A re-evaluation of the phylogeny of Old World Treefrogs

DNA barcoding and the identification of tree frogs (Amphibia: Anura: Rhacophoridae)

The DNA barcoding gene COI (cytochrome c oxidase subunit I) effectively identifies many species. Herein, we barcoded 172 individuals from 37 species belonging to nine genera in Rhacophoridae to test if the gene serves equally well to identify species of tree frogs. Phenetic neighbor joining and phylogenetic Bayesian inference were used to construct phylogenetic trees, which resolved all nine genera as monophyletic taxa except for Rhacophorus, two new matrilines for Liuixalus, and Polypedates leucomystax species complex. Intraspecific genetic distances ranged from 0.000 to 0.119 and interspecific genetic distances ranged from 0.015 to 0.334. Within Rhacophorus and Kurixalus, the intra- and interspecific genetic distances did not reveal an obvious barcode gap. Notwithstanding, we found that COI sequences unambiguously identified rhacophorid species and helped to discover likely new cryptic species via the synthesis of genealogical relationships and divergence patterns. Our results supported that COI is an effective DNA barcoding marker for Rhacophoridae.

Molecular phylogeny of Rhacophoridae (Anura): A framework of taxonomic reassignment of species within the genera Aquixalus, Chiromantis, Rhacophorus, and Philautus

Phylogenetic relationships among representative species of the family Rhacophoridae were investigated based on 2904bp of sequences from both mitochondrial (12S rRNA, 16S rRNA, the complete t-RNA for valine), and nuclear (tyrosinase, rhodopsin) genes. Maximum parsimony, maximum likelihood, and Bayesian analyses were employed to reconstruct the phylogenetic trees. This analysis, combined with previous phylogenetic studies, serves as a framework for future work in rhacophorid systematics. The monophyly of Rhacophorus is strongly confirmed except for the species R.hainanus, which is the sister taxon to A.odontotarsus. The non-monophyly of the newly designated genus Aquixalus by Delorme et al. [Delorme, M., Dubois, A., Grosjean, S., Ohler, A., 2005. Une nouvelle classification générique et subgénérique de la tribu des Philautini (Amphibia, Anura, Ranidae, Rhacophorinae). Bull. Mens. Soc. Linn. Lyon 74, 165-171] is further confirmed. Aquixalus (Aquixalus) forms a well-supported monophyletic group within Kurixalus, whereas, Aquixalus (Gracixalus) is more closely related to species of Rhacophorus, Polypedates, and Chiromantis. Philautus as currently understood, does not form a monophyletic group. Philautus (Kirtixalus) is the sister group to the clade comprising Kurixalus and Aquixalus (Aquixalus), and more remotely related to Philautus (Philautus). Chiromantisromeri does not cluster with species of Chiromantis, and forms a basal clade to all rhacophorids save Buergeria. We propose some taxonomic changes that reflect these findings, but further revision should await more detailed studies, which include combined morphological and molecular analyses, with greater species sampling.

Molecular phylogeny of Malagasy reed frogs, Heterixalus, and the relative performance of bioacoustics and color-patterns for resolving their systematics

The members of the genus Heterixalus constitute one of the endemic frog radiations in Madagascar. Here we present a complete species-level phylogeny based on DNA sequences (4876 base pairs) of three nuclear and four mitochondrial markers to clarify the phylogenetic relationships among and within all known species of this genus, as well as the phylogenetic position of the monospecific Seychellean Tachycnemis seychellensis. Although the performance to resolve supported clades of Heterixalus species differed among the investigated gene fragments when analyzed separately, we could identify five well-supported species groups within Heterixalus in the combined analysis of all gene fragments. Our data strongly support a Heterixalus-Tachycnemis clade, and indicate the probable monophyly of Heterixalus placed sister to Tachycnemis. However, the diversification of these lineages may have happened in a short interval of time, leading to an unstable placement of Tachycnemis in the single-gene fragment phylogenies. Referring to the hitherto existing classification of Heterixalus, which is predominantly based on chromatic and bioacoustic characters, we examined the relative performance of these data sets relative to our molecular phylogeny. A Bayesian tree reconstructed with a bioacoustic data set yielded a higher resemblance to the molecular phylogeny than a tree constructed using a chromatic data set, which supports the importance of bioacoustic characters for systematic analyses of these anurans.

Rearrangement of a mitochondrial tRNA gene of the concave-eared torrent frog, Amolops tormotus

In this study, the complete nucleotide sequence (17,962 bp) of the mitochondrial DNA of Amolops tormotus was determined using polymerase chain reaction (PCR). The gene content, base composition and codon usage of A. tormotus conformed to those of typical vertebrate patterns. Among 22 tRNAs, the novel position of the tRNA-His gene was in the D-loop region, which was a novel mtDNA gene rearrangement in amphibians. Phylogenetic analyses were based on a 885-bp sequence of 12S and 16S rRNA for species of Amolops and other related species, concatenated sequences of the 11 protein-encoding genes of 13 species.

Complete nucleotide sequence of the mitochondrial genome of Schlegel's tree frog Rhacophorus schlegelii (family Rhacophoridae): duplicated control regions and gene rearrangements

The complete nucleotide sequence (21,359 bp) of the mitochondrial DNA of the rhacophorid frog Rhacophorus schlegelii was determined. The gene content, nucleotide composition, and codon usage of this genome corresponded to those typical of vertebrates. However, the Rh. schlegelii genome was unusually large due to the inclusion of two control regions and the accumulation of lengthy repetitive sequences in these regions. The two control regions had 97% sequence similarity over 1,510 bp, suggesting the occurrence of concerted sequence evolution. Comparison of the gene organizations among anuran species revealed that the mitochondrial gene arrangement of Rh. schlegelii diverged from that of typical vertebrates but was similar to that of Buergeria buergeri. The positions of the tRNA-Leu(CUN) and tRNA-Thr genes were exchanged between Rh. schlegelii and B. buergeri. Based on parsimonious consideration and the basal phylogenetic position of B. buergeri, these genes seemed to have been rearranged in an ancestral lineage leading to Rh. schlegelii.

Molecular Phylogeny of the Ranid Frogs from Southwest India Based on the Mitochondrial Ribosomal RNA Gene Sequences

The Western Ghats of Southwestern India are known as one of the world's "hotspots" of biodiversity. We collected frog specimens from the family Ranidae and investigated the phylogenetic relationships among ranid species, particularly among the Fejervarya, a genus whose morphological diagnostic characteristics and phylogenetic features remain little known. We analyzed partial sequences of the mitochondrial 12S (428 bp) and 16S rDNAs (549 bp). Results showed that the members of Fejervarya form a monophyletic group with the genera Hoplobatrachus and Euphlyctis among ranid genera. This confirms the recent allocation of Fejervarya, including it within the subfamily Dicroglossinae. The mitochondrial rDNA data in our study also appeared to be useful as a marker to distinguish Fejervarya species without morphological differences. The phylogenetic tree based on the 16S rDNA sequence showed a correlation between Fejervarya phylogenies and their geographic distributions. Lastly, our results suggested the recent occurrence of a radiation event of Fejervarya species in the Indian-Sri Lankan region.

Complete nucleotide sequence and gene rearrangement of the mitochondrial genome of the bell-ring frog, Buergeria buergeri (family Rhacophoridae)

In this study we determined the complete nucleotide sequence (19,959 bp) of the mitochondrial DNA of the rhacophorid frog Buergeria buergeri. The gene content, nucleotide composition, and codon usage of B. buergeri conformed to those of typical vertebrate patterns. However, due to an accumulation of lengthy repetitive sequences in the D-loop region, this species possesses the largest mitochondrial genome among all the vertebrates examined so far. Comparison of the gene organizations among amphibian species (Rana, Xenopus, salamanders and caecilians) revealed that the positioning of four tRNA genes and the ND5 gene in the mtDNA of B. buergeri diverged from the common vertebrate gene arrangement shared by Xenopus, salamanders and caecilians. The unique positions of the tRNA genes in B. buergeri are shared by ranid frogs, indicating that the rearrangements of the tRNA genes occurred in a common ancestral lineage of ranids and rhacophorids. On the other hand, the novel position of the ND5 gene seems to have arisen in a lineage leading to rhacophorids (and other closely related taxa) after ranid divergence. Phylogenetic analysis based on nucleotide sequence data of all mitochondrial genes also supported the gene rearrangement pathway.

A molecular phylogenetic analysis of the family Rhacophoridae with an emphasis on the Asian and African genera

Using characters from mitochondrial DNA to construct maximum parsimony and maximum likelihood trees, we performed a phylogenetic analysis on representative species of 14 genera: 12 that belong to the treefrog family Rhacophoridae and two, Amolops and Rana, that are not rhacophorids. Our results support a phylogenetic hypothesis that depicts a monophyletic family Rhacophoridae. In this family, the Malagasy genera Aglyptodactylus, Boophis, Mantella, and Mantidactylus form a well-supported sister clade to all other rhacophorid genera, and Mantella is the sister taxon to Mantidactylus. Within the Asian/African genera, the genus Buergeria forms a well-supported clade of four species. The genera, except for Chirixalus, are generally monophyletic. An exception to this is that Polypedates dennysii clusters with species of Rhacophorus, suggesting that the taxonomy of the rhacophorids should be revised to reflect this relationship. Chirixalus is not monophyletic. Unexpectedly, there is strong support for Chirixalus doriae from Southeast Asia forming a clade with species of the African genus Chiromantis, suggesting that Chiromantis dispersed to Africa from Asia. Also, there is strong support for the sister taxon relationship of Chirixalus eiffingeri and Chirixalus idiootocus apart from other congeners.

Out of Asia: mitochondrial DNA evidence for an Oriental origin of tiger frogs, genus Hoplobatrachus

Most examples of intercontinental dispersal events after the Miocene contact between Africa and Asia involve mammal lineages. Among amphibians, a number of probably related groups are known from both continents, but their phylogenies are so far largely unresolved. To test the hypothesis of Miocene dispersal against a Mesozoic vicariance scenario in the context of Gondwana fragmentation, we analyzed fragments of the mitochondrial 16S rRNA gene (572 bp) in 40 specimens of 34 species of the anuran family Ranidae. Results corroborated the monophyly of tiger frogs (genus Hoplobatrachus), a genus with representatives in Africa and Asia. The African H. occipitalis was the sister group of the Asian H. crassus, H. chinensis, and H. tigerinus. Hoplobatrachus was placed in a clade also containing the Asian genera Euphlyctis and Nannophrys. Combined analysis of sequences of 16S and 12S rRNA genes (total 903 bp) in a reduced set of taxa corroborated the monophyly of the lineage containing these three genera and identified the Asian genus Fejervarya as its possible sister group. The fact that the African H. occipitalis is nested within an otherwise exclusively Asian clade indicates its probable Oriental origin. Rough molecular clock estimates did not contradict the assumption that the dispersal event took place in the Miocene. Our data further identified a similar molecular divergence between closely related Asian and African species of Rana (belonging to the section Hylarana), indicating that Neogene intercontinental dispersal also may have taken place in this group and possibly in rhacophorid treefrogs.