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Suggestions and Caveats for Naming Mtdna Haplogroup

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Suggestions and Caveats for Naming Mtdna Haplogroup may seem ambiguous. Now that it turned out that what the lineage LETTER we called M16 (3) has a sister lineage south of the Himalayas (4) but apparently does not have related lineages in East Asia, adopting Reply to van Oven: Suggestions and haplogroup M62 that encompasses both lineages (1) might be a caveats for naming mtDNA haplogroup better choice. In cases of well-established haplogroups, renaming should be done under exceptional circumstances. A superhaplogroup We agree with van Oven (1) that a uniform mitochondrial (mt) should not be named based on a single moderately or highly DNA haplogroup nomenclature is indispensable for the future variable site. So, in retrospect, the naming of M4 as based only studies, and we actually propagated the same idea a few years on the hypervariable site 16311 was most unfortunate; delib- ago (2). The current conflicts regarding the Asian haplogroup erately broadening the scope of haplogroup M13 to an entity nomenclature (1) were essentially caused by publication delay: that would be supported merely by a single site, 6023, that is at the time when we submitted the manuscript (July 14, 2009), moderately variable (5) would lead to instability in the naming there was no conflict between the haplogroup system in our system. A potentially second variant, A15924G, cannot come paper (3) and PhyloTree (mtDNA tree Build 5; http://www. for support here, because it admits a different equally phylotree.org/) to which we referred. To avoid similar problems parsimonious reconstruction. in the future, a possible solution is that researchers in the mtDNA field indicate to van Oven (1) on submission of a paper ACKNOWLEDGMENTS. This work was partially supported by a grant from that certain haplogroup names are being introduced, so that the Chinese Academy of Sciences (Special Grant for the President Scholarship Winner; Q.-P.K.). other researchers would at least not choose the same code for fi a,b,1 c a their newly identi ed haplogroups. The blocked names (possibly Qing-Peng Kong , Hans-Ju¨rgen Bandelt , Mian Zhao , Ya-Ping with some further information) could then be shown in the bulk Zhanga,b,d, and Yong-Gang Yaoe mtDNA tree on that website. aState Key Laboratory of Genetic Resources and Evolution, Kunming The haplogroup nomenclature as a uniform naming system is Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, also intended to reflect (sub)continental affiliation of the line- Yunnan Province, China; bKIZ/CUHK Joint Laboratory of Bio- ages by partly contiguous ranges of numbers and letters. For resources and Molecular Research in Common Diseases, Kunming c instance, one can easily memorize that haplogroups A–G and 650223, China; Department of Mathematics, University of Ham- d M7–M13 are prevalent in East Eurasians, whereas H–K are burg, 20146 Hamburg, Germany; Laboratory for Conservation and specific to West Eurasians and M2–M6 are specific to South Utilization of Bio-resource, Yunnan University, Kunming 650091, Yunnan Province, China; and eKey Laboratory of Animal Models Asians. Previous researchers have carefully named the newly and Human Disease Mechanisms, Kunming Institute of Zoology, identified M, N, or R subhaplogroups by using number slots for Chinese Academy of Sciences, Kunming 650223, China each broad region, which, however, turned out to be of in- sufficient size (especially in the case of South Asia, even after the 1. van Oven M (2010) Revision of the mtDNA tree and corresponding haplogroup no- menclature. Proc Natl Acad Sci USA :E38–E39. creation of an additional slot from M30 to M40). Unfortunately, 2. Kong Q-P, et al. (2006) Updating the East Asian mtDNA phylogeny: A prerequisite for this naming strategy was not generally realized, and sub- the identification of pathogenic mutations. Hum Mol Genet 15:2076–2086. 3. Zhao M, et al. (2009) Mitochondrial genome evidence reveals successful Late Paleo- sequently, it got blurred when an increasing number of basal lithic settlement on the Tibetan Plateau. Proc Natl Acad Sci USA 106:21230–21235. lineages were named quite arbitrarily. 4. Chandrasekar A, et al. (2009) Updating phylogeny of mitochondrial DNA macrohaplogroup m in India: Dispersal of modern human in South Asian corridor. PLoS One 4:e7447. According to our unpublished data, there are plenty of unnamed 5. Soares P, et al. (2009) Correcting for purifying selection: An improved human mi- basal lineages in Asia. To avoid similar conflicts regarding hap- tochondrial molecular clock. Am J Hum Genet 84:740–759. logroup nomenclature and help researchers give “proper” hap- logroup names for the novel lineages, we propose that any future Author contributions: Q.-P.K. designed research; Q.-P.K., H.-J.B., and Y.-G.Y. performed re- numbering of novel (basal) lineages should select numbers from search; Q.-P.K. analyzed data; and Q.-P.K., H.-J.B., M.Z., Y.-P.Z., and Y.-G.Y. wrote the paper. geographically prescribed slots (Fig. 1). Even then, there may be The author declares no conflict of interest. exceptional cases where the subcontinental origin of a basal lineage 1To whom correspondence should be addressed. E-mail: [email protected]. E40–E41 | PNAS | March 16, 2010 | vol. 107 | no. 11 www.pnas.org/cgi/doi/10.1073/pnas.1000977107 Downloaded by guest on September 29, 2021 L M … … … D M7 - M11 M12 G M13 M17 M21 M22 M23 M71M72 M73 M74- M120 M27 M28 M29 Q M121- M150 East & Southeast Asia East Eurasia Oceania Oceania …… … … M2 - M6 M18 M30 --M45 M48 M49 M50 M52 M53 M54 M56 M57 M58 M60 M64 M151- M200 South Asia South Asia N … … … … AN9N21N22N10 N11 N31- N50 N51 N N2 X N3 N4 N6 N7 N8 N51- N70 N71- N80 N12 N13 N14 OSN15- N30 East & East Eurasia West Eurasia West Eurasia South Oceania Oceania Southeast Asia Asia R … … … … … … … BR9R11R21- R24 R25- R29 R61- R70 R0 R1 R2 JT U R3 R4 R71- R90 R5 - R8 R30 R31 R32-- R60 R12 R14 P R15 R20 East & Southeast East Eurasia West Eurasia West Eurasia South Asia South Oceania Oceania Asia Asia Fig. 1. Scheme of basal mtDNA haplogroups in non-Africans. Haplogroups prevalent in East and Southeast Asia are marked in blue, whereas haplogroups in South Asia are in yellow, haplogroups in West Eurasia are in orange, and haplogroups in Oceania are in pink. Slots available for naming novel haplogroups in these regions are indicated by gray boxes. Kong et al. PNAS | March 16, 2010 | vol. 107 | no. 11 | E41 Downloaded by guest on September 29, 2021.
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