Toward a new history and geography of human genes informed by ancient DNA

Abstract

Genetic information contains a record of the history of our species, and technological advances have transformed our ability to access this record. Many studies have used genome-wide data from populations today to learn about the peopling of the globe and subsequent adaptation to local conditions. Implicit in this research is the assumption that the geographic locations of people today are informative about the geographic locations of their ancestors in the distant past. However, it is now clear that long-range migration, admixture and population replacement subsequent to the initial out-of-Africa expansion have altered the genetic structure of most of the world’s human populations. In light of this, we argue that it is time to critically re-evaluate current models of the peopling of the globe, as well as the importance of natural selection in determining the geographic distribution of phenotypes. We specifically highlight the transformative potential of ancient DNA. By accessing the genetic make-up of populations living at archaeologically-known times and places, ancient DNA makes it possible to directly track migrations and responses to natural selection.

A Spatial Framework for Understanding Population Structure and Admixture.

“…Geogenetic distances between samples within Africa are much greater than those between any other group (see S24 Fig), and the slope of the relationship between geographic and geogenetic distances between populations on each continent decays with distance from Africa. This pattern is consistent with a history of human colonization events characterized by serial bottlenecks [61][62][63] following an out-of-Africa expansion, and subsequent expansions into Western Eurasia, East Asia, the Americas, and Oceania (although see Pickrell and Reich [64] for a discussion of other models).…”

On the origin of mongrels: evolutionary history of free-breeding dogs in Eurasia

“…However, genetic clines may also result from alternative scenarios involving extensive post-colonization admixture [40]. Our TREEMIX analysis revealed a number of admixture events among different FBD populations, which could have contributed to the contrasting diversity patterns between mtDNA and nuclear DNA, especially if admixture was sex-biased.…”

Admixture, Population Structure, and F-Statistics

“…OR humans, whole-genome genotype data are now available for individuals from hundreds of populations (Lazaridis et al 2014;Yunusbayev et al 2015), opening up the possibility to ask more detailed and complex questions about our history (Pickrell and Reich 2014;Schraiber and Akey 2015) and stimulating the development of new tools for the analysis of the joint history of these populations (Reich et al 2009;Patterson et al 2012;Pickrell and Pritchard 2012;Lipson et al 2013;Ralph and Coop 2013;Hellenthal et al A simple and intuitive approach that has quickly gained in popularity are the F-statistics, introduced by Reich et al (2009) and summarized in Patterson et al (2012). In that framework, inference is based on "shared genetic drift" between sets of populations, under the premise that shared drift implies a shared evolutionary history.…”