DOI: 10.5061/dryad.kh7sc
title: Data from: Unexpected ancestry of Populus seedlings from a hybrid zone implies a large role for postzygotic selection in the maintenance of species

description: In the context of potential interspecific gene flow, the integrity of
 species will be maintained by reproductive barriers that reduce genetic
 exchange, including traits associated with prezygotic isolation or poor
 performance of hybrids. Hybrid zones can be used to study the importance
 of different reproductive barriers, particularly when both parental
 species and hybrids occur in close spatial proximity. We investigated the
 importance of barriers to gene flow that act early versus late in the life
 cycle of European Populus by quantifying the prevalence of homospecific
 and hybrid matings within a mosaic hybrid zone. We obtained genotypic data
 for 11,976 loci from progeny and their maternal parents and constructed a
 Bayesian model to estimate individual admixture proportions and hybrid
 classes for sampled trees, and for the unsampled pollen parent. Matings
 that included one or two hybrid parents were common, resulting in
 admixture proportions of progeny that spanned the whole range of potential
 ancestries between the two parental species. This result contrasts
 strongly with the distribution of admixture proportions in adult trees,
 where intermediate hybrids and each of the parental species are separated
 into three discrete ancestry clusters. The existence of the full range of
 hybrids in seedlings is consistent with weak reproductive isolation early
 in the life cycle of Populus. Instead, a considerable amount of selection
 must take place between the seedling stage and maturity to remove many
 hybrid seedlings. Our results highlight that high hybridization rates and
 appreciable hybrid fitness do not necessarily conflict with the
 maintenance of species integrity.
description: Sample
 IDsIndividual IDs for 621
 samples; columns give individual number; species (P. alba (AL), hybrid
 (HY), P. tremula (TR), or family sample (FA)); mom or progeny (MO, PR,
 NA); family ID; individual ID.IDs.txtGenotype likelihoods, 32 912 SNPsGenotype likelihoods in vcf file format for the full data set including all 621 individuals.variants.vcfGenotype likelihoods, 64 649 SNPsGenotype likelihoods in vcf file format for the reduced data set without seedlings, 137 individuals.variants_ref.vcfInput file, 11 979 SNPsFormatted input file to run ancestry model.input_maf05anc.txtInput file, 5 226 SNPsFormatted input file to run ancestry model.input_maf05ancred.txtAdditional input file, 11 979 SNPsInitial q values to run ancestry model.ldak2_pcg_maf05.txtAdditional input file, 5 226 SNPsInitial q values to run ancestry model.ldak2_pcg_maf05red.txtC source code, main fileC source code for genetic ancestry model.main.CC source code, functionsC source code for genetic ancestry model.func.CC source code, headerC source code for genetic ancestry model.populusancestry.hR simulation code, main filesimulations.RR simulation code, functionssimulations_func.RR simulation code, parametersparams.txtR simulation code, additional script 1Additional Perl script to obtain point estimates for genotype likelihoods.gl2genestsims.plR simulation code, additional script 2R script to obtain starting values for q to run ancestry model.initqsims.R