January 07, 2011

Major new paper on haplogroup E1b1 (E-P2)

They sequenced ~45kb in 13 E1b1 chromosomes, producing an updated phylogeny of the -haplogroup (left).

As you can see, increased phylogenetic inference comes at the cost of increasingly long-winded haplogroup designations; hopefully I'll manage to familiarize myself with the new terminology soon enough, and update this post with my comments.


From the paper:
Haplogroup E1b1 now contains two basal branches, E-V38 (E1b1a) and E-M215 (E1b1b), with V38/V100 joining the two previously separated lineages E-M2 (former E1b1a) and E-M329 (former E1b1c). Each of these two lineages has a peculiar geographic distribution. E-M2 is the most common haplogroup in sub-Saharan Africa, with frequency peaks in western (about 80%) and central Africa (about 60%). The same haplogroup is also present in North Africa, although at a lower frequency (usually below 10%) [9]–[11]. Haplogroup E-M329, on the other hand, was observed almost exclusively in eastern Africa [10], [12 and R.S. unpublished data], where E-M2 is virtually absent. The second basal branch of E1b1, E-M215, has a broad geographic distribution from southern Europe to northern and eastern Africa where it has been proposed to have originated [8]. The new topology here reported has important implications as to the origins of the haplogroup E1b1. Using the principle of the phylogeographic parsimony, the resolution of the E1b1b trifurcation in favor of a common ancestor of E-M2 and E-M329 strongly supports the hypothesis that haplogroup E1b1 originated in eastern Africa, as previously suggested [10], and that chromosomes E-M2, so frequently observed in sub-Saharan Africa, trace their descent to a common ancestor present in eastern Africa.
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) [6], [8], [10], [13]–[16] 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 [14], 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.

PLoS ONE 6(1): e16073. doi:10.1371/journal.pone.0016073

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

Beniamino Trombetta et al.

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.



  1. Are they saying that E1 originated in East Africa and likely spread from there to North Africa and from North Africa to Europe?

    Do they estimate any dates?

  2. This paper demonstrates many things:
    1) Hg. E in Europe may be very ancient
    2) Sardinia an Corsica are some of the most conservative regions of Europe
    3) The migration from Africa may have been by sea and not across Middle East
    4) If so, also the migration of R1b1a (V88+) to Africa may have been by sea from South Europe and not from Asia across Middle East
    5) Lacking the paragroups E1b1*, E1b1a* and E1b1b* it isn’t yet said that hg. E was born in Africa
    6) I found and put on Ysearch some very differentiated hg. E from the most conservative regions of the Apennine (Italy) and I invite Cruciani et alii to test them

  3. Readers aware of the fact that this is basically the "Cruciani et al" team of authors, whose articles have tended to work away at the same sample set of many years, may be interested to see the E-M35 project's wiki, where we try to keep tabs on all the results for these samples:- http://www.haplozone.net/wiki/index.php?title=Cruciani_data

  4. I was looking it up and E/ DE separated from R/I/J etc about 65,000 years ago, which is about double since the East Asian NO separated. E and R/I etc. last had common ancestry from which about 90% of male lines today are descended.

    Some say that E came to Europe about 8000 years ago and expanded from the Balkans about 5000 years ago.

  5. Hello Dinenekes...

    I don't know if you remember me, I am Vitor...I don't know if you remember from some forums about this issues...

    I made the national geographic test, And even they cannot put me in an haplogroup...so they had to make the SNP to be sure...
    I will have to test it again with some other more accurate dna test...

    btw I am greek, not portuguese from your anthoprometric calculator...

    On my work not even the german mask XLL adapt to my elongated face and nose...


    Vitor from Portugal


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