Plant Systematics and Evolution

, Volume 302, Issue 5, pp 493–513 | Cite as

Patterns of phylogenetic incongruence in Medicago found among six loci

  • Filipe de Sousa
  • Yann J. K. Bertrand
  • Bernard E. Pfeil
Original Article


The species phylogeny of Medicago L. (Leguminosae) remains unresolved, as there is significant incongruence between the published gene phylogenies. Here, we compare six of these gene phylogenies of Medicago, inferred from unlinked loci from the nuclear, chloroplast and mitochondrial genomes. Data from all loci were re-analysed, including gap-coding of initial data sets, and dated phylogenies were produced. The patterns of species relationships observed in the six dated phylogenies are compatible with several different biological processes, such as incomplete lineage sorting and hybridisation. A subset of the original sampling that included 29 taxa was also analysed using coalescent-based tree distance comparisons. The observed topological distances suggest that differences between gene phylogenies cannot be solely attributed to incomplete lineage sorting. Hybridisation is strongly suspected to have occurred in the history of many taxa in the genus, because of overlapping divergence times between suspected hybrids and each parental lineage, confirming earlier results based on only two genes. An attempt to reconcile the conflicting histories in a multispecies coalescent analysis, using multiple labels for taxa with hybrid histories, did not produce satisfactory results and may be fatally limited. We conclude that although the currently available data are not sufficient to clarify relationships in Medicago, many cases of hybridisation are probable. The phylogenetic history of the genus is therefore better understood as a network and not a single tree. This raises concerns over previous studies that have used single gene trees as summaries of the history of species relationships.


Coalescent Hybridisation Incomplete lineage sorting Medicago Phylogeny 

Supplementary material

606_2016_1278_MOESM1_ESM.xml (92 kb)
Supplementary material 1Online Resource 1. Accession Table - GenBank accession numbers of sequences used in the study. Multiple accession numbers listed under ETS-ITS are either partial 18S-ITS1-5.8S-ITS2 sequences (numbers prefixed by AY, DQ, or GQ) or ETS, ITS1, ITS2 sequences (prefixed by AJ, AF or Z). Sequences come from the following sources: Bcop, CNGC5 and rps14-cob (Maureira-Butler et al. 2008), GA3ox1 and matK (Steele et al. 2010), ETS-ITS (Bena 2001), ITS only (Campbell, T.A., unpublished GenBank submission; Ellison et al. 2006; Turini et al. 2010). (XML 93 kb)
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Supplementary material 2Online Resource 2. SplitsTree species network obtained from the concatenated dataset of six loci and 29 taxa. (NEX 8 kb)
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Supplementary material 3Online Resource 3-20. Nexus files with sequence and gap data and xml files for Bcop, CNGC5, rps14-cob, GA3ox1, matK and ITS. (NEX 61 kb)
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Supplementary material 4 (XML 108 kb)
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Copyright information

© Springer-Verlag Wien 2016

Authors and Affiliations

  • Filipe de Sousa
    • 1
  • Yann J. K. Bertrand
    • 1
  • Bernard E. Pfeil
    • 1
  1. 1.Department of Biological and Environmental SciencesUniversity of GothenburgGothenburgSweden

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