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.
chloroplast
Concatenated 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.phy
chromosome 1
Concatenated 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.phy
chromosome 2
Concatenated 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.phy
chromosome 3
Concatenated 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.phy
chromosome 4
Concatenated 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.phy
chromosome 5
Concatenated 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.phy
chromosome 6
Concatenated 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.phy
chromosome 7
Concatenated 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.phy
chromosome 8
Concatenated 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.phy
Figure S01
The 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, < 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.pdf
Figure S02
Phylogenetic 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, < 0.75. Scale bars indicate branch length in expected substitutions per site.
figS02-chromtrees_MBcon_r02.pdf
Figure S03
Genomic 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
