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Patterns of phylogenetic incongruence in Medicago found among six linkage groups

Artikel i vetenskaplig tidskrift
Författare Filipe de Sousa
Yann Bertrand
Bernard E. Pfeil
Publicerad i Plant Systematics and Evolution
Volym 302
Nummer/häfte 5
Sidor 493-513
ISSN 0378-2697
Publiceringsår 2016
Publicerad vid Institutionen för biologi och miljövetenskap
Sidor 493-513
Språk en
Länkar dx.doi.org/10.1007/s00606-016-1278-...
Ämnesord Coalescent, Hybridisation, Incomplete lineage sorting, Medicago, Phylogeny
Ämneskategorier Botanik, Biologisk systematik, Evolutionsbiologi

Sammanfattning

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.

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