DOI: 10.5061/dryad.7pj4t
title: Data from: Population genomics of divergence within an obligate pollination mutualism: selection maintains differences between Joshua tree species

description: PREMISE OF THE STUDY: Speciation is a complex process that can be shaped
 by many factors, from geographic isolation to interspecific interactions.
 In Joshua trees, selection from pollinators on style length has been
 hypothesized to contribute to the maintenance of differentiation between
 two hybridizing sister species. We used population genomics approaches to
 measure the extent of genetic differentiation between these species, test
 whether selection maintains differences between them, and determine
 whether genetic variants associated with style length show signatures of
 selection. METHODS: Using restriction-site-associated DNA
 (RAD)-sequencing, we identified 9516 single nucleotide polymorphisms
 (SNPs) across the Joshua tree genome. We characterized the genomic
 composition of trees in a narrow hybrid zone and used genomic scans to
 search for signatures of selection acting on these SNPs. We used a
 genome-wide association study to identify SNPs associated with variation
 in phenotypic traits, including style length, and asked whether those SNPs
 were overrepresented among the group under selection. KEY RESULTS: The two
 species were highly genetically differentiated (FST = 0.25), and hybrids
 were relatively rare in the hybrid zone. Approximately 20% of SNPs showed
 evidence of selection maintaining divergence. While SNPs associated with
 style length were overrepresented among those under selection (P
 &lt;&lt; 0.0001), the same was true for SNPs associated with
 highly differentiated vegetative traits. CONCLUSIONS: The two species of
 Joshua tree are clearly genetically distinct, and selection is maintaining
 differences between them. We found that loci associated with
 differentiated traits were likely to be under selection. However, many
 traits other than style length appeared to be under selection. Together
 with the dearth of intermediate hybrids, these findings reveal that these
 taxa are more strongly diverged than previously suspected and that
 selection, likely on many targets, is maintaining separation where the two
 species meet and hybridize.
description: CompleteSNPdataComplete SNP data from Joshua trees (Yucca brevifolia and Y. jaegeriana), generated by RADseq. Data is in STRUCTURE format. This data set includes SNPs and individuals with large amounts of missing data, excluded from downstream analyses. Text file saved as comma-separated values.AllGentoypes347Trees.csvTrimmedSNPDataRAD-seq data from Joshua trees (Yucca brevifolia and Y. jaegeriana). Data is in STRUCTURE format. This data set has been trimmed to remove SNPs more than 20% missing data and individuals with 30% or more missing data. This dataset was used for all analyses described in Royer et al. Text file saved as comma-separated values.GoodLoci319Trees.csvArlequinInputTrimmed SNP data from Joshua trees (Yucca brevifolia and Y. jaegeriana) formatted for analysis in Arlequin. Text file saved as tab-separated values.StructureInputRandomly selected SNPs from Joshua trees (Yucca brevifolia and Y. jaegeriana) used to classify individuals in STRUCTURE. Text file saved as tab-separated values.batch_1.structure.tsvTasselAllGenotypesSNP data from Joshua trees (Yucca brevifolia and Y. jaegeriana) in TASSEL format used for Genome-Wide Association Study. Text file saved as tab-separated values.PhenotypesPhenotypic data from Joshua trees (Yucca brevifolia and Y. jaegeriana), formatted for analysis in TASSEL. Individual names are in the first column. Trait names (header row) include units in parenthesis. Text file saved as tab-separated values.TasselAllMeasurementsJan8.txtBayesianGenomicClinesBrevifoliaDataAllele counts data from Joshua trees (Yucca brevifolia) for analysis using Bayesian Genomic Clines. Parental population file 1. Saved as plain text.BGC_Brev9430LociBayesianGenomicClinesJaegerianaDataAllele counts data from Joshua trees (Yucca jaegeriana) for analysis using Bayesian Genomic Clines. Parental population file 2. Saved as plain text.BGC_Jaeg9430LociBayesianGenomicClinesHybridZoneDataGenotype data from Joshua trees (Yucca brevifolia and Y. jaegeriana) for analysis using Bayesian Genomic Clines. Hybrid population data. Saved as plain text.BGC_Tika9430LociTreeGPSCoordinatesGPS coordinates for sampled trees in decimal minutes. Text file saved as comma-separated values.TreeCoordinates.csv