human_populations_microsat — Human population genetic differentiation (2007)

Description

Weighted network of genetic differentiation among 62 human populations worldwide, from microsatellite genotypes: 43 populations of the HGDP-CEPH Human Genome Diversity Panel studied by N. A. Rosenberg and collaborators, and 19 Native American populations studied by S. Wang and collaborators, in both cases restricted to populations with more than 10 unrelated individuals. The data were compiled by M. Cantor and collaborators for a study of nestedness across levels of biological organization, and are distributed in the repository of that study (file mep_human_Rst.txt). Nodes are populations, and an undirected edge connects every pair of populations (the network is a complete graph), weighted by their pairwise genetic differentiation R_ST (Slatkin, 1995), computed from the variance of microsatellite allele sizes (678 autosomal microsatellite loci). R_ST is 0 for genetically identical populations and grows with differentiation; small negative values arise from sampling error. Note that the documentation of the source describes the weights as the genetic similarity 1 - R_ST, but the file contains R_ST itself (with zeros on the diagonal). The populations are not identified in the source data.

The edges have the property weight, the pairwise R_ST.

Tags

Biological Genetic Weighted

Citation

N. A. Rosenberg, J. K. Pritchard, J. L. Weber, H. M. Cann, K. K. Kidd, L. A. Zhivotovsky, M. W. Feldman, "Genetic Structure of Human Populations." Science 298, 2381-2385 (2002) 10.1126/science.1078311 Sci-Hub
N. A. Rosenberg, S. Mahajan, S. Ramachandran, C. Zhao, J. K. Pritchard, M. W. Feldman, "Clines, Clusters, and the Effect of Study Design on the Inference of Human Population Structure." PLoS Genetics 1(6), e70 (2005) 10.1371/journal.pgen.0010070 Sci-Hub
S. Wang et al., "Genetic Variation and Population Structure in Native Americans." PLoS Genetics 3(11), e185 (2007) 10.1371/journal.pgen.0030185 Sci-Hub
M. Slatkin, "A measure of population subdivision based on microsatellite allele frequencies." Genetics 139(1), 457-462 (1995) 10.1093/genetics/139.1.457 Sci-Hub
M. Cantor, M. M. Pires, F. M. D. Marquitti, R. L. G. Raimundo, E. Sebastián-González, P. P. Coltri, S. I. Perez, D. R. Barneche, D. Y. C. Brandt, K. Nunes, F. G. Daura-Jorge, S. R. Floeter, P. R. Guimarães Jr., "Nestedness across biological scales." PLoS ONE 12(2), e0171691 (2017) 10.1371/journal.pone.0171691 Sci-Hub

Upstream URL OK

https://bitbucket.org/maucantor/unodf_analyses

Networks

Tip: hover over a column header for a description.

Column legend

$\left<k\right>$: Mean degree
$\sigma_k$: Standard deviation of the degrees
$\lambda_h$: Largest eigenvalue of the Hashimoto (non-backtracking) matrix
$\tau$: Random walk mixing time
$r$: Degree assortativity
$c$: Global clustering coefficient
$\oslash$: (Pseudo-) diameter
$S$: Relative size of the largest component
NPs: Node properties
EPs: Edge properties

Name	Nodes	Edges	$\left<k\right>$	$\sigma_k$	$\lambda_h$	$\tau$	$r$	$c$	$\oslash$	$S$	Kind	Mode	NPs	EPs	gt	GraphML	GML	csv
human_populations_microsat	62	1,891	61.00	0.00	60.00	inf	nan	1.00	1	1.00	Undirected	Unipartite		weight	12 KiB	14 KiB	14 KiB	10 KiB