Boris L. Blotto

Is The Amphibian Tree of Life really fatally flawed

Wiens (2007 , Q. Rev. Biol. 82, 55–56) recently published a severe critique of Frost et al.s (2006, Bull. Am. Mus. Nat. Hist. 297, 1–370) monographic study of amphibian systematics, concluding that it is “a disaster” and recommending that readers “simply ignore this study”. Beyond the hyperbole, Wiens raised four general objections that he regarded as “fatal flaws”: (1) the sampling design was insufficient for the generic changes made and taxonomic changes were made without including all type species; (2) the nuclear gene most commonly used in amphibian phylogenetics, RAG‐1, was not included, nor were the morphological characters that had justified the older taxonomy; (3) the analytical method employed is questionable because equally weighted parsimony “assumes that all characters are evolving at equal rates”; and (4) the results were at times “clearly erroneous”, as evidenced by the inferred non‐monophyly of marsupial frogs. In this paper we respond to these criticisms. In brief: (1) the study of Frost et al. did not exist in a vacuum and we discussed our evidence and evidence previously obtained by others that documented the non‐monophyletic taxa that we corrected. Beyond that, we agree that all type species should ideally be included, but inclusion of all potentially relevant type species is not feasible in a study of the magnitude of Frost et al. and we contend that this should not prevent progress in the formulation of phylogenetic hypotheses or their application outside of systematics. (2) Rhodopsin, a gene included by Frost et al. is the nuclear gene that is most commonly used in amphibian systematics, not RAG‐1. Regardless, ignoring a study because of the absence of a single locus strikes us as unsound practice. With respect to previously hypothesized morphological synapomorphies, Frost et al. provided a lengthy review of the published evidence for all groups, and this was used to inform taxonomic decisions. We noted that confirming and reconciling all morphological transformation series published among previous studies needed to be done, and we included evidence from the only published data set at that time to explicitly code morphological characters (including a number of traditionally applied synapomorphies from adult morphology) across the bulk of the diversity of amphibians (Haas, 2003, Cladistics 19, 23–90). Moreover, the phylogenetic results of the Frost et al. study were largely consistent with previous morphological and molecular studies and where they differed, this was discussed with reference to the weight of evidence. (3) The claim that equally weighted parsimony assumes that all characters are evolving at equal rates has been shown to be false in both analytical and simulation studies. (4) The claimed “strong support” for marsupial frog monophyly is questionable. Several studies have also found marsupial frogs to be non‐monophyletic. Wiens et al. (2005, Syst. Biol. 54, 719–748) recovered marsupial frogs as monophyletic, but that result was strongly supported only by Bayesian clade confidence values (which are known to overestimate support) and bootstrap support in his parsimony analysis was < 50%. Further, in a more recent parsimony analysis of an expanded data set that included RAG‐1 and the three traditional morphological synapomorphies of marsupial frogs, Wiens et al. (2006, Am. Nat. 168, 579–596) also found them to be non‐monophyletic. Although we attempted to apply the rule of monophyly to the naming of taxonomic groups, our phylogenetic results are largely consistent with conventional views even if not with the taxonomy current at the time of our writing. Most of our taxonomic changes addressed examples of non‐monophyly that had previously been known or suspected (e.g., the non‐monophyly of traditional Hyperoliidae, Microhylidae, Hemiphractinae, Leptodactylidae, Phrynobatrachus, Ranidae, Rana, Bufo; and the placement of Brachycephalus within “Eleutherodactylus”, and Lineatriton within “Pseudoeurycea”), and it is troubling that Wiens and others, as evidenced by recent publications, continue to perpetuate recognition of non‐monophyletic taxonomic groups that so profoundly misrepresent what is known about amphibian phylogeny.

Big, Bad, and Beautiful: Phylogenetic Relationships of the Horned Frogs (Anura: Ceratophryidae)

Abstract. 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.

Phylogenetic relationships of toads of the Rhinella granulosa group (Anura: Bufonidae): a molecular perspective with comments on hybridization and introgression

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.

The complex evolutionary history of the tympanic middle ear in frogs and toads (Anura)

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 Tadpole of Rhinella azarai (Gallardo, 1965) with Comments on Larval Morphology in the Rhinella granulosa Species Group (Anura: Bufonidae)

Abstract We describe the larval morphology of Rhinella azarai, a medium-sized species of the Rhinella granulosa group. None of the morphological characters allow the larvae of R. azarai to be distinguished unequivocally from those of other species in the group. However, the tadpoles show a distinctive set of character states shared with some species of the group, which may represent putative synapomorphies of the R. granulosa group or internal clades.

Concentrated evolutionary novelties in the foot musculature of Odontophrynidae (Anura: Neobatrachia), with comments on adaptations for burrowing

We studied the foot musculature of the fossorial family Odontophrynidae (composed of the genera Macrogenioglottus, Odontophrynus, and Proceratophrys) plus several outgroup taxa from Hyloidea and other burrowing taxa from across Anura. We found novel character-states supporting the monophyly of Odontophrynus, Proceratophrys, and Odontophrynus + Macrogenioglottus. The character-states observed in O. cultripes support conflicting phylogenetic positions within Odontophrynus. A comparison of some novel character-states with a diverse sample of burrowing taxa suggests that some modifications of the foot musculature might be involved in digging.

On the Monophyly and Relationships of Several Genera of Hylini (Anura: Hylidae: Hylinae), with Comments on Recent Taxonomic Changes in Hylids

Abstract. 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.

Occurrence of Tachymenis chilensis chilensis (Schlegel, 1837) (Reptilia: Serpentes: Dipsadidae) and other herpetological fauna from Epu Lauquen Natural Protected Area, Neuquén, Argentina

We report a new specimen of Tachymenis chilensis chilensis from Epu Lauquen Natural Reserve, Neuquen, Argentina. This specimen represents the northernmost voucher of T. c. chilensis in Argentina and confirms the presence of the subspecies occupying moist habitats remnants in dry areas of northern Neuquen province. Moreover, this record corresponds to the northernmost population of T. c. chilensis in a protected area in Argentina. We also found two sympatric anurans, Rhinella spinulosa and Pleurodema thaul . Both anurans also represent the first record of amphibians at Epu Lauquen Natural Reserve.