The computer program STRUCTURE does not reliably identify the main genetic clusters within species: simulations and implications for human population structure

Corander J, Marttinen P, Siren J, Tang J (2008). Enhanced Bayesian modeling in BAPS software for learning genetic structures of populations. BMC Bioinformatics 9: 539.

Evanno G, Regnaut S, Goudet J (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14: 2611–2620.

Falush D, Stephens M, Pritchard JK (2003). Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567–1587.

Hubisz MJ, Falush D, Stephens M, Pritchard JK (2009). Inferring weak population structure with the assistance of sample group information. Mol Ecol Resources 9: 1322–1332.

Ingman M, Kaessmann H, Paabo S, Gyllensten U (2000). Mitochondrial genome variation and the origin of modern humans. Nature 408: 708–713.

Kalinowski ST (2009). How well do evolutionary trees describe genetic relationships between populations? Heredity 102: 506–513.

King TL, Kalinowski ST, Schill WB, Spidle AP, Lubinski BA (2001). Population structure of Atlantic salmon (Salmo salar L.): a range-wide perspective from microsatellite DNA variation. Mol Ecol 10: 807–821.

Lawson Handley LJ, Manica A, Goudet J, Balloux F (2007). Going the distance: human population genetics in a clinical world. Trends Genet 9: 432–439.

Manica M, Prugnolle F, Balloux F (2005). Geography is a better determinant of human genetic differentiation than ethnicity. Hum Genet 118: 366–371.

Nei M (1978). Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89: 583–590.

Novembre J, Johnson T, Bryc K, Kutalik Z, Boyko AR, Auton A et al. (2008). Genes mirror geography within Europe. Nature 456: 98–103.

Patterson N, Price AL, Reich D (2006). Population structure and eigenanalysis. Plos Genet 2: e190.

Pritchard JK, Stephens M, Donnelly P (2000). Inference of population structure using multilocus genotype data. Genetics 155: 945–959.

Quintana-Murci L, Quach H, Christine Harmant C, Luca F, Massonnet B, Patin E et al. (2008). Maternal traces of deep common ancestry and asymmetric gene flow between Pygmy hunter-gatherers and Bantu-speaking farmers. PNAS 105: 1596–1601.

Rosenberg NA (2004). DISTRUCT: a program for the graphical display of population structure. Mol Ecol Notes 4: 137–138.

Rosenberg NA, Mahajan S, Ramachandran S, Zhao C, Pritchard JK, Feldman MW (2005). Clines, clusters, and the effect of study design on the inference of human population structure. PLOS Genet 1: e70.

Rosenberg NA, Burke T, Elo K, Feldman MW, Freidlin PJ, Groenen MA et al. (2001). Empirical evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds. Genetics 159: 699–713.

Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA et al. (2002). Genetic structure of human populations. Science 298: 2381–2385.

Saitou N, Nei M (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406–425.

Santafé G, Lozano JA, Larraño P (2008). Inference of population structure using genetic markers and a Bayesian model averaging approach for clustering. J Comput Biol 15: 207–220.

Schwartz MK, McKelvey KS (2008). Why sampling scheme matters: the effect of sampling scheme on landscape genetic results. Conservation Genet 10: 441–452.

Tishkoff SA, Reed FA, Friedlaender FR, Ehret C, Ranciaro A, Froment A et al. (2009). The genetic structure and history of Africans and African Americans. Science 324: 1035–1044.

Underhill PA, Kivisild T (2007). Use of y chromosome and mitochondrial DNA population structure in tracing human migrations. Annu Rev Genet 41: 539–564.

Weaver TD, Roseman CC (2008). New developments in the genetic evidence for modern human origins. Evol Anthropol 17: 69–80.

Weir BS, Cockerham CC (1984). Estimating F-statistics for the analysis of population structure. Evolution 38: 1358–1370.

Zhang Y (2008). Tree-guided Bayesian inference of population structures. Bioinformatics 24: 965–971.

Zhivotovsky LA, Rosenberg NA, Feldman MW (2003). Features of evolution and expansion of modern humans, inferred from genome wide microsatellite markers. Am J Hum Genet 72: 1171–1186.