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[QUOTE]Originally posted by Clyde Winters: [QB] [b]Technical Report: Assessment of the genetic analyses of Rasmussen et al. (2015) John Novembre, PhD, David Witonsky, Anna Di Rienzo, PhD April 4, 2016 SYNOPSIS The primary aim of the analysis undertaken here (U.S. Army Corps of Engineers, St Louis District Contract #W912P9-16-P-0010) is to provide an independent validation of the genetic evidence underlying a recent publication by Morten Rasmussen and colleagues on July 23rd, 2015, in Nature (Vol 523:455–58). Based on our analysis of the Kennewick Man’s sequence data and Colville tribe genotype data generated by Rasmussen et al., we concur with the findings of the original paper that the sample is genetically closer to modern Native Americans than to any other population worldwide. We carried out several analyses to support this conclusion, including (i)principal component analysis (PCA; Patterson et al. 2006), (ii) unsupervised genetic clustering using ADMIXTURE (Alexander, Novembre, and Lange 2009), (iii) estimation of genetic affinity to modern human populations using f3 and D statistics (Patterson et al. 2012), and (iv) a novel approach based on the geographic distribution of rare variants. Importantly, these distinct analyses, spanning three non-overlapping subsets of the data, are each consistent with Native American ancestry.[/b] Craniometric and skeletal evidence indicates that Paleoamericans were related to the Australian, Polynesian or Sub-Saharan type.Novembre et al (2016) argue that Kennewick man is related more to modern Native Americans, instead of the PaleoAmericans. In support of this hypothesis Novembre et al (2015) conclude that Kennewick man is closely related to the South American Karitiana people. The finding by Novembre et al (2015) that genetically Kennewick man related mostly to the Karitiana falsifies their population. It is falsified because Skoglund et al (2015) found that the Karitiana and other Amozonian people in South America have an Australasian heritage. The identification of a relationship between Kennewick man and the Karitiana would continue to situate this Native American in the Paleoamerican group--not contemporary Native Americans. The Amerindian haplogroups (hg) are descendant from the L3(M,N, & X) macrohaplogroup): ABCDN and X. The L3 (M,N,X) marcogroup converge at np 16223. The mtDNA haplogroups ABC and X are subclades of haplogroup N. In Table 1, we see the distribution of haplogroup N, in the Americas. The phylogeography of haplogroup C suggest that this American founder haplogroup differentiated in Siberia-Asia (24). The situation is not so clear for haplogrop B2, but A2 and D1 probably differentiated after the mongoloid Native American lineages diverged after crossing the Beringa Straits (24) Haplogroup A2 has the motif 16111T,16223c, 16290T, 16319A and 16223C (25). Haplogroup A is rare in Siberia (26). Interestingly, haplogroup A absent in western North America is common in parts of Central America and Northern America where the Spanish reported the existence of Black Native American communities(1-2). In a recent study of post-Classic Mexicans at Tlatilco , dating between 10-13 centuries the subjects carried the founder haplogroups A (36%), B (13%), C (4.3%) and D (17.4%) (27). We should note, that in Yucatec, the Mayans were predominately haplogroup A, the Maya in Hondurus, a stronghold of the Black Native Americans belonged to haplogroup C. The mtDNA haplogroup A common to Mexicans is also found among the Mande speaking people and some East Africans (28-29). Haplogroup A found among Mixe and Mixtecs (28).The Mande speakers carry mtDNA haplogroup A, which is common among Mexicans (30). In addition to the Mande speaking people of West Africa, Southeast Africa Africans also carry mtDNA haplogroup A (29). The major American Indian male lineages include R1, C,D and Q3.There is evidence of African admixture in the American y-chromosome haplogroups. The Q y-haplogroup has the highest frequency among indigenous Mexicans. The frequency hg Q varies from a high of 54% for Q-M243, and a low of 46% for QM (34). African y-chromosome are associated with YAP+ and 9bp. The YAP-à associated with A-àG transition at DYS271 is found among Native Americans. The YAP+ individuals include Mixe speakers (32-33). YAP+ is often present in haplogroups (hg) C and D. The DYS271 transition is of African origin (32).The DSY271 Alu insertion is found only in chromosomes bearing Alu insertion (YAP+) at locus DYS287 (33). The DYS271 transition was found among the Wayuu, Zenu and Inzano. The Mexican Native American y-chromosome bearing the African markers is resident in haplogroups C and D (34). R-M173 is also found in Mexico. Haplogroups R and Q are part of the CT microgroup which dates back 56kya. Haplogroup R branches from hg Q, with the SNP M242. The CT haplogroup has SNP mutation M168, along with P and M294. Haplogroup P (M45) has two branches Q (M242) and R-M207 which share the common marker M45. The M45 chromosome is subdivided by the biallelic variant M173 (35). In Africa we find P (M173), R1b (M343) and V88; and R1b1a2 (M269). Native Americans carry a high frequency of R-M173 (48). The predominate y-chromosome in North America is R-M173. R-M173 is found only in the Northeastern United States along with mtDNA haplogroup X (25%). Both haplogroups are found in Africa, but is absent in Siberia. There are varying frequencies of y-chromosome M-173 in Africa and Eurasia. Whereas only between 8% and 10% of M-173 is carried by Eurasians, 82% of the carriers of this y-chromosome are found in Africa. This is very interesting given the presence on R-M173 is found among many American Indian groups (48). R-M173 among the North American Algonquian group range from Ojibwe (79%), Chipewyan (62%), Seminole (50%), Cherokee (47%), Dogrib (40%) and Papago (38%) . These Indian groups have a long association with Africans and many live in areas were Europeans found Black Native Americans. In most studies of North American Indians, any evidence of African haplogroups are excluded from all analyses (47). Exclusion of evidence of non-Amerindian admixture and non-foundational Amerindian haplogroups is regularly left out of publications on Native American DNA (49). The R haplogroup is carried by Mexicans. The frequency of hg R varies from Tarahumara (5.6%), Otomi (14.3%), Yucateca Maya (10.5%). There is also a high frequency of haplogroup R among the Ch'ol and Chontal which stood around 15% (38). The Ch'ol and Chontal also carry E1b1b (38). The Spanish identified the Otomi as a Black Native American tribe(11). African ancestry has been found among indigenous groups that have had no historical contact with African slaves and thus support an African presence in America, already indicated by African skeletons among the Olmec and Mayan people. Lisker et al, noted that "The variation of Indian ancestry among the studied Indians shows in general a higher proportion in the more isolated groups, except for the Cora, who are as isolated as the Huichol and have not only a lower frequency but also a certain degree of black admixture. The black admixture is difficult to explain because the Cora reside in a mountainous region away from the west coast" (22). A recent study of African - Mexican admixture yielded a frequency range between 22-41% (25). In one study the researcher found that 3% of Native Americans showed African haplogroups (25). Underhill et al , noted that:" One Mayan male, previously [has been] shown to have an African Y chromosome" (31). This is very interesting because the Maya language illustrates a Mande substratum, in addition to African genetic markers (3) Plus the Chontal were identified as a Black Native American tribe (11). The African haplogroups among indigenous Mexicans include L0a1a'3, L2a1, L3b, L3d, and U6a (25). Interestingly, an individual at Laguna de los Condores, Peru dating between AD 1000-1500 carried L3 (36). Green et al also found Indians with African genes in North Central Mexico, including the L1 and L2 clusters (25). An important indicator of African admixture is 9bp (22,27). Haplogroup B is defined by 9bp (27) and is linked to haplogroup A. The 9bp marker is reported among the North Mexicans. It is common among the Mixtec (27). Some indigenous Mexicans show the G6PD deficiency. In a study of Yucatecos, Tzellzal-Tzoltzil, Mixteca and Mestizo it was found that people on the Oaxaca coast suffered from G6PD deficiency (22). Lisker also found G6PD deficiency in Costa Chica (22). The G6PD deficiency is usually carried by SSA. Indigenous Indians at Tlaxcala contains 8% African genes, but historically no Africans lived in the area (37). Researchers have also found L1, L2 & L3 clusters among many Mexicans including the Cora, Mixtec and Zapotecs (39-41) It is interesting to note that the proportion of African haplotypes roughly equivalent to the proportion of European haplotypes [among North Central Mexican Indians] cannot be explained by recent admixture of African Americans for the United States (41). This is especially the case for the Ojinaga area, which presently is, and historically has been largely isolated from U.S. African Americans. In the Ojinaga sample set, the frequency of African haplotypes was higher than that of European hyplotypes"(41). Human Leukocyte Antigens (HLA) polymorphism is used to investigate ethnic relationships and origins. Africans and Indigenous Mexicans share HLA alleles. In Table 2 we outline the relationship. Gutherie in a study of the HLAs in indigenous American populations, found that the V antigen of the Rhesus system, considered to be an indication of African ancestry, among Indians in Belize and Mexico centers of Mayan civilization (45). Dr. Gutherie also noted that A*28 common among Africans has high frequencies among Eastern Maya (45). In addition to A*28 , there is a high frequency of HLA B*35 among Mexicans and SSA (46). The frequency of HLA B*35 among indigenous Mexicans and SSA is high ranging between 22-31% among SSA populations and 30-45% among MA groups (46). It is interesting to note that the Otomi, a Mexican group identified as being of African origin and six Mayan groups show the B Allele of the ABO system that is considered to be of African origin. It is time that researchers stop claiming the first Native Americans were not Negroes. Reference: Skoglund et al (2015), Genetic evidence for two founding populations of the Americas , NATURE ,525 ( 3 SEPTEMBER):104-108. Retrieved 5/1/2016 at : [URL=http://www.nature.com/articles/nature14895.epdf?referrer_access_token=4TuRenNBfBRS7tHNMAY1qdRgN0jAjWel9jnR3ZoTv0N6yB-nEyCdRoL51ykMO5E9z_7mdrRF_UTJvxtpDQnayOfwuJnrOCxIhdm8_7djDnDo9Obq-VbpDatHfBozg8WnuFcDDHGC6D1QQbbgmyediLKefzmJLdqOP9IYieqkoaey_M8XA-n4Ua9CD3IbOslIqWUnXzIWbLwafl9bJMOQNAJlELt6cfooH162H7W_3B8%3D&tracking_referrer=mobile.nytimes.com]http://www.nature.com/articles/nature14895.epdf?referrer_access_token=4TuRenNBfBRS7tHNMAY1qdRgN0jAjWel9jnR3ZoTv0N6yB-nEyCdRoL51ykMO5E9z_7mdrRF_UTJvxtpDQnayOfwuJnrOCxIhdm8_7djDnDo9O bq-VbpDatHfBozg8WnuFcDDHGC6D1QQbbgmyediLKefzmJLdqOP9IYieqkoaey_M8XA-n4Ua9CD3IbOslIqWUnXzIWbLwafl9bJMOQNAJlELt6cfooH162H7W_3B8%3D&tracking_referrer=mobile.nytimes.com[/URL] . [/QB][/QUOTE]
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