title: Comparing spatial maps of human population-genetic variation using Procrustes analysis.
abstract: Recent applications of principal components analysis (PCA) and multidimensional scaling (MDS) in human population genetics have found that "statistical maps" based on the genotypes in population-genetic samples often resemble geographic maps of the underlying sampling locations. To provide formal tests of these qualitative observations, we describe a Procrustes analysis approach for quantitatively assessing the similarity of population-genetic and geographic maps. We confirm in two scenarios, one using single-nucleotide polymorphism (SNP) data from Europe and one using SNP data worldwide, that a measurably high level of concordance exists between statistical maps of population-genetic variation and geographic maps of sampling locations. Two other examples illustrate the versatility of the Procrustes approach in population-genetic applications, verifying the concordance of SNP analyses using PCA and MDS, and showing that statistical maps of worldwide copy-number variants (CNVs) accord with statistical maps of SNP variation, especially when CNV analysis is limited to samples with the highest-quality data. As statistical maps with PCA and MDS have become increasingly common for use in summarizing population relationships, our examples highlight the potential of Procrustes-based quantitative comparisons for interpreting the results in these maps.
authors.affiliation: University of Michigan, USA. chaolong@umich.edu
authors.forename: Chaolong
authors.initials: C
authors.lastname: Wang
authors.forename: Zachary A
authors.initials: ZA
authors.lastname: Szpiech
authors.forename: James H
authors.initials: JH
authors.lastname: Degnan
authors.forename: Mattias
authors.initials: M
authors.lastname: Jakobsson
authors.forename: Trevor J
authors.initials: TJ
authors.lastname: Pemberton
authors.forename: John A
authors.initials: JA
authors.lastname: Hardy
authors.forename: Andrew B
authors.initials: AB
authors.lastname: Singleton
authors.forename: Noah A
authors.initials: NA
authors.lastname: Rosenberg
mesh_terms: D056808:Biostatistics; D056915:DNA Copy Number Variations; D005060:Europe; D014644:Genetic Variation; D005828:Genetics, Population / Q000706:statistics & numerical data*; D006801:Humans; D008957:Models, Genetic; D015233:Models, Statistical; D015999:Multivariate Analysis; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis