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Cryptic genetic diversity is paramount in small-bodied amphibians of the genus Euparkerella (Anura: Craugastoridae) endemic to the Brazilian Atlantic forest.

Fusinatto LA, Alexandrino J, Haddad CF, Brunes TO, Rocha CF, Sequeira F - PLoS ONE (2013)

Bottom Line: Morphological similarity associated to restricted distributions and low dispersal abilities make the direct developing "Terrarana" frogs of the genus Euparkerella a good model for examining diversification processes.The analysis of 39 individuals from the four known Euparkerella species uncovered high levels of genetic diversity, especially within the two previously morphologically-defined E. cochranae and E. brasiliensis.These six units were also uncovered in the Bayesian clustering analysis, and supported by the Bayesian coalescent-based species delimitation (BPP), and Genealogical Sorting Index (GSI), providing thus strong evidence for underestimation of the current levels of diversity within Euparkerella.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Ecologia, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brasil.

ABSTRACT
Morphological similarity associated to restricted distributions and low dispersal abilities make the direct developing "Terrarana" frogs of the genus Euparkerella a good model for examining diversification processes. We here infer phylogenetic relationships within the genus Euparkerella, using DNA sequence data from one mitochondrial and four nuclear genes coupled with traditional Bayesian phylogenetic reconstruction approaches and more recent coalescent methods of species tree inference. We also used Bayesian clustering analysis and a recent Bayesian coalescent-based approach specifically to infer species delimitation. The analysis of 39 individuals from the four known Euparkerella species uncovered high levels of genetic diversity, especially within the two previously morphologically-defined E. cochranae and E. brasiliensis. Within these species, the gene trees at five independent loci and trees from combined data (concatenated dataset and the species tree) uncovered six deeply diverged and geographically coherent evolutionary units, which may have diverged between the Miocene and the Pleistocene. These six units were also uncovered in the Bayesian clustering analysis, and supported by the Bayesian coalescent-based species delimitation (BPP), and Genealogical Sorting Index (GSI), providing thus strong evidence for underestimation of the current levels of diversity within Euparkerella. The cryptic diversity now uncovered opens new opportunities to examine the origins and maintenance of microendemism in the context of spatial heterogeneity and/or human induced fragmentation of the highly threatened Brazilian Atlantic forest hotspot.

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Nuclear genes trees of Euparkerella.Bayesian phylogenetic inferences of nuclear haplotypes of four gene fragments (β-fibint7, C-myc, RAG-1 and TYR) of Euparkerella. Colors refer to populations and combinations of numbers-letters indicate localities (Figure 2 and Table S1 in File S1) corresponding to haplotypes. Posterior probabilities are indicated left to nodes. Asterisks represents posteriors equal or higher than 0.95.
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pone-0079504-g004: Nuclear genes trees of Euparkerella.Bayesian phylogenetic inferences of nuclear haplotypes of four gene fragments (β-fibint7, C-myc, RAG-1 and TYR) of Euparkerella. Colors refer to populations and combinations of numbers-letters indicate localities (Figure 2 and Table S1 in File S1) corresponding to haplotypes. Posterior probabilities are indicated left to nodes. Asterisks represents posteriors equal or higher than 0.95.

Mentions: The Bayesian inference of the mtDNA CO-I gene tree resulted in an overall highly resolved and strongly supported topology for all major relationships (Figure 3). Contrasting with the previously morphologically-defined species E. robusta and E. tridactyla, both E. brasiliensis and E. cochranae were not recovered as monophyletic groups. Euparkerella cochranae 3 (from locality 3) and E. brasiliensis (from localities 5, 6 and 7) form a well-supported clade, and E. cochranae 4 (from locality 4) together with individuals belonging to Euparkerella sp. (locality 8) form another clade with high posterior probability. The former clade appears to be highly substructured with the occurrence of two sub-clades with high posterior probability, corresponding to individuals of E. brasiliensis from localities 5 and 6, but their relationships are basically unresolved (Figure 3). Although resolution varied among nuclear loci, gene trees showed an overall lower resolution when compared to the mtDNA tree, and some phylogenetic non-concordance (Figure 4). The placement of E. cochranae 3 was non-concordant across markers, by clustering with E. cochranae 4 and E. robusta on the β-fibint7 tree, but with its position unresolved for other nuclear markers. Another non-concordant pattern between mtDNA and nuclear gene trees was the monophyly of Euparkerella sp., which was recovered by all nuclear, but not mtDNA, gene trees (Figure 4).


Cryptic genetic diversity is paramount in small-bodied amphibians of the genus Euparkerella (Anura: Craugastoridae) endemic to the Brazilian Atlantic forest.

Fusinatto LA, Alexandrino J, Haddad CF, Brunes TO, Rocha CF, Sequeira F - PLoS ONE (2013)

Nuclear genes trees of Euparkerella.Bayesian phylogenetic inferences of nuclear haplotypes of four gene fragments (β-fibint7, C-myc, RAG-1 and TYR) of Euparkerella. Colors refer to populations and combinations of numbers-letters indicate localities (Figure 2 and Table S1 in File S1) corresponding to haplotypes. Posterior probabilities are indicated left to nodes. Asterisks represents posteriors equal or higher than 0.95.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3815154&req=5

pone-0079504-g004: Nuclear genes trees of Euparkerella.Bayesian phylogenetic inferences of nuclear haplotypes of four gene fragments (β-fibint7, C-myc, RAG-1 and TYR) of Euparkerella. Colors refer to populations and combinations of numbers-letters indicate localities (Figure 2 and Table S1 in File S1) corresponding to haplotypes. Posterior probabilities are indicated left to nodes. Asterisks represents posteriors equal or higher than 0.95.
Mentions: The Bayesian inference of the mtDNA CO-I gene tree resulted in an overall highly resolved and strongly supported topology for all major relationships (Figure 3). Contrasting with the previously morphologically-defined species E. robusta and E. tridactyla, both E. brasiliensis and E. cochranae were not recovered as monophyletic groups. Euparkerella cochranae 3 (from locality 3) and E. brasiliensis (from localities 5, 6 and 7) form a well-supported clade, and E. cochranae 4 (from locality 4) together with individuals belonging to Euparkerella sp. (locality 8) form another clade with high posterior probability. The former clade appears to be highly substructured with the occurrence of two sub-clades with high posterior probability, corresponding to individuals of E. brasiliensis from localities 5 and 6, but their relationships are basically unresolved (Figure 3). Although resolution varied among nuclear loci, gene trees showed an overall lower resolution when compared to the mtDNA tree, and some phylogenetic non-concordance (Figure 4). The placement of E. cochranae 3 was non-concordant across markers, by clustering with E. cochranae 4 and E. robusta on the β-fibint7 tree, but with its position unresolved for other nuclear markers. Another non-concordant pattern between mtDNA and nuclear gene trees was the monophyly of Euparkerella sp., which was recovered by all nuclear, but not mtDNA, gene trees (Figure 4).

Bottom Line: Morphological similarity associated to restricted distributions and low dispersal abilities make the direct developing "Terrarana" frogs of the genus Euparkerella a good model for examining diversification processes.The analysis of 39 individuals from the four known Euparkerella species uncovered high levels of genetic diversity, especially within the two previously morphologically-defined E. cochranae and E. brasiliensis.These six units were also uncovered in the Bayesian clustering analysis, and supported by the Bayesian coalescent-based species delimitation (BPP), and Genealogical Sorting Index (GSI), providing thus strong evidence for underestimation of the current levels of diversity within Euparkerella.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Ecologia, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brasil.

ABSTRACT
Morphological similarity associated to restricted distributions and low dispersal abilities make the direct developing "Terrarana" frogs of the genus Euparkerella a good model for examining diversification processes. We here infer phylogenetic relationships within the genus Euparkerella, using DNA sequence data from one mitochondrial and four nuclear genes coupled with traditional Bayesian phylogenetic reconstruction approaches and more recent coalescent methods of species tree inference. We also used Bayesian clustering analysis and a recent Bayesian coalescent-based approach specifically to infer species delimitation. The analysis of 39 individuals from the four known Euparkerella species uncovered high levels of genetic diversity, especially within the two previously morphologically-defined E. cochranae and E. brasiliensis. Within these species, the gene trees at five independent loci and trees from combined data (concatenated dataset and the species tree) uncovered six deeply diverged and geographically coherent evolutionary units, which may have diverged between the Miocene and the Pleistocene. These six units were also uncovered in the Bayesian clustering analysis, and supported by the Bayesian coalescent-based species delimitation (BPP), and Genealogical Sorting Index (GSI), providing thus strong evidence for underestimation of the current levels of diversity within Euparkerella. The cryptic diversity now uncovered opens new opportunities to examine the origins and maintenance of microendemism in the context of spatial heterogeneity and/or human induced fragmentation of the highly threatened Brazilian Atlantic forest hotspot.

Show MeSH
Related in: MedlinePlus