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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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Previously argued phylogenetic hypotheses for the genus Triturus.Background colors reflect the variation in the number of rib-bearing pre-sacral vertebrae (NRBV) characterizing the five Triturus morphotypes. The two species with a green background are marbled newts and the remaining species are crested newts. The MrBayes phylogeny (left) is based on full mitochondrial genomes [19]. Posterior probabilities for all internal branches are 0.95 or higher. Note that this phylogeny is concordant with the most parsimonious interpretation of the evolution of the number of rib-bearing pre-sacral vertebrae (with the required character state changes noted in red). The *BEAST coalescent-based estimation of the species tree (right) is based on three nuclear introns (adapted from [20]). Posterior probabilities for internal branches are all below 0.95 and only those supported at over 0.75 are shown.
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pone-0111011-g001: Previously argued phylogenetic hypotheses for the genus Triturus.Background colors reflect the variation in the number of rib-bearing pre-sacral vertebrae (NRBV) characterizing the five Triturus morphotypes. The two species with a green background are marbled newts and the remaining species are crested newts. The MrBayes phylogeny (left) is based on full mitochondrial genomes [19]. Posterior probabilities for all internal branches are 0.95 or higher. Note that this phylogeny is concordant with the most parsimonious interpretation of the evolution of the number of rib-bearing pre-sacral vertebrae (with the required character state changes noted in red). The *BEAST coalescent-based estimation of the species tree (right) is based on three nuclear introns (adapted from [20]). Posterior probabilities for internal branches are all below 0.95 and only those supported at over 0.75 are shown.

Mentions: The genus Triturus (marbled and crested newts, Amphibia: Salamandridae) provides an example of a rapid radiation and the branching order has proved difficult to resolve [16]. The nine species can be divided into five groups hereafter referred to as morphotypes (Fig. 1; [17]). Morphotypes differ in body built and body built is reflected by the number of rib-bearing pre-sacral vertebrae. Arranged from stocky to slender, with the modal rib-bearing pre-sacral vertebrae count provided between parentheses, these morphotypes are: T. marmoratus and T. pygmaeus (12), T. ivanbureschi (including an as yet unnamed taxon) and T. karelinii (13), T. carnifex and T. macedonicus (14), T. cristatus (15) and T. dobrogicus (16 or 17) [18]. A full mtDNA dataset yielded a fully bifurcating and highly supported tree in which morphotypes are monophyletic (Fig. 1a; [19]). This tree supports the most parsimonious scenario of character state change in the number of rib-bearing pre-sacral vertebrae (the ancestral state for the number of rib-bearing pre-sacral vertebrae in the family Salamandridae is considered to be 13 [19]). Coalescent-based species tree estimations based on three nuclear markers for all species (Fig. 1b; [20]) and five nuclear markers for a subset of species [21] yielded contrasting results and both deviated from the species tree based on full mtDNA and morphology.


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)

Previously argued phylogenetic hypotheses for the genus Triturus.Background colors reflect the variation in the number of rib-bearing pre-sacral vertebrae (NRBV) characterizing the five Triturus morphotypes. The two species with a green background are marbled newts and the remaining species are crested newts. The MrBayes phylogeny (left) is based on full mitochondrial genomes [19]. Posterior probabilities for all internal branches are 0.95 or higher. Note that this phylogeny is concordant with the most parsimonious interpretation of the evolution of the number of rib-bearing pre-sacral vertebrae (with the required character state changes noted in red). The *BEAST coalescent-based estimation of the species tree (right) is based on three nuclear introns (adapted from [20]). Posterior probabilities for internal branches are all below 0.95 and only those supported at over 0.75 are shown.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0111011-g001: Previously argued phylogenetic hypotheses for the genus Triturus.Background colors reflect the variation in the number of rib-bearing pre-sacral vertebrae (NRBV) characterizing the five Triturus morphotypes. The two species with a green background are marbled newts and the remaining species are crested newts. The MrBayes phylogeny (left) is based on full mitochondrial genomes [19]. Posterior probabilities for all internal branches are 0.95 or higher. Note that this phylogeny is concordant with the most parsimonious interpretation of the evolution of the number of rib-bearing pre-sacral vertebrae (with the required character state changes noted in red). The *BEAST coalescent-based estimation of the species tree (right) is based on three nuclear introns (adapted from [20]). Posterior probabilities for internal branches are all below 0.95 and only those supported at over 0.75 are shown.
Mentions: The genus Triturus (marbled and crested newts, Amphibia: Salamandridae) provides an example of a rapid radiation and the branching order has proved difficult to resolve [16]. The nine species can be divided into five groups hereafter referred to as morphotypes (Fig. 1; [17]). Morphotypes differ in body built and body built is reflected by the number of rib-bearing pre-sacral vertebrae. Arranged from stocky to slender, with the modal rib-bearing pre-sacral vertebrae count provided between parentheses, these morphotypes are: T. marmoratus and T. pygmaeus (12), T. ivanbureschi (including an as yet unnamed taxon) and T. karelinii (13), T. carnifex and T. macedonicus (14), T. cristatus (15) and T. dobrogicus (16 or 17) [18]. A full mtDNA dataset yielded a fully bifurcating and highly supported tree in which morphotypes are monophyletic (Fig. 1a; [19]). This tree supports the most parsimonious scenario of character state change in the number of rib-bearing pre-sacral vertebrae (the ancestral state for the number of rib-bearing pre-sacral vertebrae in the family Salamandridae is considered to be 13 [19]). Coalescent-based species tree estimations based on three nuclear markers for all species (Fig. 1b; [20]) and five nuclear markers for a subset of species [21] yielded contrasting results and both deviated from the species tree based on full mtDNA and morphology.

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