DOI: 10.5061/dryad.nh4366s
title: Data from: Subsampling reveals that unbalanced sampling affects STRUCTURE results in a multi-species dataset

description: Studying the genetic population structure of species can reveal important
 insights into several key evolutionary, historical, demographic, and
 anthropogenic processes. One of the most important statistical tools for
 inferring genetic clusters is the program STRUCTURE. Recently, several
 papers have pointed out that STRUCTURE may show a bias when the sampling
 design is unbalanced, resulting in spurious joining of underrepresented
 populations and spurious separation of overrepresented populations.
 Suggestions to overcome this bias include subsampling and changing the
 ancestry model, but the performance of these two methods has not yet been
 tested on actual data. Here, I use a dataset of twelve high-alpine plant
 species to test whether unbalanced sampling affects the STRUCTURE
 inference of population differentiation between the European Alps and the
 Carpathians. For four of the twelve species, subsampling of the Alpine
 populations –to match the sample size between the Alps and the
 Carpathians– resulted in a drastically different clustering than the full
 dataset. On the other hand, STRUCTURE results with the alternative
 ancestry model were indistinguishable from the results with the default
 model. Based on these results, the subsampling strategy seems a more
 viable approach to overcome the bias than the alternative ancestry model.
 However, subsampling is only possible when there is an a priori
 expectation of what constitute the main clusters. Though these results do
 not mean that the use of STRUCTURE should be discarded, it does indicate
 that users of the software should be cautious about the interpretation of
 the results when sampling is unbalanced.
description: dataThis folder contains for
 every species the data for the AFLP markers. These are formatted in plain
 text files with each AFLP marker represented by a single column. A zero
 (0)represents absence of an marker band and a one (1) represents presence
 of a marker band. Preceding the AFLP data are four columns with metadata:
 1) individual: The name of the individual consisting of a three-digit code
 indicating the cell on the IntraBioDiv grid where the individual was
 sampled, followed by a hyphen and an index number. 2) usable: A Boolean
 (t/f) indicating whether the data is of sufficient quality to make the
 individual usable 3) longitude: the x-coordinate of the sampling location
 in decimal degrees 4) latitude: the y-coordinate of the sampling location
 in decimal degreesR scripts used for
 parsing resultsThis folder contains
 several scripts to read the results of the Structure analyses and all
 replicate subsampling and produce plots. Note that the working directory
 for R should be set to the folder "Results with default
 parameters".R scripts used for
 subsampling and structureThis folder contains for
 each species the script that reads the datafile, writes it in Structure
 format and also creates 500 Structure files where the populations of the
 Alps have been subsampled to match the number of populations from the
 Carpathians. For each file it then proceeds to run a Structure analysis
 with ten replicate runs per datafile (the mainparams and extraparams files
 required by Structure are also included). The script also reads all the
 output produced by Structure and parses it. Note that this script requires
 the Structure executable in order to run correctly. Also the script takes
 an inordinate amount of time to finish.Results with alternative
 ancestry modelThis folder contains for
 every species the results of a Structure analysis on the full dataset (so
 no subsampling) using the alternative ancestry model suggested by Wang
 (2017). The results are distributed over three folders, depending on the
 value used for the initial alpha setting of Structure: Alpha=0.3,
 Alpha=0.5 and Alpha=1.0. For Alpha=0.3 and Alpha=1.0 only the results for
 k=2 clusters are shown; for Alpha=0.5 results are shown for values of K
 ranging from 1 to 11. In all cases, ten replicate runs were performed per
 value of K.Results Arabis
 alpinaThis folder contains for
 this species the full and subsampled input files for Structure plus the
 results of the Structure analyses on the full and 500 subsampled datasets
 (in total 15,618 files per species). The full dataset and the first 100
 subsampled datasets have been run for values of K from 1 to 11. The other
 400 subsampled datasets have been run only for K=2. In all cases, ten
 replicate runs were performed per value of K. -The Structure input files
 are named "infileStructure_", followed by the three-letter
 species abbreviation and an index number from 1 to 501 (e.g.
 "infileStructure_Hun_465.txt"). The file with index number 1
 contains the full dataset; the files with indexes 2 to 501 contain
 subsampled datasets where the number of population in the Alps matched
 that in the Carpathians. -The Structure output files are named:
 "structOut_", followed by the three-letter species abbreviation,
 the number of clusters, the replicate structure run for this value of k,
 and the index number of the inputfile from 1 to 501 (e.g.
 "structOut_Hun_k2_rep4_orep465_f"). -In addition, this folder
 contains some plots and files with parsed output, plus the mainparams and
 extraparams files used by Structure.Structure_Aal.zipResults Carex sempervirenssee previous description for detailsStructure_Cse.zipResults Dryas octopetalaSee above for detailsStructure_Doc.zipResults Geum montanumSee above for detailsStructure_Gmo.zipResults Geum reptansSee above for detailsStructure_Gre.zipResults Hedysarum hedysaroidesSee above for detailsStructure_Hhe.zipResults Hypochaeris unifloraSee above for detailsStructure_Hun.zipResults Juncus trifidusSee above for detailsStructure_Jtr.zipResults Luzula alpinopilosaSee above for detailsStructure_Lal.zipResults Loiseleuria procumbensSee above for detailsStructure_Lpr.zipResults Sesleria caeruleaSee above for detailsStructure_Sco.zipResults Saxifraga stellarisSee above for detailsStructure_Sst.zip