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Data concatenation, Bayesian concordance and coalescent-based analyses of the species tree for the rapid radiation of Triturus newts.

Wielstra B, Arntzen JW, van der Gaag KJ, Pabijan M, Babik W - PLoS ONE (2014)

Bottom Line: The data concatenation based species tree shows high branch support but branching order is considerably affected by allele choice in the case of heterozygotes in the concatenation process.Bayesian concordance analysis expresses the conflict between individual gene trees for part of the Triturus species tree as low concordance factors.The coalescent-based species tree is relatively similar to a previously published species tree based upon morphology and full mtDNA and any conflicting internal branches are not highly supported.

View Article: PubMed Central - PubMed

Affiliation: Naturalis Biodiversity Center, Leiden, The Netherlands; Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom.

ABSTRACT
The phylogenetic relationships for rapid species radiations are difficult to disentangle. Here we study one such case, namely the genus Triturus, which is composed of the marbled and crested newts. We analyze data for 38 genetic markers, positioned in 3-prime untranslated regions of protein-coding genes, obtained with 454 sequencing. Our dataset includes twenty Triturus newts and represents all nine species. Bayesian analysis of population structure allocates all individuals to their respective species. The branching patterns obtained by data concatenation, Bayesian concordance analysis and coalescent-based estimations of the species tree differ from one another. The data concatenation based species tree shows high branch support but branching order is considerably affected by allele choice in the case of heterozygotes in the concatenation process. Bayesian concordance analysis expresses the conflict between individual gene trees for part of the Triturus species tree as low concordance factors. The coalescent-based species tree is relatively similar to a previously published species tree based upon morphology and full mtDNA and any conflicting internal branches are not highly supported. Our findings reflect high gene tree discordance due to incomplete lineage sorting (possibly aggravated by hybridization) in combination with low information content of the markers employed (as can be expected for relatively recent species radiations). This case study highlights the complexity of resolving rapid radiations and we acknowledge that to convincingly resolve the Triturus species tree even more genes will have to be consulted.

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Species trees resulting from the coalescent-based estimation in *BEAST for the genus Triturus, based on 38 nuclear markers positioned in 3′ untranslated regions, sequenced for 20 individuals.Internal branches supported with pp = 1.0 are marked with an asterisk. The inferred position of the root for Triturus is shown. Background colors reflect variation in the number of rib-bearing pre-sacral vertebrae characterizing Triturus morphotypes as in Fig. 1 and the character stage changes required are noted in red.
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pone-0111011-g005: Species trees resulting from the coalescent-based estimation in *BEAST for the genus Triturus, based on 38 nuclear markers positioned in 3′ untranslated regions, sequenced for 20 individuals.Internal branches supported with pp = 1.0 are marked with an asterisk. The inferred position of the root for Triturus is shown. Background colors reflect variation in the number of rib-bearing pre-sacral vertebrae characterizing Triturus morphotypes as in Fig. 1 and the character stage changes required are noted in red.

Mentions: The result of the coalescent-based analysis with *BEAST (hereafter *BEAST phylogeny) is presented in Fig. 5. This tree is based on three runs; it excludes five runs that plateaued at a lower likelihood value within the burn-in of one billion generations. The individual trees resulting from all eight runs are available on Dryad. Part of the ESS values in the individual analyses, including those runs used to create the consensus tree, were (well) below 200. This finding shows that, even with runs of two billion-generations, stabilization within and convergence between runs did not occur. Considering we conducted eight independent, long runs, this appears inherent to the nature of our dataset. Still the results provide insight into the Triturus species tree.


Data concatenation, Bayesian concordance and coalescent-based analyses of the species tree for the rapid radiation of Triturus newts.

Wielstra B, Arntzen JW, van der Gaag KJ, Pabijan M, Babik W - PLoS ONE (2014)

Species trees resulting from the coalescent-based estimation in *BEAST for the genus Triturus, based on 38 nuclear markers positioned in 3′ untranslated regions, sequenced for 20 individuals.Internal branches supported with pp = 1.0 are marked with an asterisk. The inferred position of the root for Triturus is shown. Background colors reflect variation in the number of rib-bearing pre-sacral vertebrae characterizing Triturus morphotypes as in Fig. 1 and the character stage changes required are noted in red.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4206468&req=5

pone-0111011-g005: Species trees resulting from the coalescent-based estimation in *BEAST for the genus Triturus, based on 38 nuclear markers positioned in 3′ untranslated regions, sequenced for 20 individuals.Internal branches supported with pp = 1.0 are marked with an asterisk. The inferred position of the root for Triturus is shown. Background colors reflect variation in the number of rib-bearing pre-sacral vertebrae characterizing Triturus morphotypes as in Fig. 1 and the character stage changes required are noted in red.
Mentions: The result of the coalescent-based analysis with *BEAST (hereafter *BEAST phylogeny) is presented in Fig. 5. This tree is based on three runs; it excludes five runs that plateaued at a lower likelihood value within the burn-in of one billion generations. The individual trees resulting from all eight runs are available on Dryad. Part of the ESS values in the individual analyses, including those runs used to create the consensus tree, were (well) below 200. This finding shows that, even with runs of two billion-generations, stabilization within and convergence between runs did not occur. Considering we conducted eight independent, long runs, this appears inherent to the nature of our dataset. Still the results provide insight into the Triturus species tree.

Bottom Line: The data concatenation based species tree shows high branch support but branching order is considerably affected by allele choice in the case of heterozygotes in the concatenation process.Bayesian concordance analysis expresses the conflict between individual gene trees for part of the Triturus species tree as low concordance factors.The coalescent-based species tree is relatively similar to a previously published species tree based upon morphology and full mtDNA and any conflicting internal branches are not highly supported.

View Article: PubMed Central - PubMed

Affiliation: Naturalis Biodiversity Center, Leiden, The Netherlands; Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom.

ABSTRACT
The phylogenetic relationships for rapid species radiations are difficult to disentangle. Here we study one such case, namely the genus Triturus, which is composed of the marbled and crested newts. We analyze data for 38 genetic markers, positioned in 3-prime untranslated regions of protein-coding genes, obtained with 454 sequencing. Our dataset includes twenty Triturus newts and represents all nine species. Bayesian analysis of population structure allocates all individuals to their respective species. The branching patterns obtained by data concatenation, Bayesian concordance analysis and coalescent-based estimations of the species tree differ from one another. The data concatenation based species tree shows high branch support but branching order is considerably affected by allele choice in the case of heterozygotes in the concatenation process. Bayesian concordance analysis expresses the conflict between individual gene trees for part of the Triturus species tree as low concordance factors. The coalescent-based species tree is relatively similar to a previously published species tree based upon morphology and full mtDNA and any conflicting internal branches are not highly supported. Our findings reflect high gene tree discordance due to incomplete lineage sorting (possibly aggravated by hybridization) in combination with low information content of the markers employed (as can be expected for relatively recent species radiations). This case study highlights the complexity of resolving rapid radiations and we acknowledge that to convincingly resolve the Triturus species tree even more genes will have to be consulted.

Show MeSH