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peer review demolishes Winters M-173
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[QUOTE]Originally posted by Clyde Winters: [QB] [QUOTE]Originally posted by the lioness,: [qb] http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0007447 2009 [b]Updating Phylogeny of Mitochondrial DNA Macrohaplogroup M in India: Dispersal of Modern Human in South Asian Corridor Adimoolam Chandrasekar et al[/b] Published: October 13, 2009 DOI: 10.1371/journal.pone.000744 [b]Abstract[/b] To construct maternal phylogeny and prehistoric dispersals of modern human being in the Indian sub continent, a diverse subset of 641 complete mitochondrial DNA (mtDNA) genomes belonging to macrohaplogroup M was chosen from a total collection of 2,783 control-region sequences, sampled from 26 selected tribal populations of India. On the basis of complete mtDNA sequencing, we identified 12 new haplogroups - M53 to M64; redefined/ascertained and characterized haplogroups M2, M3, M4, M5, M6, M8′C′Z, M9, M10, M11, M12-G, D, M18, M30, M33, M35, M37, M38, M39, M40, M41, M43, M45 and M49, which were previously described by control and/or coding-region polymorphisms. Our results indicate that the mtDNA lineages reported in the present study (except East Asian lineages M8′C′Z, M9, M10, M11, M12-G, D ) are restricted to Indian region.The deep rooted lineages of macrohaplogroup ‘M’ suggest in-situ origin of these haplogroups in India. Most of these deep rooting lineages are represented by multiple ethnic/linguist groups of India. Hierarchical analysis of molecular variation (AMOVA) shows substantial subdivisions among the tribes of India (Fst = 0.16164). The current Indian mtDNA gene pool was shaped by the initial settlers and was galvanized by minor events of gene flow from the east and west to the restricted zones. Northeast Indian mtDNA pool harbors region specific lineages, other Indian lineages and East Asian lineages. We also suggest the establishment of an East Asian gene in North East India through admixture rather than replacement. [b]Origin of Macrohaplogroup M[/b] L3 lineages other than M and N are absent in India and among non-African mitochondria in general [2]–[3], [49]. M, N and R haplogroups of mtDNA have no indication of an African origin. However, it is proposed that the origin of haplogroup M is in Africa [34], in view of its high frequency in Ethiopia. But in 2006, by [35] demonstrated that the presence of M1 and U6 in Africa is due to a back migration. Sequencing of 81 entire human mitochondrial DNAs belonging to haplogroups M1 and U6 revealed that these predominantly North African Clades arose in Southwestern Asia and moved together to Africa about 40,000 to 45,000 years ago. Only some sub-sets of M1a (with an estimated coalescence time of 28.8±4.9ky), U6a2 (with an estimated coalescence time of 24.0±7.3ky), and U6d (with an estimated coalescence time of 20.6±7.3ky) diffused to East and North Africa through the Levant, leaving the origin of macrohaplogroup M unresolved. Haplogroup M has been found ubiquitous in India, although its frequency is somewhat higher in southern Indian populations than in northern Indian populations and to a large extent autochthonous because neither the East nor the West Eurasian mtDNA pools include such lineages at notable frequencies [37], [58]. Our findings, (for example, deep time depth >50,000 years of western, central, southern and eastern Indian haplogroups M2, M38, M54, M58, M33, M6, M61, M62 and distribution of macrohaplogroup M) do not rule out the possibility of macrohaplogroup M arising in Indian population. Migration routes of modern human Recent mtDNA evidence on modern human out of Africa migration route suggests a single dispersal by a southern coastal route to India and further, to East Asia and Australia [17], [20], [22], [23], [66], [69]. The North Asian route could not get support from mtDNA due to the lack of basal M, R, N lineages in northern Asians, thereby ruling out the existence of a northern Asian route [29]–[30], [70]–[71]. Proven back migration of sub lineages of M and U into Africa [35], and the absence of L3 lineages or ancestral lineage for L3, M and N in India, leaves two issues unresolved: evidences for the southern route hypothesis from India and origin of M haplogroup. However, in the present study, the basal diversity (37 nodes) and founder ages (57,000–75,000 years) of macrohaplogroup M in India reveals initial settlement of African exodus in India. Our database also reveals evidences that Andaman islanders and Australians have ancestral maternal roots in India [24], [43]. In summary, the present study provides evidence that several Indian mtDNA M lineages are deep rooted and in situ origin. In North East India the coalescent time of East Asian lineages dates back to Last Glacial Maximum (LGM). Further, the combination of virtually all previously reported lineages from South and East Asia and our newly produced Indian complete mtDNA sequences have helped to define several novel (sub) haplogroups. The present work further ascertained previously reported haplogroups, and refined the phylogenetic tree of South Asia. This updated phylogenetic tree provides an essential reference guide for diseases, anthropological and forensic studies among Asian populations. [/qb][/QUOTE]This is my response to this article. [QUOTE][list] [*]Macrohaplogroup M Did not Originate in India Posted by Clyde98 on 21 Aug 2011 at 06:11 GMT by Clyde Winters Chandrasekar et al provide a good discussion of the phylogeny of Indian macrohaplogroup M. Although they claimed to have examined all of the M haplogroups in India they failed to discuss haplogroup M1, which is also found in India [3-4]. This failure to discuss all the M lineages in India cast doubt on the conclusions of the authors of this study. The researchers argue that the M macrohaplogroup in India developed in situ. They base this claim on the research of Gonzalez et al [1]. Chandrasekar et al maintain that the research in [1] indicates that M1 probably originated in Southwest Asia and through a back migration hg M and U6 returned to Africa. This is false hg M probably originated in Africa, not Asia [3]. Chandrasekar et al claim that hg M arose in Southwest Asia 40kya. This date is ludicrous because Neanderthals lived in that region at this time. The only anatomically modern humans in Western Eurasia at this time were Cro-Magnon man who carried haplogroup N. To estimate the coalescence age of haplogroup M1 Gonzalez et al [1] analyzed 13 complete sequences of haplogroup M1. Gonzalez et al claims that the M1c lineage is the oldest M1 subclade based on the coalescence age estimation of the M1 subgroup: M1a (16756 +-5997), M1b (10155 +-3590) and M1c (19040+-4916). This makes M1a and M1b the youngest clades. The available sample for M1c was complete sequences from individuals found in Jordan, Senegal, and Spain. The small data set make a precise estimation of the errors in the data uncertain. The limited sample for M1c makes it difficult to effectively quantify the estimation error for the data, since error increases from level to level in models possessing a hierarchical structure. The small sample size makes the confidence intervals overlap. This calls into question the conclusions of Gonzalez et al [1] in relation to the ages of hg M1 despite the differing levels of hierarchy. In addition to the evidence of the coalescence age estimation in support of the antiquity of M1c, Gonzalez et al believe the presence of M1c among Jordanians is an important indicator for the ancient origin of this clade. The evidence of M1c in Jordan, does not really add to the hypothesis that M1c is the oldest clade because the presence of this clade in the Middle East can be explained by the thousands of West Africans who have taken the hajj to Mecca, and remained in the Middle East, instead of returning to West Africa. The Valencia sample can also be explained by the history of Islam. There is a direct link between Senegal and Yusuf ibn Tashufin. Yusuf founded the Almoravids. The Almoravid empire extended from Senegal to Spain [2]. This link comes from the fact that many of the followers of Tashufin came from the ribats or ‘religious schools’ he had established in northern Senegal. Troops from these ribats formed the backbone of Tashufin’s army when he invaded Spain in 1086[2]. These African Muslims ruled much of Spain until 1492. Since M1c is presently found in Senegal, the carrier of M1c reported by Gonzalez et al in Valencia may be a descendent of these African Almoravids that ruled Spain for over 700 years Sub-Saharan Africans probably spread hg M1c to Eurasia. Gonzalez et al reported that the carriers of the M1c subset were from Jordan, Senegal and Valencia [1]. It was revealed above that 1) many of the Muslim troops in Tashufin’s army that conquered Spain in 1086 AD, came from Senegal; and 2) many West Africans after taking the Hajj, visited Jerusalem and settled in the Middle East. Even if we eliminate the Jordan sample, the evidence from Valencia and Senegal gives a 67% probability that M1c originated in Senegal, not Asia or North Africa because of the historical presence of Sub-Saharan Africans in both areas . This provides support for an African origin of M1. Chandrasekar et al claim that India is the only region where there is a variety of M subclades is also false. In Africa, for example in addition to M1, we also find haplogroups M3,M30 and M33. Chandrasekar et al claims that there is no influence of African haplogroups in India. The presence of M1 among South Indian Dravidian speakers make it clear that African mtDNA is found in India [1][3]. This along with African y-chromosomes and African HLA among Dravidian tribal groups indicate a recent African influence among South Indians [4-6]. This is not surprising since Dravidian speakers formerly belonged to the C-Group culture of Nubia, and only entered India 5kya [4]. The distribution of continental African populations carrying M haplogroups favors Africa as the place of origin for this macrohaplogroup instead of India. The population distributions for the M macrohaplogroup in Africa make it clear that haplogroup M originated in Africa, not Asia or North Africa. Reference: 1. Gonzalez , A. Jose M Larruga , Khaled K Abu-Amero , Yufei Shi , Jose Pestano and Vicente M Cabrera. (2007).Mitochondrial lineage M1 traces an early human backflow to Africa, BMC Genomics , 8:223 doi:10.1186/1471-2164-8-223. Retrieved on 9/15/2010 http://www.biomedcentral.... 2. Bovill,E.W. (1970). The Golden trade of the Moors. London: Oxford University Press. 3. Winters,C. (2010). The African Origin of the M1 Haplogroup Introduction. Current Research Journal of Biological Sciences. Retrieved 8/20/2011 http://olmec98.net/afro_m... 4. Winters, C.(2007). Did the Dravidian Speakers Originate in Africa? BioEssays,27(5):497-498. 5.Winters, C. (2010). Y-chromosome evidence of an African origin of Dravidian Agriculture. Int J Genet & Molec Bio, 2(3):030-033. Retrieved 6/4/2010 at: http://www.academicjourna... 6. Winters, C. (2010). 9bp and the Relationship Between African and Dravidian Speakers. Current Research Journal of Biological Sciences 2(4): 229-231. http://maxwellsci.com/pri... See: http://www.plosone.org/annotation/listThread.action?root=6633 . [/QUOTE] [/list] [/QB][/QUOTE]
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