africans are nearly all E?
    Well, it makes more sense if you look at the maternal lineages. There's evidence for a connection with Nilotes there, for example the L3 in West Africa came from the East through the Nile area. Also, those E1a/E1b1a migrations westwards took place so long ago that their basal markers went extinct in the Nile Basin but can still be found in Ethiopia.

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