Contrasting patterns of Y chromosome variation in Ashkenazi Jewish and host non-Jewish European populations

Abstract

The molecular basis of more than 25 genetic diseases has been described in Ashkenazi Jewish populations. Most of these diseases are characterized by one or two major founder mutations that are present in the Ashkenazi population at elevated frequencies. One explanation for this preponderance of recessive diseases is accentuated genetic drift resulting from a series of dispersals to and within Europe, endogamy, and/or recent rapid population growth. However, a clear picture of the manner in which neutral genetic variation has been affected by such a demographic history has not yet emerged. We have examined a set of 32 binary markers (single nucleotide polymorphisms; SNPs) and 10 microsatellites on the non-recombining portion of the Y chromosome (NRY) to investigate the ways in which patterns of variation differ between Ashkenazi Jewish and their non-Jewish host populations in Europe. This set of SNPs defines a total of 20 NRY haplogroups in these populations, at least four of which are likely to have been part of the ancestral Ashkenazi gene pool in the Near East, and at least three of which may have introgressed to some degree into Ashkenazi populations after their dispersal to Europe. It is striking that whereas Ashkenazi populations are genetically more diverse at both the SNP and STR level compared with their European non-Jewish counterparts, they have greatly reduced within-haplogroup STR variability, especially in those founder haplogroups that migrated from the Near East. This contrasting pattern of diversity in Ashkenazi populations is evidence for a reduction in male effective population size, possibly resulting from a series of founder events and high rates of endogamy within Europe. This reduced effective population size may explain the high incidence of founder disease mutations despite overall high levels of NRY diversity.

Signatures of founder effects, admixture, and selection in the Ashkenazi Jewish population

“…Using these proxy ancestral populations, we calculated the amount of European admixture in the AJ population to be 35 to 55%. Previous estimates of admixture levels have varied widely depending on the chromosome or specific locus being considered (18), with studies of Y-chromosome haplogroups estimating from 5 to 23% European admixture (8,9). Our higher estimate is in part a result of the use of different proxies for the Jewish ancestral population.…”

“…For example, some have posited that selection can explain the increase in rare recessive disorders, arguing for a heterozygous advantage for the mutant alleles (14)(15)(16). Moreover, Y-chromosome studies, in contrast to mtDNA results, reveal that Y-chromosome diversity in the AJ population is comparable to their non-Jewish European neighbors (8,17). Admixture estimates using markers at a few autosomal loci or based on STRUCTURE clustering results have also shown much higher European admixture than reflected in the Y chromosome (13,18,19).…”

“…Strong evidence of founder events also comes from studies of mitochondrial DNA (mtDNA), which show significantly less diversity of mtDNA haplotypes among the AJ population (6,7). Ychromosome studies also indicate only a low amount of admixture with neighboring Europeans (8)(9)(10). Additionally, some reports have measured higher LD in the AJ genome compared with reference populations (11,12).…”

Afghanistan from a Y-chromosome perspective

“…To assess the phylogenetic relationships between the two Afghan collections and 16 geographically targeted reference populations (Table 1), [19][20][21][22] a correspondence analysis (CA) 23 plot, Maximum-Likelihood (ML) 24 dendrogram and Analysis of Figure 2 Hierarchical phylogenetic relationships of Y-chromosome haplogroups and their percentages in Afghanistan. The following 77 markers were typed but were not polymorphic in the populations: C3a-M93, C3b-P39, C3c-M77, C3d-M407, C3e-P53.1, C3f-P62, DE-YAP, F1-P92, F2-M427, F2-M428, F3-P96, F3-M282, F4-P254, G1-M285, G2a1a-P18, G2a2-M286, H1a1-M197, H1a2-M97, H1a3-M39, H2-Apt, I-M258, J1a-M62, J1b-M365, J1c-M390, J1d-P56, J1e-PAGE8, J2a1-M47, J2a2-M67, J2a2a-M92, J2a2b-M163, J2a4-M137, J2a6-M289, J2a7-M318, J2a8-M319, J2a9-M339, J2a10-M340, J2a11-M419, J2a12-P81, J2a13-P279, J2b2a-M99, J2b2b-M280, J2b2c-M321, J2b2d-P84, K1-M147, K2-P60, K3-P79, K4-P261, L2-M317, M-P256, NO-M214, O-M175, Q1a1-M120, Q1a2-M25, Q1a3a-M3, Q1a4-P48, Q1a5-P89, Q1a6-M323, Q1b-M378, R1a1a1-M56, R1a1a2-M157, R1a1a3-M204, R1a1a4-P98, R1a1a5-PK5, R1a1a6-M434, R1a1a7-M458, R1b1b1a-M412, R1b1b1a1a-M405/U106, R1b1b1a1b1-U152, R1b1b1a1b2a-M222, R1b1b1a1b2b-M37, R1b1b1a1b2c1-P66, R1b1b1a1b3-M65, R1b1b1a1b4-M153, R1b1b1a1b5-M167, R1b1b-M335, S-M230 and T-M184.…”

Linking the sub-Saharan and West Eurasian gene pools: maternal and paternal heritage of the Tuareg nomads from the African Sahel

“…The geographic location used is the centre of the distribution area, from where the individual samples of each population were collected. Comparative data for H1 and H3 were taken from Finnila et al, 27 Herrnstadt et al, 28 Pereira et al, 29 Cherni et al 30 and Ennafaa et al; 31 and those for haplogroup V from Torroni et al, 10 Pereira et al, 32 Behar et al 33 and Cherni et al 30 …”