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

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.

Using mitochondrial DNA to test the hypothesis of a European post-glacial human recolonization from the Franco-Cantabrian refuge

“…The high frequency and diversity found for it in Pyrenean populations (Lopez-Parra et al, 2009) seems to confirm that hypothesis. However, in contrast to I-M253, I-M26 has an extremely low frequency in Scandinavia and most probably had a minor role in the recolonization of this region (Rootsi et al, 2004).…”

“…However, Y-chromosome analysis of Iberia pointed to the I-M26 subclade as the most prevalent there (Flores et al, 2004;Alonso et al, 2005;Lopez-Parra et al, 2009). It has been suggested that a region of Iberia-Southern France could be the origin of this subclade (Rootsi et al, 2004). The high frequency and diversity found for it in Pyrenean populations (Lopez-Parra et al, 2009) seems to confirm that hypothesis.…”

“…As occurs for H1a, the H3 highest diversity is in North-central Europe. The Y-chromosome I-M253 subclade has been proposed as another lineage signalling a northward expansion from the Iberian Peninsula-Southern France refuge after the LGM (Rootsi et al, 2004). However, Y-chromosome analysis of Iberia pointed to the I-M26 subclade as the most prevalent there (Flores et al, 2004;Alonso et al, 2005;Lopez-Parra et al, 2009).…”

Tracing the genetic origin of Europe's first farmers reveals insights into their social organization

“…B 282: 20150339 (L281) [40], which has been found in the extant Sardinian population [57]. Haplogroups I1 and I2a1 are most frequent in present-day populations of Europe, with the highest frequencies in Scandinavian [58][59][60] and southeast European populations, respectively [58]. We used PCA and genetic distance maps to identify affinities of the Carpathian Basin samples with 49 516 NRY SNP profiles from present-day Eurasian and African populations (electronic supplementary material).…”

The phylogenetic and geographic structure of Y-chromosome haplogroup R1a

“…[1][2][3][4][5] The International Society of Genetic Genealogy 10 has aggregated these variants and those discovered with previous technologies into a public resource that population surveys can leverage to further elucidate the geographic origins of and structure within haplogroups. [6][7][8][9][10][11][12][13] Y-chromosome haplogroup R (hg R) is one of 20 that comprise the standardized global phylogeny. 14 It consists of two main components: R1-M173 and R2-M479 15 (Figure 1).…”