DOI: 10.5061/dryad.2d4m9
title: Data from: The program STRUCTURE does not reliably recover the correct population structure when sampling is uneven: sub-sampling and new estimators alleviate the problem

description: Inferences of population structure and more precisely the identification
 of genetically homogeneous groups of individuals are essential to the
 fields of ecology, evolutionary biology, and conservation biology. Such
 population structure inferences are routinely investigated via the program
 STRUCTURE implementing a Bayesian algorithm to identify groups of
 individuals at Hardy-Weinberg and linkage equilibrium. While the method is
 performing relatively well under various population models with even
 sampling between subpopulations, the robustness of the method to uneven
 sample size between subpopulations and/or hierarchical levels of
 population structure has not yet been tested despite being commonly
 encountered in empirical datasets. In this study, I used simulated and
 empirical microsatellite datasets to investigate the impact of uneven
 sample size between subpopulations and/or hierarchical levels of
 population structure on the detected population structure. The results
 demonstrated that uneven sampling often leads to wrong inferences on
 hierarchical structure and downward biased estimates of the true number of
 subpopulations. Distinct subpopulations with reduced sampling tended to be
 merged together, whilst at the same time, individuals from extensively
 sampled subpopulations were generally split, despite belonging to the same
 panmictic population. Four new supervised methods to detect the number of
 clusters were developed and tested as part of this study and were found to
 outperform the existing methods using both evenly and unevenly sampled
 datasets. Additionally, a sub-sampling strategy aiming to reduce sampling
 unevenness between subpopulations is presented and tested. These results
 altogether demonstrate that when sampling evenness is accounted for, the
 detection of the correct population structure is greatly improved.
description: Model 1 datasets (island
 model), full datasetsThis zipped file
 contains 50 datasets simulated under an island model with 10
 subpopulations and 200 individuals per subpopulation. The files, in Fstat
 format, were created by the EASYPOP program.M1.zipModel 1 datasets (island model), sampling strategy No. 1This zipped file contains 50 datasets simulated under an island model, with 10 subpopulations evenly sampled and a total of 620 individuals (sampling strategy no. 1; cf. Table 1). The files, in Fstat format, were simulated in the EASYPOP program and sampled in R via a custom written script.M1_SS1.zipModel 1 datasets (island model), sampling strategy No. 2.1This zipped file contains 50 datasets simulated under an island model, with 10 subpopulations unevenly sampled and a total of 620 individuals (sampling strategy no. 2; cf. Table 1). The files, in Fstat format, were simulated in the EASYPOP program and sampled in R via a custom written script.M1_SS2-1.zipModel 1 datasets (island model), sampling strategy No. 2.2This zipped file contains 50 datasets simulated under an island model, with 10 subpopulations sampled (20 individuals sampled in eight subpopulations and 10 in the remaining two), and a total of 180 individuals (cf. 'Sub-Sampling' section in M&M). The files, in Fstat format, were simulated in the EASYPOP program and sampled in R via a custom written script.M1_SS2-2.zipModel 1 datasets (island model), sampling strategy No. 3This zipped file contains 50 datasets simulated under an island model, with 6 subpopulations evenly sampled (4 subpopulations not sampled) and a total of 150 individuals (sampling strategy no. 3; cf. Table 1). The files, in Fstat format, were simulated in the EASYPOP program and sampled in R via a custom written script.M1_SS3.zipModel 1 datasets (island model), sampling strategy No. 4This zipped file contains 50 datasets simulated under an island model, with 6 subpopulations unevenly sampled (4 subpopulations not sampled) and a total of 150 individuals (sampling strategy no. 4; cf. Table 1). The files, in Fstat format, were simulated in the EASYPOP program and sampled in R via a custom written script.M1_SS4.zipModel 2 datasets (hierarchical island model), full datasetsThis zipped file contains 50 datasets simulated under a hierarchical island model with 10 subpopulations and 200 individuals per subpopulation. The files, in Fstat format, were created by the EASYPOP program.M2.zipModel 2 datasets (hierarchical island model), sampling strategy No. 1This zipped file contains 50 datasets simulated under a hierarchical island model, with 10 subpopulations evenly sampled and a total of 620 individuals (sampling strategy no. 1; cf. Table 1). The files, in Fstat format, were simulated in the EASYPOP program and sampled in R via a custom written script.M2_SS1.zipModel 2 datasets (hierarchical island model), sampling strategy No. 2.1This zipped file contains 50 datasets simulated under a hierarchical island model, with 10 subpopulations unevenly sampled and a total of 620 individuals (sampling strategy no. 2; cf. Table 1). The files, in Fstat format, were simulated in the EASYPOP program and sampled in R via a custom written script.M2_SS2-1.zipModel 2 datasets (hierarchical island model), sampling strategy No. 2.2This zipped file contains 50 datasets simulated under a hierarchical island model, with 10 subpopulations sampled (20 individuals sampled in eight subpopulations and 10 in the remaining two), and a total of 180 individuals (cf. 'Sub-Sampling' section in M&M). The files, in Fstat format, were simulated in the EASYPOP program and sampled in R via a custom written script.M2_SS2-2.zipModel 2 datasets (hierarchical island model), sampling strategy No. 3This zipped file contains 50 datasets simulated under a hierarchical island model, with 6 subpopulations evenly sampled (4 subpopulations not sampled) and a total of 150 individuals (sampling strategy no. 3; cf. Table 1). The files, in Fstat format, were simulated in the EASYPOP program and sampled in R via a custom written script.M2_SS3.zipModel 2 datasets (hierarchical island model), sampling strategy No. 4This zipped file contains 50 datasets simulated under a hierarchical island model, with 6 subpopulations unevenly sampled (4 subpopulations not sampled) and a total of 150 individuals (sampling strategy no. 4; cf. Table 1). The files, in Fstat format, were simulated in the EASYPOP program and sampled in R via a custom written script.M2_SS4.zipModel 3 datasets (hierarchical stepping stone model), full datasetsThis zipped file contains 50 datasets simulated under a hierarchical stepping stone model with 10 subpopulations and 200 individuals per subpopulation. The files, in Fstat format, were created by the EASYPOP program.M3.zipModel 3 datasets (hierarchical stepping stone model), sampling strategy No. 1This zipped file contains 50 datasets simulated under a hierarchical stepping stone model, with 10 subpopulations evenly sampled and a total of 620 individuals (sampling strategy no. 1; cf. Table 1). The files, in Fstat format, were simulated in the EASYPOP program and sampled in R via a custom written script.M3_SS1.zipModel 3 datasets (hierarchical stepping stone model), sampling strategy No. 2.1This zipped file contains 50 datasets simulated under a hierarchical stepping stone model, with 10 subpopulations unevenly sampled and a total of 620 individuals (sampling strategy no. 2; cf. Table 1). The files, in Fstat format, were simulated in the EASYPOP program and sampled in R via a custom written script.M3_SS2-1.zipModel 3 datasets (hierarchical stepping stone model), sampling strategy No. 2.2This zipped file contains 50 datasets simulated under a hierarchical stepping stone model, with 10 subpopulations sampled (20 individuals sampled in eight subpopulations and 10 in the remaining two), and a total of 180 individuals (cf. 'Sub-Sampling' section in M&M). The files, in Fstat format, were simulated in the EASYPOP program and sampled in R via a custom written script.M3_SS2-2.zipModel 3 datasets (hierarchical stepping stone model), sampling strategy No. 3This zipped file contains 50 datasets simulated under a hierarchical stepping stone model, with 6 subpopulations evenly sampled (4 subpopulations not sampled) and a total of 150 individuals (sampling strategy no. 3; cf. Table 1). The files, in Fstat format, were simulated in the EASYPOP program and sampled in R via a custom written script.M3_SS3.zipModel 3 datasets (hierarchical stepping stone model), sampling strategy No. 4This zipped file contains 50 datasets simulated under a hierarchical stepping stone model, with 6 subpopulations unevenly sampled (4 subpopulations not sampled) and a total of 150 individuals (sampling strategy no. 4; cf. Table 1). The files, in Fstat format, were simulated in the EASYPOP program and sampled in R via a custom written script.M3_SS4.zipModel 4 datasets (island model), full datasetsThis zipped file contains 50 datasets simulated under a hierarchical stepping stone model with 10 subpopulations and 200 individuals per subpopulation. The parameters used to simulate Model 4 were identical to those used for Model 1, except that the migration rate was doubled (set to 0.02) (cf. Table S1 for Fst values). The files, in Fstat format, were created by the EASYPOP program.M4.zipModel 4 datasets (island model), sampling strategy No. 1This zipped file contains 50 datasets simulated under a hierarchical stepping stone model, with 10 subpopulations evenly sampled and a total of 620 individuals (sampling strategy no. 1; cf. Table 1). The parameters used to simulate Model 4 were identical to those used for Model 1, except that the migration rate was doubled (set to 0.02) (cf. Table S1 for Fst values). The files, in Fstat format, were simulated in the EASYPOP program and sampled in R via a custom written script.M4_SS1.zipModel 5 datasets (hierarchical island model), full datasetsThis zipped file contains 50 datasets simulated under a hierarchical stepping stone model with 10 subpopulations and 200 individuals per subpopulation. The parameters used to simulate Model 5 were identical to those used for Model 2, except that the migration rates between subpopulations within and between archipelagos were doubled (set to 0.02 & 0.002 respectively) (cf. Table S1 for Fst values).The files, in Fstat format, were created by the EASYPOP program.M5.zipModel 5 datasets (hierarchical island model), sampling strategy No. 1This zipped file contains 50 datasets simulated under a hierarchical stepping stone model, with 10 subpopulations evenly sampled and a total of 620 individuals (sampling strategy no. 1; cf. Table 1). The parameters used to simulate Model 5 were identical to those used for Model 2, except that the migration rates between subpopulations within and between archipelagos were doubled (set to 0.02 & 0.002 respectively) (cf. Table S1 for Fst values). The files, in Fstat format, were simulated in the EASYPOP program and sampled in R via a custom written script.M5_SS1.zipModel 6 datasets (hierarchical stepping stone model), full datasetsThis zipped file contains 50 datasets simulated under a hierarchical stepping stone model with 10 subpopulations and 200 individuals per subpopulation. The parameters used to simulate Model 6 were identical to those used for Model 3, except that the migration rates between subpopulations on one side versus across the contact zone were doubled (set to 0.02 & 0.002 respectively) (cf. Table S1 for Fst values).The files, in Fstat format, were created by the EASYPOP program.M6.zipModel 6 datasets (hierarchical stepping stone model), sampling strategy No. 1This zipped file contains 50 datasets simulated under a hierarchical stepping stone model, with 10 subpopulations evenly sampled and a total of 620 individuals (sampling strategy no. 1; cf. Table 1). The parameters used to simulate Model 6 were identical to those used for Model 3, except that the migration rates between subpopulations on one side versus across the contact zone were doubled (set to 0.02 & 0.002 respectively) (cf. Table S1 for Fst values). The files, in Fstat format, were simulated in the EASYPOP program and sampled in R via a custom written script.M6_SS1.zip