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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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Calibrated multispecies coalescent of the diploid Hordeum species as calculated with *Beast from all loci excluding NUC. Numbers along the branches are posterior probability values/concordance factors of the clades. Ages (in millions of years) were inferred from the crown clade age of B. distachyon + Triticeae at 44.4 Ma and from the divergence between Hordeum and Triticum lineages at 15.32 Ma (Marcussen et al. 2014); calibration points are depicted by asterisks, divergence dates are reported in Table 4.
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Figure 2: Calibrated multispecies coalescent of the diploid Hordeum species as calculated with *Beast from all loci excluding NUC. Numbers along the branches are posterior probability values/concordance factors of the clades. Ages (in millions of years) were inferred from the crown clade age of B. distachyon + Triticeae at 44.4 Ma and from the divergence between Hordeum and Triticum lineages at 15.32 Ma (Marcussen et al. 2014); calibration points are depicted by asterisks, divergence dates are reported in Table 4.

Mentions: The MSC species tree (Fig. 2) resulted in a slightly different topology providing a better resolution for the closely related American species. The main disagreement concerned the three southern Patagonian species (H. comosum, H. patagonicum, and H. pubiflorum) found to be monophyletic and H. chilense/H. flexuosum as sister clade to the Patagonian clade. A second disagreement occurred with the Asian clade and the relationships within this clade where MSC provided high support (0.95 pp) for the monophyly of the clade but with H. roshevitzii outside although without any significant support within the clade (0.45 pp for H. brevisubulatum and H. roshevitzii). However, the differences are minor and do not influence the recognition of the major clades within Hordeum. In all analyses the recently proposed infrageneric taxonomic groups within Hordeum (Blattner 2009) were found to be monophyletic, for the first time with high support values (Fig. 1).


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)

Calibrated multispecies coalescent of the diploid Hordeum species as calculated with *Beast from all loci excluding NUC. Numbers along the branches are posterior probability values/concordance factors of the clades. Ages (in millions of years) were inferred from the crown clade age of B. distachyon + Triticeae at 44.4 Ma and from the divergence between Hordeum and Triticum lineages at 15.32 Ma (Marcussen et al. 2014); calibration points are depicted by asterisks, divergence dates are reported in Table 4.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 2: Calibrated multispecies coalescent of the diploid Hordeum species as calculated with *Beast from all loci excluding NUC. Numbers along the branches are posterior probability values/concordance factors of the clades. Ages (in millions of years) were inferred from the crown clade age of B. distachyon + Triticeae at 44.4 Ma and from the divergence between Hordeum and Triticum lineages at 15.32 Ma (Marcussen et al. 2014); calibration points are depicted by asterisks, divergence dates are reported in Table 4.
Mentions: The MSC species tree (Fig. 2) resulted in a slightly different topology providing a better resolution for the closely related American species. The main disagreement concerned the three southern Patagonian species (H. comosum, H. patagonicum, and H. pubiflorum) found to be monophyletic and H. chilense/H. flexuosum as sister clade to the Patagonian clade. A second disagreement occurred with the Asian clade and the relationships within this clade where MSC provided high support (0.95 pp) for the monophyly of the clade but with H. roshevitzii outside although without any significant support within the clade (0.45 pp for H. brevisubulatum and H. roshevitzii). However, the differences are minor and do not influence the recognition of the major clades within Hordeum. In all analyses the recently proposed infrageneric taxonomic groups within Hordeum (Blattner 2009) were found to be monophyletic, for the first time with high support values (Fig. 1).

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