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Species-Level Phylogeny and Polyploid Relationships in Hordeum (Poaceae) Inferred by Next-Generation Sequencing and In Silico Cloning of Multiple Nuclear Loci.

Brassac J, Blattner FR - Syst. Biol. (2015)

Bottom Line: For diploid taxa, a Bayesian concordance analysis and a coalescent-based dated species tree was inferred from all gene trees.The resulting multilocus phylogeny reveals for the first time species phylogeny and progenitor-derivative relationships of all di- and polyploid Hordeum taxa within a single analysis.Our study proves that it is possible to obtain a multilocus species-level phylogeny for di- and polyploid taxa by combining PCR with next-generation sequencing, without cloning and without creating a heavy load of sequence data.

View Article: PubMed Central - PubMed

Affiliation: Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Germany; brassac@ipk-gatersleben.de.

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Phylogenetic tree derived from the concatenated supermatrix consisting of 13 loci of the diploid Hordeum taxa and six out-group species calculated with Bayesian inference. Posterior probability values of the clades are indicated close to the nodes. Infrageneric treatment of the genus and genome denominations (bold letters along branches) in Hordeum follow Blattner (2009).
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Figure 1: Phylogenetic tree derived from the concatenated supermatrix consisting of 13 loci of the diploid Hordeum taxa and six out-group species calculated with Bayesian inference. Posterior probability values of the clades are indicated close to the nodes. Infrageneric treatment of the genus and genome denominations (bold letters along branches) in Hordeum follow Blattner (2009).

Mentions: The BI of the supermatrix (Fig. 1) produced a completely congruent tree topology with the primary concordance tree (Supplementary Fig. S15). Within Hordeum all clades were highly supported except for H. californicum, which was only moderately supported (0.85 pp). As in the primary concordance tree, H. patagonicum was found paraphyletic with H. pubiflorum nested within the H. patagonicum grade. Within the South American clade, characterized by short internal branches, the nucleotide diversity was too low to resolve all sister relationships. The exclusion of NUC, the locus with the most missing data, from the supermatrix had no effect on the topology of the resulting tree. The consensus tree of 98 MP trees derived from the supermatrix (Supplementary Fig. S16) was very similar to the BI tree. Exceptions included the non-monophyly of H. comosum, placed on a polytomy within the series Critesion, and the paraphyly of H. brevisubulatum, with one individual (PI440419) clustering with low support as sister to the two other Asian species. The inclusion of seven additional nuclear loci and six chloroplast loci (Petersen et al. 2011), although for a data set with only one individual per diploid species, resulted in a highly supported topology (lowest pp 0.94) and confirmed generally the topology obtained with the supermatrix (Supplementary Fig. S17). Hordeumpusillum clustering as sister to the two sister species H. intercedens and H. euclaston, and H. chilense/H. flexuosum forming the sister clade to the one containing H. pusillum were the only species differentially affected in the 26-loci analysis.


Species-Level Phylogeny and Polyploid Relationships in Hordeum (Poaceae) Inferred by Next-Generation Sequencing and In Silico Cloning of Multiple Nuclear Loci.

Brassac J, Blattner FR - Syst. Biol. (2015)

Phylogenetic tree derived from the concatenated supermatrix consisting of 13 loci of the diploid Hordeum taxa and six out-group species calculated with Bayesian inference. Posterior probability values of the clades are indicated close to the nodes. Infrageneric treatment of the genus and genome denominations (bold letters along branches) in Hordeum follow Blattner (2009).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4538882&req=5

Figure 1: Phylogenetic tree derived from the concatenated supermatrix consisting of 13 loci of the diploid Hordeum taxa and six out-group species calculated with Bayesian inference. Posterior probability values of the clades are indicated close to the nodes. Infrageneric treatment of the genus and genome denominations (bold letters along branches) in Hordeum follow Blattner (2009).
Mentions: The BI of the supermatrix (Fig. 1) produced a completely congruent tree topology with the primary concordance tree (Supplementary Fig. S15). Within Hordeum all clades were highly supported except for H. californicum, which was only moderately supported (0.85 pp). As in the primary concordance tree, H. patagonicum was found paraphyletic with H. pubiflorum nested within the H. patagonicum grade. Within the South American clade, characterized by short internal branches, the nucleotide diversity was too low to resolve all sister relationships. The exclusion of NUC, the locus with the most missing data, from the supermatrix had no effect on the topology of the resulting tree. The consensus tree of 98 MP trees derived from the supermatrix (Supplementary Fig. S16) was very similar to the BI tree. Exceptions included the non-monophyly of H. comosum, placed on a polytomy within the series Critesion, and the paraphyly of H. brevisubulatum, with one individual (PI440419) clustering with low support as sister to the two other Asian species. The inclusion of seven additional nuclear loci and six chloroplast loci (Petersen et al. 2011), although for a data set with only one individual per diploid species, resulted in a highly supported topology (lowest pp 0.94) and confirmed generally the topology obtained with the supermatrix (Supplementary Fig. S17). Hordeumpusillum clustering as sister to the two sister species H. intercedens and H. euclaston, and H. chilense/H. flexuosum forming the sister clade to the one containing H. pusillum were the only species differentially affected in the 26-loci analysis.

Bottom Line: For diploid taxa, a Bayesian concordance analysis and a coalescent-based dated species tree was inferred from all gene trees.The resulting multilocus phylogeny reveals for the first time species phylogeny and progenitor-derivative relationships of all di- and polyploid Hordeum taxa within a single analysis.Our study proves that it is possible to obtain a multilocus species-level phylogeny for di- and polyploid taxa by combining PCR with next-generation sequencing, without cloning and without creating a heavy load of sequence data.

View Article: PubMed Central - PubMed

Affiliation: Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Germany; brassac@ipk-gatersleben.de.

Show MeSH