Phylogenetic signal variation in the genomes of medicago (Fabaceae)

Jeremy B. Yoder, Roman Briskine, Joann Mudge, Andrew Farmer, Timothy Paape, Kelly Steele, George D. Weiblen, Arvind K. Bharti, Peng Zhou, Gregory D. May, Nevin D. Young, Peter Tiffin

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39 Scopus citations

Abstract

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 Medicago 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. Subsampling the data reveals considerable variation in phylogenetic signal and power in smaller subsets of the data. Even when sampling 5000 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.

Original languageEnglish (US)
Pages (from-to)424-438
Number of pages15
JournalSystematic Biology
Volume62
Issue number3
DOIs
StatePublished - May 1 2013

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Keywords

  • Medicago
  • phylogenomics
  • whole-genome resequencing

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

Cite this

Yoder, J. B., Briskine, R., Mudge, J., Farmer, A., Paape, T., Steele, K., Weiblen, G. D., Bharti, A. K., Zhou, P., May, G. D., Young, N. D., & Tiffin, P. (2013). Phylogenetic signal variation in the genomes of medicago (Fabaceae). Systematic Biology, 62(3), 424-438. https://doi.org/10.1093/sysbio/syt009