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.
processed_reads1
File 1/13 containing processed reads after running process radtags. Contains separate .fq files for each sample.
processed_reads2
File 2/13 containing processed reads after running process radtags. Contains separate .fq files for each sample.
processed_reads3
File 3/13 containing processed reads after running process radtags. Contains separate .fq files for each sample.
processed_reads4
File 4/13 containing processed reads after running process radtags. Contains separate .fq files for each sample.
processed_reads5
File 5/13 containing processed reads after running process radtags. Contains separate .fq files for each sample.
processed_reads6
File 6/13 containing processed reads after running process radtags. Contains separate .fq files for each sample.
processed_reads7
File 7/13 containing processed reads after running process radtags. Contains separate .fq files for each sample.
processed_reads8
File 8/13 containing processed reads after running process radtags. Contains separate .fq files for each sample.
processed_reads9
File 9/13 containing processed reads after running process radtags. Contains separate .fq files for each sample.
processed_reads10
File 10/13 containing processed reads after running process radtags. Contains separate .fq files for each sample.
processed_reads11
File 11/13 containing processed reads after running process radtags. Contains separate .fq files for each sample.
processed_reads12
File 12/13 containing processed reads after running process radtags. Contains separate .fq files for each sample.
processed_reads13
File 13/13 containing processed reads after running process radtags. Contains separate .fq files for each sample.
fullseq.phylip
Sequence alignments in interleaved phylip format used to build phylogeny, including invariant sites.
structure_all_clades
Input 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_cladeD
Input 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_clades
Q 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_cladeD
Q 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_file
Genotype 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_file
SNP 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_dstat
Individual 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.