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AIM: We investigate the biogeographical history and diversification in a treefrog lineage distributed in contrasting (open and forested) ecoregions of South America, including three biodiversity hotspots. We evaluate the role of dispersal and whether other factors such as diversity‐dependence or paleotemperatures could explain the diversification pattern for this group. Especially focusing on the savanna endemics, we illuminate the processes governing the species assembly and evolution of the Cerrado savanna. LOCATION: South American ecoregions south of the Amazon (i.e. Atlantic Forest, Cerrado, Araucaria Forest, Pampas, Central and Southern Andes). TAXON: Boana pulchella group. METHODS: We built the most complete time‐calibrated phylogeny for the group to date. We then reconstructed ancestral ranges using the dispersal‐extinction‐cladogenesis (DEC) model comparing different dispersal scenarios considering distance, adjacency and ecological similarity among regions. Centre‐of‐origin hypotheses in forest and open ecoregions were also tested. Using biogeographical stochastic mapping, we additionally estimated the contribution of range shifts across different biomes. Lastly, we evaluated several diversification models, including the effect of time, diversity‐dependence and temperature‐dependence on speciation and extinction rates. RESULTS: The Boana pulchella group originated during the Early Miocene (~17.5 MYA) and underwent high speciation rates during the Middle Miocene Climatic Optimum, with a decreasing trend following the Miocene Climatic Transition. We found no support for a single ecoregion acting as a centre of origin and diversification; instead, we inferred recurrent range shifts with dispersal among dissimilar adjacent ecoregions. Speciation linearly dependent on paleotemperatures, with either no or very low constant extinction rates, best explained the slowdown diversification pattern. MAIN CONCLUSIONS: Our results support a species assembly of Cerrado savanna in South America during the Miocene with intermittent interchange with rain forest habitats. Past climate changes impacted the rate new species originated with apparently no impact on extinction. Finally, the repeated habitat shifts among open/dry and forested/humid ecoregions, rather than long‐term in‐situ diversification in single areas, highlights the very dynamic historical interchange between contrasting habitats in South America, possibly contributing to its high species diversity.

The sequestration by neotropical poison frogs (Dendrobatidae) of an amazing array of defensive alkaloids from oribatid soil mites has motivated an exciting research theme in chemical ecology, but the details of mite-to-frog transfer remain hidden. To address this, McGugan et al. (2016, Journal of Chemical Ecology 42:537-551) used the little devil poison frog (Oophaga sylvatica) and attempted to simultaneously characterize the prey mite alkaloids, the predator skin alkaloids, and identify the mites using DNA sequences. Heethoff et al. (2016, Journal of Chemical Ecology 42:841-844) argued that none of the mite families to which McGugan et al. allocated the prey was thought to possess alkaloids. Heethoff et al. concluded from analyses including additional sequences that the mite species were unlikely to be close relatives of the defended mites. We re-examine this by applying more appropriate phylogenetic methods to broader and denser taxonomic samples of mite sequences using the same gene (CO1). We found, over trees based on CO1 datasets, only weak support (except in one case) for branches critical to connecting the evolution of alkaloid sequestration with the phylogeny of mites. In contrast, a well-supported analysis of the 18S ribosomal gene suggests at least two independent evolutionary origins of oribatid alkaloids. We point out impediments in the promising research agenda, namely a paucity of genetic, chemical, and taxonomic information, and suggest how phylogenetics can elucidate at a broader level the evolution of chemical defense in prey arthropods, sequestration by predators, and the impact of alkaloids on higher-order trophic interactions.

Groundwater-dependent species are among the least-known components of global biodiversity, as well as some of the most vulnerable because of rapid groundwater depletion at regional and global scales. The karstic Edwards–Trinity aquifer system of west-central Texas is one of the most species-rich groundwater systems in the world, represented by dozens of endemic groundwater-obligate species with narrow, naturally fragmented distributions. Here, we examine how geomorphological and hydrogeological processes have driven population divergence and speciation in a radiation of salamanders ( Eurycea ) endemic to the Edwards–Trinity system using phylogenetic and population genetic analysis of genome-wide DNA sequence data. Results revealed complex patterns of isolation and reconnection driven by surface and subsurface hydrology, resulting in both adaptive and nonadaptive population divergence and speciation. Our results uncover cryptic species diversity and refine the borders of several threatened and endangered species. The US Endangered Species Act has been used to bring state regulation to unrestricted groundwater withdrawals in the Edwards (Balcones Fault Zone) Aquifer, where listed species are found. However, the Trinity and Edwards–Trinity (Plateau) aquifers harbor additional species with similarly small ranges that currently receive no protection from regulatory programs designed to prevent groundwater depletion. Based on regional climate models that predict increased air temperature, together with hydrologic models that project decreased springflow, we conclude that Edwards–Trinity salamanders and other codistributed groundwater-dependent organisms are highly vulnerable to extinction within the next century.

Rapid radiation coupled with low genetic divergence often hinders species delimitation and phylogeny estimation even if putative species are phenotypically distinct. Some aposematic species, such as poison frogs (Dendrobatidae), have high levels of intraspecific color polymorphism, which can lead to overestimation of species when phenotypic divergence primarily guides species delimitation. We explored this possibility in the youngest origin of aposematism (3–7 MYA) in poison frogs, Epipedobates, by comparing genetic divergence with color and acoustic divergence. We found low genetic divergence (2.6% in the 16S gene) despite substantial differences in color and acoustic signals. While chemical defense is inferred to have evolved in the ancestor of Epipedobates, aposematic coloration evolved at least twice or was lost once in Epipedobates, suggesting that it is evolutionarily labile. We inferred at least one event of introgression between two cryptically colored species with adjacent ranges (E. boulengeri and E. machalilla). We also find evidence for peripheral isolation resulting in phenotypic divergence and potential speciation of the aposematic E. tricolor from the non-aposematic E. machalilla. However, we were unable to estimate a well-supported species tree or delimit species using multispecies coalescent models. We attribute this failure to factors associated with recent speciation including mitochondrial introgression, incomplete lineage sorting, and too few informative molecular characters. We suggest that species delimitation within young aposematic lineages such as Epipedobates will require genome-level molecular studies. We caution against relying solely on DNA barcoding for species delimitation or identification and highlight the value of phenotypic divergence and natural history in delimiting species.

We present a near comprehensive, densely sampled, multilocus phylogenetic estimate of species relationships within the anuran family Ceratobatrachidae, a morphologically and ecologically diverse group of frogs from the island archipelagos of Southeast Asia and the South-West Pacific. Ceratobatrachid frogs consist of three clades: a small clade of enigmatic, primarily high-elevation, semi-aquatic Sundaland species currently assigned to Ingerana (for which we erect a new genus), which is the sister taxon of two large, monophyletic radiations, each situated on islands on either side of Wallace's Line. One radiation is composed of Philippine species of Platymantis and the other contains all taxa from the eastern Indonesian, New Guinean, Solomon, Bismarck, and Fijian archipelagos. Several additional genera (Batrachylodes, Discodeles, Ceratobatrachus, and Palmatorappia) are nested within Platymantis, and of these Batrachylodes and Discodeles are nonmonophyletic. To address the widespread paraphyly of the genus Platymantis and several additional nomenclatural issues, we undertook a wholesale nomenclatural reorganization of the family. Given our partially unresolved phylogeny, and in order to impart a conservative, stable taxonomy, involving a minimal number of genus-species couplet changes, we propose a conservative classification representing a few compromises. These changes are designed to preserve maximally the presumed original intent of taxonomy (widely used group names associated with morphological and ecological diversity of particular species or groups of species) while implementing a hierarchical system that is consistent with the estimate of phylogeny based on new molecular data. © 2015 The Linnean Society of London

The Neotropical leaf litter frog genus Pristimantis is very species-rich, with 526 species described to date, but the full extent of its diversity is much higher and remains unknown. This study explores the phylogenetic processes and resulting evolutionary patterns of diversification in Pristimantis. Given the well-recognised failure of morphology- and community-based species groups to describe diversity within the genus, we apply a new test for the presence and phylogenetic distribution of higher evolutionary units. We developed a phylogeny based on 260 individuals encompassing 149 Pristimantis presumed species, sampled at mitochondrial and nuclear genes (3718 base pair alignment), combining new and available sequence data. Our phylogeny broadly agrees with previous studies, both in topology and age estimates, with the origin of Pristimantis at 28.97 (95% HDP =21.59 – 37.33) million years ago (MYA). New taxa that we add to the genus, which had not previously been included in Pristimantis phylogenies, suggest considerable diversity remains to be described. We assessed patterns of lineage origin and recovered 14 most likely (95% CI: 13–19) phylogenetic clusters or higher evolutionary significant units (hESUs) within Pristimantis. Diversification rates decrease towards the present following a density-dependent pattern for Pristimantis overall and for most hESU clusters, reflecting historical evolutionary radiation. The timing of diversification suggests that geological events in the Miocene, such as Andes orogenesis and Pebas system formation and drainage, may have had a direct or indirect impact on the evolution of Pristimantis and thus contributed to the origins of evolutionary independent phylogenetic clusters.

The tepuis of South America are massive flattop mountains with cliffs up to 1000m and summits up to 3100m. Tepuis hold enormous endemicity levels, but little is known about the origins of the endemic flora and fauna. Recently diverged lineages offer the possibility of understanding the origins of summit endemicity by examining population dynamics and dispersal. We examine species delimitation, clade relationships, and demographic patterns of three recently diverged lineages of Tepuihyla, an endemic treefrog clade. These three lineages represent two currently recognized species, T. edelcae and T. rodriguezi. Given the low divergences in both nuclear and mitochondrial genes among lineages, we find unexpectedly high numbers of unique nuclear haplotypes and moderate levels of lineage sorting. We also find support from multiple analyses for a cryptic, undescribed summit species within T. edelcae. We suggest that the genetic and distribution patterns of the four most recently diverged Tepuihyla lineages support a concurrent speciation event during the Pliocene, and suggest a biogeographic hypothesis in which a widespread climatic change made mid- and low-elevation habitat unsuitable for the common ancestor within the timeframe of their divergence.

Published data from DNA sequences, morphology of 11 extant and 15 extinct frog taxa, and stratigraphic ranges of fossils were integrated to open a window into the deep-time evolution of Xenopus. The ages and morphological characters of fossils were used as independent datasets to calibrate a chronogram. We found that DNA sequences, either alone or in combination with morphological data and fossils, tended to support a close relationship between Xenopus and Hymenochirus, although in some analyses this topology was not significantly better than the Pipa + Hymenochirus topology. Analyses that excluded DNA data found strong support for the Pipa + Hymenochirus tree. The criterion for selecting the maximum age of the calibration prior influenced the age estimates, and our age estimates of early divergences in the tree of frogs are substantially younger than those of published studies. Node-dating and tip-dating calibrations, either alone or in combination, yielded older dates for nodes than did a root calibration alone. Our estimates of divergence times indicate that overwater dispersal, rather than vicariance due to the splitting of Africa and South America, may explain the presence of Xenopus in Africa and its closest fossil relatives in South America.

Frogs (Anura) are one of the most diverse groups of vertebrates and comprise nearly 90% of living amphibian species. Their worldwide distribution and diverse biology make them well-suited for assessing fundamental questions in evolution, ecology, and conservation. However, despite their scientific importance, the evolutionary history and tempo of frog diversification remain poorly understood. By using a molecular dataset of unprecedented size, including 88-kb characters from 95 nuclear genes of 156 frog species, in conjunction with 20 fossil-based calibrations, our analyses result in the most strongly supported phylogeny of all major frog lineages and provide a timescale of frog evolution that suggests much younger divergence times than suggested by earlier studies. Unexpectedly, our divergence-time analyses show that three species-rich clades (Hyloidea, Microhylidae, and Natatanura), which together comprise ∼88% of extant anuran species, simultaneously underwent rapid diversification at the Cretaceous-Paleogene (K-Pg) boundary (KPB). Moreover, anuran families and subfamilies containing arboreal species originated near or after the KPB. These results suggest that the K-Pg mass extinction may have triggered explosive radiations of frogs by creating new ecological opportunities. This phylogeny also reveals relationships such as Microhylidae being sister to all other ranoid frogs and African continental lineages of Natatanura forming a clade that is sister to a clade of Eurasian, Indian, Melanesian, and Malagasy lineages. Biogeographical analyses suggest that the ancestral area of modern frogs was Africa, and their current distribution is largely associated with the breakup of Pangaea and subsequent Gondwanan fragmentation.

Although the impact of Pleistocene glacial cycles on the diversification of the tropical biota was once dismissed, increasing evidence suggests that Pleistocene climatic fluctuations greatly affected the distribution and population divergence of tropical organisms. Landscape genomic analyses coupled with paleoclimatic distribution models provide a powerful way to understand the consequences of past climate changes on the present-day tropical biota. Using genome-wide SNP data and mitochondrial DNA, combined with projections of the species distribution across the late Quaternary until the present, we evaluate the effect of paleoclimatic shifts on the genetic structure and population differentiation of Hypsiboas lundii, a treefrog endemic to the South American Cerrado savanna. Our results show a recent and strong genetic divergence in H. lundii across the Cerrado landscape, yielding four genetic clusters that do not seem congruent with any current physical barrier to gene flow. Isolation by distance (IBD) explains some of the population differentiation, but we also find strong support for past climate changes promoting range shifts and structuring populations even in the presence of IBD. Post-Pleistocene population persistence in four main areas of historical stable climate in the Cerrado seems to have played a major role establishing the present genetic structure of this treefrog. This pattern is consistent with a model of reduced gene flow in areas with high climatic instability promoting isolation of populations, defined here as "isolation by instability," highlighting the effects of Pleistocene climatic fluctuations structuring populations in tropical savannas.

Poison frogs resist their own chemical defense Poison frogs produce a neurotoxin that protects them from predation. The frogs, however, run the risk of intoxicating themselves. Studying the frog neurotoxin epibatidine, which binds to acetylcholine receptors, Tarvin et al. found a single amino acid substitution. The substitution changes the configuration of the acetylcholine receptor, so that it decreases its sensitivity to the toxin. But acetylcholine signaling is essential for normal life. Expressing frog receptors in human cells revealed that different amino acid substitutions have occurred in different lineages that allow the frog to resist its own toxins while still letting target neurotransmitters function effectively. Science , this issue p. 1261

In the majority of frogs, males but not females produce vocalizations to attract mates. Sexual selection can influence the evolution of these vocalizations by modifying the frog's morphology. The larynx is the main organ responsible for sound production; thus, it constitutes a target of selection. The goal of this study was to determine qualitatively and quantitatively the sexual differences in the developmental sequence of larynges of Physalaemus pustulosus ( = Engystomops pustulosus). We examined larynges of individuals ranging from recent metamorphs to adults. We provide quantitative measurements of laryngeal area and volume, vocal cords, and fibrous mass 1 (FM1), as well as qualitative descriptions of the developmental origin of vocal cords and FM1. Larynges of small male and female juveniles (less than 16 mm SVL) are similar, both externally and internally. The area of these larynges is no more than 1 mm2; no vocal cords or FM1 are present in either sex at this developmental stage. In individuals lar...

Complex phenotypes typically have a correspondingly multifaceted genetic component. However, the genotype–phenotype association between chemical defense and resistance is often simple: genetic changes in the binding site of a toxin alter how it affects its target. Some toxic organisms, such as poison frogs (Anura: Dendrobatidae), have defensive alkaloids that disrupt the function of ion channels, proteins that are crucial for nerve and muscle activity. Using protein-docking models, we predict that three major classes of poison frog alkaloids (histrionicotoxins, pumiliotoxins, and batrachotoxins) bind to similar sites in the highly conserved inner pore of the muscle voltage-gated sodium channel, Nav1.4. We predict that poison frogs are somewhat resistant to these compounds because they have six types of amino acid replacements in the Nav1.4 inner pore that are absent in all other frogs except for a distantly related alkaloid-defended frog from Madagascar, Mantella aurantiaca. Protein-docking models and comparative phylogenetics support the role of these replacements in alkaloid resistance. Taking into account the four independent origins of chemical defense in Dendrobatidae, phylogenetic patterns of the amino acid replacements suggest that 1) alkaloid resistance in Nav1.4 evolved independently at least five times in these frogs, 2) variation in resistance-conferring replacements is likely a result of differences in alkaloid exposure across species, and 3) functional constraint shapes the evolution of the Nav1.4 inner pore. Our study is the first to demonstrate the genetic basis of autoresistance in frogs with alkaloid defenses.

Complex interactions between topographic heterogeneity, climatic and environmental gradients, and thermal niche conservatism are commonly assumed to indicate the degree of biotic diversification in montane regions. Our aim was to investigate factors that disrupt gene flow between populations and to determine if there is evidence of downslope asymmetric migration in highland frogs with wide elevational ranges and thermal niches. We determined the role of putative impediments to gene flow (as measured by least-cost path (LCP) distances, topographic complexity, and elevational range) in promoting genetic divergence between populations of 2 tropical Andean frog sister species (Dendropsophus luddeckei, N = 114; Dendropsophus labialis, N = 74) using causal modeling and multiple matrix regression. Although the effect of geographic features was species specific, elevational range and LCP distances had the strongest effect on gene flow, with mean effect sizes (Mantel r and regression coefficients β), between 5 and 10 times greater than topographic complexity. Even though causal modeling and multiple matrix regression produced congruent results, the latter provided more information on the contribution of each geographic variable. We found moderate support for downslope migration. We conclude that the climatic heterogeneity of the landscape, the elevational distance between populations, and the inability to colonize suboptimal habitats due to thermal niche conservatism influence the magnitude of gene flow. Asymmetric migration, however, seems to be influenced by life history traits.

Ranaviruses have been implicated in recent declines in global amphibian populations. Compared with the familyIridoviridae, to which the genusRanavirusbelongs, ranaviruses have a wide host range in that species/strains are known to infect fish, amphibians and reptiles, presumably due to recent host-switching events. We used eight sequenced ranavirus genomes and two selection-detection methods (site based and branch based) to identify genes that exhibited signatures of positive selection, potentially due to the selective pressures at play during host switching. We found evidence of positive selection acting on four genes via the site-based method, three of which were newly acquired genes unique to ranavirus genomes. Using the branch-based method, we identified eight additional candidate genes that exhibited signatures ofdN/dS(non-synonymous/synonymous substitution rate) >1 in the clade where intense host switching had occurred. We found that these branch-specific patterns of elevateddN/dSwere enriched in a small group of viral genes that have been acquired most recently in the ranavirus genome, compared with core genes that are shared among all members of the familyIridoviridae. Our results suggest that the group of newly acquired genes in the ranavirus genome may have undergone recent adaptive changes that have facilitated interspecies and interclass host switching.

Living amphibians exhibit a diversity of ecologies, life histories, and species-rich lineages that offers opportunities for studies of adaptive radiation. We characterize a diverse clade of frogs (Kaloula, Microhylidae) in the Philippine island archipelago as an example of an adaptive radiation into three primary habitat specialists or ecotypes. We use a novel phylogenetic estimate for this clade to evaluate the tempo of lineage accumulation and morphological diversification. Because species-level phylogenetic estimates for Philippine Kaloula are lacking, we employ dense population sampling to determine the appropriate evolutionary lineages for diversification analyses. We explicitly take phylogenetic uncertainty into account when calculating diversification and disparification statistics and fitting models of diversification. Following dispersal to the Philippines from Southeast Asia, Kaloula radiated rapidly into several well-supported clades. Morphological variation within Kaloula is partly explained by ecotype and accumulated at high levels during this radiation, including within ecotypes. We pinpoint an axis of morphospace related directly to climbing and digging behaviors and find patterns of phenotypic evolution suggestive of ecological opportunity with partitioning into distinct habitat specialists. We conclude by discussing the components of phenotypic diversity that are likely important in amphibian adaptive radiations.

Most global hotspots of biodiversity and endemism are in montane regions. One explanation is that montane regions have intrinsically higher speciation rates than lowland regions because complex mountain topography and climate variation facilitate genetic isolation among populations. Here, we ask from an intraspecific perspective whether frog species whose haplotypes are connected by topographically/climatically complex regions display strong genetic isolation (greater scaled genetic distances), compared with species whose haplotypes are connected by less complex regions. We analysed published DNA sequences of several frog species from tropical Central and South America for the mitochondrial cob, cox1 and 16S rRNA genes. Pairwise genetic distances among haplotypes within each species were scaled to the geographic distances between each pair of haplotypes. Topographic complexity was positively correlated with scaled genetic distances, and isolation-by-resistance was supported only in species from more topographically complex regions. This suggests that heterogeneous topographies increase landscape resistance, which in turn favours the appearance of isolation-by-resistance. Moreover, we found that the potential barriers that restrict gene flow within species are more closely related to factors associated with temperature and topography than to precipitation.

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 High-Andean Frog (Dendropsophus labialis) is distributed along the Eastern Andes of Colombia between 1900 and 3600 m. We analyzed multiple traits to determine if acoustics and morphology covary with genealogical history or if they evolved following independent trajectories. We generated a phylogeny of D. labialis populations with the use of mitochondrial ribosomal gene (12S, val-RNA, 16S) and nuclear gene (proopiomelanocortin A [POMC]) sequences. Two well-supported clades that correspond to geographic distribution were recovered. Acoustic variation diverges according to genealogical history, but external morphology does not follow this pattern. The strong and congruent divergence observed in acoustic and genetic characters indicates that these two clades correspond to morphologically cryptic, parapatric species. We describe the Northern Clade as a new species (Dendropsophus luddeckei; the Southern Clade retains the name D. labialis). The low level of molecular divergence between two outgroup...

Complex phenotypes can be modeled as networks of component traits connected by genetic, developmental, or functional interactions. Aposematism, which has evolved multiple times in poison frogs (Dendrobatidae), links a warning signal to a chemical defense against predators. Other traits are involved in this complex phenotype. Most aposematic poison frogs are ant specialists, from which they sequester defensive alkaloids. We found that aposematic species have greater aerobic capacity, also related to diet specialization. To characterize the aposematic trait network more fully, we analyzed phylogenetic correlations among its hypothesized components: conspicuousness, chemical defense, diet specialization, body mass, active and resting metabolic rates, and aerobic scope. Conspicuous coloration was correlated with all components except resting metabolism. Structural equation modeling on the basis of trait correlations recovered “aposematism” as one of two latent variables in an integrated phenotypic network, the other being scaling with body mass and physiology (“scale”). Chemical defense and diet specialization were uniquely tied to aposematism whereas conspicuousness was related to scale. The phylogenetic distribution of the aposematic syndrome suggests two scenarios for its evolution: ( i ) chemical defense and conspicuousness preceded greater aerobic capacity, which supports the increased resource-gathering abilities required of ant–mite diet specialization; and ( ii ) assuming that prey are patchy, diet specialization and greater aerobic capacity evolved in tandem, and both traits subsequently facilitated the evolution of aposematism.

Detection of genetic and behavioural diversity within morphologically similar species has led to the discovery of cryptic species complexes. We tested the hypothesis that US populations of the canyon treefrog (Hyla arenicolor) may consist of cryptic species by examining mate-attraction signals among three divergent clades defined by mtDNA. Using a multi-locus approach, we re-analysed phylogenetic relationships among the three clades and a closely related, but morphologically and behaviourally dissimilar species, the Arizona treefrog (H. wrightorum). We found evidence for introgression of H. wrightorum's mitochondrial genome into H. arenicolor. Additionally, the two-clade topology based on nuclear data is more congruent with patterns of call variation than the three-clade topology from the mitochondrial dataset. The magnitude of the call divergence is probably insufficient to promote isolation of the nuclear DNA-defined clades should they become sympatric, but further divergence in call properties significant in species identification could promote speciation in the future.

We describe a new species of Chiasmocleis (Anura: Microhylidae) from lowland rainforests in the western Amazon basin of Peru (near Iquitos, Departamento de Loreto). The species differs from congeners in the Amazon basin by its large size (it is the largest known Chiasmocleis species), bright yellow iris, a grey dorsum with reddish blotches posteriorly and on limbs, and a creamy white venter with bold dark mottling with pale centers. The new species also differs from two other sympatric Chiasmocleis species at 12S–16S mitochondrial DNA (6.1% and 11.9% sequence divergence between the new species and C. ventrimaculata and C. bassleri, respectively). A comparison of the new species with other microhylids found in the western Amazon basin is provided.

Behavioural isolation from divergence in male advertisement calls and female preferences is hypothesized to cause genetic divergence and speciation in the Amazonian frogs Physalaemus petersi and P. freibergi, yet the importance of call variation and landscape features in genetic divergence is unresolved. We tested for correlations between genetic divergence at microsatellite loci and (1) call variables; and (2) landscape variables among 10 populations of these frogs. Genetic divergence was not correlated with geographical distance, rivers or elevation. There was a strong positive relationship, however, between genetic divergence and inter-population differences in one call variable, whine dominant frequency. Effective population sizes varied among sites (range = 15-846) and were often small, suggesting that genetic drift could influence call evolution. Evidence for fine-scale genetic structure within sites was also found. Our results support the hypothesis that behavioural isolation from divergence in male calls and female preferences causes genetic divergence and speciation.

The sixth edition of the Scientific and Standard English Names of Amphibians and Reptiles of North America (Crother, 2008, SSAR Herpetological Circular 37:1–84) is the “Official Names List” for the three major North American herpetological societies. Although this publication is intended to aid users of scientific and common names, we argue that current practices for authoring, reviewing, and using this list, in some cases, generate taxonomic chaos. By this we mean that users are uncertain of which name to use and/or the rationale for using a particular name, and efficient communication is hindered by this confusion. Most importantly, through inadequate and inconsistent review of this list, the societies have endorsed unnecessary and arbitrary name changes and are uncritically promoting individual taxonomic viewpoints when a clear choice on the most appropriate name has not been reached by the community. This problem is exemplified by North American anurans for which 57 of the 100 species have sc...

We analyzed and described quantitative differences in morphology and calls of Physalaemus petersi and P. freibergi, both members of the monophyletic Physalaemus pustulosus species group. We found significant differences between the two species in both morphometric and call parameters. Physalaemus petersi has proportionately longer legs and a narrower dorsum and head than P. freibergi. The calls of P. petersi are higher in frequency and longer than P. freibergi. Discriminant Function Analysis (DFA) of morphometric variables correctly classified 76.7–87.4% of individuals to species. DFA of call variables correctly classified 96.8–100.0% of males to species. Physalaemus petersi is found north of the Rio Maranon and Rio Amazonas in eastern Ecuador, northeastern Peru, and southeastern Colombia; P. freibergi is found south of these rivers in Amazonian Brazil, southeastern Peru, and Amazonian Bolivia. Calls and geographic locations are the most reliable means of identifying these species in the field.

Geographic patterns of species diversity in southeast Australia have been attributed to changes in Pleistocene climate, but related phylogeographic patterns and processes are relatively understudied. 12S and 16S mitochondrial DNA sequences in Crinia signifera populations were used to infer historical patterns and processes in southeast Australia. Phylogenetic analysis identified three geographically restricted ancient lineages and several geographically restricted sub-clades. Present-day features that may prevent gene flow are absent between these geographic regions. Divergence among the three lineages corresponds to a late Miocene origin, approximately 9 million years ago (mya). The geographic breaks among the lineages are consistent with Miocene-Pliocene uplift in the Great Dividing Range and elevated sea levels in East Gippsland. Divergence among sub-clades in Victoria and South Australia is estimated to be within the early Pliocene, whereas sub-clades in New South Wales are estimated to have diverged near the Plio-Pleistocene boundary, approximately 2 mya. Geographic limits of sub-clades are consistent with geographic variation in advertisement calls, but are inconsistent with phylogeographic limits previously identified in other southeastern species.

Although the trilling chorus frogs (subclade within Pseudacris: Hylidae) have been important in studies of speciation, continental patterns of genetic diversity within and among species have not been elucidated. As a result, this North American clade has been the subject of substantial taxonomic debate. In this study, we examined the phylogenetic relationships among the trilling Pseudacris and tested previously hypothesized scenarios for speciation using 2.4 kb of mitochondrial 12S and 16S rRNA genes from 253 populations. Bayesian phylogenetic analyses, in combination with published morphological and behavioral data, support recognition of at least nine species, including an undescribed species from the south-central United States. Evidence is presented for substantial geographic subdivision within P. brachyphona (northern and southern clades) and P. feriarum (coastal and inland clades). Discordance between morphology/behavior and molecular data in several individuals suggests occasional hybridization between sympatric species. These results require major revision of range limits for several taxa, in particular, P. maculata, P. triseriata, and P. feriarum. Hypothesis tests using parametric bootstrapping strongly reject previously proposed scenarios for speciation in the group. The tests also support recognition of the geographically restricted taxon P. kalmi as a distinct species. Results of this study provide both a firm phylogenetic basis for future studies of speciation in the trilling Pseudacris and a taxonomic framework for conservation efforts.

True frogs of the genus Rana are widely used as model organisms in studies of development, genetics, physiology, ecology, behavior, and evolution. Comparative studies among the more than 100 species of Rana rely on an understanding of the evolutionary history and patterns of diversification of the group. We estimate a well-resolved, time-calibrated phylogeny from sequences of six nuclear and three mitochondrial loci sampled from most species of Rana, and use that phylogeny to clarify the group's diversification and global biogeography. Our analyses consistently support an "Out of Asia" pattern with two independent dispersals of Rana from East Asia to North America via Beringian land bridges. The more species-rich lineage of New World Rana appears to have experienced a rapid radiation following its colonization of the New World, especially with its expansion into montane and tropical areas of Mexico, Central America, and South America. In contrast, Old World Rana exhibit different trajectories of diversification; diversification in the Old World began very slowly and later underwent a distinct increase in speciation rate around 29-18 Ma. Net diversification is associated with environmental changes and especially intensive tectonic movements along the Asian margin from the Oligocene to early Miocene. Our phylogeny further suggests that previous classifications were misled by morphological homoplasy and plesiomorphic color patterns, as well as a reliance primarily on mitochondrial genes. We provide a phylogenetic taxonomy based on analyses of multiple nuclear and mitochondrial gene loci. [Amphibians; biogeography; diversification rate; Holarctic; transcontinental dispersal.

We describe a new genus and two new species of gymnophthalmid lizards based on specimens collected from Brazilian Amazonia, mostly in the "arc of deforestation". The new genus is easily distinguished from other Gymnophthalmidae by having very wide, smooth, and imbricate nuchals, arranged in two longitudinal and 6-10 transverse rows from nape to brachium level, followed by much narrower, strongly keeled, lanceolate, and mucronate scales. It also differs from all other Gymnophthalmidae, except Iphisa, by the presence of two longitudinal rows of ventrals. The new genus differs from Iphisa by having two pairs of enlarged chinshields (one in Iphisa); posterior dorsal scales lanceolate, strongly keeled and not arranged in longitudinal rows (dorsals broad, smooth and forming two longitudinal rows), and lateral scales keeled (smooth). Maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses based on morphological and molecular data indicate the new species form a clade that is most closely related to Iphisa. We also address several nomenclatural issues and present a revised classification of Gymnophthalmidae.

One proposed mechanism of speciation is divergent sexual selection, whereby divergence in female preferences and male signals results in behavioural isolation. Despite the appeal of this hypothesis, evidence for it remains inconclusive. Here, we present several lines of evidence that sexual selection is driving behavioural isolation and speciation among populations of an Amazonian frog ( Physalaemus petersi ). First, sexual selection has promoted divergence in male mating calls and female preferences for calls between neighbouring populations, resulting in strong behavioural isolation. Second, phylogenetic analysis indicates that populations have become fixed for alternative call types several times throughout the species' range, and coalescent analysis rejects genetic drift as a cause for this pattern, suggesting that this divergence is due to selection. Finally, gene flow estimated with microsatellite loci is an average of 30 times lower between populations with different call types than between populations separated by a similar geographical distance with the same call type, demonstrating genetic divergence and incipient speciation. Taken together, these data provide strong evidence that sexual selection is driving behavioural isolation and speciation, supporting sexual selection as a cause for speciation in the wild.

We present a phylogeny of the Neotropical genus Engystomops (= Physalaemus pustulosus species group) based on sequences of approximately 2.4 kb of mtDNA, (12S rRNA, valine-tRNA, and 16S rRNA) and propose a phylogenetic nomenclature. The phylogeny includes all described taxa and two unnamed species. All analyses indicate that Engystomops is monophyletic and contains two basal allopatric clades. Clade I (Edentulus) includes E. pustulosus and the Amazonian E. petersi + E. cf. freibergi. Clade II (Duovox) includes all species distributed in W Ecuador and NW Peru. Brevivox, a clade of small-sized species is strongly supported within Duovox. Populations of Engystomops pustulosus fall into two well-supported clades, each of which occupies two disjunct portions of the species range. Overall, our phylogeny is congruent with most previous hypotheses. This study is among the few published species-level phylogenies of Neotropical amphibians derived from molecular datasets. A review of the proportion of new species detected by similar studies suggests that the increasing use of molecular techniques will lead to the discovery of a vast number of species of Neotropical amphibians.

Many animals advertise their chemical defense to predators with conspicuous coloration and unpalatability, but little is known about the information in these signal elements. To effectively avoid predation, is it more advantageous to invest in increased conspicuousness or greater noxiousness, or to allocate equally to both signal modalities? Using natural variation among poison frog species measured with spectral reflectance and toxicity assays, we tested the relative importance of warning signal components with predator-learning and avoidance experiments. We demonstrate that closely related species use alternative strategies: increasing either conspicuousness or toxicity affords equivalent avoidance by predators and provides protection to nontoxic mimic species. These equally effective predator avoidance tactics demonstrate different aposematic solutions for two potentially costly signal components, providing a mechanism for natural diversity in warning signals.

Polyploidization is one of the few mechanisms that can produce instantaneous speciation. Multiple origins of tetraploid lineages from the same two diploid progenitors are common, but here we report the first known instance of a single tetraploid species that originated repeatedly from at least three diploid ancestors. Parallel evolution of advertisement calls in tetraploid lineages of gray tree frogs has allowed these lineages to interbreed, resulting in a single sexually interacting polyploid species despite the separate origins of polyploids from different diploids. Speciation by polyploidization in these frogs has been the source of considerable debate, but the various published hypotheses have assumed that polyploids arose through either autopolyploidy or allopolyploidy of extant diploid species. We utilized molecular markers and advertisement calls to infer the origins of tetraploid gray tree frogs. Previous hypotheses did not sufficiently account for the observed data. Instead, we found that tetraploids originated multiple times from extant diploid gray tree frogs and two other, apparently extinct, lineages of tree frogs. Tetraploid lineages then merged through interbreeding to result in a single species. Thus, polyploid species may have complex origins, especially in systems in which isolating mechanisms (such as advertisement calls) are affected directly through hybridization and polyploidy.

We describe a new species of leptodactylid frog of the genus Physalaemus from the lowlands of western Ecuador. It belongs to the P. pustulosus species group and differs from other group members in its smaller size, skin texture, tadpole characters, and advertisement call. The new species has wide variation in size and color pattern both at the intra- and inter-population levels. This variation matches that observed in P. montubio and P. randi, and render difficult its diagnosis on the basis of morphological features. A phylogenetic analysis of morphological characters shows that the new species belongs to a clade distributed west of the Andes in Ecuador and northern Peru, sister to (P. petersi + P. pustulosus). A phylogeny based on mtDNA shows that P. montubio and P. randi form a clade sister to (P. coloradorum + P. sp. nov.). The calls of these three species have two components with different acoustic features that arguably match the frequency sensitivity of the ear of conspecific females, in a manner si...

Defensive mechanisms, including noxious or toxic substances, are favored by predation-driven natural selection. The acquisition of noxious/toxic substances can be either endogenous, in which the substances are produced by the organism, or exogenous, in which the substances are produced by another organism and are sequestered. Evidence indicates that the defensive skin alkaloids of Neotropical poison frogs (Dendrobatidae) have an exogenous source: a diet of ants and other small alkaloid-containing arthropods, which we term the diet-toxicity hypothesis. A critical prediction of the diet-toxicity hypothesis is that independent origins of dietary specialization will be found to be correlated with independent origins of skin alkaloids. We tested this prediction in an integrated framework using comparative methods with new and published data on feeding ecology and chemical defense for 15 species of dendrobatids in five genera. We found a significant correlation between alkaloid profiles and degree of dietary specialization. This reveals a recurring association of dietary specialization and alkaloid sequestration in dendrobatids, which suggests parallel evolutionary trends in the origins of defensive mechanisms.

We describe two new species of the leptodactylid frog genus Physalaemus from the lowlands of western Ecuador. Both species belong to the P. pustulosus species group. They differ from other group members, except P. coloradorum, in their smaller size. They can be distinguished from P. coloradorum by their less tuberculate dorsal skin and a more depressed loreal region. The new species differ from each other markedly in advertisement call. Although the ranges overlap, body size, flank gland length, and parotoid gland length (relative to snout-vent length) are also significantly different. Overall the new species are similar in color patterns and body shape; they are difficult to diagnose from each other with morphological characters.

The interface of the Asian and Australian faunal zones is defined by a network of deep ocean trenches that separate intervening islands of the Philippines and Wallacea (Sulawesi, the Lesser Sundas, and the Moluccas). Studies of this region by Wallace marked the genesis of the field of biogeography, yet few workers have used molecular methods to investigate the biogeography of taxa whose distribution spans this interface. Some taxa, such as the fanged frogs of the ranid genus Limnonectes, have distributions on either side of the zoogeographical lines of Wallace and Huxley, offering an opportunity to ask how frequently these purported barriers were crossed and by what paths. To examine diversification of Limnonectes in Southeast Asia, the Philippines, and Wallacea, we estimated a phylogeny from mitochondrial DNA sequences obtained from a robust geographic sample. Our analyses suggest that these frogs dispersed from Borneo to the Philippines at least twice, from Borneo to Sulawesi once or twice, from Sulawesi to the Philippines once, and from the Philippines to Sulawesi once. Dispersal to the Moluccas occurred from Sulawesi and to the Lesser Sundas from Java/Bali. Species distributions are generally concordant with Pleistocene aggregate island complexes of the Philippines and with areas of endemism on Sulawesi. We conclude that the recognition of zoogeographic lines, though insightful, may oversimplify the biogeography of widespread taxa in this region.

Aposematism is the association, in a prey organism, of the presence of a warning signal with unprofitability to predators. The origin of aposematism is puzzling, because of its predicted low probability of establishment in a population due to the prey's increased conspicuousness. Aposematism is a widespread trait in invertebrate taxa, but, in vertebrates, it is mostly evident in amphibians, reptiles, and fishes. Poison frogs (Dendrobatidae) are one of the most well known examples of the co-occurrence of warning coloration and toxicity. This monophyletic group of mostly diurnal leaf-litter Neotropical anurans has both toxic/colorful and palatable/cryptic species. Previous studies suggested a single origin of toxicity and warning coloration, dividing the family in two discrete groups of primitively cryptic and more derived aposematic frogs. Recent molecular phylogenetic analyses using mostly aposematic taxa supported this conclusion and proposed a single tandem origin of toxicity and conspicuous warning coloration. By using expanded taxon and character sampling, we reexamined the phylogenetic correlation between the origins of toxicity and warning coloration. At least four or five independent origins of aposematism have occurred within poison frogs; by using simulations, we rejected hypotheses of one, two, or three origins of aposematism ( P < 0.002). We also found that diet specialization is linked with the evolution of aposematism. Specialization on prey, such as ants and termites, may have evolved independently at least two times.

Multimodal signals facilitate communication with conspecifics during courtship, but they can also alert eavesdropper predators. Hence, signallers face two pressures: enticing partners to mate and avoiding detection by enemies. Undefended organisms with limited escape abilities are expected to minimize predator recognition over mate attraction by limiting or modifying their signalling. Alternatively, organisms with anti-predator mechanisms such as aposematism (i.e. unprofitability signalled by warning cues) might elaborate mating signals as a consequence of reduced predation. We hypothesize that calls diversified in association with aposematism. To test this, we assembled a large acoustic signal database for a diurnal lineage of aposematic and cryptic/non-defended taxa, the poison frogs. First, we showed that aposematic and non-aposematic species share similar extinction rates, and aposematic lineages diversify more and rarely revert to the nonaposematic phenotype. We then characterized mating calls based on morphological (spectral), behavioural/physiological (temporal) and environmental traits. Of these, only spectral and temporal features were associated with aposematism. We propose that with the evolution of antipredator defences, reduced predation facilitated the diversification of vocal signals, which then became elaborated or showy via sexual selection. © 2014 The Author(s) Published by the Royal Society. All rights reserved.