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Evolutionary networks from RADseq loci point to hybrid origins of Medicago carstiensis and Medicago cretacea

Artikel i vetenskaplig tidskrift
Författare José Luis Blanco-Pastor
Yann Bertrand
I. M. Liberal
Y. L. Wei
E. C. Brummer
Bernard E. Pfeil
Publicerad i American Journal of Botany
Volym 106
Nummer/häfte 9
Sidor 1219-1228
ISSN 0002-9122
Publiceringsår 2019
Publicerad vid Institutionen för biologi och miljövetenskap
Sidor 1219-1228
Språk en
Länkar dx.doi.org/10.1002/ajb2.1352
Ämnesord alfalfa, assembly, Fabaceae, GBS, gene trees, hybridization, Medicago, multidimensional scaling, bayesian-inference, sequence capture, hybridization, introgression, phylogeny, model, demography, thousands, history, taxa, Plant Sciences
Ämneskategorier Botanik

Sammanfattning

Premise Although hybridization has played an important role in the evolution of many plant species, phylogenetic reconstructions that include hybridizing lineages have been historically constrained by the available models and data. Restriction-site-associated DNA sequencing (RADseq) has been a popular sequencing technique for the reconstruction of hybridization in the next-generation sequencing era. However, the utility of RADseq for the reconstruction of complex evolutionary networks has not been thoroughly investigated. Conflicting phylogenetic relationships in the genus Medicago have been mainly attributed to hybridization, but the specific hybrid origins of taxa have not been yet clarified. Methods We obtained new molecular data from diploid species of Medicago section Medicago using single-digest RADseq to reconstruct evolutionary networks from gene trees, an approach that is computationally tractable with data sets that include several species and complex hybridization patterns. Results Our analyses revealed that assembly filters to exclusively select a small set of loci with high phylogenetic information led to the most-divergent network topologies. Conversely, alternative clustering thresholds or filters on the number of samples per locus had a lower impact on networks. A strong hybridization signal was detected for M. carstiensis and M. cretacea, while signals were less clear for M. rugosa, M. rhodopea, M. suffruticosa, M. marina, M. scutellata, and M. sativa. Conclusions Complex network reconstructions from RADseq gene trees were not robust under variations of the assembly parameters and filters. But when the most-divergent networks were discarded, all remaining analyses consistently supported a hybrid origin for M. carstiensis and M. cretacea.

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