How Much R1b?

One of the outstanding questions from the halplogroup frequency estimation I did yesterday concerns the frequency of R1b.

Today I revisited the estimate, using the data from the Giacomo paper and a table of regional populations.

Now there are couple of limitations to this analysis. First, Giacomo didn't specifically measure R1b: he reports P*(x R1a). P is the parent of haplogroups Q and R, and so P is actually measuring the frequency of "true" P, Q, R1b, and R2. Undifferentiated P is fairly rare in Europe, but it exists in small amounts along with Q (except Q3, which is largely associated with Native American populations) and R2. Thus, the reported frequency of P*(xR1a) actually overstates the frequency of R1b by a little bit.

The second problem is that Giacomo did not report all other haplogroups, though I think he got all the major ones. Still, this will also cause the R1b proxy to skew a little high.

Anyway, using his data I estimated the P*(xR1a) frequency for each region and then took a weighted average using the regional population as the weight. I got a weighted frequency of about 45%, which means that (given the caveats above) I think the frequency of R1b in Italy is maybe 40-42%, or not far off the estimate I made yesterday.

Haplogroup L

One of the project's members is a confirmed member of Y-Haplogroup L, which is fairly uncommon in Italy and is most often associated with the Indian subcontinent.

Our member has collected some interesting information about his haplogroup. Worth a read.

Haplogroups of Italy

Using a variety of sources (cited below), I have compiled an estimate of Y-DNA haplogroup frequencies in Italy. Because the sources examined different haplogroups (often with a variety of nomenclature systems) in different geographies within Italy, some extrapolation and adjustments were necessary.

Still, I think having these estimates compiled in one location will be useful to the participants in the Italy DNA Project. For reference, I have compiled the observed frequency of each haplogroup for our project's current participants.

Haplogroup	Estimated Frequency of Haplogroups in Italian Population	Calculated Frequency of Haplogroups in Italy DNA Project
E3b1	12%	14.5%
E3b3	3%	0%
G2	6%	7.5%
I1a	2%	5.0%
I1b	1%	12.0%
I1c	2%	0%
J1	2%	2.5%
J2	25%	31.5%
K	3%	0%
L	1%	2.5%
Q3	1%	0%
R1a1	2%	2.5%
R1b	40%	22.0%

F. Cruciani et al., "Phylogeographic Analysis of Haplogroup E3b (E-M215) Y Chromosomes Reveals Multiple Migratory Events Within and Out Of Africa", American Journal of Human Genetics, 74(5): 1014-1022.

F. Di Giacomo et al., "Clinal patterns of human Y chromosomal diversity in continental Italy and Greece are dominated by drift and founder effects." Molecular Phylogenetics and Evolution, 28(3): 387-395.

M. Pericic et al., "High-resolution phylogenetic analysis of southeastern Europe traces major episodes of paternal gene flow among Slavic populations", Molecular Biology and Evolution, 2005 Oct;22(10):1964-75.

S. Rootsi et al., "Phylogeography of Y-chromosome haplogroup I reveals distinct domains of prehistoric gene flow in europe", American Journal of Human Genetics 75(1): 128-37.

Z. Rosser et al., "Y-Chromosomal Diversity in Europe Is Clinal and Influenced Primarily by Geography, Rather than by Language", American Journal of Human Genetics, 67(6): 1526-1543.

O. Semino et al., "The genetic legacy of Paleolithic Homo sapiens sapiens in extant Europeans: a Y chromosome perspective", Science, 290(5494): 1155-1159.

O. Semino et al., "Origin, Diffusion, and Differentiation of Y-Chromosome Haplogroups E and J: Inferences on the Neolithization of Europe and Later Migratory Events in the Mediterranean Area", American Journal of Human Genetics, 74(5): 1023-0134.