A paradigm shift in our view of species drives current trends in biological classification.

Discontent about changes in species classifications has grown in recent years. Many of these changes are seen as arbitrary, stemming from unjustified conceptual and methodological grounds, or leading to species that are less distinct than those recognised in the past. We argue that current trends in species classification are the result of a paradigm shift toward which systematics and population genetics have converged and that regards species as the phylogenetic lineages that form the branches of the Tree of Life.

The advertisement call of the treefrog Nyctimantis rugiceps Boulenger, 1882 (Anura: Hylidae), with notes on its natural history and toxicity.

Nyctimantis rugiceps Boulenger, 1882 (Fig. 1A) is a Neotropical treefrog (Duellman Trueb 1976; Faivovich et al. 2005) known only from disjunct localities in Amazonian Colombia, Ecuador, and Peru (Pérez-Villota et al.

A new species of Phrynopus from the northeastern Andes of Peru, its phylogenetic position, and notes on the relationships of Holoadeninae (Anura: Craugastoridae).

We report the discovery of a geographically disjunct and morphologically distinctive species of direct-developing frog of the genus Phrynopus (Phrynopus mariellaleo sp. nov.) that changes considerably our understanding of the distribution of species in this Andean genus.

A new morphologically cryptic species of Phyllomedusa (Anura: Phyllomedusidae) from Amazonian forests of northern Peru revealed by DNA sequences.

We describe and name Phyllomedusa chaparroi sp. nov., a medium-sized species (snout-vent length in adult males 67.

A new species of poison-dart frog (Anura: Dendrobatidae) from Manu province, Amazon region of southeastern Peru, with notes on its natural history, bioacoustics, phylogenetics, and recommended conservation status.

We describe and name a new species of poison-dart frog from the Amazonian slopes of the Andes in Manu Province, Madre de Dios Department, Peru; specifically within the Amarakaeri Communal Reserve and the buffer zone of Manu National Park. Ameerega shihuemoy sp. nov.

Molecular systematics of teioid lizards (Teioidea/Gymnophthalmoidea: Squamata) based on the analysis of 48 loci under tree-alignment and similarity-alignment.

We infer phylogenetic relationships within Teioidea, a superfamily of Nearctic and Neotropical lizards, using nucleotide sequences. Phylogenetic analyses relied on parsimony under tree-alignment and similarity-alignment, with length variation (i.e.

Phylogenetic systematics of egg-brooding frogs (Anura: Hemiphractidae) and the evolution of direct development.

Egg-brooding frogs (Hemiphractidae) are a group of 105 currently recognized Neotropical species, with a remarkable diversity of developmental modes, from direct development to free-living and exotrophic tadpoles. Females carry their eggs on the back and embryos have unique bell-shaped gills. We inferred the evolutionary relationships of these frogs and used the resulting phylogeny to review their taxonomy and test hypotheses on the evolution of developmental modes and bell-shaped gills.

A new species of Andean frog of the genus Bryophryne from southern Peru Anura: Craugastoridae) and its phylogenetic position, with notes on the diversity of the genus.

We describe a new species of terrestrial frog of the genus Bryophryne (Anura: Craugastoridae) from the wet puna and elfin forests of the Amazonian versant of the Andes. The new species seems to be restricted to high altitude environments at elevations between 3506-3651 m in the area now protected by Megantoni National Sanctuary and Manu National Park (Distrito de Echarate, Provincia La Convención, Departamento Cusco, Peru). The new species is characterized by lacking vomerine processes of vomers, by having tympanic annulus and tympanic membrane not evident through the skin, smooth dorsal skin with scattered warts, conspicuous dorsolateral, middorsal, and occipital folds, warty flanks, areolate skin on ventral surfaces of the body, and by lacking finger and toe fringes and basal web on feet.

Molecular systematics of terraranas (Anura: Brachycephaloidea) with an assessment of the effects of alignment and optimality criteria.

Brachycephaloidea is a monophyletic group of frogs with more than 1000 species distributed throughout the New World tropics, subtropics, and Andean regions. Recently, the group has been the target of multiple molecular phylogenetic analyses, resulting in extensive changes in its taxonomy. Here, we test previous hypotheses of phylogenetic relationships for the group by combining available molecular evidence (sequences of 22 genes representing 431 ingroup and 25 outgroup terminals) and performing a tree-alignment analysis under the parsimony optimality criterion using the program POY.

Molecular phylogenetics, species diversity, and biogeography of the Andean lizards of the genus Proctoporus (Squamata: Gymnophthalmidae).

The family Gymnophthalmidae comprises ca. 220 described species of Neotropical lizards distributed from southern Mexico to Argentina. It includes 36 genera, among them Proctoporus, which contains six currently recognized species occurring across the yungas forests and wet montane grasslands of the Amazonian versant of the Andes from central Peru to central Bolivia.

From Amazonia to the Atlantic forest: molecular phylogeny of Phyzelaphryninae frogs reveals unexpected diversity and a striking biogeographic pattern emphasizing conservation challenges.

Documenting the Neotropical amphibian diversity has become a major challenge facing the threat of global climate change and the pace of environmental alteration. Recent molecular phylogenetic studies have revealed that the actual number of species in South American tropical forests is largely underestimated, but also that many lineages are millions of years old. The genera Phyzelaphryne (1 sp.

Phylogeny of North African Agama lizards (Reptilia: Agamidae) and the role of the Sahara desert in vertebrate speciation.

The origin of Saharan biodiversity is poorly understood, in part because the geological and paleoclimatic events that presumably shaped species diversity are still controversial, but also because few studies have explored causal explanations for the origin of Saharan diversity using a phylogenetic framework. Here, we use mtDNA (16S and ND4 genes) and nDNA (MC1R and CMOS genes) to infer the relationships and biogeographic history of North African agamas (genus Agama). Agamas are conspicuous, diverse and abundant African lizards that also occur in the Saharan xeric and mesic environments.

The integrative future of taxonomy.

Background: Taxonomy is the biological discipline that identifies, describes, classifies and names extant and extinct species and other taxa. Nowadays, species taxonomy is confronted with the challenge to fully incorporate new theory, methods and data from disciplines that study the origin, limits and evolution of species.

Results: Integrative taxonomy has been proposed as a framework to bring together these conceptual and methodological developments.

Tests of biogeographic hypotheses for diversification in the Amazonian forest frog, Physalaemus petersi.

Several hypotheses have been proposed to explain the biogeographic processes that generate the high species richness of the Amazon basin. We tested two of them in a terra firme (upland) forest frog species, Physalaemus petersi: (1) the riverine barrier hypothesis; and (2) the elevational gradient hypothesis. Mitochondrial DNA sequence data (2.