The phylogeny of Dendropsophini (Anura: Hylidae: Hylinae).

The relationships of the hyline tribe Dendropsophini remain poorly studied, with most published analyses dealing with few of the species groups of Dendropsophus. In order to test the monophyly of Dendropsophini, its genera, and the species groups currently recognized in Dendropsophus, we performed a total evidence phylogenetic analysis. The molecular dataset included sequences of three mitochondrial and five nuclear genes from 210 terminals, including 12 outgroup species, the two species of Xenohyla, and 93 of the 108 recognized species of Dendropsophus. The phenomic dataset includes 46 terminals, one per species (34 Dendropsophus, one Xenohyla, and 11 outgroup species). Our results corroborate the monophyly of Dendropsophini and the reciprocal monophyly of Dendropsophus and Xenohyla. Some species groups of Dendropsophus are paraphyletic (the D. microcephalus, D. minimus, and D. parviceps groups, and the D. rubicundulus clade). On the basis of our results, we recognize nine species groups; for three of them (D. leucophyllatus, D. microcephalus, and D. parviceps groups) we recognize some nominal clades to highlight specific morphology or relationships and facilitate species taxonomy. We further discuss the evolution of oviposition site selection, where our results show multiple instances of independent evolution of terrestrial egg clutches during the evolutionary history of Dendropsophus.

Phylogenetic relationships of the Boana pulchella Group (Anura: Hylidae).

In this paper we present a phylogenetic analysis of the treefrogs of the Boana pulchella Group with the goals of (1) providing a rigorous test of its monophyly; (2) providing a test of relationships supported in previous studies; and (3) exploring the relationships of the several species not included in previous analyses. The analyses included>300 specimens of 37 of the 38 species currently included in the group, plus 36 outgroups, exemplars of the diversity of Boana and the other genera of the hylid tribe Cophomantini. The dataset included eight mitochondrial genes (12S, 16S, CytB, COI, ND1, tRNAIle, tRNALeu, and tRNAVal) and five nuclear genes (RHO, TYR, RAG-1, CXCR4, SIAH1). The phylogenetic analyses recover the monophyly of the B. pulchella Group with lower support than previous studies, as a result of the inclusion of the B. claresignata Group, which is recovered as its sister taxon. Within the B. pulchella Group, the inclusion of almost all species of the group had little impact on previous notions of its phylogeny, except for the rejection of the hypothesized B. polytaenia Clade (B. goiana and B. phaeopleura are nested in the clade here called the B. prasina Clade), which is redefined. Phylogenetic support is strong for five major clades, which collectively include all but three of the species sampled: the B. balzani Clade (B. aguilari, B. balzani, B. gladiator, B. melanopleura, B. palaestes), the redefined B. polytaenia Clade (B. botumirim, B. buriti, B. cipoensis, B. jaguariaivensis, B. leptolineata, B. polytaenia, B. stenocephala, and two undescribed species), the B. prasina Clade (B. bischoffi, B. caingua, B. cordobae, B. goiana, B. guentheri, B. marginata, B. phaeopleura, B. prasina, B. pulchella, and one undescribed species), the B. riojana Clade (B. callipleura, B. marianitae, B. riojana), and the B. semiguttata Clade (B. caipora, B. curupi, B. joaquini, B. poaju, B. semiguttata, B. stellae, and two undescribed species). The monophyly of the B. prasina + B. riojana Clades, and that of the B. polytaenia + B. semiguttata Clades are well-supported. The relationships among these two clades, the B. balzani Clade, B. ericae + B. freicanecae, and B. cambui (representing the deepest phylogenetic splits within the B. pulchella Group) are recovered with weak support. We discuss the phenotypic evidence supporting the monophyly of the B. pulchella Group, and the taxonomy of several species, identifying three new synonyms of Boana polytaenia, one new synonym of Boana goiana, and one new synonym of B. riojana.

Preliminary phylogenetic analysis of the Andean clade and the placement of new Colombian blueberries (Ericaceae, Vaccinieae).

The blueberry tribe Vaccinieae (Ericaceae) is particularly diverse in South America and underwent extensive radiation in Colombia where many endemics occur. Recent fieldwork in Colombia has resulted in valuable additions to the phylogeny and as well in the discovery of morphologically noteworthy new species that need to be phylogenetically placed before being named. This is particularly important, as the monophyly of many of the studied genera have not been confirmed. In order to advance our understanding of the relationships within neotropical Vaccinieae and advice the taxonomy of the new blueberry relatives, here we present the most comprehensive phylogenetic analysis for the Andean clade. Anthopterus, Demosthenesia, and Pellegrinia are among the putative Andean genera recovered as monophyletic, while other eight Andean genera were not. The analyses also showed that genera that have been traditionally widely defined are non-monophyletic and could be further split into more discrete groups. Four newly discovered Colombian Vaccinieae are placed in the monophyletic Satyria s.s. and the Psammisia I clade. Although these new species are endemic to the Colombian Western Cordillera and Chocó biogeographic region and three are not known outside of Las Orquídeas National Park, they do not form sister pairs.

Phylogenetic relationships of a Patagonian frog radiation, the Alsodes + Eupsophus clade (Anura: Alsodidae), with comments on the supposed paraphyly of Eupsophus.

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.

A phylogenetic analysis of Pleurodema (Anura: Leptodactylidae: Leiuperinae) based on mitochondrial and nuclear gene sequences, with comments on the evolution of anuran foam nests.

Species of the genus Pleurodema are relatively small, plump frogs that mostly occur in strong-seasonal and dry environments. The genus currently comprises 14 species distributed from Panama to southern Patagonia. Here we present a phylogenetic analysis of Pleurodema, including all described species and several outgroups. Our goals include testing its monophyly and the monophyly of the species groups that were historically proposed, and studying the evolution of some character systems, particularly macroglands and egg-clutch structure; this last point also provided the chance for a discussion of foam nest evolution in anurans. Our dataset includes portions of the mitochondrial genes cytochromeb, 12S, 16S, and the intervening tRNAVal ; the nuclear gene sequences include portions of rhodopsin exon 1 and seven in absentia homolog I. Our results support a clade composed of Pleurodema and including the monotypic SomuncuriaLynch, 1978 nested within it. The latter genus is therefore considered a junior synonym of Pleurodema and its sole species is added to this genus. Furthermore, our results indicate the non-monophyly of several species groups proposed previously. We recognize four clades in Pleurodema: the P. bibroni clade (P. bibroni, P. cordobae and P. kriegi), the P. thaul clade (P. bufoninum, P. marmoratum, P. somuncurensis and P. thaul), the P. brachyops clade (P. alium, P. borellii, P. brachyops, P. cinereum, P. diplolister and P. tucumanum) and the P. nebulosum clade (P. guayapae and P. nebulosum). Our results further indicate the need for a taxonomic reassessment of P. borellii and P. cinereum (as did previous studies), P. guayapae and P. nebulosum, and the three species in the P. bibroni clade. Pleurodema shows a striking pattern of variation in presence/absence of lumbar glands. Our results indicate multiple losses or independent gains of this character associated with defensive displays. The reproductive modes of Pleurodema include four different egg-clutch structures. The optimization of these indicates that there are at least two independent transformations from the plesiomorphic mode of foam nests to egg-clutch structures involving gelatinous masses of different sorts (ovoid plates, masses, or strings). We hypothesize that these independent transformations could involve changes at the behavioural (the loss of foam beating behaviour by the parent) and/or structural level (transformations involving the pars convoluta dilata, the section of the oviduct where the foam-making substance is secreted). Finally, our study of foam nest evolution in Pleurodema is extended to the other groups of anurans where foam-nesting occurs, on the basis of available data and recent phylogenetic hypotheses. In the different hyloid groups where it occurs, foam-nesting evolved from clutches laid in water. However, in all ranoids in which foam-nesting occurs, it evolved from terrestrial clutches, with eggs laid hanging in vegetation, or, if the clutches are laid on a restricted volume of water, involving endotrophic development. © The Willi Hennig Society 2012.

Phylogenetic relationships of family groups in Pentatomoidea based on morphology and DNA sequences (Insecta: Heteroptera).

Phylogenetic relationships within the Pentatomoidea are investigated through the coding and analysis of character data derived from morphology and DNA sequences. In total, 135 terminal taxa were investigated, representing most of the major family groups; 84 ingroup taxa are coded for 57 characters in a morphological matrix. As many as 3500 bp of DNA data are adduced for each of 52 terminal taxa, including 44 ingroup taxa, comprising the 18S rRNA, 16S rRNA, 28S rRNA, and COI gene regions. Character data are analysed separately and in the form of a total evidence analysis. Major conclusions of the phylogenetic analysis include: the concept of Urostylididae is restricted to that of earlier authors; the Saileriolinae is raised to family rank and treated as the sister group of all Pentatomoidea exclusive of Urostylididae sensu stricto; a broadly conceived Cydnidae, as recognized by Dolling, 1981, is not supported; the placement of Thaumastellidae within the Pentatomoidea is affirmed and the taxon is recognized at family rank rather than as a subfamily of Cydnidae, although its exact phylogenetic position within the Pentatomoidea remains equivocal; the Parastrachiinae is treated as also including Dismegistus Amyot & Serville and placed within a broadly conceived Corimelaenidae, the latter group being treated at family rank; the family-group taxa Dinidoridae and Tessaratomidae probably represent a monophyletic group, but the recognition of monophyletic subgroups will benefit from additional representation in the sequence data set; and the Lestoniidae is treated as the sister group of the Acanthosomatidae. The Acanthosomatidae and Scutelleridae are consistently recovered as monophyletic. The monophyly of the Pentatomidae appears unequivocal, inclusive of the Aphylinae and Cyrtocorinae, on the basis of morphology, the latter two taxa not being represented in the molecular data set. © The Willi Hennig Society 2008.

Linking of digital images to phylogenetic data matrices using a morphological ontology.

Images are paramount in documentation of morphological data. Production and reproduction costs have traditionally limited how many illustrations taxonomy could afford to publish, and much comparative knowledge continues to be lost as generations turn over. Now digital images are cheaply produced and easily disseminated electronically but pose problems in maintenance, curation, sharing, and use, particularly in long-term data sets involving multiple collaborators and institutions. We propose an efficient linkage of images to phylogenetic data sets via an ontology of morphological terms; an underlying, fine-grained database of specimens, images, and associated metadata; fixation of the meaning of morphological terms (homolog names) by ostensive references to particular taxa; and formalization of images as standard views. The ontology provides the intellectual structure and fundamental design of the relationships and enables intelligent queries to populate phylogenetic data sets with images. The database itself documents primary morphological observations, their vouchers, and associated metadata, rather than the conventional data set cell, and thereby facilitates data maintenance despite character redefinition or specimen reidentification. It minimizes reexamination of specimens, loss of information or data quality, and echoes the data models of web-based repositories for images, specimens, and taxonomic names. Confusion and ambiguity in the meanings of technical morphological terms are reduced by ostensive definitions pointing to features in particular taxa, which may serve as reference for globally unique identifiers of characters. Finally, the concept of standard views (an image illustrating one or more homologs in a specific sex and life stage, in a specific orientation, using a specific device and preparation technique) enables efficient, dynamic linkage of images to the data set and automatic population of matrix cells with images independently of scoring decisions.

A molecular perspective on the phylogeny of the Hyla pulchella species group (Anura, Hylidae).

A molecular phylogenetic analysis of the Hyla pulchella species group was performed to test its monophyly, explore the interrelationships of its species, and evaluate the validity of the taxa that were considered subspecies of H. pulchella. Approximately 2.8 kb from the mitochondrial genes 12s, tRNA valine, 16s, and Cytochrome b were sequenced. The analysis included 50 terminals representing 10 of the 14-15 species currently recognized in the H. pulchella group, including samples from several localities for some taxa, several outgroups, as well as two species previously suspected to be related with the group (Hyla guentheri and Hyla bischoffi). The results show that the H. pulchella and Hyla circumdata groups are distantly related, and, therefore, should be recognized as separate groups. As currently defined, the H. pulchella group is paraphyletic with respect to the Hyla polytaenia group; therefore, we recognize the Hyla polytaenia clade in the H. pulchella group. Two subspecies of H. pulchella recognized by some authors are considered full species including Hyla pulchella riojana because it is only distantly related to H. pulchella, and Hyla pulchella cordobae because molecular and non-molecular evidence suggests that it is specifically distinct. With the inclusion of the H. polytaenia clade, H. guentheri, and H. bischoffi, and the recognition of the two former subspecies of H. pulchella as distinct species, the H. pulchella group now comprises 25 described species. All representatives of the H. pulchella group with an Andean distribution are monophyletic and nested within a clade from the Atlantic forest from south-southeastern Brazil/northeastern Argentina, and Cerrado gallery forest from central Brazil.