Abstract
Haplogroup E1b1, defined by the marker P2, is the most represented human Y chromosome haplogroup in Africa. A phylogenetic tree showing the internal structure of this haplogroup was published in 2008. A high degree of internal diversity characterizes this haplogroup, as well as the presence of a set of chromosomes undefined on the basis of a derived character. Here we make an effort to update the phylogeny of this highly diverse haplogroup by including seven mutations which have been newly discovered by direct resequencing. We also try to incorporate five previously-described markers which were not, however, reported in the 2008 tree. Additionally, during the process of mapping, we found that two previously reported SNPs required a new position on the tree. There are three key changes compared to the 2008 phylogeny. Firstly, haplogroup E-M2 (former E1b1a) and haplogroup E-M329 (former E1b1c) are now united by the mutations V38 and V100, reducing the number of E1b1 basal branches to two. The new topology of the tree has important implications concerning the origin of haplogroup E1b1. Secondly, within E1b1b1 (E-M35), two haplogroups (E-V68 and E-V257) show similar phylogenetic and geographic structure, pointing to a genetic bridge between southern European and northern African Y chromosomes. Thirdly, most of the E1b1b1* (E-M35*) paragroup chromosomes are now marked by defining mutations, thus increasing the discriminative power of the haplogroup for use in human evolution and forensics.
Highlights
Human Y chromosome haplogroups are defined by unique mutations within the male specific region of the Y chromosome (MSY)
The lack of recombination in this portion of the genome makes it possible to reconstruct an unequivocal haplogroup phylogenetic tree, which can be related to the geographic distribution of the individual branches of the tree, by an approach known as ‘‘phylogeography’’ [1]
Five mutations (M293, V68, V92, V95 and V100) that had been previously described [3,4,5] but not included in the tree reported by Karafet et al [2], were phylogenetically characterized
Summary
Human Y chromosome haplogroups are defined by unique mutations within the male specific region of the Y chromosome (MSY). The high genealogical resolution of this system, established by recent advances in mutationdetection technology, and the phylogeographic method have together proven highly informative in tracing patterns of human prehistoric colonization and migrations. A parsimonious phylogenetic tree for 20 major haplogroups (AT) representing worldwide Y chromosomal variation was proposed in 2008 [2]. We focused on the structure of haplogroup E1b1. Within haplogroup E, which represents the majority of the Y chromosomes found in Africa, E1b1 is the haplogroup which has the greatest geographic distribution. To gain a better understanding of the structure of this complicated haplogroup, we performed a high resolution analysis by sequencing, on the average, 45.4 kb in each of 13 E1b1 Y chromosomes (Table S1). Incorporating the information obtained from this analysis into the previously reported tree produced an extensively revised phylogeny for the haplogroup E1b1 resulting in 52 distinct haplogroups
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