DOI: 10.5061/dryad.5bd62
title: Data from: Genomewide variation provides insight into evolutionary relationships in a monkeyflower species complex (Mimulussect.Diplacus)

description: PREMISE OF THE STUDY: Evolutionary radiations provide excellent
 opportunities to study the origins of biodiversity, but rapid divergence
 and ongoing gene flow make inferring evolutionary relationships among taxa
 difficult. Consequently, multiple tools that combine morphological and
 genomic analyses may be necessary to provide a clear picture of
 relationships. We used an integrative approach to shed light on
 relationships within a diverse radiation of monkeyflowers (Mimulus section
 Diplacus) with a controversial taxonomic history. METHODS: Using
 genome-wide SNP data, we performed a combination of phylogenetic and
 population genomic analyses to infer the evolutionary relationships within
 the group. Tests for hybridization were performed to reveal sources of
 shared variation, and multivariate analyses of floral trait data were
 conducted to examine the relationship between phenotypic and phylogenetic
 information. KEY RESULTS: We identified four primary clades with evidence
 for some shared variation among them. We also detected evidence for recent
 gene flow between closely related subclades and populations. Strong
 discordance between floral trait and molecular data provides evidence for
 divergent and convergent phenotypic evolution. CONCLUSIONS: Mimulus
 section Diplacus exhibits all of the hallmarks of a rapid radiation,
 including diverse taxa that are at different stages of divergence,
 extensive shared variation among taxa, and complex patterns of phenotypic
 evolution. Our findings will direct future evolutionary research and have
 important taxonomic implications, highlighting the need for a new revision
 of section Diplacus.
description: READMEprocessed_reads1File 1/13 containing processed reads after running process radtags. Contains separate .fq files for each sample.processed_reads2File 2/13 containing processed reads after running process radtags. Contains separate .fq files for each sample.processed_reads3File 3/13 containing processed reads after running process radtags. Contains separate .fq files for each sample.processed_reads4File 4/13 containing processed reads after running process radtags. Contains separate .fq files for each sample.processed_reads5File 5/13 containing processed reads after running process radtags. Contains separate .fq files for each sample.processed_reads6File 6/13 containing processed reads after running process radtags. Contains separate .fq files for each sample.processed_reads7File 7/13 containing processed reads after running process radtags. Contains separate .fq files for each sample.processed_reads8File 8/13 containing processed reads after running process radtags. Contains separate .fq files for each sample.processed_reads9File 9/13 containing processed reads after running process radtags. Contains separate .fq files for each sample.processed_reads10File 10/13 containing processed reads after running process radtags. Contains separate .fq files for each sample.processed_reads11File 11/13 containing processed reads after running process radtags. Contains separate .fq files for each sample.processed_reads12File 12/13 containing processed reads after running process radtags. Contains separate .fq files for each sample.processed_reads13File 13/13 containing processed reads after running process radtags. Contains separate .fq files for each sample.fullseq.phylipSequence alignments in interleaved phylip format used to build phylogeny, including invariant sites.structure_all_cladesInput file for Structure including individuals from clades A-D. Column 1 gives the sample names, column 2 is the population ID (set to 1), and the remaining columns give genotypes.structure_cladeDInput file for Structure including individuals from clade D only. Column 1 gives the sample name, column 2 is the population ID and the remaining columns provide genotypes.Qscores_k4_all_cladesQ scores from Structure for K = 4 including individuals from clades A-D. Column 1 gives the sample name and columns 2-5 give the Q scores.Qscores_k3_cladeDQ scores from structure for K = 3 including individuals from clade D only. Column 1 gives the sample name and columns 2-4 give the Q scores.admixtools_geno_fileGenotype information in eigenstrat format for Admixtools. Each column is an individual (order given in .ind file) and each row provides genotype data for a single SNP.admixtools_snp_fileSNP file in eigenstrat format for Admixtools. Column 1 contains SNP ids, column 2 is the chromosome (set to 1), column 3 gives position in cM, column 4 gives position in BP (set to arbitrary values), column 5 gives the reference allele, and column 6 gives the variant allele. Positions are used for jackknife resampling to generate a Z score, however the position of SNPs along the genome is not known.admix_tools_ind_dstatIndividual file in eigenstrat format for Admixtools. Column one gives the individual ID, and the order corresponds to eigenstratgeno file. Column 2 gives gender, set to U. Column 3 gives the population ID, provided for ABBA/BABA test.