Different Genetic Components in the Ethiopian Population, Identified by mtDNA and Y- Chromosome Polymorphisms Giuseppe Passarino, Ornella Semino, Lluís.

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Different Genetic Components in the Ethiopian Population, Identified by mtDNA and Y- Chromosome Polymorphisms Giuseppe Passarino, Ornella Semino, Lluís Quintana-Murci, Laurent Excoffier, Michael Hammer, A. Silvana Santachiara-Benerecetti The American Journal of Human Genetics Volume 62, Issue 2, Pages 420-434 (February 1998) DOI: 10.1086/301702 Copyright © 1998 The American Society of Human Genetics Terms and Conditions

Figure 1 One of 49 MP trees obtained by PAUP analysis after 1,000 replications. This tree includes 21 Y-chromosome superhaplotypes (S1–S21; table 8). It is 23 steps in length and has consistency and retention indexes (CI and RI) of .522 and .711, respectively. Markers (YAP+, YAP−, sY81-G, 49a,f-A1, and 12f2 8-kb) characterizing the most important lineages are indicated. The lengths of the horizontal branches are proportional to the number of mutational events, and triangular areas are proportional to superhaplotype frequencies. The strict consensus tree of the 49 MP trees is illustrated in the inset: it is 35 steps in length and has a CI of .343 and a RI of .395. Haplotypes are in the same order as in the main figure. The American Journal of Human Genetics 1998 62, 420-434DOI: (10.1086/301702) Copyright © 1998 The American Society of Human Genetics Terms and Conditions

Figure 2 TaqI electrophoretic patterns detected by 49a,f probes in one gorilla (G) and in one chimpanzee (C), compared with human haplotypes 15 (A3C1D2F1I1), 7 (A2C0D1F1I0), 29 (A2/3C1D2F1I1), and 4 (A1C0D0F1I1) The American Journal of Human Genetics 1998 62, 420-434DOI: (10.1086/301702) Copyright © 1998 The American Society of Human Genetics Terms and Conditions

Figure 3 Parsimony tree correlating mtDNA types, obtained by means of the six classical enzymes, that have been found in Ethiopians (present study), Khoisan (Soodyall and Jenkins 1992), Niger-Congo speakers of southern Africa (Johnson et al. 1983; Soodyall and Jenkins 1993), and western Africans (Scozzari et al. 1988, 1994; Graven et al. 1995). This is one of the 3,000 parsimony trees generated by the TBR algorithm (Swofford 1992). It is 72 steps long, with CI and RI indexes of .583 and .746, respectively. The lengths of the horizontal branches are proportional to the number of mutational events. mtDNA types found in Ethiopia are in boldface. The HpaI site at nt 3592 defines most of the African types. Only one of the branches is defined by the absence of this site. The American Journal of Human Genetics 1998 62, 420-434DOI: (10.1086/301702) Copyright © 1998 The American Society of Human Genetics Terms and Conditions

Figure 4 A, PCA of 11 populations tested for HpaI, BamHI, HaeII, MspI, and AvaII mtDNA RFLPs. The first axis represents 64.1% of the total variance, and the second axis represents 16.7% of the total variance. Populations represented are Ethiopians (present study), Nama and Sekele (Soodyall and Jenkins 1992), Bantu (Johnson et al. 1983), Senegalese 1 (Mandekalu: Graven et al. 1995), Senegalese 2 (Wolof and Peul: Scozzari et al. 1988), Cameroonians (Scozzari et al. 1994), Jews (from Iraq, Yemen, and Turkey), and Israeli Arabs (Ritte et al. 1993b). Since the DdeI10394AluI10397 classification revealed ethnic heterogeneity within the Ethiopian mtDNA type 1, the frequency of this type (54.6%) has been subdivided as follows: 15.6% mtDNA type 1 DdeI10394AluI10397 (++), which is Asian and is absent in all the comparison populations; 17.0% mtDNA type 1 DdeI10394AluI10397 (+−), which is African and was compared with 88.8% (see table 4) of the mtDNA type 1 frequencies of the African control populations; and 22.0% mtDNA type 1 DdeI10394AluI10397 (−−), which was compared with 12% of the mtDNA type 1 frequencies of the African populations and with the entire frequency of the Caucasoid control sample. B, PCA of seven populations classified for the Y-chromosome YAP/12f2/49a,f compound haplotypes. The first axis represents 45.4% of the total variance, and the second axis represents 33.1% of the total variance. Populations represented are Ethiopians and Senegalese (present study); southern African blacks, Indians, Lemba, and Europeans (Spurdle and Jenkins 1996); and Jews (25 from Spurdle and Jenkins [1996] and 65 from A. S. Santachiara-Benerecetti [unpublished data]). The American Journal of Human Genetics 1998 62, 420-434DOI: (10.1086/301702) Copyright © 1998 The American Society of Human Genetics Terms and Conditions