A predominantly neolithic origin for Y-chromosomal DNA variation in North Africa

Abstract

We have typed 275 men from five populations in Algeria, Tunisia, and Egypt with a set of 119 binary markers and 15 microsatellites from the Y chromosome, and we have analyzed the results together with published data from Moroccan populations. North African Y-chromosomal diversity is geographically structured and fits the pattern expected under an isolation-by-distance model. Autocorrelation analyses reveal an east-west cline of genetic variation that extends into the Middle East and is compatible with a hypothesis of demic expansion. This expansion must have involved relatively small numbers of Y chromosomes to account for the reduction in gene diversity towards the West that accompanied the frequency increase of Y haplogroup E3b2, but gene flow must have been maintained to explain the observed pattern of isolation-by-distance. Since the estimates of the times to the most recent common ancestor (TMRCAs) of the most common haplogroups are quite recent, we suggest that the North African pattern of Y-chromosomal variation is largely of Neolithic origin. Thus, we propose that the Neolithic transition in this part of the world was accompanied by demic diffusion of Afro-Asiatic-speaking pastoralists from the Middle East.

Figure A1

Network of haplogroup E3b2*(xE3b2a) microsatellite haplotypes in North Africa. Circles represent haplotypes; their areas are proportional to their frequencies in the total North African sample, and their colors indicate the population of origin. Population codes are reported in table 1 and fig. 1. Lines across the network branches represent haplotypes that were not observed.

Figure 1

A, Phylogeny of Y-chromosomal haplogroups. The name of each haplogroup is shown at the tip of the lineage (1) according to Underhill et al. (2000) and (2) according to the Y Chromosome Consortium (2002). The polymorphisms screened in this study are shown along the branches. Lineage colors correspond to the haplogroup cluster colors of fig. 1B). Lineages shown by dashed lines were not observed in any of the populations discussed. Haplogroups observed in our samples are shown in boldface. The § symbol denotes 12f2_a. B, Frequency distribution of Y haplogroup clusters in African, Middle Eastern, and European samples. Populations include the samples from table 1, as well as Moroccan Arabs (M-Ara), North Central Moroccan Berbers (NM-Ber), Saharawis (Sah), South Moroccan Berbers (SM-Ber) (Bosch et al. 2001); Sudanese (Sud), Ethiopians (Eth), Europeans (Europe), Malians (Mali), Central Africans (C-Afr), South Africans (S-Afr), Khoisan (Khoi), Middle Easterners (Mid-East) (Underhill et al. 2000); Ethiopian Jews (Eth-J), Mossi (Mossi), Rimaibe (Rim), Fali (Fali), Ouldeme (Ould), Bamileke (Bamil), and Ewondo (Ewo) (Cruciani et al. 2002).

Figure 2

Population gene diversity and haplogroup E3b2 frequency in North Africa as a function of longitude. The linear regressions of gene (i.e., haplogroup) diversity (grey line) and E3b2 frequency (black line) onto longitude are shown. The population codes are reported in table 1 and figure 1 (in italics for gene diversity and in roman type for E3b2 frequency).

Figure 3

MDS analyses based on binary marker genetic distances among the North African, sub-Saharan African, European, and Middle Eastern populations from fig. 1B, tested using 116 binary markers (stress value 0.15). The population codes are reported in table 1 and figure 1.

Figure 4

Spatial autocorrelation analyses. A, Correlogram of the AIDA II indices calculated for North Africa. B, Correlogram of the AIDA II indices for North Africa and the Middle East (Syrian, Turkish, and Lebanese samples of Semino et al. [2000]). C, Correlogram of the Moran’s I index for the haplogroup E3b2* (overall correlogram significance P=.001). ***, P<.001; ns, not significant.