Reappraising the evolutionary history of the largest known gecko, the presumably extinct Hoplodactylus delcourti, via high-throughput sequencing of archival DNA.

Hoplodactylus delcourti is a presumably extinct species of diplodactylid gecko known only from a single specimen of unknown provenance. It is by far the largest known gekkotan, approximately 50% longer than the next largest-known species. It has been considered a member of the New Zealand endemic genus Hoplodactylus based on external morphological features including shared toe pad structure. We obtained DNA from a bone sample of the only known specimen to generate high-throughput sequence data suitable for phylogenetic analysis of its evolutionary history. Complementary sequence data were obtained from a broad sample of diplodactylid geckos. Our results indicate that the species is not most closely related to extant Hoplodactylus or any other New Zealand gecko. Instead, it is a member of a clade whose living species are endemic to New Caledonia. Phylogenetic comparative analyses indicate that the New Caledonian diplodactylid clade has evolved significantly more disparate body sizes than either the Australian or New Zealand clades. Toe pad structure has changed repeatedly across diplodactylids, including multiple times in the New Caledonia clade, partially explaining the convergence in form between H. delcourti and New Zealand Hoplodactylus. Based on the phylogenetic results, we place H. delcourti in a new genus.

A revision of Angolan species in the genus Pedioplanis Fitzinger (Squamata: Lacertidae), with the description of a new species.

The genus Pedioplanis reaches its northernmost limit in western Angola, where it is represented by three species, Pedioplanis benguelensis, P. haackei and P. huntleyi. The taxonomic status of P. benguelensis remains problematic, mainly due to the vague original description and the loss of the original type material. Here we provide a revision of the Angolan representatives of the genus, with the description of a new species, Pedioplanis serodioi sp. nov., from the lowlands of southwestern Angola. Phylogenetic analyses using a combination of mitochondrial (16S and ND2) and nuclear (RAG-1) markers, as well as morphological data, support the recognition of the new species. For purposes of nomenclatural stability, we designate a neotype for P. benguelensis and provide motivation to correct the spelling of the specific epithet to benguelensis. The clarification of the status of P. benguelensis and the description of a new species contribute to a better understanding of the taxonomy and biogeography of the genus Pedioplanis, as well as the general biogeographic context of southwestern Angola, adding to the growing evidence in favor of the recognition of this region as a hotspot of lizard diversity and endemism. An updated key to the genus is also provided.

A new species of Rain Frog (Brevicipitidae, Breviceps) endemic to Angola.

Recent molecular phylogenetic work has found that Breviceps Merrem, 1820 comprises two major clades, one of which, the B. mossambicus group, is widely distributed across southern sub-Saharan Africa. This group is notable for harboring abundant cryptic diversity. Of the four most recently described Breviceps species, three are members of this group, and at least five additional lineages await formal description. Although Breviceps has long been known to occur in Angola, no contemporary material has been collected until recently. The three most widespread taxa, B. adspersus, B. mossambicus, and B. poweri, may all occur in Angola, but accurate species assignment remains challenging given the rampant morphological similarity between these taxa, and, until recently, the lack of genetic resources. Phylogenetic, morphological, and acoustic analyses of recently collected samples from disparate localities within Angola provide evidence for an undescribed species that is sister to B. poweri. The new species can be diagnosed from its sister taxon by lacking pale spots along the flanks, a pale patch above the vent, and a short, dark band below the nares (all present in B. poweri). Additionally, the male advertisement call differs from the three other Breviceps that might occur in Angola in having both a longer interval between consecutive calls and a higher average dominant frequency. We here describe this lineage as a distinct species, currently only known from Angola, and discuss the presence of other Breviceps taxa within Angola.

ResumoInvestigações moleculares recentes revelaram que o género Breviceps Merrem, 1820, é composto por duas linhagens principais, uma das quais, o grupo B. mossambicus, é amplamente distribuído na região sul da África subsaariana. Este grupo é notável por albergar uma abundante diversidade críptica. Das quatro espécies de Breviceps recentemente descritas, três pertencem a este grupo, e pelo menos outras cinco linhagens adicionais aguardam a sua descrição formal. Apesar de o género ser conhecido de Angola desde há muito tempo, só muito recentemente foram colhidos novos espécimes. Os três taxa mais amplamente distribuídos, B. adspersus, B. mossambicus e B. poweri podem todos, porventura, ocorrer em Angola, no entanto a correta identificação destas espécies têm sido problemática devido às semelhanças morfológicas extremas entre este taxa, e, até muito recente, a completa ausência de material genético. Análises filogenéticas, morfológicas e acústicas dos espécimes recentemente colhidos em diferentes locais de Angola apontam para a existência de uma espécie nova para a ciência, irmã de B. poweri. A nova espécie pode ser diferenciada do seu táxon irmão pela falta de marcas pálidas nos flancos, mancha pálida acima do ventre e pequena banda negra abaixo do nariz (presentes em B. poweri). Para além destas características, o chamamento dos machos difere das outras três espécies de Breviceps que podem ocorrer em Angola por ter um maior intervalo entre chamamentos consecutivos e uma maior frequência média dominante. Descrevemos aqui esta linhagem como uma espécie distinta, atualmente apenas conhecida de Angola, e discutimos a presença de outras espécies de Breviceps em Angola.

A review of the African snake-eyed skinks (Scincidae: Panaspis) from Angola, with the description of a new species.

The genus Panaspis in Angola is represented by four species, most of them part of taxonomically and nomenclaturally challenging species-complexes. We present a taxonomic revision of the group in the region and describe one new species, Panaspis mocamedensis sp. nov., endemic to the lowland areas of the Namibe province, southwestern Angola. Phylogenetic analysis using a combination of mitochondrial (16S, cytb) and nucleares (RAG1, PDC) markers, as well as morphological and meristic data support the recognition of the new species. In addition, these data support the presence of nominotypical Panaspis cabindae, P. wahlbergi and P. maculicollis in Angola. Reexamination of the Angolan population of P. breviceps was based on morphological analysis, as no molecular data from Angola is available for this species. According to our results, this population likely represents the nominotypical form, but due to its complex taxonomic and nomenclatural history and the lack of molecular data, this population needs to be reconsidered when molecular data become available. The description of a new species and revision of the Angolan Panaspis contributes to a better understanding of the true species richness of the Angolan herpetofauna, as well as to understanding the major biogeographic patterns of the region. A key to Angolan Panaspis species is also presented.

The development of cephalic armor in the tokay gecko (Squamata: Gekkonidae: Gekko gecko).

Armored skin resulting from the presence of bony dermal structures, osteoderms, is an exceptional phenotype in gekkotans (geckos and flap-footed lizards) only known to occur in three genera: Geckolepis, Gekko, and Tarentola. The Tokay gecko (Gekko gecko LINNAEUS 1758) is among the best-studied geckos due to its large size and wide range of occurrence, and although cranial dermal bone development has previously been investigated, details of osteoderm development along a size gradient remain less well-known. Likewise, a comparative survey of additional species within the broader Gekko clade to determine the uniqueness of this trait has not yet been completed. Here, we studied a large sample of gekkotans (38 spp.), including 18 specimens of G. gecko, using X-rays and high-resolution computed tomography for visualizing and quantifying the dermal armor in situ. Results from this survey confirm the presence of osteoderms in a second species within this genus, Gekko reevesii GRAY 1831, which exhibits discordance in timing and pattern of osteoderm development when compared with its sister taxon, G. gecko. We discuss the developmental sequence of osteoderms in these two species and explore in detail the formation and functionality of these enigmatic dermal ossifications. Finally, we conducted a comparative analysis of endolymphatic sacs in a wide array of gekkotans to explore previous ideas regarding the role of osteoderms as calcium reservoirs. We found that G. gecko and other gecko species with osteoderms have highly enlarged endolymphatic sacs relative to their body size, when compared to species without osteoderms, which implies that these membranous structures might fulfill a major role of calcium storage even in species with osteoderms.

A new earless species of Poyntonophrynus (Anura, Bufonidae) from the Serra da Neve Inselberg, Namibe Province, Angola.

African pygmy toads of the genus Poyntonophrynus are some of the least known species of African toads. The genus comprises ten recognized species endemic to sub-Saharan Africa, five of which are restricted to southwestern Africa. Recent field research in Angola provided new material for three species of Poyntonophrynus, including a morphologically distinctive population from the Serra da Neve Inselberg. Based on a combination of external morphology, high-resolution computed tomography scanning, and molecular phylogenetic analysis, the Serra da Neve population is described as new species that is nested within the genus. The most striking character that differentiates the newly described species from its congeners is the lack of a tympanic middle ear, a condition common in the family Bufonidae, but so far not known for Poyntonophrynus. The description of this new species from southwestern Angola reinforces the biogeographic importance of the region and further suggests that southwestern Africa is the cradle of diversity for this genus.

Phylogenomic support for evolutionary relationships of New World direct-developing frogs (Anura: Terraranae).

Phylogenomic approaches have proven able to resolve difficult branches in the tree of life. New World direct-developing frogs (Terraranae) represent a large evolutionary radiation in which interrelationships at key points in the phylogeny have not been adequately determined, affecting evolutionary, biogeographic, and taxonomic interpretations. We employed anchored hybrid enrichment to generate a data set containing 389 loci and >600,000 nucleotide positions for 30 terraranan and several outgroup frog species encompassing all major lineages in the clade. Concatenated maximum likelihood and coalescent species-tree approaches recover nearly identical topologies with strong support for nearly all relationships in the tree. These results are similar to previous phylogenetic results but provide additional resolution at short internodes. Among taxa whose placement varied in previous analyses, Ceuthomantis is shown to be the sister taxon to all other terraranans, rather than deeply embedded within the radiation, and Strabomantidae is monophyletic rather than paraphyletic with respect to Craugastoridae. We present an updated taxonomy to reflect these results, and describe a new subfamily for the genus Hypodactylus.

The measure of success: geographic isolation promotes diversification in Pachydactylus geckos.

BACKGROUND: Geckos of the genus Pachydactylus and their close relatives comprise the most species-rich clade of lizards in sub-Saharan Africa. Many explanations have been offered to explain species richness patterns of clades. In the Pachydactylus group, one possible explanation is a history of diversification via geographic isolation. If geographic isolation has played a key role in facilitating diversification, then we expect species in more species-rich subclades to have smaller ranges than species in less diverse subclades. We also expect traits promoting geographic isolation to be correlated with small geographic ranges. In order to test these expectations, we performed phylogenetic analyses and tested for correlations among body size, habitat choice, range sizes, and diversification rates in the Pachydactylus group. RESULTS: Both body size and habitat use are inferred to have shifted multiple times across the phylogeny of the Pachydactylus group, with large size and generalist habitat use being ancestral for the group. Geographic range size is correlated with both of these traits. Small-bodied species have more restricted ranges than large-bodied species, and rock-dwelling species have more restricted ranges than either terrestrial or generalist species. Rock-dwelling and small body size are also associated with higher rates of diversification, and subclades retaining ancestral conditions for these traits are less species rich than subclades in which shifts to small body size and rocky habitat use have occurred. The phylogeny also illustrates inadequacies of the current taxonomy of the group. CONCLUSIONS: The results are consistent with a model in which lineages more likely to become geographically isolated diversify to a greater extent, although some patterns also resemble those expected of an adaptive radiation in which ecological divergence acts as a driver of speciation. Therefore, the Pachydactylus group may represent an intermediate between clades in which radiation is adaptive versus those in which it is non-adaptive.

Molecular and morphological data support recognition of a new genus of New World direct-developing frog (Anura: Terrarana) from an under-sampled region of South America.

We describe a new genus of New World direct-developing frog (Terrarana) from the northern Andes of Venezuela and adjacent Colombia. Tachiramantis gen. nov. includes three species formerly placed in the large genus Pristimantis. Molecular phylogenetic analysis of data from five nuclear and mitochondrial genes shows that Tachiramantis is not part of Pristimantis or any other named genus in its family (Craugastoridae or Strabomantidae). Morphological evidence further supports the distinctiveness of Tachiramantis, which has several aspects of skull morphology that are rare or absent in Pristimantis and synapomorphic for Tachiramantis, including frontoparietal-prootic fusion and degree of vomer development. The terminal phalanges, which narrow greatly before expanding at the tips, may represent an additional morphological synapomorphy. One species, T. prolixodiscus, also displays a fenestra between the posterior portions of the frontoparietals, a character state otherwise present in only 1 of 98 other sampled terraranan species. We use mapped ranges of most New World direct-developing frogs to show that Tachiramantis occurs in a geographic region that had been under-sampled in previous molecular studies of New World direct-developing frogs. Other under-sampled regions are identified in western Peru, Colombia, and northern Central America; these regions should provide fruitful target taxa for future phylogenetic studies.

A new tuberculated Pristimantis (Anura, Terrarana, Strabomantidae) from the Venezuelan Andes, redescription of Pristimantis pleurostriatus, and variation within Pristimantis vanadisae.

A new tuberculated Pristimantis is described from the eastern versant of the Venezuelan Andes. The new species is found in cloud forest at around 1600 masl on the eastern side of the Cordillera de Mérida. It is distinguished from other similar tuberculated species by its round, ill-defined canthus rostralis, ill-defined canthal stripe, and absence of pale spots on the groin and posterior surface of thighs. Pristimantis pleurostriatus is a poorly known species found in cloud forest on the western slopes of the Venezuelan Andes. We redescribe the species based on topotypic specimens. Pristimantis vanadisae is a polychomatic species varying dramatically in pattern; four chromotypes are described. Molecular data are presented which distinguish among tuberculated and other species of Pristimantis in the Cordillera de Merida. Molecular data also support placement of Mucubatrachus and Paramophrynella in Pristimantis.

A preliminary phylogeny of the Palearctic naked-toed geckos (Reptilia: Squamata: Gekkonidae) with taxonomic implications.

Palearctic naked-toed geckos are a group of gekkonid geckos that range from North Africa to northern India and western China, with their greatest diversity in Iran and Pakistan. Relationships among the constituent genera remain incompletely resolved and the monophyly of key genera remains unverified. Further, competing classifications are in current use and many species have been allocated to different genera by different authors. We used both mitochondrial (ND2) and nuclear genes (RAG1, PDC) to explore relationships among representatives of all but one genus in the group (Rhinogecko), including four genera not previously included in phylogenetic analyses (Asiocolotes, Altigekko, Indogekko, and Siwaligekko). Siwaligekko (and presumably other Tibeto-Himalayan species often referred to Cyrtopodion) are more closely related to tropical Asian Cyrtodactylus than to Palearctic naked-toed geckos. Sampled species of Asiocolotes and Altigekko are sister taxa, but both genera are here considered junior subjective synonyms of Altiphylax. Cyrtopodion sensu lato is non-monophyletic; Mediodactylus and Tenuidactylus, which have variably been considered as subgenera or synonyms of Cyrtopodion are both valid genera. Indogekko is embedded within Cyrtopodion and is here treated as a subgenus. Bunopus and Crossobamon are closely related to one-another, and with Agamura are interdigitated among taxa previously assigned to Cyrtopodion. Our data confirm the previous identification of a Saharo-Arabian Stenodactylus/Tropiocolotes/Pseudoceramodactylus clade and verify that Microgecko and Alsophylax are not members of the main clade of Palearctic naked-toed geckos. Osteological differences between Tropiocolotes and Microgecko, formerly treated as congeneric, are discussed and illustrated. The divergence between Cyrtodactylus and the Palearctic naked-toed clade predates the initial collision of the Indian and Eurasian plates, but deeper divergences within both groups are consistent with mountain building in the Himalayas and adjacent ranges as promoting cladogenic events. Miocene divergences within Tenuidactylus are consistent with vicariant speciation caused by uplift events in the Iranian and Transcaspian regions. Taxonomic implications of our phylogenetic results are discussed and a preliminary allocation of all species of padless Palearctic gekkonids to genus is provided.

Phylogeny of bent-toed geckos (Cyrtodactylus) reveals a west to east pattern of diversification.

The Asian/Pacific genus Cyrtodactylus is the most diverse and among the most widely distributed genera of geckos, and more species are continually being discovered. Major patterns in the evolutionary history of Cyrtodactylus have remained largely unknown because no published study has broadly sampled across the geographic range and morphological diversity of the genus. We assembled a data set including sequences from one mitochondrial and three nuclear loci for 68 Cyrtodactylus and 20 other gekkotan species to infer phylogenetic relationships within the genus and identify major biogeographic patterns. Our results indicate that Cyrtodactylus is monophyletic, but only if the Indian/Sri Lankan species sometimes recognized as Geckoella are included. Basal divergences divide Cyrtodactylus into three well-supported groups: the single species C. tibetanus, a clade of Myanmar/southern Himalayan species, and a large clade including all other Cyrtodactylus plus Geckoella. Within the largest major clade are several well-supported subclades, with separate subclades being most diverse in Thailand, Eastern Indochina, the Sunda region, the Papuan region, and the Philippines, respectively. The phylogenetic results, along with molecular clock and ancestral area analyses, show Cyrtodactylus to have originated in the circum-Himalayan region just after the Cretaceous/Paleogene boundary, with a generally west to east pattern of colonization and diversification progressing through the Cenozoic. Wallacean species are derived from within a Sundaland radiation, the Philippines were colonized from Borneo, and Australia was colonized twice, once via New Guinea and once via the Lesser Sundas. Overall, these results are consistent with past suggestions of a Palearctic origin for Cyrtodactylus, and highlight the key role of geography in diversification of the genus.

Evolution of gliding in Southeast Asian geckos and other vertebrates is temporally congruent with dipterocarp forest development.

Gliding morphologies occur in diverse vertebrate lineages in Southeast Asian rainforests, including three gecko genera, plus frogs, snakes, agamid lizards and squirrels. It has been hypothesized that repeated evolution of gliding is related to the dominance of Asian rainforest tree floras by dipterocarps. For dipterocarps to have influenced the evolution of gliding in Southeast Asian vertebrates, gliding lineages must have Eocene or later origins. However, divergence times are not known for most lineages. To investigate the temporal pattern of Asian gliding vertebrate evolution, we performed phylogenetic and molecular clock analyses. New sequence data for geckos incorporate exemplars of each gliding genus (Cosymbotus, Luperosaurus and Ptychozoon), whereas analyses of other vertebrate lineages use existing sequence data. Stem ages of most gliding vertebrates, including all geckos, cluster in the time period when dipterocarps came to dominate Asian tropical forests. These results demonstrate that a gliding/dipterocarp correlation is temporally viable, and caution against the assumption of early origins for apomorphic taxa.

Origin of invasive Florida frogs traced to Cuba.

Two of the earliest examples of successful invasive amphibians are the greenhouse frog (Eleutherodactylus planirostris) and the Cuban treefrog (Osteopilus septentrionalis) in Florida. Although both are generally assumed to be recent introductions, they are widespread on Caribbean islands and also have been proposed as natural colonizers. We obtained nucleotide sequence data for both species and their closest relatives in their native and introduced ranges. Phylogenetic analyses trace the origin of E. planirostris to a small area in western Cuba, while O. septentrionalis is derived from at least two Cuban sources, one probably a remote peninsula in western Cuba. The tropical-to-temperate invasion began with colonization of the Florida Keys followed by human-mediated dispersal within peninsular Florida. The subtropical Keys may have served as an adaptive stepping stone for the successful invasion of the North American continent.

Major Caribbean and Central American frog faunas originated by ancient oceanic dispersal.

Approximately one-half of all species of amphibians occur in the New World tropics, which includes South America, Middle America, and the West Indies. Of those, 27% (801 species) belong to a large assemblage, the eleutherodactyline frogs, which breed out of water and lay eggs that undergo direct development on land. Their wide distribution and mode of reproduction offer potential for resolving questions in evolution, ecology, and conservation. However, progress in all of these fields has been hindered by a poor understanding of their evolutionary relationships. As a result, most of the species have been placed in a single genus, Eleutherodactylus, which is the largest among vertebrates. Our DNA sequence analysis of a major fraction of eleutherodactyline diversity revealed three large radiations of species with unexpected geographic isolation: a South American Clade (393 sp.), a Caribbean Clade (171 sp.), and a Middle American Clade (111 sp.). Molecular clock analyses reject the prevailing hypothesis that these frogs arose from land connections with North and South America and their subsequent fragmentation in the Late Cretaceous (80-70 Mya). Origin by dispersal, probably over water from South America in the early Cenozoic (47-29 million years ago, Mya), is more likely.

Molecular phylogeny and biogeography of West Indian frogs of the genus Leptodactylus (Anura, Leptodactylidae).

Three endemic species of the aquatic-breeding frog genus Leptodactylus are recognized from the West Indies: Leptodactylus albilabris (Puerto Rico and the Virgin Islands), Leptodactylus dominicensis (Hispaniola), and Leptodactylus fallax (Lesser Antilles). DNA sequences were obtained from several mitochondrial genes to resolve taxonomic questions involving these species and to provide insights into their origin and distribution in the islands. We found low levels of sequence divergence between L. dominicensis and L. albilabris, supporting morphological evidence that the former species is a junior synonym of the latter species. Phylogenetic analysis supported previous species-group allocations, finding that L. albilabris is a member of the fuscus group and L. fallax is a member of the pentadactylus group. Molecular time estimates for the divergence of L. albilabris from its closest relative in South America (24-58 million years ago, Ma) and for L. fallax from its closest relative in South America (23-34Ma) indicate that they colonized the West Indies independently by over-water dispersal in the mid-Cenozoic. The absence of detectable sequence divergence between the two extant populations of L. fallax (Dominica and Montserrat), a species used for human food and now critically endangered, suggests that one or both arose by human introduction from an island or islands where that species originated. The relatively minor genetic differentiation of populations of L. albilabris can be explained by vicariance and dispersal in the Pleistocene and Holocene, although human introduction of some populations cannot be ruled out.