R1b1 Neighbor-Net

I have used SplitsTree4, an excellent piece of phylogenetic software that I regret not learning earlier, to produce a phylogenetic network using the Neighbor-Net method.

I'll try not to bore you with the nitty-gritty, but Neighbor-Net is a type of distance based phylogenetic network. I think of it a as a hybrid between the median-joining networks produced by Fluxus and the Neighbor-Joining trees produced by programs like Phylip. I encourage you, if you don't mind the tecnical details, to read the paper by Bryant and Moulton presenting Neighbor-Net.

Unlike a phylogenetic tree, which shows the most likely or most parsimonious tree, a network shows many (or all) feasible trees in one 2D representation. In effect, it allows us visually represent the ambiguity we have about which of the feasible trees is the the true tree.

In this case, the input was pairwise distance matrix constructed (using Dean McGee's Y-Utility) from STR haplotypes at Ysearch and the R1b1b Haplogroup Project. It shows the relationship of a representative sample of the known sublcades of R1b1 (R1b1b in blue and R1b1c in red) to the other clusters of R1b1* for which no SNPs downstream of P25 have yet been identified.

Each of sublcade and/or cluster can be seen to "radiate" out from the center of the network. Each node is labeled with a ysearch ID (except the R1b1b folks, which are labeled with FTDNA kit numbers). I don't want to overstate any conclusions, but generally speaking the longer the "neck" is for each cluster the more time passed between its split from the group and the era in which the MRCA for that subclade/cluster lived.