Abstract
Over the past two decades numerous new trees of modern human populations have been published extensively but little attention has been paid to formal phylogenetic synthesis. We utilized the “matrix representation with parsimony” (MRP) method to infer a composite phylogeny (supertree) of modern human populations, based on 257 genetic/genomic, as well as linguistic, phylogenetic trees and 44 admixture plots from 200 published studies (1990–2014). The resulting supertree topology includes the most basal position of S African Khoisan followed by C African Pygmies, and the paraphyletic section of all other sub-Saharan peoples. The sub-Saharan African section is basal to the monophyletic clade consisting of the N African–W Eurasian assemblage and the consistently monophyletic Eastern superclade (Sahul–Oceanian, E Asian, and Beringian–American peoples). This topology, dominated by genetic data, is well-resolved and robust to parameter set changes, with a few unstable areas (e.g., West Eurasia, Sahul–Melanesia) reflecting the existing phylogenetic controversies. A few populations were identified as highly unstable “wildcard taxa” (e.g. Andamanese, Malagasy). The linguistic classification fits rather poorly on the supertree topology, supporting a view that direct coevolution between genes and languages is far from universal.
Highlights
Over the past two decades numerous new trees of modern human populations have been published extensively but little attention has been paid to formal phylogenetic synthesis
The resulting supertree topology includes the most basal position of S African Khoisan followed by C African Pygmies, and the paraphyletic section of all other sub-Saharan peoples
No unified picture of modern human evolution based on genetic data is available, as studies that infer human population history have used different types of genetic markers, from “classical polymorphisms” and uniparental markers to genome-wide allele frequency data and data based on whole-genome sequencing[11]
Summary
Over the past two decades numerous new trees of modern human populations have been published extensively but little attention has been paid to formal phylogenetic synthesis. The sub-Saharan African section is basal to the monophyletic clade consisting of the N African–W Eurasian assemblage and the consistently monophyletic Eastern superclade (Sahul–Oceanian, E Asian, and Beringian–American peoples) This topology, dominated by genetic data, is well-resolved and robust to parameter set changes, with a few unstable areas (e.g., West Eurasia, Sahul–Melanesia) reflecting the existing phylogenetic controversies. A large body of comparative data currently exists for a phylogenetic synthesis, integration of all kinds of raw data using a “supermatrix approach” (or “total evidence approach”22) remains unfeasible for the human population, due to the distance-based (instead of character-based) nature of some source data and lack of widely overlapping datasets In light of these problems, a possible strategy is to focus on published www.nature.com/scientificreports/
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