Network Analyses of Y-Chromosomal Types in Europe, Northern Africa, and Western Asia Reveal Specific Patterns of Geographic Distribution

Abstract

In a study of 908 males from Europe, northern Africa, and western Asia, the variation of four Y-linked dinucleotide microsatellites was analyzed within three "frames" that are defined by mutations that are nonrecurrent, or nearly so. The rapid generation and extinction of new dinucleotide length variants causes the haplotypes within each lineage to diverge from one another. We constructed networks of "adjacent" haplotypes within each frame, by assuming changes of a single dinucleotide unit. Two small and six large networks were obtained, the latter including 94.9% of the sampled Y chromosomes. We show that the phenetic relationships among haplotypes, represented as a network, result largely from common descent and subsequent molecular radiation. The grouping of haplotypes of the same network thus fits an evolutionarily relevant criterion. Notably, this method allows the total diversity within a sample to be partitioned. Networks can be considered optimal markers for population studies, because reliable frequency estimates can be obtained in small samples. We present synthetic maps describing the incidence of different Y-chromosomal lineages in the extant human populations of the surveyed areas. Dinucleotide diversity also was used to infer time intervals for the coalescence of each network.

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

“…Consistent with previous results [13,27], a jump of more than two repeats at both DYS413a and DYS413b subdivides the FIGURE 2 Network of adjacent microsatellite haplotypes within the haplogroup YAP(Ϫ)/p12f2(8kb) (HG9 in Rosser et al [7]). All possible adjacent relationships are indicated by unbroken connecting lines, while dashed lines denote a two-repeat difference.…”

“…As previously reported [13,27,33,34], haplogroup 2.2 is essentially confined to Sardinia, where it was found at high frequencies (17%-56%) in all population samples (Table 1). Very few instances of this haplogroup were observed in the surrounding regions, including nearby Corsica.…”

“…This hypothesis was confirmed by the analysis of HG2. The lower part of Figure 3 depicts a subset of HG2 characterized by the allele with 11 repeats at YCAIIb, an allele already known to be at high frequency in Sardinia [13,27,33,34]. In this study, 130 such alleles were observed and none of them was found in other haplogroups, indicating, also in this case, that most likely a single deletion event on a HG2 background gave rise to all members of HG2.2 ( Figure 1).…”

“…Microsatellite haplotypes with the same combined repeat length were placed at the same horizontal level and the network was constructed by sequentially adding haplotypes differing by a single repeat unit [26,27].…”

“…In an initial attempt to use Y-chromosome variation to investigate the origin of European Y chromosomes, networks of microsatellites differing by one repeat were constructed for haplogroups defined by only two stable markers [13,27]. That analysis provided new information about the mutational process of microsatellites, and suggested that the occurrence of rare multistep changes in the repeat number could be used to define more geographically coherent lineages within widely distributed haplogroups.…”