Multilocus molecular phylogenetic analysis of the montane Craugastor podiciferus species complex (Anura: Craugastoridae) in Isthmian Central America

Streicher, Jeffrey W.; Crawford, Andrew J.; Edwards, Cody W.

doi:10.1016/j.ympev.2009.07.011

Cited by 33 publications

(20 citation statements)

References 60 publications

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“…The considerable distances between some Craugastor species indicates the existence of a species complex, as indicated previously for Craugastor podiciferus by Streicher et al (2009). In respect to Osteopilus septentrionalis , which is widely distributed in Cuba, a similar pattern was observed by the Cyt b gene (Heinicke et al 2011).…”

Section: Discussionsupporting

confidence: 76%

Evaluating the diversity of Neotropical anurans using DNA barcodes

Estupiñán¹,

Ferrari²,

Gonçalves³

et al. 2016

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This study tested the effectiveness of COI barcodes for the discrimination of anuran species from the Amazon basin and other Neotropical regions. Barcodes were determined for a total of 59 species, with a further 58 species being included from GenBank. In most cases, distinguishing species using the barcodes was straightforward. Each species had a distinct COI barcode or codes, with intraspecific distances ranging from 0% to 9.9%. However, relatively high intraspecific divergence (11.4-19.4%) was observed in some species, such as Ranitomeya ventrimaculata, Craugastor fitzingeri, Hypsiboas leptolineatus, Scinax fuscomarginatus and Leptodactylus knudseni, which may reflect errors of identification or the presence of a species complex. Intraspecific distances recorded in species for which samples were obtained from GenBank (Engystomops pustulosus, Atelopus varius, Craugastor podiciferus, and Dendropsophus labialis) were greater than those between many pairs of species. Interspecific distances ranged between 11-39%. Overall, the clear differences observed between most intra-and inter-specific distances indicate that the COI barcode is an effective tool for the identification of Neotropical species in most of the cases analyzed in the present study.

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Section: Discussionsupporting

confidence: 76%

Evaluating the diversity of Neotropical anurans using DNA barcodes

Estupiñán¹,

Ferrari²,

Gonçalves³

et al. 2016

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“…Moreover, if shared past events led to the formation of current genetic patterns, then comparing phylogeographic patterns of sympatric species may enhance our understanding of the relative roles performed by the forces of climatic, geological and ecological conditions in structuring within-species genetic variation [18], [19], [20]. Molecular studies of different amphibians in the montane Neotropics have revealed high levels of genetic diversity across small geographic areas [21], [22], [23]. However, in South America and especially in Colombia, there are only a few molecular studies on genetic diversity of widely distributed montane amphibian taxa endemic to particular regions [9].…”

Section: Introductionmentioning

confidence: 99%

Comparative Phylogeography of Direct-Developing Frogs (Anura: Craugastoridae: Pristimantis) in the Southern Andes of Colombia

et al. 2012

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The Andes of South America hosts perhaps the highest amphibian species diversity in the world, and a sizable component of that diversity is comprised of direct-developing frogs of the genus Pristimantis (Anura: Craugastoridae). In order to better understand the initial stages of species formation in these frogs, this study quantified local-scale spatial genetic structuring in three species of Pristimantis. DNA sequences of two mitochondrial gene fragments (16S and COI) were obtained from P. brevifrons, P. palmeri and P. jubatus at different locations in the Cordillera Occidental. We found high levels of genetic diversity in the three species, with highly structured populations (as measured by F ST) in P. brevifrons and P. palmeri while P. jubatus showed panmixia. Large effective population sizes, inferred from the high levels of genetic diversity, were found in the three species and two highly divergent lineages were detected within P. jubatus and P. palmeri. Estimated divergence times among populations within P. brevifrons and P. palmeri coincide with the Pleistocene, perhaps due to similar responses to climatic cycling or recent geological history. Such insights have important implications for linking alpha and beta diversity, suggesting regional scale patterns may be associated with local scale processes in promoting differentiation among populations in the Andes.

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“…Bayesian inference was performed as previously described [24]. The optimal model for each data set was estimated by the program Modeltest 3.7 [25].…”

Section: Methodsmentioning

confidence: 99%

A Comparison of Genetic Diversity of COX-III Gene in Lowland Chickens and Tibetan Chickens

Liu

Zhang

et al. 2017

BioMed Research International

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To obtain a full understanding of the genetic diversity of the cytochrome oxidase III gene (COX-III) and its association with high altitude adaptation in Tibetan chickens, we sequenced COX-III in 12 chicken populations (155 Tibetan chickens and 145 other domestic chickens). We identified a total of 11 single nucleotide polymorphisms (SNPs) and 12 haplotypes (Ha1–Ha12). Low genetic diversity (haplotype diversity = 0.531 ± 0.087, nucleotide diversity = 0.00125) was detected for COX-III, and haplotype diversity of Tibetan chicken populations (0.750 ± 0.018) was markedly higher than lowland chicken populations (0.570 ± 0.028). Obvious genetic differentiation (nucleotide divergence = 0.092~0.339) and conspicuous gene communication (gene flow = 0.33~32.22) among 12 populations suggested that Tianfu black-bone fowl (white feather) was possibly introduced from Tibetan chicken. SNP m.10587 T>C affects the specific functions of the COX enzyme. Haplotype Ha3 was found in Tibetan chickens, and SNP m.10115G>A caused an amino acid substitution (Val62Ile) associated with phospholipid binding, while mutations m.10017C>A and m.10555G>A and the previously reported SNP m.10065T>C reduced the hydropathy index to some extent. Together, this indicates that the mitochondrial membrane is more hydrophobic in Tibetan chickens.

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Multilocus molecular phylogenetic analysis of the montane Craugastor podiciferus species complex (Anura: Craugastoridae) in Isthmian Central America

Cited by 33 publications

References 60 publications

Evaluating the diversity of Neotropical anurans using DNA barcodes

Evaluating the diversity of Neotropical anurans using DNA barcodes

Comparative Phylogeography of Direct-Developing Frogs (Anura: Craugastoridae: Pristimantis) in the Southern Andes of Colombia

A Comparison of Genetic Diversity of COX-III Gene in Lowland Chickens and Tibetan Chickens

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