Efficient Sequencing of Anuran mtDNAs and a Mitogenomic Exploration of the Phylogeny and Evolution of Frogs

Abstract

Anura (frogs and toads) constitute over 88% of living amphibian diversity but many important questions about their phylogeny and evolution remain unresolved. For this study, we developed an efficient method for sequencing anuran mitochondrial DNAs (mtDNAs) by amplifying the mitochondrial genome in 12 overlapping fragments using frog-specific universal primer sets. Based on this method, we generated 47 nearly complete, new anuran mitochondrial genomes and discovered nine novel gene arrangements. By combining the new data and published anuran mitochondrial genomes, we assembled a large mitogenomic data set (11,007 nt) including 90 frog species, representing 39 of 53 recognized anuran families, to investigate their phylogenetic relationships and evolutionary history. The resulting tree strongly supported a paraphyletic arrangement of archaeobatrachian (=nonneobatrachian) frogs, with Leiopelmatoidea branching first, followed by Discoglossoidea, Pipoidea, and Pelobatoidea. Within Neobatrachia, the South African Heleophrynidae is the sister-taxon to all other neobatrachian frogs and the Seychelles-endemic Sooglossidae is recovered as the sister-taxon to Ranoidea. These phylogenetic relationships agree with many nuclear gene studies. The chronogram derived from two Bayesian relaxed clock methods (MultiDivTime and BEAST) suggests that modern frogs (Anura) originated in the early Triassic about 244 Ma and the appearance of Neobatrachia took place in the late Jurassic about 163 Ma. The initial diversifications of two species-rich superfamilies Hyloidea and Ranoidea commenced 110 and 133 Ma, respectively. These times are older than some other estimates by approximately 30-40 My. Compared with nuclear data, mtDNA produces compatible time estimates for deep nodes (>150 Ma), but apparently older estimates for more shallow nodes. Our study shows that, although it evolves relatively rapidly and behaves much as a single locus, mtDNA performs well for both phylogenetic and divergence time inferences and will provide important reference hypotheses for the phylogeny and evolution of frogs.

The phylogenetic position and diversity of the enigmatic mongrel frog Nothophryne Poynton, 1963 (Amphibia, Anura)

“…Phylogenetic trees were rooted at Hemisotidae + Brevicipitidae, because this node is considered basal within Ranoidea (following Frost et al, 2006;Pyron and Wiens, 2011;Siu-Ting et al, 2014;Zhang et al, 2013). We used the Petropedetidae (chosen to minimise missing data) were included as outgroup taxa.…”

Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous–Paleogene boundary

“…However, despite intensive molecular phylogenetic studies (2-7), areas of uncertainty and disagreement persist among clades that are crucial for interpreting broad-scale macroevolutionary patterns. In addition, a general consensus on divergence times of the major anuran lineages is also lacking (7,8).…”

The mitochondrial genomes of three species of poison frogs (Anura: Dendrobates)

“…We observed 129 nucleotide differences among the mitogenome sequences of a captive D. leucomelas and one collected in the wild, and 53 differences between our D. auratus sequence and a previously published one (Zhang et al 2013), corresponding to uncorrected p-distances of 0.9 and 0.4%, respectively. All D. tinctorius in our study came from the same captive-bred strain, and specimens Dt3, Dt4, Dt5, Dt6, and Dt9 were full siblings.…”

“…New sequences were submitted to GenBank (accession numbers MF069434-MF069441). Sequences were aligned to published complete or near-complete mitochondrial genomes of dendrobatid and aromobatid frogs (Zhang et al 2013;Machado et al 2016;Vacher et al 2016) with MAFFT v.7 (Katoh and Standley 2013). The mitogenome sequence of Bufo tibetanus was used as outgroup.…”