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Comparative Study

Phylogeography of Y-chromosome Haplogroup I Reveals Distinct Domains of Prehistoric Gene Flow in Europe

Siiri Rootsi et al. Am J Hum Genet.

Abstract

To investigate which aspects of contemporary human Y-chromosome variation in Europe are characteristic of primary colonization, late-glacial expansions from refuge areas, Neolithic dispersals, or more recent events of gene flow, we have analyzed, in detail, haplogroup I (Hg I), the only major clade of the Y phylogeny that is widespread over Europe but virtually absent elsewhere. The analysis of 1,104 Hg I Y chromosomes, which were identified in the survey of 7,574 males from 60 population samples, revealed several subclades with distinct geographic distributions. Subclade I1a accounts for most of Hg I in Scandinavia, with a rapidly decreasing frequency toward both the East European Plain and the Atlantic fringe, but microsatellite diversity reveals that France could be the source region of the early spread of both I1a and the less common I1c. Also, I1b*, which extends from the eastern Adriatic to eastern Europe and declines noticeably toward the southern Balkans and abruptly toward the periphery of northern Italy, probably diffused after the Last Glacial Maximum from a homeland in eastern Europe or the Balkans. In contrast, I1b2 most likely arose in southern France/Iberia. Similarly to the other subclades, it underwent a postglacial expansion and marked the human colonization of Sardinia approximately 9,000 years ago.

Figures

Figure  1
Figure 1
A, Phylogram of Hg I and its subclades within the context of the superhaplogroup F. Mutation labeling follows the Y Chromosome Consortium nomenclature (Y Chromosome Consortium ; Jobling and Tyler-Smith 2003). Markers M21 and M72 (Underhill et al. 2001) and the three new markers—M258 (a T→C transition at position 123), M284 (ACAAdel at position 105), and M307 (a G→A transversion at position 282)—were examined in a subset of 236 Y chromosomes, representative of the entire collection, by using the DHPLC method. The primers used for the new markers were as follows: F, 5′-tatatagcatatgttaaatgtttaggt-3′ and R, 5′-gacttttgaataatttgcatctttc-3′ for M258; F, 5′-ggcagttttcatttaagcaga-3′and R, 5′-agcgaaactttcagcacttc-3′ for M284; and F, 5′-ttattggcatttcaggaagtg-3′ and R, 5′-gggtgaggcaggaaaatagc-3′ for M307. When the DHPLC method was not used, M170 was detected as described by Ye et al. (2002); M253 was detected by using published primers (Cinnioğlu et al. 2004) and restriction analysis with HincII; P37 was assayed by TaaI digestion using the primers given by YCC (2002); and M223, M26, and the novel M227 (a C→G transversion at position 157) were studied by sequencing using published primers (Underhill et al. 2001) and the primers F, 5′-gagtgccaagctgaggatg-3′ and R, 5′-tccttgcagccgctgaggag-3′, respectively. A minority (n=67) of widely geographically distributed Hg I Y chromosomes (table 1) not tested for M258 and not harboring derived alleles at the sites M253, P37, and M223 were aggregated into paragroup I*. B–F, Frequency distribution of haplogroup I (B) and its subclades: I1a (C), I1c (D), I1b* (E), and I1b2 (F). Maps were obtained by applying the frequencies from table 1 in Surfer (version 7) software (Golden Software).
Figure  2
Figure 2
Network of haplogroup I. The network was obtained by using the biallelic markers and six STR loci (DYS19, DYS388, DYS390, DYS391, DYS392, and DYS393) in 533 Hg I chromosomes from 34 populations (Andalusian, Basques [French and Spanish], Bearnais, French [southern France, Low Normandy, Lyon, and Poitier], Swiss, Dutch, Italian [northern Italy, central Italy, Calabria1, Calabria2 of Albanese origin, Apulia, and Sardinia], Croat, Bosnian, Albanian, Macedonian, Moldavian, Gagauz, Greek, Swedish, Norwegian, Saami, Estonian, Polish, Czech, Slovak, Hungarian, Ukrainian, Turkish, and Jewish). The phylogenetic relationships between the 58 microsatellite haplotypes (out of the 156 observed) with frequency >1 were determined by using the program NETWORK 4.0b (Fluxus Engineering Web site). Networks were calculated by the median-joining method (ɛ=0) (Bandelt et al. 1995), weighting the STR loci according to the average of their relative variability in the haplogroup I subclades and after having processed the data with the reduced-median method. Circles represent microsatellite haplotypes. Unless otherwise indicated by a number on the pie, the area of the circles and the area of the sectors are proportional to the haplotype frequency in the haplogroup (the smallest circle corresponds to two individuals) and in the geographic area indicated by the color. The inset reveals, in more detail, the relationship between I1b2 and I1b* in a subsample of 103 Y chromosomes from 20 populations. The network was determined as described above but, in this case, in addition to the above mentioned six STR loci, the YCAIIa, YCAIIb, and DYS389 microsatellites and the 49a,f system were also considered. Here, the smallest circle of the network corresponds to a single Y chromosome. Very stable YCAII motifs characterize both I1b* (YCAIIa-21/YCAIIb-21) and I1b2 (YCAIIa-21/YCAIIb-11), supporting the hypothesis that single-banded patterns and very short alleles are due to deletion events rather than stepwise mutations.

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