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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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The distribution of the two marbled and seven crested newt species, represented by different colors, and the geographical position of sampled individuals (a).Sampling details can be found in Table 1. BAPS plot showing that each individual is allocated to its respective species (b).
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pone-0111011-g002: The distribution of the two marbled and seven crested newt species, represented by different colors, and the geographical position of sampled individuals (a).Sampling details can be found in Table 1. BAPS plot showing that each individual is allocated to its respective species (b).

Mentions: We chose samples from a comprehensive DNA database stored in the collection of Naturalis Biodiversity Center available from an earlier study [24]. This DNA was initially extracted using the DNeasy Tissue Kit (Qiagen) from tail tips taken from animals under anesthesia that were subsequently released back into the wild (a method which does not negatively affect survival [25]). We sampled 2–3 individuals for each of the seven crested newt species and one individual for each of the two marbled newt species. It should be noted that one taxon that we refer to as ‘Triturus candidate species’ is yet to be named [26]. We employed a wide geographical spread within species, but our sampling scheme avoided localities positioned close to interspecific hybrid zones, to minimize effects of introgression (Fig. 2; Table 1) [27].


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)

The distribution of the two marbled and seven crested newt species, represented by different colors, and the geographical position of sampled individuals (a).Sampling details can be found in Table 1. BAPS plot showing that each individual is allocated to its respective species (b).
© Copyright Policy
Related In: Results  -  Collection

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

pone-0111011-g002: The distribution of the two marbled and seven crested newt species, represented by different colors, and the geographical position of sampled individuals (a).Sampling details can be found in Table 1. BAPS plot showing that each individual is allocated to its respective species (b).
Mentions: We chose samples from a comprehensive DNA database stored in the collection of Naturalis Biodiversity Center available from an earlier study [24]. This DNA was initially extracted using the DNeasy Tissue Kit (Qiagen) from tail tips taken from animals under anesthesia that were subsequently released back into the wild (a method which does not negatively affect survival [25]). We sampled 2–3 individuals for each of the seven crested newt species and one individual for each of the two marbled newt species. It should be noted that one taxon that we refer to as ‘Triturus candidate species’ is yet to be named [26]. We employed a wide geographical spread within species, but our sampling scheme avoided localities positioned close to interspecific hybrid zones, to minimize effects of introgression (Fig. 2; Table 1) [27].

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