Trombetta et al. (2011)

From Haplowiki

Trombetta et al. (2011)

A New Topology of the Human Y Chromosome Haplogroup E1b1 (E-P2) Revealed through the Use of Newly Characterized Binary Polymorphisms

http://www.plosone.org/article/info:doi/10.1371/journal.pone.0016073

Received: November 17, 2010; Accepted: December 6, 2010; Published: January 6, 2011

Authors

Beniamino Trombetta 1, Fulvio Cruciani 1, Daniele Sellitto 1,2, Rosaria Scozzari 1*

1 Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Rome, Italy, 2 Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Rome, Italy * E-mail: rosaria.scozzari@uniroma1.it

Note: this is the Cruciani et al. team and this article uses many of the same samples as in their previous articles. See:-

• Scozzari et al. (2001)
• Cruciani et al. (2002)
• Cruciani et al. (2004)
• Cruciani et al. (2006)
• Cruciani et al. (2007)
• Cruciani et al. (2008)
• Cruciani data

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.

Notable quotes

Appropriate internal wikilinks have been inserted where the original paper had internal links to footnotes for the same references.

• The V68 mutation was recently reported to be phylogenetically equivalent to M78 in a sample of 239 African chromosomes Cruciani et al. (2008). Here, undifferentiated paragroup E-V68*(xM78) chromosomes were observed in 3 among 9 E-M35* previously reported chromosomes from Europe Cruciani et al. (2004).
• A newly discovered mutation, V257, combined all the E-M81 and a subset (4/9 from Europe, 1/1 Marrakesh Berber and 1/1 Oromo from Kenya) of the E-M35* chromosomes reported by Cruciani et al. Cruciani et al. (2004).
• The V23 mutation was found to mark a new lineage within the E-M34 clade. Two out of 16 E-M34 Y chromosomes which had been previously observed in Africa Cruciani et al. (2004) turned out to carry this mutation.
• The mutation M293 mutation Henn et al. (2008) was shown to be positioned upstream of the P72 marker (Figure 1), which defines the E1b1b1f lineage in the tree by Karafet et al. Karafet et al. (2008). All the sixteen Y chromosomes from southern Africa and 4/19 Y chromosomes from eastern Africa described by Cruciani et al. Cruciani et al. (2004) as belonging to paragroup E-M35* turned out to carry the M293 mutation.
• The E-M35* undifferentiated state of two Jews and one Amhara from Ethiopia previously reported Cruciani et al. (2004) has now been resolved by two mutations (V42 and V92, respectively), that identify two additional clades within the E-M35 haplogroup. *Finally, we have found that M281 does not define a separate sub-lineage within E-M35; rather it is phylogenetically indistinct from the newly discovered V16 mutation and marks all the five E-M215* chromosomes reported by Cruciani et al. Cruciani et al. (2008).

More speculatively:

Within E-M35, there are striking parallels between two haplogroups, E-V68 and E-V257. Both contain a lineage which has been frequently observed in Africa (E-M78 and E-M81, respectively) Underhill et al. (2000), Cruciani et al. (2008), Semino et al. (2004), Bosch et al. (2001), Arredi et al. (2004), Cruciani et al. (2007), Luis et al. (2004) and a group of undifferentiated chromosomes that are mostly found in southern Europe (Table S2). An expansion of E-M35 carriers, possibly from the Middle East as proposed by other Authors Arredi et al. (2004), and split into two branches separated by the geographic barrier of the Mediterranean Sea, would explain this geographic pattern. However, the absence of E-V68* and E-V257* in the Middle East (Table S2) makes a maritime spread between northern Africa and southern Europe a more plausible hypothesis. A detailed analysis of the Y chromosomal microsatellite variation associated with E-V68 and E-V257 could help in gaining a better understanding of the likely timing and place of origin of these two haplogroups.