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Morphology and molecular systematics support a new species of Pseudogonatodes (Squamata: Gekkota: Sphaerodactylidae) from Venezuela with a remarkable telescoped skull
Abstract and Figures
We describe a new species of miniaturized gecko (genus Pseudogonatodes) from the Peninsula de Paria in northeastern Venezuela. Externally, the new species resembles Pseudogonatodes furvus and Pseudogonatodes manessi, from the Sierra Nevada de Santa Marta in Colombia and the Central Coastal Range in Venezuela, respectively; however, it differs from these species in terms of molecular genetic data (12S rRNA, 16S rRNA, and c-mos), osteological characters, and scale counts. The new species is unique in skull osteology, and we adopt the term ‘telescoped’ from the literature to describe the overlap of bones in the snout, in particular the premaxilla fully separating the nasal bones and contacting the frontal bone. The new species is also the only known species of Pseudogonatodes with fused parietal bones. Using molecular data, we present the first phylogeny of Pseudogonatodes, including six of the nine species in the genus. The new species is sister to P. manessi, which is consistent with biogeographical patterns in the mountainous areas of northern Venezuela. The phylogenetic results also indicate that Pseudogonatodes guianensis is non-monophyletic and raise the possibility of resurrecting the name Pseudogonatodes amazonicus. However, large sampling gaps in Amazonia prevent us from rigorously assessing species limits and proposing a taxonomic change.
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Pseudogonatodes is a poorly known genus of small bodied, diurnal, ground-dwelling geckos widely distributed in northern South America. No additional species have been described in over two decades. Herein we describe a new species from the eastern slope of the Cordillera de Mérida in the Venezuelan Andes. The new species is readily diagnosable morphologically from the other seven recognized species of Pseudogonatodes by having a single postnasal scale—a putative autapomorphy. Furthermore, it is characterized by a unique combination of phenotypic characters that includes granular dorsal scales, three large postrostrals, five to six loreals, mental U-shaped, four to six postmentals, 26–29 ventrals between anterior levels of fore- and hind limbs, third lamella under fourth toe not distinctly enlarged, and subcaudal pattern 1’1”. In addition to characterizing the external morphology, we present a description of the skull, based on 3D digital models reconstructed from high resolution computed microtomography scans. The discovery of this new species highlights the still underestimated diversity of this group of Neotropical dwarf geckos and underscores the need for further studies on its systematics and taxonomy.
Advances in both morphological and molecular techniques have uncovered many lineages across the tree of life, and Neotropical vertebrates are no exception. Sphaerodactylus geckos (Sphaerodactylidae) are abundant and important components of the Neotropical herpetofauna, but few studies have thoroughly investigated them using a combination of morphology and modern molecular genetic methods. Here, we combine morphological and genetic data to describe a new species of Sphaerodactylus from the northwestern karst region of Puerto Rico. The new species is compared to other closely related and sympatric species of Sphaerodactylus. Morphological analysis shows that the combination of small body size (median SVL ¼ 21.5 mm), lepidosis, skull morphology, and coloration of the head differentiates the new species from its closest relatives, including the related species, Sphaerodactylus klauberi. Comparing sequences of the mitochondrial 16S rRNA gene showed a genetic distance between S. klauberi and the new species of 5.1-5.6%, which is similar to genetic distances among other recognized gecko species. This is the first new species of Sphaerodactylus to be described from Puerto Rico in nearly a century, highlighting the continued need to evaluate and chronicle biological diversity even in well-studied regions. Las filogenias moleculares han elucidado múltiples linajes en el á rbol de la vida, incluyendo varios vertebrados neotropicales. Las salamanquitas del género Sphaerodactylus (Sphaerodactylidae) son abundantes y forman una parte importante de la herpetofauna neotropical. Este género ha sido investigado recientemente utilizando métodos moleculares modernos. En este artículo se describe una nueva especie del género Sphaerodactylus, procedente de la región ká rstica del noroeste de Puerto Rico. Los individuos de la nueva especie fueron comparados con especies afines y simpá tricas. El aná lisis morfológico muestra que la combinación entre el tamaño corporal, escamación, morfología del crá neo y coloración cefá lica, distinguen a la especie nueva de otras especies cercanas filogenéticamente, incluyendo su especie hermana Sphaerodactylus klauberi. Al comparar secuencias del gen mitocondrial 16S rRNA se observó una distancia genética de 5.1-5.6% entre la especie nueva y S. klauberi, dicha distancia es similar a la que existe entre otras especies descritas de salamaquitas. Ha pasado casi un siglo desde que laúltima especie de Sphaerodactylus de Puerto Rico fue descrita,ésto resalta la necesidad de seguir evaluando y catalogando la biodiversidad, inclusive en á reas que han sido investigadas a profundidad.
The Molecular Evolutionary Genetics Analysis (MEGA) software has matured to contain a large collection of methods and tools of computational molecular evolution. Here, we describe new additions that make MEGA a more comprehensive tool for building timetrees of species, pathogens, and gene families using rapid relaxed-clock methods. Methods for estimating divergence times and confidence intervals are implemented to use probability densities for calibration constraints for node-dating and sequence sampling dates for tip-dating analyses, which will be supported by new options for tagging sequences with spatiotemporal sampling information, an expanded interactive Node Calibrations Editor, and an extended Tree Explorer to display timetrees. We have now added a Bayesian method for estimating neutral evolutionary probabilities of alleles in a species using multispecies sequence alignments and a machine learning method to test for the autocorrelation of evolutionary rates in phylogenies. The computer memory requirements for the maximum likelihood analysis are reduced significantly through reprogramming, and the graphical user interface (GUI) has been made more responsive and interactive for very big datasets. These enhancements will improve the user experience, quality of results, and the pace of biological discovery. Natively compiled GUI and command-line versions of MEGA11 are available for Microsoft Windows, Linux, and macOS from www.megasoftware.net.
We examine, for the first time, biogeographic patterns in a series of tropical montane coastal systems in northern South America. We use amphibians and reptiles, which constitute the most critical communities based upon the prevalence of endemic taxa, to assess the region’s biodiversity. The montane coastal system spans an east-west distance of 925 km. It includes peaks ranging from 549 m to 2765 m above sea level and encompasses the montane complexes of northern Venezuela (including Isla de Margarita), an outlier at Santa Marta (Colombia), and ranges on the islands Trinidad and Tobago. The area supports 14 family level amphibian clades and 23 family level reptile clades. Fieldwork, museum specimen surveys, and a literature review suggest that biodiversity decreases at higher elevations. Here we examine the biogeographic patterns in the region to assess the role of the montane systems as possible refugia. We also look at the possible island and sky island effects using data from altitudes >200 m. At lower elevations, we tabulated 294 species, comprising 112 amphibians and 182 reptiles. About 45% of these taxa are endemic or exclusive to different sub-regions. At mid-elevation montane cloud forests, we find a much-reduced biodiversity with a total of 125 species (66 amphibians and 59 reptiles) exclusive or restricted to the region, and few species shared between systems. We find that biogeographical patterns follow a natural topographic disposition above 200 m in elevations. At the lower elevation cut off, there are 118 species (26 amphibians and 92 reptiles) shared among two or more of the studied mountain systems, suggesting a common origin and dispersal events, despite what seem to be topographic barriers. Biogeographical relationships support a topographic disposition of the region with close associations between the islands of Trinidad and Tobago, the Paria Range and the Turimiquire Massif, and close associations between the Sierra Nevada de Santa Marta and the Sierra de San Luis. Overall, the biogeographic relationships between amphibians and reptiles are similar. Species diversity in the eastern Caribbean region is less rich than in the west. This study includes the first herpetological surveys at the two easternmost mountains (Cerro La Cerbatana and Campeare) belonging to the Paria Range biogeographic unit, and aims to contribute to a better understanding of the rich biodiversity of the region.
Pseudogonatodes furvus is an endemic gecko from the region of the Sierra Nevada de Santa Marta, an isolated massif located in the continental Caribbean region of Colombia. Pseudogonatodes furvus is the type species of the genus, and its morphology and natural history remain poorly known. This lizard was described based on two specimens. After its description, the species has only been mentioned in a handful of taxonomic studies of Pseudogonatodes, in which a few morphological characters of P. furvus have been mentioned. One other paper reported two new localities, without providing new information on the external morphology, especially the lepidosis of the newly obtained specimens. Here we review the external morphology of P. furvus, based on examination of the holotype and six additional specimens. We provide an extended diagnosis and definition, description of holotype, variation, comparisons with other Pseudogonatodes, geographic distribution (adding a fourth locality to the known distribution for the species), and conservation status. Additionally, we describe osteological features for the diagnosis of the genus.
We describe a new species of diurnal gecko, Gonatodes castanae sp. nov. from the foothills of the Serranía de San Lucas, municipality of Norosí, Department of Bolívar, Colombia. The new species differs from all species in the genus by the combination of the following characters: moderate size, subcaudal scale pattern type B (1’1’1’’), typically two rows of lateral scales on the digits, and aspects of color pattern in males (dorsum, flanks, limbs and tail with white ocelli on a black background) and females (dorsum, flanks, limbs and tail with brown to black reticulations and withe spots on a greenish-yellow background). The validity of the new species is also supported by molecular analyses. This species inhabits relicts of riverine forests at about 150 m above sea level (a.s.l.). Gonatodes castanae increases the number of known species in this genus to 34 and the species registered for Colombia to eight.
IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. Here, we describe notable features of IQ-TREE version 2 and highlight the key advantages over other software.
The Molecular Evolutionary Genetics Analysis (MEGA) software enables comparative analysis of molecular sequences in phylogenetics and evolutionary medicine. Here, we introduce the macOS version of the MEGA software. This new version eliminates the need for virtualization and emulation programs previously required to use MEGA on Apple computers. MEGA for macOS utilizes memory and computing resources efficiently for conducting evolutionary analyses on Apple computers. It has a native Cocoa graphical user interface that is programmed to provide a consistent user experience across macOS, Windows, and Linux. MEGA for macOS is available from www.megasoftware.net free of charge.
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. Distribution of osteoderms in the skull of a large sized Tokay gecko (Gekko gecko).
Determining the mechanisms that create and maintain biodiversity is a central question in ecology and evolution. Speciation is the process that creates biodiversity. Speciation is mediated by incompatibilities that lead to reproductive isolation between divergent populations and these incompatibilities can be observed in hybrid zones. Gecko lizards are a speciose clade possessing an impressive diversity of behavioral and morphological traits. In geckos, however, our understanding of the speciation process is negligible. To address this gap, we used genetic sequence data (both mitochondrial and nuclear markers) to revisit a putative hybrid zone between Sphaerodactylus nicholsi and S. townsendi in Puerto Rico, initially described in 1984. First, we addressed discrepancies in the literature on the validity of both species. Second, we sampled a 10 km-wide transect across the putative hybrid zone and tested explicit predictions about its dynamics using cline models. Third, we investigated potential causes for the hybrid zone using species distribution modeling and simulations; namely, whether unique climatic variables within the hybrid zone might elicit selection for intermediate phenotypes. We find strong support for the species-level status of each species and no evidence of movement, or unique climatic variables near the hybrid zone. We suggest that this narrow hybrid zone is geographically-stable and is maintained by a combination of dispersal and selection. Thus, this work has identified an extant model system within geckos that that can be used for future investigations detailing genetic mechanisms of reproductive isolation in an understudied vertebrate group.
The Peruvian sphaerodactyl gecko, Pseudogonatodes barbouri, is among the smallest reptile species in South America. Morphological information about this species, or even the genus, is limited. In this study, we produced a bone-by-bone description from the skull and atlantoaxial complex to contribute new phenotypic information about this poorly known lizard. To achieve this objective, we employed a divide-and-conquer approach in which each author digitally isolated one or two bones from the skull and produced a written description of these elements, thereby reducing 3D imaging processing and description to a fraction of time. In addition to a reduced phalanx in the fourth toe of both the hand and foot, the genus is characterized by having nasal bones with a broad lateral wing, an ectopterygoid that clasps the pterygoid, and an anterior shifting of the paroccipital process and as consequence the position of the quadrate, and squamosal not participating in the quadrate suspension. There are also modifications in fenestration and foramina and a trend towards synostosis of the jaw bones (e.g., coronoid + splenial, compound bone + surangular). Pseudogonatodes bears four long processes on the intercentrum of the axis; which is a character of New World sphaerodactyls.
Well-resolved phylogenetic hypotheses and ontogenetic data are often necessary for investigating the evolution of structural novelty. The Sphaerodactylidae comprises 12 genera of predominantly miniaturized geckos. The genera Aristelliger and Teratoscincus are exceptions, with taxa reaching snout-to-vent lengths far exceeding those of other sphaerodactylids. These two genera possess enigmatic, supraorbital ossifications — parafrontal bones — which are encountered nowhere else among squamates. At the time of their discovery, these structures were believed to be the result of evolutionary convergence. Although relationships between other sphaerodactylids remain unresolved, recent molecular and morphological data have supported a close relationship between Aristelliger and Teratoscincus. We investigated the ontogeny of parafrontal bones to better understand relationships between sphaerodactylid body size and the presence of parafrontals, and to evaluate whether ontogenetic data support the homology of parafrontals between Aristelliger and Teratoscincus. We hypothesize that the parafrontals of Aristelliger and Teratoscincus are homologous and that there is a threshold body size in sphaerodactylids below which parafrontals do not develop, thus explaining their absence from the miniaturized taxa. The presence of parafrontals was investigated in all sphaerodactylid genera using cleared-and-stained, radiographed, and skeletonized specimens. Total surface area of parafrontals was measured for seven species of Aristelliger and six species of Teratoscincus throughout their ontogeny. Histology was used to investigate the cellular composition of the parafrontals throughout their ontogeny. Our data suggest that parafrontals have evolved in parallel from a homologous, parafrontal precursor and that the onset of parafrontal development is not strictly dependent on a threshold body size. This article is protected by copyright. All rights reserved.
The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an efficient alternative to SBS and other bootstrap approaches.
Here, we present UFBoot2, which substantially accelerates UFBoot and reduces the risk of overestimating branch supports due to polytomies or severe model violations. Additionally, UFBoot2 provides suitable bootstrap resampling strategies for phylogenomic data. UFBoot2 is 778 times (median) faster than SBS and 8.4 times (median) faster than RAxML rapid bootstrap on tested datasets. UFBoot2 is implemented in the IQ-TREE software package version 1.6 and freely available at http://www.iqtree.org.
Gonatodes rayito sp. nov. is described from the western versant of the Cordillera de Mérida, Venezuela. Like most species of Gonatodes the new species is sexually dichromatic and is one of only a few in the genus in which individuals have a conspicuous, pale middorsal stripe. The new species is similar to, and has been confused in the past with, G. petersi and G. vittatus. It differs from both species in several aspects of color pattern, and also from G. vittatus in size and scale counts. The validity of Gonatodes rayito sp. nov. is also strongly supported by a phylogenetic analysis using a fragment of the ornithine decarboxylase nuclear gene.
Riama is the most speciose genus of the Neotropical lizard family Gymnophthalmidae. Its more than 30 montane species occur throughout the northern Andes, the Cordillera de la Costa (CC) in Venezuela, and Trinidad. We present the most comprehensive phylogenetic analysis of Riama to date based on a total evidence (TE) approach and direct optimization of molecular and morphological evidence. Analyses use DNA sequences from four loci and 35 phenotypic characters. The dataset consists of 55 ingroup terminals representing 25 of the 30 currently recognized species of Riama plus five undescribed taxa, including an endemic species from the Sierra Nevada de Santa Marta (SNSM) in Colombia, and 66 outgroup terminals of 47 species. Analysis results in a well supported hypothesis in which Riama is polyphyletic, with its species falling into three clades. The Tepuian Anadia mcdiarmidi nests within one clade of Riama, and the recently resurrected Pantodactylus nests within Cercosaura. Accordingly, we propose a monophyletic taxonomy that reflects historical relationships. Analysis of character evolution indicates that the presence/absence of prefrontals—a cornerstone of the early genus-level taxonomy of cercosaurines—is optimally explained as having been plesiomorphically present in the most recent common ancestor of Cercosaurinae and lost in that of the immediately less inclusive clade. Multiple independent reversals to present and subsequent returns to absent occur within this clade. To evaluate the impact of phenotypic evidence on our results, we compare our TE results with results obtained from analyses using only molecular data. Although phenotypic evidence comprises only 1.2% of the TE matrix, its inclusion alters both the topology and support values of the clades that do not differ. Finally, current phylogenetic evidence reveals a SNSM–CC–Trinidad–tepuis biogeographical link. We hypothesize that an ancient connection facilitated the exchange of species between the SNSM and the CC.
Geckos are among the most diverse radiations of lizards; however, the lack of baseline natural history data on the reproductive biology for many species creates a challenge for predicting their long-term persistence. This study aims to fill a gap in our understanding of the reproductive biology of an enigmatic nocturnal gecko endemic to the islands of Curaçao and Bonaire: Gonatodes antillensis. Using ra-diographs of specimens from natural history collections, we conduct the first investigation of the potential role of endolymphatic sacs in the reproduction of the species. We find that females have larger endolymphatic sacs than males, with further quantification of endolymphatic sac sizes between females with or without visible eggs supporting the hypothesis that calcium stores are built up in the early reproductive phase and depleted during the development of the egg. Additionally, we combined data on endolymphatic sacs sizes with examinations of gravidity to expand the known reproductive interval of the species into fall and winter months and suggest the possibility of year-round reproduction. Along with providing baseline data, our findings raise a new conservation concern for the species. The spread of the invasive gecko Hemidactylus mabouia has resulted in a notable decline in the abundance of Gonatodes antillensis across its native range. This decline has been attributed to Hemidactylus mabouia acting as both a competitor and possible predator of Gonatodes antillensis. However, stress can inhibit calcium uptake in endolymphatic sacs, and these findings raise the possibility that Hemidacty-lus mabouia may also be indirectly affecting the reproductive success of this species.
Pseudogonatodes lunulatus (Roux, 1927) was described from a single specimen collected in the village El Mene, Acosta municipality, northeastern Falcón state, Venezuela. Although the species has been reported for other Venezuelan and Colombian localities, an extensive study on taxonomy and geographic distribution in the country had not been performed. In this sense, we examined and compared a larger sample of 20 specimens deposited in several national and foreign museums. Additionally, we substantially expand the known distribution of the species to the north of the Orinoco River. KEY WORDS. Pseudogonatodes, taxonomy, habitat. RESUMEN Pseudogonatodes lunulatus (Roux, 1927) fue descrito de un único ejemplar recolectado en la población El Mene, municipio Acosta, al noreste del estado Falcón, Venezuela. Aunque la especie ha sido señalada para otras localidades de Venezuela y Colombia, un estudio extenso acerca de su taxonomía y distribución geográfica en el país no había sido efectuado. En este sentido, se pudo examinar y comparar una muestra mayor de 20 especímenes depositados en varios museos nacionales y extranjeros. Adicionalmente, se extiende sustancialmente la distribución conocida de la especie al norte del río Orinoco.
Based on morphological and molecular data, we describe three new species of the genus Lepidoblepharis with granular dorsals from Panama (Lepidoblepharis emberawoundule sp. nov., Lepidoblepharis rufigularis sp. nov., and Lepidoblepharis victormartinezi sp. nov.). The results of our molecular analyses confirm the existence of five deeply differentiated genealogical lineages among Panamanian Lepidoblepharis. We present detailed descriptions of their morphology, including some new valuable scalation characters (ventral and subfemoral escutcheon) and hemipenes, as well as comparisons with the other two species of the genus known to occur in Panama (L. sanctaemartae and L. xanthostigma) and their South American congeners. Last, we provide an updated identification key for the genus Lepidoblepharis in Central America.
Fieldwork in the cloud forest of Venezuela’s remote Península de Paria in 2001 resulted in the collection of several specimens that could unquestionably be classified as members of the genus Pristimantis. Subsequent analysis of comparative material in museum collections brought the total number of specimens to 44, and these collectively represent five new species. Two of these species, P. geminus sp. nov. and P. nubisilva sp. nov., have phenotypes remarkably similar to the Trinidadian P. urichi, supporting a prediction that Pristimantis from easternmost Venezuela may have given rise to Trinidadian forms. Pristimantis hoogmoedi sp. nov. is easily identified by its large size and red eyes. Two of the species, P. longicorpus sp. nov. and P. pariagnomus sp. nov., are very distinct morphologically but are known only from the holotypes. The former is characterized by an elongate body form supported by relatively short limbs, whereas the latter has very distinctive hand morphology and is likely the smallest Venezuelan frog. Chromosome banding studies of P. nubisilva sp. nov. and P. hoogmoedi sp. nov. revealed chromosome numbers of 2n = 36 and 2n = 26, respectively, with an unusual submetacentric fusion chromosome 11;18 in some males of the former and a unique meiotic pairing of chromosomes in males of the latter. All five species can be readily distinguished by their osteology, such as by the extent of the sphenethmoid and features on the roof of the mouth, as well as by the shape and rearrangement of mesopodial elements. The unexpectedly high diversity of Pristimantis in this region, along with high endemism of amphibians and reptiles in general, underscores the position of the Península de Paria as a center for frog biodiversity in Venezuela. The similarity of these Paria species to Pristimantis from Trinidad, Tobago and the central Cordillera de la Costa represents a tangible piece of evidence for the close biogeographic link of the anuran fauna of these landmasses.
Geckos are the only major lizard group consisting mostly of nocturnal species. Nocturnality is presumed to have evolved early in gecko evolution and geckos possess numerous adaptations to functioning in low light and at low temperatures. However, not all gecko species are nocturnal and most diurnal geckos have their own distinct adaptations to living in warmer, sunlit environments. We reconstructed the evolution of gecko activity patterns using a newly generated time-calibrated phylogeny. Our results provide the first phylogenetic analysis of temporal activity patterns in geckos and confirm an ancient origin of nocturnality at the root of the gecko tree. We identify multiple transitions to diurnality at a variety of evolutionary time scales and transitions back to nocturnality occur in several predominantly diurnal clades. The scenario presented here will be useful in reinterpreting existing hypotheses of how geckos have adapted to varying thermal and light environments. These results can also inform future research of gecko ecology, physiology, morphology and vision as it relates to changes in temporal activity patterns. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, ●●, ●●–●●.
Pseudogonatodes peruvianus n. sp. is described from the Rio Utcubamba Valley on the eastern slope of the Andes, Department of Cajamarca, northwestern Peru. It is most closely related to P. furvus of Colombia by having relatively long digits, lacking an expanded lamella and being scansorial in behavior. It is also related to P. amazonicus of Brazil in coloration, body size and having granular dorsals.
A new sphaerodactylid gecko of the genus Gonatodes is described from La Blanquilla Island, located 170 km north of the Venezuelan mainland. This new species exhibits the following suite of characters that immediately separate it from other taxa in the genus: vertically elliptic pupil, small size, uniformly reddish brown, non-sexually dimorphic coloration, and a subcaudal scale pattern type C (1'1 ''). The new species is the fourth Gonatodes endemic to Caribbean islands, the other three being G. antillensis (Bonaire, Curacao, the archipelagos of Las Aves and Los Roques), G. daudini (Union Island, The Grenadines), and G. ocellatus (Tobago). Finally, we discuss the close phylogenetic relationship (based on nuclear genes c-mos and NT3) between the new species and Gonatodes daudini, as well as its zoogeographical implications, showing interesting parallels with that of other Caribbean lizards.
In phylogenomics the analysis of concatenated gene alignments, the so-called supermatrix, is commonly accompanied by the assumption
of partition models. Under such models each gene, or more generally partition, is allowed to evolve under its own evolutionary
model. Though partition models provide a more comprehensive analysis of supermatrices, missing data may hamper the tree search
algorithms due to the existence of phylogenetic (partial) terraces. Here we introduce the phylogenetic terrace aware (PTA)
data structure for the efficient analysis under partition models. In the presence of missing data PTA exploits (partial) terraces
and induced partition trees to save computation time. We show that an implementation of PTA in IQ-TREE leads to a substantial
speedup of up to 4.5 and 8 times compared with the standard IQ-TREE and RAxML implementations, respectively. PTA is generally
applicable to all types of partition models and common topological rearrangements thus can be employed by all phylogenomic
inference software.
Only two species of the microteiid lizard genus Euspondylus (E. acutirostris and E. phelpsorum) had been reported from Venezuela. New records of the poorly known gymnophthalmid lizard Euspondylus acutirostris are reported extending its known range along the Coastal Range and Sierra de Aroa (north-central Venezuela) and Sierra de San Luis (northwestern Venezuela), all records occurring at the cloud forest above 1000 m. Seven body measurements were included and morphological variation is described based on at least 17 new specimens. Sexual dimorphism is determined in, at least, eight characteristics of size and squamation. Specimens were found in epiphytic bromeliads and the ground. The populations from Sierra de Aroa and Sierra de San Luis (only one specimen known from each locality), differ from those of the Coastal Range (supposedly the nominal population) in some morphological and coloration features, suggesting that the former two could represent different taxonomical entities. A new species of Euspondylus is described based on a female (taken within a bromeliad) from Cerro El Humo, Sucre, northeastern Venezuela. It differs from congeners mainly by having keeled scales on the limbs and a very acute snout.
Little is known about the natural history of the Sphaerodactylus species endemic to the three islands located in the Mona Passage separating the Greater Antillean islands of Hispaniola and Puerto Rico. In this study, parts of two mitochondrial genes, 16S rRNA and 12S rRNA, were sequenced to determine the relationships between the sphaerodactylids that live in the Mona Passage and other Caribbean species from the same genus. While the main goal was to identify the biogeographical origin of these species, we also identified a genetically distinct type of dwarf gecko that warrants future evaluation as a possible new species. According to the reconstructed phylogenies, we propose a stepwise model of colonization wherein S. nicholsi from southwestern Puerto Rico or a very close ancestor gave rise through a founder event to Sphaerodactylus monensis on Mona Island. In a similar fashion, S. monensis or a very close ancestor on Mona Island gave rise to S. levinsi on Desecheo Island. This study also suggests that the most recent common ancestor between the species from the islands in the Mona Passage and Puerto Rico existed approximately 3 MYA.
A new species of Sphaerodactylus (Squamata: Gekkota: Sphaerodactylidae) is described from an amber inclusion from the late Early Miocene or early Middle Miocene (15 to 20 million years ago) of the Dominican Republic. Unlike earlier amber-embedded specimens assigned to this genus, the new specimen is largely skeletal, with some integument remaining. A combination of 258 (of 674) osteological and external characters could be scored for the new species in a cladistic analysis of 21 gekkotan species, including representatives of all sphaerodactylid genera. The most parsimonious trees obtained confirm the placement of the amber gecko within the genus Sphaerodactylus and a comparison with extant Hispaniolan and Puerto Rican congeners suggests phenetic similarity both with members of S. difficilis complex and the S. shrevei species group. Character mapping on the basis of the phylogenetic analysis permits the preliminary identification of morphological characters diagnostic of the Sphaerodactylidae, Sphaerodactylini, and Sphaerodactylus. Osteological features of the new species are discussed in the broader context of sphaerodactyl, sphaerodactylid, and gekkotan variation. Extant Hispaniolan Sphaerodactylus display significant ecomorphological variation and it is likely that the many known, though not yet described, amber-embedded specimens will eventually reveal similar patterns in their Miocene congeners.
Two new species of Pseudogonatodes Ruthven, 1915, are described, one from the Rio Juruá Basin, in the state of Acre, Brazil (Amazonian rainforest), the other from Rancho Grande, in the state Aragua, Venezuela (cloud forest). Both have granular dorsals and relatively numerous fourth toe lamellae, of which the third (from tip to base of toe) is not distinctly larger than the two distal ones. The species from the Rio Juruá is small, with dark belly, and recognised, among other characteristics, by its tall, conical to flat-conical dorsals. That from Rancho Grande is relatively large, with low number of ventrals, and mental with a straight or convex posterior segment medially, among other distinctive characteristics. Some remarks on the geographic distribution of sphaerodactyl lizards in South America are presented, including a new record for Coleodactylus meridionalis. Duas novas espécies de Pseudogonatodes Ruthven, 1915 são descritas, uma procedente da bacia do rio Juruá, estado do Acre, Brasil (floresta amazônica), a outra de Rancho Grande, estado Aragua, Venezuela (floresta nublada). Ambas as espécies possuem escamas dorsais granulares e lamelas do quarto artelho relativamente numerosas, entre as quais a terceira lamela (a partir da extremidade distal do artelho) não é especialmente aumentada em relação às duas distais. A espécie do Rio Juruá é pequena, com ventre escuro, e reconhecível, entre outros caracteres, pelas escamas dorsais altas e cônicas a cônico-achatadas. A espécie de Rancho Grande é relativamente grande, com um baixo número de escamas ventrais, e margem posterior da mental com um segmento mediano formando uma linha transversal reta ou convexa, entre outros caracteres distintivos. São apresentadas também algumas observações sobre a distribuição geográfica de lagartos Sphaerodactylidae na América do Sul, incluindo um novo registro para Coleodactylus meridionalis.
A new species of gymnophthalmid lizard is describes from the montane forests of the peninsula de Paria in northeastern Venezuela. The new species is one of the three gymnophtalmid species known to be endemic to the region, and the fourth species of Riama from Venezuela. It is likely the sister species to R. shrevei of Trinidad, but can be distinguished from the latter species by having a nosoloreal suture, fewer scale rows encircling the midbody, and by having a higher number of transverse dorsal scale rows.
Nonparametric bootstrap has been a widely used tool in phylogenetic analysis to assess the clade support of phylogenetic trees.
However, with the rapidly growing amount of data, this task remains a computational bottleneck. Recently, approximation methods
such as the RAxML rapid bootstrap (RBS) and the Shimodaira–Hasegawa-like approximate likelihood ratio test have been introduced
to speed up the bootstrap. Here, we suggest an ultrafast bootstrap approximation approach (UFBoot) to compute the support
of phylogenetic groups in maximum likelihood (ML) based trees. To achieve this, we combine the resampling estimated log-likelihood
method with a simple but effective collection scheme of candidate trees. We also propose a stopping rule that assesses the
convergence of branch support values to automatically determine when to stop collecting candidate trees. UFBoot achieves a
median speed up of 3.1 (range: 0.66–33.3) to 10.2 (range: 1.32–41.4) compared with RAxML RBS for real DNA and amino acid alignments,
respectively. Moreover, our extensive simulations show that UFBoot is robust against moderate model violations and the support
values obtained appear to be relatively unbiased compared with the conservative standard bootstrap. This provides a more direct
interpretation of the bootstrap support. We offer an efficient and easy-to-use software (available at http://www.cibiv.at/software/iqtree) to perform the UFBoot analysis with ML tree inference.
A new species of dendrobatid frog of the genus Mannophryne is described from Península de Paria, Estado Sucre, Venezuela. The new taxon, closely related to M. trinitatis, an endemic species of Trinidad, was for a long time considered a continental population of this species. External morphology and call characteristics provide taxonomic distinction between the continental and the insular species, while mitochondrial DNA supports a sister taxon relationship between them. The new species differs from the other members of the genus by its small size (mean snout-vent length 21.5 mm in females, 19.4 mm in males), unpigmented and not well-defined collar and reduced foot webbing. Additionally, the new taxon can be distinguished from Mannophryne trinitatis by: 1) dorsal coloration with a well contrasted pattern; 2) pale dorsolateral stripes not well defined; 3) a paler brown pigmentation on palms and soles; 4) diffuse inguinal stripes; 5) dark markings absent along the anterior margins of forelimbs; 6) advertisement call with a single frequency-modulated note; and 7) differences in 16S and COI mtDNA sequences. Comments on natural history, biogeography and conservation status are provided.
The phylogenetic relationships and species boundaries of the diurnal geckos of the genus Gonatodes in the Guayana region are examined. Seven species of Gonatodes are recognized for the region, six of which are endemic to this region and form a monophyletic group together with G. hasemani from the southern part of the Amazon Basin. Two of the six species in this group are new to science, one of which is endemic to Venezuela and it is described here. Taxonomic accounts are provided for all the Venezuelan species of Gonatodes that are endemic to the Guayana region. The phylogenetic relationships of Gonatodes suggest that the diversity of this genus in the Guayana region has resulted mostly from in situ diversification rather than multiple colonization events by different lineages. The phylogenetic analyses also support that G. antillensis, the only nocturnal species in the genus, is indeed nested within Gonatodes, indicating re-evolution of some traits associated with nocturnal life. Finally, we comment on a recently proposed framework of temporal diversification in Gonatodes and suggest that we are still a long way from attaining a complete understanding about the systematics of this genus.
Se describe un nuevo Colostethus de la Península de Paria en el noreste de Venezuela. La nueva especie habitá en las vertientes del Cerro El Humo à altitudes cerca de 1000 m. Morfológicamente, este estrechamente relacionada con Colostethus bromelicola del tramo central de la Cordillera de la Costa venezolana. Se distingue claramente de las demás especies conocidas para el género de coloración dorsal, ausencia de plieges laterales en los dedos de la mano, ausencia de proceso lingual, y coloración ventral blanquecina. Con esta se eleva à 33 el número de especies pertenecientes al género Colostethus para Venezuela.
La serpiente Taeniophallus nebularis, especie nueva, se conoce de un solo ejemplar colectado en bosque nublado montano, 800 m sobre el nivel del mar, en la Península de Paria, en el noreste de Venezuela. Se trata de un colúbrido “xenodontino” de pequeño tamaño (macho adulto con un largo total de 492 mm); escamas dorsales en 19-19-17 hileras, lisas, con fosas apicales en pares en la parte anterior; marrón dorsalmente y grisáceo lateralmente, con patrón poco definido; banda postocular blanca; amarillo brillante en región media del vientre con bordes laterales negros en patrón aserrado. La especie es fácilmente diagnosticable, aunque su colocación en el genero Taeniophallus es problemática. Algunos caracteres sugestivos son compartidos con T. brevirostris y T. nicagus. Estas dos últimas, presumiblemente las especies relacionadas más cercanas geográficamente a T. nebularis, se encuentran en la cuenca Amazónica y en las Guayanas, indicando un paralelismo biogeográfico con ciertas plantas. Taeniophallus occipitalis, especie con extrema reducción de hileras de escamas dorsales y un patrón de color distintivo posiblemente derivado de un precursor similar a T. brevirostris, está ampliamente distribuida al sur del Amazonas. Cuatro especies adicionales de Taeniophallus sensu lato constituyen el grupo monofilético affinis con centro de distribución en el sureste de Brasil. El genero Echinantera (también con un centro de distribución en el sureste de Brasil) es algunas veces expandido a incluir todo las especies en Taeniophallus. Echinantera s.s. es visto como un grupo demostrablemente monofilético que contiene seis especies, mientras que las relaciones entre los subgrupos de Taeniophallus s.l. y con respecto a Echinantera permanecen inciertas. La divergencia evolutiva en los órganos copulativos es extraordinaria en las especies otrora similares Taeniophallus nicagus y T. brevirostris, lo cual sugiere que no se puede asignar de forma segura peso a los caracteres del hemipene en especies presumiblemente cercanas. El hemipenes de T. nebularis difiere de los de los otros taxa estudiados en ser conspicuamente bilobado en casi un tercio de su longitud. Sin embargo, cierto grado de bilobación es simplesiomórfico para estas serpientes, como se evidencia por la presencia o ausencia de bilobación débil en algunas especies y división de la inserción del músculo retractor en todas. La región desnuda en el lado asulcado del hemipenes en T. nebularis también pudiera ser simplesiomórfico para Taeniophallus s.l. y Echinantera s.s., pero la homología y nivel de generalidad de este carácter no es claro todavía.
Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data.Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl.Contact:
peter@biomatters.com
Phylogenetic comparative methods comprise the general endeavor of using an estimated phylogenetic tree (or set of trees) to make secondary inferences: about trait evolution, diversification dynamics, biogeography, community ecology, and a wide range of other phenomena or processes. Over the past ten years or so, the phytools R package has grown to become an important research tool for phylogenetic comparative analysis. phytools is a diverse contributed R library now consisting of hundreds of different functions covering a variety of methods and purposes in phylogenetic biology. As of the time of writing, phytools included functionality for fitting models of trait evolution, for reconstructing ancestral states, for studying diversification on trees, and for visualizing phylogenies, comparative data, and fitted models, as well numerous other tasks related to phylogenetic biology. Here, I describe some significant features of and recent updates to phytools , while also illustrating several popular workflows of the phytools computational software.
Snakes comprise nearly 4,000 extant species found on all major continents except Antarctica. Morphologically and ecologically diverse, they include burrowing, arboreal, and marine forms, feeding on prey ranging from insects to large mammals. Snakes are strikingly different from their closest lizard relatives, and their origins and early diversification have long challenged and enthused evolutionary biologists. The origin and early evolution of snakes is a broad, interdisciplinary topic for which experts in palaeontology, ecology, physiology, embryology, phylogenetics, and molecular biology have made important contributions. The last 25 years has seen a surge of interest, resulting partly from new fossil material, but also from new techniques in molecular and systematic biology. This volume summarises and discusses the state of our knowledge, approaches, data, and ongoing debates. It provides reviews, syntheses, new data and perspectives on a wide range of topics relevant to students and researchers in evolutionary biology, neontology, and palaeontology.
We describe a new sphaerodactylid lizard of the genus Gonatodes from the western flank of the Cordillera Oriental, Santander Department, Colombia based on morphological and molecular data. The new species is distinguished from all congeners by having a medium body size, by the absence of both a supraciliary spine and of clusters of distinctly enlarged conical scales on the sides and by having a subcaudal scale pattern (1’1”) and a cryptic dorsal color pattern in both sexes. Additionally, we describe for the first time the hemipenial morphology for a species of the genus. The new species increases the number of Gonatodes known from Colombia to eight and is the only known species of the country, as well as the second known mainland species of the genus not exhibiting sexual dichromatism
Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates by incorporating a model of rate heterogeneity across sites not previously considered in this context and by allowing concurrent searches of model space and tree space.
Eighty-nine species of lizards, six of which polytypic (forming a total of 97 taxa), are presently known from Brazilian Amazonia. This number includes six species and one subspecies described as new to science in this paper: Stenocercus fimbriatus, Lepidoblepharis hoogmoedi, Leposoma osvaldoi, L. snethlageae, Tretioscincus oriximinensis, Tupinambis longilineus, and Anolis nitens tandai. Stenocercus dumerilii is resurrected from the synonymy of S. tricristatus. Bachia cophias is considered a junior synonym of B. flavescens. B. peruana is a new record from Brazil. Anolis nitens has priority over A. chrysolepis. The Amazonian Tupinambis is shown to be T. teguixin (of which T. nigropunctatus is a junior synonym). The name T. merianae should be used for T. teguixin sensu Boulenger (1885b). Mabuya ficta is a junior synonym of M. bistriata, while the name M. nigropunctata should be used for M. bistriata sensu Vanzolini & Williams (1980). Of all species extensive descriptions and ecological data, if available, are presented. A zoogeographical analysis based on the combined distribution maps of the various species shows a main division in Amazonia of a western and an eastern fauna. A southwestern group is also recognised and, although defined by a smaller number of species, a Guianan group. The lizard fauna from Rondônia shows multiple affinities. The distribution of lizards in enclaves of open formations in Amazonia does not support the idea of continuous areas of savannas throughout Amazonia in relatively recent times.
Amphisbaenians are a poorly known group of squamate reptiles with over 150 extant species in 23 genera. They live almost exclusively under loose or sandy soil in tropical to temperate areas around the world, and their anatomy is modified in many ways related to this lifestyle. Most recent studies recognize four families within Amphishaenia - Bipedidae, Amphisbaenidae, Trogonophidae, and Rhineuridae. Only the Rhineuridae are well represented in the fossil record. Two exclusively fossil families, Hyporhinidae and Crythiosauridae, have also been recognized in some studies. In this paper, a phylogenetic study of the Amphisbaenia is presented based on morphological characters investigated in living and fossil forms. Amphisbaenian monophyly is supported, but the recent identification of the late Cretaceous Sineoamphisbaena hextabularis† as a primitive amphisbaenian is not supported. The monophyly of two of the four families of extant amphisbaenians is upheld, with one family being more inclusive than previously thought. Amphisbaenidae is substantially revised, with several taxa previously included in the family being more closely related to rhineurids, and with Blanus representing a basal amphisbaenian. Rhineuridae is also revised to include the previously recognized fossil family Hyporhinidae. Trogonophidae is the sister-group to the remaining amphisbaenids, and together they form the sister-group to the expanded rhineurid clade. Bipes is the most basal amphisbaenian and Blanus is the Sister-group to all remaining amphisbaenians. Crythiosauridae is removed from the Amphisbaenia because no support was found for its inclusion. The deep nesting of rhineurids within Amphisbaenia found here contrasts with their extensive fossil record beginning in the late Paleocene. This hypothesis implies significant gaps in the fossil record of all other amphisbaenian taxa, and the reacquisition of some seemingly primitive features in some fossil rhineurids. However, the condition of the limbs in extinct rhineurids is uncertain and, if they are found to be present, the related characters could place them in a more basal position, which would then alter interpretations of character evolution. The basal positions of Bipes and Blanus imply that a round-headed cranial shape is the primitive condition for Amphishaenia in contrast to some previous hypotheses. In this analysis, amphisbaenians are nested within Squamata, in contrast to a hypothesized relationship as the sister-group to the remainder of squamates (alone, with snakes, or with another group of limbless burrowing lizards, Dibamidae). Weak support was found for a relationship between amphisbaenians and Dibamidae as previously suggested by some other analyses, but this is liased mainly on reduction and absence features and the sister-group to Amphisbaenia is considered here to be inconclusive. Sineoamphisbaena† is found to be related to maerocephalosaurs, an extinct group previously placed with Teiidae, but placed basally among squamates by this analysis. Morphological analyses of squamates in this study include numerous features associated with reduced or absent limbs and limb girdles, as well as other specializations presumed to be related to a burrowing lifestyle. These characters are often hypothesized to have heen convergently acquired among limbless squamate clades and have been excluded or downweighted in some previous analyses. This approach is difficult to implement here because further anatomical investigations of these structures revealed useful variation for resolving relationships within amphisbaenians. Future studies will require new approaches that can address the convergence problem in a manner that does not involve the added problem of removing characters informative at other levels. They should also include the addition of novel data sets.
Mosasaurus hoffmanni, one of the latest known mosasaurs, comes from the Upper Maastrichtian, Upper Cretaceous Chalk of The Netherlands. Although the first specimen was discovered over 200 years ago, it is here fully described for the first time to provide detailed insights into its anatomy, functional morphology and evolution. Many characters of the skull show that M. hoffmanni was among the most advanced mosasaurs. The skull is robustly constructed and is the least kinetic in the Mosasauridae and, with a tightly assembled palatal complex, provided greater cranial stability in this large-headed mosasaur. The cranial musculature is highly modified. The four-bar linkage system of lizards and early mosasaurs is non-functional in M. hoffmanni. The elements of the lower jaw are also more tightly united than in other mosasaurs. Tooth crowns are divided into several distinct, unique cutting surfaces or prisms. A functional analysis of the marginal teeth shows that they are particularly adapted to powerful bite forces although pterygoidal teeth are small and reduced in importance in ratchet feeding. Moderately large orbits and poorly developed olfactory organs suggest that Mosasaurus hoffmanni was a surface-swimming animal. A relatively lower level of binocular vision than in some other mosasaurs may indicate a somewhat uncomplicated habitat. Geological and palaeontological evidence indicates that M. hoffmanni lived in fairly deep nearshore waters of 40-50 m depth, with changing temperatures and rich vertebrate and invertebrate life. Several severely broken and healed mandibles suggest either a violent lifestyle in predation or in fighting.
1Apart from their elongation, the skulls of pygopods are gecko-like in general form and in the elements present. Cranial morphology supports the views of gecko-pygopod affinities which have been expressed by McDowell & Bogert (1954) and Underwood (1957).2Of the various pygopod genera, the skull of Pygopus is the least modified, while that of Delma is very similar to it.3The most extreme elongation of the pre-optic and post-optic regions of the skull occurs in Lialis. In Aprasia, differential elongation of dorsal and ventral regions of the skull anteriorly results in the mouth being ventral instead of terminal.4Pletholax is the only known genus amongst pygopods and Australian geckos in which the frontals are not fused, and is further characterized by the fact that certain bones of the head overlap.5Lialis is unique among pygopods in lacking a jugal.6Aprasia invariably lacks maxillary teeth. Furthermore, premaxillary teeth are lacking in juveniles of this genus, and also in adult females except those of A. striolata.7As in Australian geckos, only a single splinter-like temporal bone may be recognized between the parietal and quadrate.8The hyobranchial apparatus is extremely gecko-like in form.9The reduced, U-shaped pectoral girdle of Aprasia is re-interpreted. It is suggested that the elements present are the two cartilaginous suprascapulae, the two bony clavicles, and a median piece representing the clavicular symphysis.10The pectoral girdle of Pletholax gracilis is unique amongst known pygopods and Australian geckos in the presence of a bony interclavicle.11The three elements of the pelvic girdle, namely the pubis, ischium and ilium, are invariably present. However, different pygopod genera show various stages of hind limb reduction, from Pygopus in which even four digits of the foot are present, to Aprasia, in which only one bone, the femur, is present in the hind limb rudiment.12The morphological distinctiveness of various pygopod genera is discussed in terms of heterochrony. Differences between adult species and genera, though genetically based, are subsequently related to the time of embryonic appearance of certain structures as compared with neighbouring structures, and to their varying rates of development.
A molecular phylogeny was reconstructed for 26 recognized genera of the Gymnophthalmidae using a total of 2379 bp of mitochondrial (12S, 16S and ND4) and nuclear (18S and c-mos) DNA sequences. We performed maximum parsimony (MP) and maximum likelihood (ML) analyses, and data partitions were analysed separately and in combination under MP. ML analyses were carried out only on the combined sequences for computational simplicity. Robustness for the recovered nodes was assessed with bootstrap and partitioned Bremer support (PBS) analyses. The total molecular evidence provided a better-resolved hypothesis than did separate analysis of individual partitions, and the PBS analysis indicates congruence among independent partitions for support of some internal nodes. Based on this hypothesis, a new classification for the family is proposed. Alopoglossus, the sister group of all the other Gymnophthalmidae was allocated to a new subfamily Alopoglossinae, and Rhachisaurus (a new genus for Anotosaura brachylepis) to the new Rhachisaurinae. Two tribes are recognized within the subfamily Gymnophthalminae: Heterodactylini and Gymnophthalmini, and two others within Cercosaurinae (Ecpleopini and Cercosaurini). Some ecological and evolutionary implications of the phylogenetic hypothesis are considered, including the independent occurrence of limb reduction, body elongation, and other characters associated with fossoriality.
Aim Geckos (Reptilia: Squamata), due to their great age and global distribution, are excellent candidates to test hypotheses of Gondwanan vicariance against post‐Gondwanan dispersal. Our aims are: to generate a phylogeny of the sphaerodactyl geckos and their closest relatives; evaluate previous phylogenetic hypotheses of the sphaerodactyl geckos with regard to the other major gecko lineages; and to use divergence date estimates to inform a biogeographical scenario regarding Gondwanan relationships and assess the roles of vicariance and dispersal in shaping the current distributions of the New World sphaerodactyl geckos and their closest Old World relatives.
Location Africa, Asia, Europe, South America, Atlantic Ocean.
Methods We used parsimony and partitioned Bayesian methods to analyse data from five nuclear genes to generate a phylogeny for the New World sphaerodactyl geckos and their close Old World relatives. We used dispersal–vicariance analysis to determine ancestral area relationships among clades, and divergence times were estimated from the phylogeny using nonparametric rate smoothing.
Results We recovered a monophyletic group containing the New World sphaerodactyl genera, Coleodactylus , Gonatodes , Lepidoblepharis , Pseudogonatodes and Sphaerodactylus , and the Old World Gekkotan genera Aristelliger , Euleptes , Quedenfeldtia , Pristurus , Saurodactylus and Teratoscincus . The dispersal–vicariance analysis indicated that the ancestral area for this clade was North Africa and surrounding regions. The divergence between the New World spaherodactyl geckos and their closest Old World relative was estimated to have occurred c . 96 Myr bp .
Main conclusions Here we provide the first molecular genetic phylogenetic hypothesis of the New World sphaerodactyl geckos and their closest Old World relatives. A combination of divergence date estimates and dispersal–vicariance analysis informed a biogeographical scenario indicating that the split between the sphaerodactyl geckos and their African relatives coincided with the Africa/South America split and the opening of the Atlantic Ocean. We resurrect the family name Sphaerodactylidae to represent the expanded sphaerodactyl clade.
Sphaerodactyl geckos comprise five genera distributed across Central and South America and the Caribbean. We estimated phylogenetic relationships among sphaerodactyl genera using both separate and combined analyses of seven nuclear genes. Relationships among genera were incongruent at different loci and phylogenies were characterized by short, in some cases zero length, internal branches and poor phylogenetic support at most nodes. We recovered a polyphyletic Coleodactylus, with Coleodactylus amazonicus being deeply divergent from the remaining Coleodactylus species sampled. The C. amazonicus lineage possessed unique codon deletions in the genes PTPN12 and RBMX while the remaining Coleodactylus species had unique codon deletions in RAG1. Topology tests could not reject a monophyletic Coleodactylus, but we show that short internal branch lengths decreased the accuracy of topology tests because there were not enough data along short branches to support one phylogenetic hypothesis over another. Morphological data corroborated results of the molecular phylogeny, with Coleodactylus exhibiting substantial morphological heterogeneity. We identified a suite of unique craniofacial features that differentiate C. amazonicus not only from other Coleodactylus species, but also from all other geckos. We describe this novel sphaerodactyl lineage as a new genus, Chatogekko gen. nov. We present a detailed osteology of Chatogekko, characterizing osteological correlates of miniaturization that provide a framework for future studies in sphaerodactyl systematics and biology.