MadSci Network: Genetics

Re: What Eurasian and American Indian populations carry mtDNA haplogroup X?

Date: Wed May 31 12:24:24 2000
Posted By: Gabriel Vargas M.D.,Ph.D., Post-doc/Fellow, Neurosciences/Psychiatry
Area of science: Genetics
ID: 958063812.Ge

I looked in the web for mtDNA and native Americans and came up with several 
web sites. The most interesting and relevant one to your question is the 
following paper presented at the INTERNATIONAL SYMPOSIUM: The Origin of 
Humankind Venezia, Palazzo Loredan in May 1998.

Global Mitochondrial DNA 
Variation and the Origin of Native Americans

Douglas C. Wallace, Michael D. Brown, Theodore G. Schurr, Estella Chen, 
Yu-Sheng Chen, Yelena B. Starikovskaya and
Rem I. Sukernik.
Center for Molecular Medicine
Emory University Medical School
Atlanta, GA 30322

The complete sequence of 39 mitochondrial DNAs (mtDNAs) have confirmed that 
all human mtDNAs form a single phylogenetic tree, the mtDNAs from each 
continent (Europe, Asia and Africa) cluster together, and African mtDNAs 
are the most divergent, hence the oldest, followed by Asian and then 
European mtDNAs. Comparison with chimpanzee mtDNA roots the human mtDNA 
tree in Africa and gives an estimated coalescence time of 149,000 years 
before present (YBP), with 95% confidence limits of 81,000-231,000 YBP.

Surveys of continent-specific mtDNA variation using restriction site 
polymorphisms (RSPs) and control region (CR) sequences have extended this 
analysis. Using RSP data, the overall sequence diversity of African mtDNAs 
has been estimated at 0.369%, giving an estimated coalescence time of 
between 130,000 and 170,000 YBP. Phylogenetic analysis of African mtDNA 
RSPs has revealed that approximately two thirds of African mtDNAs belong to 
a group of related mtDNA haplotypes, designated macro-haplogroup L, defined 
by the presence of a Hpal site ar nucleotide pair (np) 3592. The remaining 
African mtDNAs divide into four haplogroups which are more similar to 
European and Asian mtDNAs, than to those of macro-haplogroup L. 
Macro-haplogroup L is subdivided into haplogroups L1 and L2, and, vithin 
these haplogroups, distinct lineages are observed for the !Kung, Western 
Pygmy, Eastern Pygmy, and Senegalese. Phylogenetic and sequence divergence 
estimates indicate that the !Kung and Western Pygmys are the oldest African 
populations and that the Eastern and Western Pygmys had independent 

Analysis of European mtDNA variation has revealed that 99% of European 
mtDNAs fall into nine haplogroups (H, I, J, K T, U, V, W, and X). The 
European mtDNA coalescence time is between 40,000 and 50,000 YBP.
Central Asian mtDNAs generally fall into two macro-haplogroups. About 55% 
of Asian mtDNAs harbor two linked RSPs, a DdeI site at np 10394 and an AluI 
site at np 10397; while almost all of the remainder of Asian mtDNAs lack 
these sites. Asian mtDNAs which lack the 10394/10397 sites are subdivided 
into a number of haplogroups, including "A" which is defined by a HaeIII 
site gain at np 663 and "B" which is defined bu a 9 np COII-tRNALys 
intergenic deletion. Asian mtDNAs harboring the 10394/10397 sites are also 
subdivided into haplogroups including haplogroup "C" defined by a combined 
HincII site loss at np 13259 and AluI site gain at np 13262; and "D" 
defined by an AluI site loss at np 5176. The coalescence time for the Asian 
10394/10397 lineage is about 56 to 73,000 YBP.

Analysis of Native American mtDNAs revealed that mosto fall into four major 
haplogroups (A, B, C and D). Each of these haplogroups encompasses a 
coherent lineage of Native American specific mtDNA haplotypes which trace 
back to a founding haplotype that is also present in Asia. This implies 
that Native Americans were founded by a limited number of Asian ancestors. 
Analysis of the distribution of haplogroups A, B, C, and D among Native 
Americans revealed that the Amerind speaking Paleo-Indians of North, 
Central, and South America harbor all four haplogroups; the Na-Dene 
speakers of the Pacific Northwest as well as the Navajo and Apache of the 
Southwest harbor predominantly A; and the Eskimos and Aleuts harbor 
haplogroups A and D. This suggests that each of these groups of populations 
is genetically distinct. The coalescence time for Amerind haplogroups A, C, 
and D is about 20,000 to 30,000 YBP, suggesting that the first Americans 
arrived in the New World prior to the emergence of the Clovis lithic 
culture. Haplogroup B may have arrived independently and mixed with the 
populations carrying haplogroups A, C, and D. By contrast, the coalescence 
time of Na-Dene haplogroup A suggests that this population radiated into 
the Americans about 7 to 9,000 YBP.

In addition to the primary Native American haplogroups, we have also 
identified a rare fifth haplogroup "X" in the northern Amerinds and the 
Navajo. This haplogroup is defined by the absence of a DdeI site at np 
1715, the presence of an AccI site at np 14465, and several CR variants. 
Interestingly, distantly related haplogroup X mtDNAs have been found in 
Europe, but have not been detected in Asia. The coalescence a time of 
haplogroup X in the Americas is between 12 and 36,000 YBP, suggesting it 
represents a distinct migration to the New World.

MtDNA analysis of aboriginal Siberian populations has revealed that 
haplogroups C and D are widely distributed throughout Siberia, while 
haplogroup B is virtually absent. Haplogroup A is present at relatively low 
frequencies throughout Siberia, but increases to 68% in the Chukchi of the 
Chokotka peninsula adjacent to Alaska. Haplogroups C (11%), D (12%), and G 
(9%) are also found in the Chukchi. The neighboring Koryaks of the 
Kamchatka peninsula have 4% A, 37% C, 11% D, 43% G, 10% Y and 4%Z. Hence, 
the haplogroup distribution of the Chukchi most closely resembles that of 
Native Americans.

Analyses of the haplogroup A CR sequence variation in populations 
surrounding the Bering Strait has indicated that ancient Beringian 
populations also expanded into northern North America after the last major 
glacial period. The ancestral Beringian population is delineated by the CR 
np 16111 T polymorphism which gave rise to all Native American groups. The 
later Beringian populations are defined by a subsequent polymorphism at np 
16192 T which is found in the haplogroup A mt DNA of modern Koyaks, 
Chukchi, Siberian and Alaskan Eskimos and Na-Dene Indians.

In summary, modern Native American population have been derived from at 
least two and possibily three expansions out of northeastern Asia, the 
first occurring about 20,000 to 30,000 YBP.

hope this helps,
gabriel vargas md/phd

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