Update 20/05/2015: Large-scale recent expansion of European patrilineages
I wonder what the hardcore Y-DNA genetic genealogists will say about this effort? I know that many of those guys have been working with full Y-chromosome sequences for a while now. It's open access with lots of supplementary info.
Abstract: Many studies of human populations have used the male-specific region of the Y chromosome (MSY) as a marker, but MSY sequence variants have traditionally been subject to ascertainment bias. Also, dating of haplogroups has relied on Y-specific short tandem repeats (STRs), involving problems of mutation rate choice, and possible long-term mutation saturation. Next-generation sequencing can ascertain single nucleotide polymorphisms (SNPs) in an unbiased way, leading to phylogenies in which branch-lengths are proportional to time, and allowing the times-to-most-recent-common-ancestor (TMRCAs) of nodes to be estimated directly. Here we describe the sequencing of 3.7 Mb of MSY in each of 448 human males at a mean coverage of 51x, yielding 13,261 high-confidence SNPs, 65.9% of which are previously unreported. The resulting phylogeny covers the majority of the known clades, provides date estimates of nodes, and constitutes a robust evolutionary framework for analysing the history of other classes of mutation. Different clades within the tree show subtle but significant differences in branch lengths to the root. We also apply a set of 23 Y-STRs to the same samples, allowing SNP- and STR-based diversity and TMRCA estimates to be systematically compared. Ongoing purifying selection is suggested by our analysis of the phylogenetic distribution of non-synonymous variants in 15 MSY single-copy genes.
Here are a couple of interesting quotes. You can see the samples they're talking about on the tree below. As per the second paragraph, it seems there's a paper about to be published at Nature Communications on European Y-chromosome haplogroups based on some heavy resequencing data (see Batini et al. in the references list). Can't wait for that.
(viii) Rare deep-rooting hg Q lineages in NW Europe: Hg Q has been most widely investigated in terms of the peopling of the Americas from NE Asia (Karafet et al. 1999). Here, as well as an example of the common native American Q-M3 lineage, we included examples of rare European hg Q chromosomes. One of the English chromosomes belongs to the deepest-rooting lineage within Q (Q-M378) and may reflect the Jewish diaspora (Hammer et al. 2009); the other is distantly related, shares a deep node with the Mexican Q-M3 chromosome, and has an STR-haplotype closely related to those of scarce Scandinavian hg Q chromosomes (unpublished data).
(ix) Structure within the west Eurasian hg R: The TMRCA of hg R is 19 KYA, and within it both hgs R1a and R1b comprise young, star-like expansions discussed extensively elsewhere (Batini et al. submitted). The addition of Central Asian chromosomes here contributes a sequence to the deepest subclade of R1b-M269, while another, in a Bhutanese individual, forms an outgroup almost as old as the R1a/R1b split.
Hallast et al., The Y-chromosome tree bursts into leaf: 13,000 high-confidence SNPs covering the majority of known clades, Molecular Biology & Evolution, published online December 2, 2014, doi: 10.1093/molbev/msu327