Data from: Phylogenetic signal variation in the genomes of Medicago (Fabaceae)

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.