DOI: 10.5061/dryad.vp634306
title: Data from: Phylogenetic signal variation in the genomes of Medicago (Fabaceae)

description: Genome-scale data offer the opportunity to clarify phylogenetic
 relationships that are difficult to resolve with few loci, but they can
 also identify genomic regions with evolutionary history distinct from that
 of the species history. We collected whole-genome sequence data from 29
 taxa in the legume genus Medicago, then aligned these sequences to the M.
 truncatula reference genome to confidently identify 87,596 variable
 homologous sites. We used this data set to estimate phylogenetic
 relationships among Medicago species, to investigate the number of sites
 needed to provide robust phylogenetic estimates, and to identify specific
 genomic regions supporting topologies in conflict with the genome-wide
 phylogeny. Our full genomic data set resolves relationships within the
 genus that were previously intractable. Sub-sampling the data reveals
 considerable variation in phylogenetic signal and power in smaller subsets
 of the data. Even when sampling 5,000 sites, no random sample of the data
 supports a topology identical to that of the genome-wide phylogeny.
 Phylogenetic relationships estimated from 500-site sliding windows
 revealed genome regions supporting several alternative species
 relationships among recently-diverged taxa, consistent with the expected
 effects of deep coalescence or introgression in the recent history of
 Medicago.
description: chloroplastConcatenated alignment of single-nucleotide variants from the chloroplast in 29 taxa of genus Medicago (Fabaceae), collected by whole-genome resequencing and alignment to the M. truncatula reference genome.chl_29_ab.phychromosome 1Concatenated alignment of single-nucleotide variants from chromosome 1 in 29 taxa of genus Medicago (Fabaceae), collected by whole-genome resequencing and alignment to the M. truncatula reference genome.chr1_29_ab.phychromosome 2Concatenated alignment of single-nucleotide variants from chromosome 2 in 29 taxa of genus Medicago (Fabaceae), collected by whole-genome resequencing and alignment to the M. truncatula reference genome.chr2_29_ab.phychromosome 3Concatenated alignment of single-nucleotide variants from chromosome 3 in 29 taxa of genus Medicago (Fabaceae), collected by whole-genome resequencing and alignment to the M. truncatula reference genome.chr3_29_ab.phychromosome 4Concatenated alignment of single-nucleotide variants from chromosome 4 in 29 taxa of genus Medicago (Fabaceae), collected by whole-genome resequencing and alignment to the M. truncatula reference genome.chr4_29_ab.phychromosome 5Concatenated alignment of single-nucleotide variants from chromosome 5 in 29 taxa of genus Medicago (Fabaceae), collected by whole-genome resequencing and alignment to the M. truncatula reference genome.chr5_29_ab.phychromosome 6Concatenated alignment of single-nucleotide variants from chromosome 6 in 29 taxa of genus Medicago (Fabaceae), collected by whole-genome resequencing and alignment to the M. truncatula reference genome.chr6_29_ab.phychromosome 7Concatenated alignment of single-nucleotide variants from chromosome 7 in 29 taxa of genus Medicago (Fabaceae), collected by whole-genome resequencing and alignment to the M. truncatula reference genome.chr7_29_ab.phychromosome 8Concatenated alignment of single-nucleotide variants from chromosome 8 in 29 taxa of genus Medicago (Fabaceae), collected by whole-genome resequencing and alignment to the M. truncatula reference genome.chr8_29_ab.phyFigure S01The posterior consensus topology estimated from the concatenated nuclear genomic dataset in our Bayesian analysis (left) compared to a maximum parsimony topology estimated from the same data set (right). On both trees, support for nodes (posterior support for the Bayesian consensus, bootstrap support from 500 replicates for the MP tree) is indicated: black filled circles, ≥ 0.95; gray, between 0.95 and 0.75; white, &lt; 0.75. On the right-hand tree, arrows indicate nodes in conflict with the Bayesian consensus. Scale bar indicates branch length in expected substitutions per site.figS01-MB-PA_comp.pdfFigure S02Phylogenetic estimates from sites on each of the chromosomes and the chloroplast. Each tree is the Bayesian consensus tree estimated for the concatenated variable sites on each chromosome and the chloroplast, with posterior support indicated at each node: black filled circles, ≥ 0.95; gray, between 0.95 and 0.75; white, &lt; 0.75. Scale bars indicate branch length in expected substitutions per site.figS02-chromtrees_MBcon_r02.pdfFigure S03Genomic location of sliding windows with strong (≥ 0.95) posterior support for the four topological rearrangements most commonly given strong support by individual sliding windows. Filled circles indicate the weighted conflict score for the consensus tree estimated from a given sliding window of 500 consecutive sites; red circles indicate windows whose consensus topology strongly supports the given rearrangement.figS03-recurrent_conflict4_r04.pdf