A Quantitative Comparison of the Similarity between Genes and Geography in Worldwide Human Populations
Chaolong Wang1*, Sebastian Zöllner2, Noah A. Rosenberg3
1 Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America, 2 Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, United States of America, 3 Department of Biology, Stanford University, Stanford, California, United States of America
Abstract
Multivariate statistical techniques such as principal components analysis (PCA) and multidimensional scaling (MDS) have been widely used to summarize the structure of human genetic variation, often in easily visualized two-dimensional maps. Many recent studies have reported similarity between geographic maps of population locations and MDS or PCA maps of genetic variation inferred from single-nucleotide polymorphisms (SNPs). However, this similarity has been evident primarily in a qualitative sense; and, because different multivariate techniques and marker sets have been used in different studies, it has not been possible to formally compare genetic variation datasets in terms of their levels of similarity with geography. In this study, using genome-wide SNP data from 128 populations worldwide, we perform a systematic analysis to quantitatively evaluate the similarity of genes and geography in different geographic regions. For each of a series of regions, we apply a Procrustes analysis approach to find an optimal transformation that maximizes the similarity between PCA maps of genetic variation and geographic maps of population locations. We consider examples in Europe, Sub-Saharan Africa, Asia, East Asia, and Central/South Asia, as well as in a worldwide sample, finding that significant similarity between genes and geography exists in general at different geographic levels. The similarity is highest in our examples for Asia and, once highly distinctive populations have been removed, Sub-Saharan Africa. Our results provide a quantitative assessment of the geographic structure of human genetic variation worldwide, supporting the view that geography plays a strong role in giving rise to human population structure.
Author Summary
The spatial pattern of human genetic variation provides a basis for investigating the history of human migrations. Statistical techniques such as principal components analysis (PCA) and multidimensional scaling (MDS) have been used to summarize spatial patterns of genetic variation, typically by placing individuals on a two-dimensional map in such a way that pairwise Euclidean distances between individuals on the map approximately reflect corresponding genetic relationships. Although similarity between these statistical maps of genetic variation and the geographic maps of sampling locations is often observed, it has not been assessed systematically across different parts of the world. In this study, we combine genome-wide SNP data from more than 100 populations worldwide to perform a formal comparison between genes and geography in different regions. By examining a worldwide sample and samples from Europe, Sub-Saharan Africa, Asia, East Asia, and Central/South Asia, we find that significant similarity between genes and geography exists in general in different geographic regions and at different geographic levels. Surprisingly, the highest similarity is found in Asia, even though the geographic barrier of the Himalaya Mountains has created a discontinuity on the PCA map of genetic variation.
Citation: Wang C, Zöllner S, Rosenberg NA (2012) A Quantitative Comparison of the Similarity between Genes and Geography in Worldwide Human Populations. PLoS Genet 8(8): e1002886. doi:10.1371/journal.pgen.1002886
Editor: Scott M. Williams, Dartmouth College, United States of America
Received: March 2, 2012; Accepted: June 24, 2012; Published: August 23, 2012
Copyright: © 2012 Wang et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This work was supported by National Institutes of Health grants R01 GM081441 and R01 HG005855, by the Burroughs Wellcome Fund, and by a Howard Hughes Medical Institute International Student Research Fellowship. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
* E-mail: chaolong@umich.edu
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