No abstract

The frog clade composed of the alsodid genera Alsodes + Eupsophus is the most species‐rich of the Patagonian endemic frog clades, including nearly 31 of the slightly more than 50 species of that region. The biology of this group of frogs is poorly known, its taxonomy quite complex (particularly Alsodes), and its diversity in chromosome number striking when compared with other frogs (collectively, there are species having 2n = 22, 2n = 26, 2n = 28, 2n = 30 or 2n = 34). We present a phylogenetic analysis of this Patagonian frog clade based on mitochondrial and nuclear gene sequences. We sequenced five mitochondrial genes (cytochrome b, cytochrome oxidase I, 12S, 16S, NADH dehydrogenase subunit 1) with three intervening tRNAs, and fragments of three nuclear genes (seven in absentia homolog 1, rhodopsin exon 1, RAG‐1), for a maximum of 6510 bp for multiple specimens from 26 of the 31 species. We recovered Eupsophus as polyphyletic, with E. antartandicus, E. sylvaticus, and E. taeniatus in Batrachylidae, in accordance with most previous hypotheses. Based on this result, we transfer E. antartandicus and E. taeniatus back to Batrachyla, and E. sylvaticus to Hylorina (resurrected from the synonymy of Eupsophus), remediating the paraphyly of Eupsophus. Our results strongly corroborate the monophyly of Alsodes + Eupsophus (sensu stricto), the individual monophyly of these genera, and the monophyly of the species groups of Eupsophus. They also show the non‐monophyly of all non‐monotypic species groups of Alsodes proposed in the past. Our results expose several taxonomic problems particularly in Alsodes, and to a lesser extent in Eupsophus. This phylogenetic context suggests a rich evolutionary history of karyotypic diversification in the clade, in part corroborating previous hypotheses. In Alsodes, we predict three independent transformations of chromosome number from the plesiomorphic 2n = 26. All these, strikingly, involve increments or reductions of pairs of haploid chromosomes. Finally, the phylogenetic pattern recovered for Alsodes and Eupsophus suggests a trans‐Andean origin and diversification of the group, with multiple, independent ingressions over cis‐Andean regions.

Most anurans possess a tympanic middle ear (TME) that transmits sound waves to the inner ear; however, numerous species lack some or all TME components. To understand the evolution of these structures, we undertook a comprehensive assessment of their occurrence across anurans and performed ancestral character state reconstructions. Our analysis indicates that the TME was completely lost at least 38 independent times in Anura. The inferred evolutionary history of the TME is exceptionally complex in true toads (Bufonidae), where it was lost in the most recent common ancestor, preceding a radiation of >150 earless species. Following that initial loss, independent regains of some or all TME structures were inferred within two minor clades and in a radiation of >400 species. The reappearance of the TME in the latter clade was followed by at least 10 losses of the entire TME. The many losses and gains of the TME in anurans is unparalleled among tetrapods. Our results show that anurans, and especially bufonid toads, are an excellent model to study the behavioural correlates of earlessness, extratympanic sound pathways, and the genetic and developmental mechanisms that underlie the morphogenesis of TME structures.

The Neotropical hylid genus Sphaenorhynchus includes 15 species of small, greenish treefrogs widespread in the Amazon and Orinoco basins, and in the Atlantic Forest of Brazil. Although some studies have addressed the phylogenetic relationships of the genus with other hylids using a few exemplar species, its internal relationships remain poorly understood. In order to test its monophyly and the relationships among its species, we performed a total evidence phylogenetic analysis of sequences of three mitochondrial and three nuclear genes, and 193 phenotypic characters from all species of Sphaenorhynchus. Our results support the monophyly of Sphaenorhynchus with molecular and phenotypic evidence, with S. pauloalvini as the earliest diverging taxon, followed by S. carneus, as the sister taxon of all remaining species of the genus. We recognize three species groups in Sphaenorhynchus (the S. lacteus, S. planicola and S. platycephalus groups), to facilitate its taxonomic study; only three species (S. carneus, S. pauloalvini and S. prasinus) remain unassigned to any group. Sequence data were not available for only two species (S. bromelicola and S. palustris) for which we scored phenotypic data; wildcard behaviour was detected only in S. bromelicola nested inside the S. platycephalus group. On the basis of the resulting phylogenetic hypothesis, we discuss the evolution of oviposition site and a number of phenotypic characters that could be associated with heterochronic events in the evolutionary history of this group.

Despite major progress in deciphering the amphibian tree of life by molecular phylogenetics, we identified two questions remaining to be answered regarding relationships within Hyloidea, the clade of South American origin that comprises most extant anuran diversity. A few genera like Rupirana and Crossodactylodes have enigmatic phylogenetic positions, and relationships among major lineages within some families like Leptodactylidae remain ambiguous. To resolve these specific questions we used two approaches (1) a complete matrix approach representing >6.6 kb, including most major Hyloidea lineages (61 terminals) combining different methods of phylogenetic reconstruction and measures of node support; and (2) a supermatrix approach >11.6 kb with a focus on Leptodactylidae. Both Rupirana and Crossodactylodes are unambiguously grouped with Paratelmatobius and Scythrophrys. The clade comprising these four genera is named Crossodactylodinae and embedded within Leptodactylidae. Crossodactylodinae is moderately supported as sister group of Leptodactylinae from (1) and as the sister group of the other Leptodactylidae from (2) with low support. Genera within Crossodactylodinae are scattered along a north-south axis in the Atlantic forest and their origins are very ancient (Paleocene). Such results stress the importance of the northern Atlantic forest in terms of conservation. Moreover, the position of Pseudopaludicola, which is well supported as the sister group to all other Leiuperinae, suggests that foam-nest building may have arisen independently in Leptodactylinae and Leiuperinae. Moreover, in spite of being of similar age, foam-nest builders are more widespread than nonfoam-nest breeders and have higher species diversity. Nevertheless, the bulk of the diversity within foam-nest breeders arose some 20 Myr later than the character itself.

The Rhinella granulosa group consists of 13 species of toads distributed throughout open areas of South America and Panama. In this paper we perform a phylogenetic analysis considering all but one species of the group, employing five nuclear and four mitochondrial genes, for up to 7910 bp per specimen. Separate phylogenetic analyses under direct optimization (DO) of nuclear and mitochondrial sequences recovered the R. granulosa group as monophyletic and revealed topological incongruence that can be explained mainly by multiple events of hybridization and introgression, both mitochondrial and nuclear. The DO combined analysis, after the exclusion of putatively introgressed or heterozygous genomes, resulted in a phylogenetic hypothesis for the R. granulosa group in which most of the species are recovered as monophyletic, but with interspecific relationships poorly supported. The optimization of morphological (adult and larval), chromosomal, and behavioural characters resulted in 12 putative phenotypic synapomorphies for this species group and some other synapomorphies for internal clades. Our results indicate the need for additional population genetic studies on R. dorbignyi and R. fernandezae to corroborate the taxonomic status of both taxa. Finally, we discuss biological and genetic characteristics of Bufonidae, as possible explanations for the common occurrence of hybridization and introgression observed in some lineages of this family.

We present a molecular phylogenetic analysis of the hylid tribe Hylini, with the goals of testing the monophyly of the genera Duellmanohyla, Isthmohyla, and Ptychohyla and providing a discussion on the monophyly of Bromeliohyla, Charadrahyla, Ecnomiohyla, Exerodonta, Megastomatohyla, and Sarcohyla. Our results indicate the paraphyly of Ptychohyla, with Bromeliohyla and Duellmanohyla nested within it, and, as in previous analyses, the paraphyly of Duellmanohyla (due to Ptychohyla legleri and P. salvadorensis being nested within it). To resolve this situation, we restrict the contents of Ptychohyla, redelimit those of Duellmanohyla and Bromeliohyla, and erect two new genera, one to include the former Ptychohyla panchoi and P. spinipollex, and the other for the former Ptychohyla acrochorda, P. sanctaecrucis, P. zoque, and tentatively, P. erythromma. Exerodonta as currently defined is not monophyletic, inasmuch as Exerodonta juanitae is nested within Charadrahyla. Consequently, we transfer this species and, tentatively, E. pinorum to Charadrahyla. Also, we discuss some possible taxonomic problems within Exerodonta. Our results indicate that Isthmohyla is polyphyletic, the bromeliad-dwelling Isthmohyla melacaena being the sister taxon of our only exemplar of Bromeliohyla, B. bromeliacia. For this reason, we transfer I. melacaena to Bromeliohyla, rendering Isthmohyla monophyletic. The former Isthmohyla pictipes Group is shown to be paraphyletic due to having the non-monophyletic I. pseudopuma Group within it. Accordingly, we recognize a redelimited I. pseudopuma Group (contents: I. infucata and I. pseudopuma), an I. zeteki Group (contents: I. picadoi and I. zeteki), and a newly defined I. tica Group (contents: I. angustilineata, I. calypsa, I. debilis, I. graceae, I. lancasteri, I. pictipes, I. tica, I. rivularis, and, tentatively, I. insolita and I. xanthosticta). The three groups of Isthmohyla are supported by molecular evidence with jackknife support values > 90%, and two of them by putative morphological synapomorphies. We discuss the recognition of Dryophytes, Hyliola, Rheohyla, and Sarcohyla and whether it is useful to recognize Anotheca, Diaglena, and Triprion as three distinct, monotypic genera. Finally, we discuss a recent taxonomic proposal involving changes in rank and from ranked to unranked names in hylids that overall we consider to have been poorly justified and only superficially discussed.

The horned frog family, Ceratophryidae, currently comprises three genera and 12 extant species, distributed from the Caribbean lowlands to the Pampean grasslands. Horned frogs are fossorial species that are remarkable in terms of their adult and larval morphology, karyotype, behavior, and other aspects of their biology. In this paper we present a molecular phylogenetic analysis with the goals of: (1) exploring the relationships among the species of Ceratophryidae; (2) studying the evolution of polyploidy; (3) studying the evolution of cocoon formation and larval development duration associated with surviving in semiarid environments; and (4) reviewing the ceratophryid fossil record that could be relevant as calibration points in molecular divergence estimations. The analysis included 11 of the 12 extant species and, when possible, multiple exemplars per species, as well as multiple outgroups. Sequence data were obtained on seven mitochondrial and six nuclear genes for up to 8200 bp per specimen. Our results indicate that the individual monophyly of Ceratophrys and Lepidobatrachus is well corroborated. The monotypic Chacophrys is recovered as the sister taxon of Lepidobatrachus, but with Jackknife frequency < 50%. Lepidobatrachus asper is the sister taxon of L. laevis + L. llanensis. Relationships within Ceratophrys are congruent with an earlier proposal, with a clade composed of the species possessing a dorsal bony shield (Ce. aurita, Ce. cranwelli, Ce. joazeirensis, and Ce. ornata), and another clade composed of Ce. stolzmanni, Ce. calcarata, and Ce. cornuta. Unlike earlier proposals, the octoploid species (Ce. aurita, Ce. joazeirensis, and Ce. ornata) are not monophyletic, as the diploid Ce. cranwelli, and Ce. ornata are sister taxa. This result implies an ambiguous optimization of ploidy levels, with either a single origin of octoploidy with a subsequent reversal to diploidy, or two independent origins of octoploidy being equally parsimonious; both alternatives are quite unusual from the perspective of chromosome evolution. Our results suggest that ceratophryids diversified in semiarid environments and three independent events resulted in three species subsequently occupying temperate or tropical humid areas. This early diversification in semiarid areas explains the retention of characteristics associated with these environments (like the production of a cocoon of dead skin during estivation, and possibly an accelerated larval period and development) in species present in humid areas. A revision of the fossil record of this family of frogs indicates that there are only two fossil remains that could serve as calibration points for molecular clock estimation, but a number of issues associated with them preclude their use.