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Evolutionary relationships of the critically endangered frog Ericabatrachus baleensis Largen, 1991 with notes on incorporating previously unsampled taxa into large-scale phylogenetic analyses.

Siu-Ting K, Gower DJ, Pisani D, Kassahun R, Gebresenbet F, Menegon M, Mengistu AA, Saber SA, de Sá R, Wilkinson M, Loader SP - BMC Evol. Biol. (2014)

Bottom Line: We obtained fresh samples of the now rare and Critically Endangered Ericabatrachus baleensis and generated DNA sequences for two mitochondrial and four nuclear genes.We discuss the implications of our results for the taxonomy, biogeography and conservation of E. baleensis, and suggest a two-tiered approach to the inclusion and analyses of new data in order to assess the phylogenetic relationships of previously unsampled taxa.Such approaches will be important in the future given the increasing availability of relevant mega-alignments and potential framework phylogenies.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Environmental Sciences, University of Basel, Biogeography Research Group, Basel 4056, Switzerland. simon.loader@unibas.ch.

ABSTRACT

Background: The phylogenetic relationships of many taxa remain poorly known because of a lack of appropriate data and/or analyses. Despite substantial recent advances, amphibian phylogeny remains poorly resolved in many instances. The phylogenetic relationships of the Ethiopian endemic monotypic genus Ericabatrachus has been addressed thus far only with phenotypic data and remains contentious.

Results: We obtained fresh samples of the now rare and Critically Endangered Ericabatrachus baleensis and generated DNA sequences for two mitochondrial and four nuclear genes. Analyses of these new data using de novo and constrained-tree phylogenetic reconstructions strongly support a close relationship between Ericabatrachus and Petropedetes, and allow us to reject previously proposed alternative hypotheses of a close relationship with cacosternines or Phrynobatrachus.

Conclusions: We discuss the implications of our results for the taxonomy, biogeography and conservation of E. baleensis, and suggest a two-tiered approach to the inclusion and analyses of new data in order to assess the phylogenetic relationships of previously unsampled taxa. Such approaches will be important in the future given the increasing availability of relevant mega-alignments and potential framework phylogenies.

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Small-scale Bayesian tree under GTR model showing the phylogenetic placement of Ericabatrachus baleensis (in bold). Support values for the nodes correspond to posterior probabilities (left) and non-parametric bootstraps (right). Values with “*” represent maximal support (100%), values lower than 40% are denoted by “-”.
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Figure 3: Small-scale Bayesian tree under GTR model showing the phylogenetic placement of Ericabatrachus baleensis (in bold). Support values for the nodes correspond to posterior probabilities (left) and non-parametric bootstraps (right). Values with “*” represent maximal support (100%), values lower than 40% are denoted by “-”.

Mentions: Focused, smaller-scale Bayesian and ML analyses (66-taxon data set) recover Ericabatrachus as most likely the sister group to Petropedetes (Figure 3). The posterior probability for this position under the GTR + G, CAT + G, or CAT-GTR + G models is invariably equal to one. ML bootstrap support is only marginally increased (to ~ 67%). The topologies obtained in different analyses of the 66-taxon data set are almost identical, varying only in the positions of Occidoziga lima, Phrynobatrachus kreffti, and Micrixalus. AU tests show that the phylogenetic placement of Ericabatrachus obtained in our Bayesian and ML results fits the 66-taxon data significantly better than any previously proposed hypothesis.


Evolutionary relationships of the critically endangered frog Ericabatrachus baleensis Largen, 1991 with notes on incorporating previously unsampled taxa into large-scale phylogenetic analyses.

Siu-Ting K, Gower DJ, Pisani D, Kassahun R, Gebresenbet F, Menegon M, Mengistu AA, Saber SA, de Sá R, Wilkinson M, Loader SP - BMC Evol. Biol. (2014)

Small-scale Bayesian tree under GTR model showing the phylogenetic placement of Ericabatrachus baleensis (in bold). Support values for the nodes correspond to posterior probabilities (left) and non-parametric bootstraps (right). Values with “*” represent maximal support (100%), values lower than 40% are denoted by “-”.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4008257&req=5

Figure 3: Small-scale Bayesian tree under GTR model showing the phylogenetic placement of Ericabatrachus baleensis (in bold). Support values for the nodes correspond to posterior probabilities (left) and non-parametric bootstraps (right). Values with “*” represent maximal support (100%), values lower than 40% are denoted by “-”.
Mentions: Focused, smaller-scale Bayesian and ML analyses (66-taxon data set) recover Ericabatrachus as most likely the sister group to Petropedetes (Figure 3). The posterior probability for this position under the GTR + G, CAT + G, or CAT-GTR + G models is invariably equal to one. ML bootstrap support is only marginally increased (to ~ 67%). The topologies obtained in different analyses of the 66-taxon data set are almost identical, varying only in the positions of Occidoziga lima, Phrynobatrachus kreffti, and Micrixalus. AU tests show that the phylogenetic placement of Ericabatrachus obtained in our Bayesian and ML results fits the 66-taxon data significantly better than any previously proposed hypothesis.

Bottom Line: We obtained fresh samples of the now rare and Critically Endangered Ericabatrachus baleensis and generated DNA sequences for two mitochondrial and four nuclear genes.We discuss the implications of our results for the taxonomy, biogeography and conservation of E. baleensis, and suggest a two-tiered approach to the inclusion and analyses of new data in order to assess the phylogenetic relationships of previously unsampled taxa.Such approaches will be important in the future given the increasing availability of relevant mega-alignments and potential framework phylogenies.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Environmental Sciences, University of Basel, Biogeography Research Group, Basel 4056, Switzerland. simon.loader@unibas.ch.

ABSTRACT

Background: The phylogenetic relationships of many taxa remain poorly known because of a lack of appropriate data and/or analyses. Despite substantial recent advances, amphibian phylogeny remains poorly resolved in many instances. The phylogenetic relationships of the Ethiopian endemic monotypic genus Ericabatrachus has been addressed thus far only with phenotypic data and remains contentious.

Results: We obtained fresh samples of the now rare and Critically Endangered Ericabatrachus baleensis and generated DNA sequences for two mitochondrial and four nuclear genes. Analyses of these new data using de novo and constrained-tree phylogenetic reconstructions strongly support a close relationship between Ericabatrachus and Petropedetes, and allow us to reject previously proposed alternative hypotheses of a close relationship with cacosternines or Phrynobatrachus.

Conclusions: We discuss the implications of our results for the taxonomy, biogeography and conservation of E. baleensis, and suggest a two-tiered approach to the inclusion and analyses of new data in order to assess the phylogenetic relationships of previously unsampled taxa. Such approaches will be important in the future given the increasing availability of relevant mega-alignments and potential framework phylogenies.

Show MeSH