17-locus additive tree

© 2000 Kenneth K. Kidd, Yale University. All rights reserved.
This figure may be reproduced for classroom use only.

 This tree of 29 populations is an interim partial analysis of data on 17 unlinked loci. Eight of those loci are multiallelic haplotype systems involving 2 to 4 polymorphic sites, seven are biallelic SNPs or indels, and two are VNTRs but with only two common alleles each. Tau genetic distances (Kidd and Cavalli-Sforza, 1974) were calculated and an additive tree fit to those values. Neighbor joining and other methods were used to generate starting tree structures and then minor variants of those topologies were evaluated to see whether better least-squares fits could be obtained. The tree shown is the best found from among several dozen almost equally good trees. The other good trees differed in how populations interconnected within European, East Asian, or American clusters. The basic geographic structure is well supported by the data, the specific relationships of geographically "close" populations is not especially meaningful. On a subset of only 15 independent biallelic markers, one from each of the eight haplotyped loci plus the seven other biallelic loci, a very similar tree results and the population synthesized as fixed for the ancestral alleles at all of the 15 loci (based on testing chimpanzees, gorillas, bonobos, and sometimes orangutans) connects to that tree very close to the Mbuti pygmies, placing the root among the African populations.

Principal Components Analysis on 17-Independent Loci