Combined Use of Biallelic and Microsatellite Y-Chromosome Polymorphisms to Infer Affinities among African Populations

Abstract

To define Y-chromosome haplotypes, we studied seven biallelic polymorphic sites. We combined data with those from four dinucleotide-repeat polymorphisms, to establish Y-chromosome compound superhaplotypes. Eight biallelic haplotypes that matched the dendrogram proposed by other investigators were identified in 762 Y chromosomes from 25 African populations. For each biallelic site, coalescence time of lineages carrying the derived allele was estimated and compared with previous estimates. The "ancestral" haplotype (haplotype 1A) was observed among Ethiopians, "Khoisan" (!Kung and Khwe), and populations from northern Cameroon. Microsatellite distributions within this haplotype showed that the Khoisan haplotypes 1A are widely divergent from those of the other two groups. Populations from northern Africa and northern Cameroon share a haplotype (i.e., 1C), which is not observed in other African populations but represents a major Eurasian cluster. Haplotypes 1C of northern Cameroon are clearly distinct from those of Europe, whereas haplotypes 1C of northern African are well intermingled with those of the other two groups. Apportionment of diversity for the Y-chromosomal biallelic haplotypes was calculated after populations were clustered into different configurations. Despite some correspondence between language affiliation and genetic similarity, geographic proximity seems to be a better predictor of genetic affinity.

Human Y-chromosome variation in the Western Mediterranean area: implications for the peopling of the region

“…The haplogroup most commonly observed in this study was HG1, which is known to be the most common in Western Europe [7], and has been recently found at appreciable frequencies also in some populations from sub-Saharan Africa [18]. We observed frequencies of HG1 higher than 50% in populations from Southern Spain, Asturias, France, and Denmark.…”

“…In Africa, HG25.2 is observed in 29% of Arabs and 71% of Berbers from Morocco, but is not found in those Ethiopian populations in which a high frequency of the ancestral HG25.1 is observed (R. Scozzari and associates, unpublished results [18]). Outside Northern Africa, HG25.2 was seen at generally low frequencies in Spain, France, and Italy, although no traces could be detected in the Near East.…”

“…SRY 4064 [17,18], PN2 [1,3], and DYS271 [19] were tested in all YAP(ϩ) and some YAP(Ϫ); 2. SRY 10831 [17,18] and M9 [8] were tested in all YAP(Ϫ) and some YAP(ϩ); 3. M13 [8] was tested in all samples that carried the ancestral allele at both SRY 10831 and M9, and a few of the other samples; 4.…”

“…However, the postulated recent Iberian origin of this haplogroup [39] appears to be in contrast with its finding in our Russian sample (8%). Finally, the sub-Saharan-specific haplogroups 7.1, 7.2, 21, and 8 [4,18] were very uncommon and found only in six Berbers, one Arab, one Bedouin, three Palestinians, and seven Sardinians, which indicates that male-mediated gene flow across the Sahara has been very low both in historic and prehistoric times. [36] and Hammer et al [37], and the HG9 data from Rosser et al [7] and Quintana-Murci et al [38].…”

Human Y chromosome haplogroup R-V88: a paternal genetic record of early mid Holocene trans-Saharan connections and the spread of Chadic languages

“…Haplogroup E-DYS271, which accounts for 470% of the Y chromosomes in most of the populations south of the Sahara, is found on an average at a frequency of 2-3% in Northern Africa, whereas haplogroups J-M304, E-M81, and E-M78, which on the whole account for 50-90% of the northern African male-specific region of the Y chromosome (MSY) gene pool, have been only rarely observed in west/central sub-Saharan Africa. [12][13][14][15][16][17][18][19][20][21][22][23][24][25] A group of chromosomes of potential interest to past trans-Saharan connections is the paragroup R1b1* (R-P25*). Cruciani et al 18 found this paragroup (at that time defined as haplogroup 117, or R-M173*(xSRY 10831 , M18, M73, M269)) to be present at high frequencies (up to 95%) in populations from northern Cameroon.…”