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

Puechmaille SJ

Date Published: January 19, 2016

DOI: http://dx.doi.org/10.5061/dryad.2d4m9

 

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Title Model 1 datasets (island model), full datasets
Downloaded 29 times
Description This 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.
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Title Model 1 datasets (island model), sampling strategy No. 1
Downloaded 18 times
Description This 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.
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Title Model 1 datasets (island model), sampling strategy No. 2.1
Downloaded 21 times
Description This 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.
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Title Model 1 datasets (island model), sampling strategy No. 2.2
Downloaded 18 times
Description This 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.
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Title Model 1 datasets (island model), sampling strategy No. 3
Downloaded 17 times
Description This 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.
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Title Model 1 datasets (island model), sampling strategy No. 4
Downloaded 14 times
Description This 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.
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Title Model 2 datasets (hierarchical island model), full datasets
Downloaded 21 times
Description This 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.
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Title Model 2 datasets (hierarchical island model), sampling strategy No. 1
Downloaded 16 times
Description This 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.
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Title Model 2 datasets (hierarchical island model), sampling strategy No. 2.1
Downloaded 13 times
Description This 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.
Download M2_SS2-1.zip (2.508 Mb)
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Title Model 2 datasets (hierarchical island model), sampling strategy No. 2.2
Downloaded 14 times
Description This 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.
Download M2_SS2-2.zip (1.273 Mb)
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Title Model 2 datasets (hierarchical island model), sampling strategy No. 3
Downloaded 13 times
Description This 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.
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Title Model 2 datasets (hierarchical island model), sampling strategy No. 4
Downloaded 18 times
Description This 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.
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Title Model 3 datasets (hierarchical stepping stone model), full datasets
Downloaded 16 times
Description This 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.
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Title Model 3 datasets (hierarchical stepping stone model), sampling strategy No. 1
Downloaded 13 times
Description This 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.
Download M3_SS1.zip (2.225 Mb)
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Title Model 3 datasets (hierarchical stepping stone model), sampling strategy No. 2.1
Downloaded 16 times
Description This 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.
Download M3_SS2-1.zip (2.225 Mb)
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Title Model 3 datasets (hierarchical stepping stone model), sampling strategy No. 2.2
Downloaded 22 times
Description This 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.
Download M3_SS2-2.zip (2.225 Mb)
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Title Model 3 datasets (hierarchical stepping stone model), sampling strategy No. 3
Downloaded 15 times
Description This 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.
Download M3_SS3.zip (2.225 Mb)
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Title Model 3 datasets (hierarchical stepping stone model), sampling strategy No. 4
Downloaded 15 times
Description This 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.
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Title Model 4 datasets (island model), full datasets
Downloaded 15 times
Description This 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.
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Title Model 4 datasets (island model), sampling strategy No. 1
Downloaded 15 times
Description This 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.
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Title Model 5 datasets (hierarchical island model), full datasets
Downloaded 15 times
Description This 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.
Download M5.zip (2.593 Mb)
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Title Model 5 datasets (hierarchical island model), sampling strategy No. 1
Downloaded 16 times
Description This 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.
Download M5_SS1.zip (2.596 Mb)
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Title Model 6 datasets (hierarchical stepping stone model), full datasets
Downloaded 12 times
Description This 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.
Download M6.zip (2.369 Mb)
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Title Model 6 datasets (hierarchical stepping stone model), sampling strategy No. 1
Downloaded 20 times
Description This 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.
Download M6_SS1.zip (2.370 Mb)
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When using this data, please cite the original publication:

Puechmaille SJ (2016) The program STRUCTURE does not reliably recover the correct population structure when sampling is uneven: sub-sampling and new estimators alleviate the problem. Molecular Ecology Resources 16(3): 608-627. http://dx.doi.org/10.1111/1755-0998.12512

Additionally, please cite the Dryad data package:

Puechmaille SJ (2016) 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. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.2d4m9
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