A, Y-chromosomal haplogroup frequencies in the Malagasy and in potential ancestral populations. The maximum parsimony phylogeny relating the 41 Y-chromosomal haplogroups defined in the present study is shown above the absolute frequencies of those lineages in the different populations. The phylogeny is labeled with single-letter clades, and branches are labeled with the markers that define them. The lineage nomenclature is the updated version of that proposed by the YCC (YCC ; Jobling and Tyler-Smith ). The gray shading on the phylogeny indicates the nine sets of markers typed together in multiplexes. B, Pie charts illustrating the relative frequencies of the different haplogroups (colored to agree with the coloring of the phylogeny) shown on a map of the Indian Ocean. The Taiwanese population sample represents individuals pooled from four different aboriginal groups. Samples in these Island Southeast Asian and Pacific populations that were identified elsewhere as representing recent paternal European admixture in published lower-resolution Y-chromosomal marker typing of the same populations (Hurles et al. ) were not typed in the present study. East African data come from Luis et al. ().

A, Phylogeny of mt sequence types found in the Malagasy and their CoGs. The maximum parsimony phylogeny of the 14 maternal lineages defined in the present study builds on the phylogeny constructed by Kivisild et al. (). The tips of the phylogeny are labeled with the number of Malagasy mt genomes found in each lineage. The phylogeny is also labeled with the major clades and the variable sites that define individual branches. The gray shading on the phylogeny indicates the seven coding variants that are typed together in a single multiplex. B, A map of the Old World, showing the positions of the CoGs of the 14 different mt sequence types (blackened circles, triangles, and squares) and the lineage group to which that sequence type belongs. Strictly speaking, mtDNA type “L” encompasses mtDNA types “M” and “N,” which are Eurasian subgroups of “L”; however, for simplicity, “L” here denotes “L” lineages excluding “M” and “N” types. The number within each shape indicates the frequency of that lineage within the data set. For most mt types, it was sufficient to enter only their HVSI sequences. However, to obtain monophyletic hits in the geographic database for two Malagasy HVSI sequence types found in paraphyletic mt lineages, it was also necessary to consider their coding SNP haplotypes, to eliminate spurious matches in geographical regions in which these haplotypes are known to be absent. Full HVSI sequence types are given in .