[Show abstract][Hide abstract] ABSTRACT: The decline of amphibian populations, particularly frogs, is often cited as an example in support of the claim that Earth is undergoing its sixth mass extinction event. Amphibians seem to be particularly sensitive to emerging diseases (e.g., fungal and viral pathogens), yet the diversity and geographic distribution of infectious agents are only starting to be investigated. Recent work has linked a previously undescribed protist with mass-mortality events in the United States, in which infected frog tadpoles have an abnormally enlarged yellowish liver filled with protist cells of a presumed parasite. Phylogenetic analyses revealed that this infectious agent was affiliated with the Perkinsea: a parasitic group within the alveolates exemplified by Perkinsus sp., a " marine " pro-tist responsible for mass-mortality events in commercial shellfish populations. Using small subunit (SSU) ribosomal DNA (rDNA) se-quencing, we developed a targeted PCR protocol for preferentially sampling a clade of the Perkinsea. We tested this protocol on freshwater environmental DNA, revealing a wide diversity of Per-kinsea lineages in these environments. Then, we used the same protocol to test for Perkinsea-like lineages in livers of 182 tadpoles from multiple families of frogs. We identified a distinct Perkinsea clade, encompassing a low level of SSU rDNA variation different from the lineage previously associated with tadpole mass-mortality events. Members of this clade were present in 38 tadpoles sampled from 14 distinct genera/phylogroups, from five countries across three continents. These data provide, to our knowledge, the first evidence that Perkinsea-like protists infect tadpoles across a wide taxonomic range of frogs in tropical and temperate environments , including oceanic islands. frog decline | emerging disease | parasite | alveolates | molecular diversity
Proceedings of the National Academy of Sciences 08/2015; DOI:10.1073/pnas.1500163112 · 9.81 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The dominant hypothesis for the evolutionary origin of snakes from 'lizards' (non-snake squamates) is that stem snakes acquired many snake features while passing through a profound burrowing (fossorial) phase. To investigate this we examined the visual pigments and their encoding opsin genes in a range of squamate reptiles, focusing on fossorial lizards and snakes. We sequenced opsin transcripts isolated from retinal cDNA and used microspectrophotometry to measure directly the spectral absorbance of the photoreceptor visual pigments in a subset of samples. In snakes, but not lizards, dedicated fossoriality (as in Scolecophidia and the alethinophidian Anilius scytale) corresponds with loss of all visual opsins other than RH1 (λmax 490-497nm); all other snakes (including less dedicated burrowers) also have functional sws1 and lws opsin genes. In contrast, the retinas of all lizards sampled, even highly fossorial amphisbaenians with reduced eyes, express functional lws, sws1, sws2 and rh1 genes, and most also express rh2 (i.e., they express all five of the visual opsin genes present in the ancestral vertebrate). Our evidence of visual pigment complements suggests that the visual system of stem snakes was partly reduced, with two (RH2, SWS2) of the ancestral vertebrate visual pigments being eliminated, but that this did not extend to the extreme additional loss of SWS1 and LWS that subsequently occurred (probably independently) in highly fossorial extant scolecophidians and A. scytale. We therefore consider it unlikely that the ancestral snake was as fossorial as extant scolecophidians, whether or not the latter are para- or monophyletic This article is protected by copyright. All rights reserved.
This article is protected by copyright. All rights reserved.
[Show abstract][Hide abstract] ABSTRACT: Limited previous studies on caecilian taste organs have demonstrated the presence of very few taste buds in the oral epithelium, while providing somewhat contradictory reports of their distribution within the oropharynx and across taxa. Here we report on the gross morphology of the tongue and explore the distribution, number and morphology of taste organs of five caecilian species representing five families, focussing upon variation within the group and investigating whether larvae and adults have the same type of taste organs. We find that taste buds are widespread in the oropharynx of caecilians and that they occur both in adults and larvae of a species with a biphasic life history. Thus Gymnophiona differ substantially from Batriachia, which have distinct larval and adult taste organs.
Zoologischer Anzeiger - A Journal of Comparative Zoology 04/2015; 257. DOI:10.1016/j.jcz.2015.04.007 · 1.82 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: A new species of indotyphlid caecilian amphibian, Gegeneophis tejaswini sp. nov., is described based on eight specimens from lowlands of the most northerly district of the state of Kerala in the southern part of the Western Ghats region, India. This species is distinguished from all other Gegeneophis in annulation characters and genetics (> 6% different from most similar nominal species for 883 base pairs of mitochondrial 12S and 16S rRNA gene sequence data). The high degree of morphological similarity of G. krishni, G. mhadeiensis and the new species underlines that, for some Gegeneophis, larger samples and/or new characters will be needed to further advance the taxonomy of this genus.
[Show abstract][Hide abstract] ABSTRACT: Effective and targeted conservation action requires detailed information about species, their distribution,
systematics and ecology as well as the distribution of threat processes which affect them. Knowledge of
reptilian diversity remains surprisingly disparate, and innovative means of gaining rapid insight into the
status of reptiles are needed in order to highlight urgent conservation cases and inform environmental
policy with appropriate biodiversity information in a timely manner. We present the first ever global
analysis of extinction risk in reptiles, based on a random representative sample of 1500 species (16%
of all currently known species). To our knowledge, our results provide the first analysis of the global conservation
status and distribution patterns of reptiles and the threats affecting them, highlighting conservation
priorities and knowledge gaps which need to be addressed urgently to ensure the continued
survival of the world’s reptiles. Nearly one in five reptilian species are threatened with extinction, with
another one in five species classed as Data Deficient. The proportion of threatened reptile species is highest
in freshwater environments, tropical regions and on oceanic islands, while data deficiency was highest
in tropical areas, such as Central Africa and Southeast Asia, and among fossorial reptiles. Our results
emphasise the need for research attention to be focussed on tropical areas which are experiencing the
most dramatic rates of habitat loss, on fossorial reptiles for which there is a chronic lack of data, and
on certain taxa such as snakes for which extinction risk may currently be underestimated due to lack
of population information. Conservation actions specifically need to mitigate the effects of humaninduced
habitat loss and harvesting, which are the predominant threats to reptiles.
[Show abstract][Hide abstract] ABSTRACT: Insights into morphological diversification can be obtained from the ways the species of a clade occupy morphospace. Projecting a phylogeny into morphospace provides estimates of evolutionary trajectories as lineages diversified information that can be used to infer the dynamics of evolutionary processes that produced patterns of morphospace occupation. We present here a large-scale investigation into evolution of morphological variation in the skull of caecilian amphibians, a major clade of vertebrates. Because caecilians are limbless, predominantly fossorial animals, diversification of their skull has occurred within a framework imposed by the functional demands of head-first burrowing. We examined cranial shape in 141 species, over half of known species, using X-ray computed tomography and geometric morphometrics. Mapping an existing phylogeny into the cranial morphospace to estimate the history of morphological change (phylomorphospace), we find a striking pattern: most species occupy distinct clusters in cranial morphospace that closely correspond to the main caecilian clades, and each cluster is separated by unoccupied morphospace. The empty spaces in shape space are unlikely to be caused entirely by extinction or incomplete sampling. The main caecilian clades have different amounts of morphological disparity, but neither clade age nor number of species account for this variation. Cranial shape variation is clearly linked to phyletic divergence, but there is also homoplasy, which is attributed to extrinsic factors associated with head-first digging: features of caecilian crania that have been previously argued to correlate with differential microhabitat use and burrowing ability, such as subterminal and terminal mouths, degree of temporal fenestration (stegokrotaphy/zygokrotaphy), and eyes covered by bone, have evolved and many combinations occur in modern species. We find evidence of morphological convergence in cranial shape, among species that have eyes covered by bone, resulting in a narrow bullet-shaped head. These results reveal a complex history, including early expansion of morphospace and both divergent and convergent evolution resulting in the diversity we observe today.
[Show abstract][Hide abstract] ABSTRACT: A new species of the erythrosuchid archosauriform reptile Garjainia Ochev, 1958 is described on the basis of disarticulated but abundant and well-preserved cranial and postcranial material from the late Early Triassic (late Olenekian) Subzone A of the Cynognathus Assemblage Zone of the Burgersdorp Formation (Beaufort Group) of the Karoo Basin of South Africa. The new species, G. madiba, differs from its unique congener, G. prima from the late Olenekian of European Russia, most notably in having large bony bosses on the lateral surfaces of the jugals and postorbitals. The new species also has more teeth and a proportionately longer postacetabular process of the ilium than G. prima. Analysis of G. madiba bone histology reveals thick compact cortices comprised of highly vascularized, rapidly forming fibro-lamellar bone tissue, similar to Erythrosuchus africanus from Subzone B of the Cynognathus Assemblage Zone. The most notable differences between the two taxa are the predominance of a radiating vascular network and presence of annuli in the limb bones of G. madiba. These features indicate rapid growth rates, consistent with data for many other Triassic archosauriforms, but also a high degree of developmental plasticity as growth remained flexible. The diagnoses of Garjainia and of Erythrosuchidae are addressed and revised. Garjainia madiba is the geologically oldest erythrosuchid known from the Southern Hemisphere, and demonstrates that erythrosuchids achieved a cosmopolitan biogeographical distribution by the end of the Early Triassic, within five million years of the end-Permian mass extinction event. It provides new insights into the diversity of the Subzone A vertebrate assemblage, which partially fills a major gap between classic 'faunal' assemblages from the older Lystrosaurus Assemblage Zone (earliest Triassic) and the younger Subzone B of the Cynognathus Assemblage Zone (early Middle Triassic).
PLoS ONE 11/2014; 9(11):e111154. DOI:10.1371/journal.pone.0111154 · 3.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: For amphibians, non-lethal sampling methods have been developed and evaluated for only two of the three extant orders, with the limbless caecilians (Gymnophiona) thus far overlooked. Here we assess 16 different methods in five caecilian species representing five families with differing morphologies and ecologies. DNA was successfully extracted and amplified for multiple genetic markers using all tested methods in at least some cases although yields are, unsurprisingly, generally substantially lower than for DNA extractions from (lethally sampled) liver. Based on PCR performance, DNA yield and sampling considerations, buccal swabs, skin scrapes, blood pricks and dermal scalepocket biopsies performed the best.
[Show abstract][Hide abstract] ABSTRACT: The indotyphlid caecilian amphibian Idiocranium russeli Parker, 1936 is the only nominal species in its genus. Apart from two additional, largely overlooked locality records that we consider to be of an undescribed species, I. russeli is known with certainty from only a single collection of c.50 specimens from a single locality in 1933. We report new material from fieldwork in 2012 carried out in the vicinity of the type locality. Digging surveys at 34 sites for a total of >2000 person minutes found 50 I. russeli at 15 of these sites, extending the known range of the species by more than 40 km south and from an elevation of c.670 m to 104–820 m. The species probably occurs in nearby Nigeria and in some protected areas, is tolerant of some human disturbance, and is likely to move from Data Deficient to Least Concern on the IUCN Red List. Males have relatively longer and wider heads than females. Total length measured for preserved specimens is less than for freshly anaesthetized specimens, by up to 14.1%. Previously, preserved I. russeli were reported as having a maximum length of 114 mm, but the new sample includes specimens with total lengths of 145 mm in preservation and 167 mm when fresh. The sex of the smallest independent specimens (total length 62 mm in preservation) could be determined from examination of the gonads, hatchlings are c.30 mm, and I. russeli is confirmed as one of the smallest known caecilian species.
Journal of Natural History 09/2014; 49(3-4). DOI:10.1080/00222933.2014.939733 · 0.93 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The Eastern Afromontane Region (EAR) contains numerous endemic species, yet its reptile diversity remains relatively poorly understood. We used molecular data to examine species diversity of the Sub-Saharan chameleon genus Trioceros. In particular, we focus on establishing species boundaries for taxa with disjunct distributions across the fragmented mountains of the EAR, including T. affinis, T. balebicornutus, T. deremensis, T. harennae, T. tempeli and T. werneri. We applied three species-delimiting approaches, General Mixed Yule-Coalescent (GMYC), a Bayesian implementation of the GMYC, and Bayes Factor Delimitation to estimate species diversity. Using a dated phylogeny, we also examined spatial and temporal diversification patterns in Trioceros. We found strong congruence between different species delimitation approaches, with all methods suggesting that species diversity is currently underestimated. In particular, T. werneri consists of at least four candidate species (i.e. species awaiting description) with some mountain ranges (Uluguru and Udzungwa) having potentially more than one species. Most interspecific divergences between extant Trioceros lineages are estimated to be >5 Mya, consistent with a Pliocene origin of the endemic montane fauna, as exhibited in other taxonomic groups. Multiple, overlapping geographic events (climate and/or geomorphological changes) might account for speciation patterns in Trioceros given the dating results.
[Show abstract][Hide abstract] ABSTRACT: The hyperoliid frog Tachycnemis seychellensis, the only species of its genus, is endemic to the four largest granitic islands of the Seychelles archipelago and is reliant on freshwater bodies for reproduction. Its presence in the Seychelles is thought to be the product of a transoceanic dispersal, diverging from the genus Heterixalus, its closest living relative (currently endemic to Madagascar), between approximately 10-35Ma. A previous study documented substantial intraspecific morphological variation among island populations and also among populations within the largest island (Mahé). To assess intraspecific genetic variation and to infer the closest living relative(s) of T. seychellensis, DNA sequence data were generated for three mitochondrial and four nuclear markers. These data support a sister-group relationship between T. seychellensis and Heterixalus, with the divergence between the two occurring between approximately 11-19Ma based on cytb p-distances. Low levels of genetic variation were found among major mitochondrial haplotype clades of T. seychellensis (maximum 0.7% p-distance concatenated mtDNA), and samples from each of the islands (except La Digue) comprised multiple mitochondrial haplotype clades. Two nuclear genes (rag1 and tyr) showed no variation, and the other two (rho, pomc) lacked any notable geographic structuring, counter to patterns observed within presumably more vagile Seychelles taxa such as lizards. The low levels of genetic variation and phylogeographic structure support an interpretation that there is a single but morphologically highly variable species of Seychelles treefrog. The contrasting genetic and morphological intraspecific variation may be attributable to relatively recent admixture during low sea-level stands, ecophenotypic plasticity, local adaptation to different environmental conditions, and/or current and previously small population sizes. Low genetic diversity but substantial morphological variation is unusual within anurans.
[Show abstract][Hide abstract] ABSTRACT: Euparkeria capensis is resolved as the sister taxon to Archosauria in many cladistic phylogenies and provides a key outgroup which may approximate the ancestral archosaur morphology. Several other taxa have been referred to the family Euparkeriidae, but the monophyly of this taxon remains doubtful and largely untested. To test this monophyly, the archosauriform and putative euparkeriid Dorosuchus neoetus from the Mid-Triassic of Russia is re-examined in the light of recent work on the evolution of stem archosaurs. Dorosuchus neoetus is found to possess a number of morphological features that place it close to Archosauria, including a sigmoidal femur with a clear attachment region for the m. caudifemoralis musculature, but no unambiguous archosaurian apomorphies. Dorosuchus neoetus is included for the first time in a numerical cladistic analysis and is recovered as the sole sister taxon to Archosauria + Phytosauria. A monophyletic Euparkeriidae including D. neoetus and E. capensis is slightly less parsimonious. In addition, a mandible and pterygoid that were previously referred to D. neoetus subsequent to the original description of the species are also included separately within the phylogenetic analysis and are recovered within Archosauria, possibly raising questions as to their correct taxonomic referral. However, this phylogenetic placement is based primarily on the absence of palatal teeth, but the presence or absence of palatal teeth exhibits considerable homoplasy within Archosauriformes. Based on other aspects of their morphology, we do not reject the referral of these elements to D. neoetus.
[Show abstract][Hide abstract] ABSTRACT: A new species of striped ichthyophiid caecilian, Ichthyophis multicolor sp. nov., is described on the basis of morphological and molecular data from a sample of 14 specimens from Ayeyarwady Region, Myanmar. The new species resembles superficially the Indian I. tricolor Annandale, 1909 in having both a pale lateral stripe and an adjacent dark ventrolateral stripe contrasting with a paler venter. It differs from I. tricolor in having many more annuli, and in many details of cranial osteology, and molecular data indicate that it is more closely related to other Southeast Asian Ichthyophis than to those of South Asia. The caecilian fauna of Myanmar is exceptionally poorly known but is likely to include chikilids as well as multiple species of Ichthyophis.
[Show abstract][Hide abstract] ABSTRACT: AimThe persistence and stability of habitats through time are considered predictors of high levels of biodiversity in some environments. Long-term habitat persistence and stability may explain the species-rich, endemic forest fauna and flora of the Eastern Afromontane Biodiversity Region (EABR). Using complementary phylogenetic and biogeographical approaches, we examine evolutionary patterns in EABR brevicipitid frogs. Using these data, we test whether brevicipitid history reflects patterns of long-term forest persistence and/or stability across the EABR.LocationEast Africa.MethodsA dated phylogeny for brevicipitids was constructed using two nuclear and three mitochondrial markers. Alternative diversification models were used to determine signal for constant or varying net diversification rates. Using our dated tree, we identified areas of high phylogenetic diversity (PD), and inferred ancestral areas using likelihood and Bayesian approaches.ResultsBrevicipitids have a long history, with generic diversification among extant lineages pre-dating the Oligocene (> 33 Ma). Ancestral-area reconstructions indicate the presence of brevicipitids in the EABR since the Oligocene, and support a scenario of palaeoendemics surviving in EABR refugia. Ancestral-area reconstructions indicate that the central Eastern Arc Mountains (EAM) formed the initial centre of diversification of forest brevicipitids. Measures of PD show that diversity varies across the EABR but is highest in the EAM. Constant net diversification rate in brevicipitids is a significantly better fit than alternative, rate-variable models.Main conclusionsThe degree of persistence of forest habitats appears to be a contributing factor to the varying levels of diversity across the EABR in brevicipitids (and other organisms). In contrast to the Southern Highlands and Ethiopian Bale Mountains, the EAM stands out as an area that enabled the constant accumulation of brevicipitid species over a long period of time.
Journal of Biogeography 04/2014; 41(9). DOI:10.1111/jbi.12331 · 4.97 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: According to current understanding, five lineages of amphibians, but no other tetrapods, are secondarily lungless and are believed to rely exclusively on cutaneous gas exchange. One explanation of the evolutionary loss of lungs interprets lunglessness as an adaptation to reduce buoyancy in fast-flowing aquatic environments, reasoning that excessive buoyancy in such an environment would cause organisms being swept away. While not uncontroversial, this hypothesis provides a plausible potential explanation of the evolution of lunglessness in four of the five lungless amphibian lineages. The exception is the most recently reported lungless lineage, the newly described Guyanan caecilian genus and species Caecilita iwokramae Wake & Donnelly, 2010, which is inconsistent with the reduced disadvantageous buoyancy hypothesis by virtue of it seemingly being terrestrial and having a terrestrial ancestry. Re-examination of the previously only known specimen of C. iwokramae and of recently collected additional material reveal that this species possesses a reasonably well-developed right lung and is a species of the pre-existing caecilian genus Microcaecilia Taylor, 1968. We therefore place Caecilita in the synonymy of Microcaecilia, and re-evaluate the plausibility of the reduced disadvantageous buoyancy hy- pothesis as a general explanation of the evolution of lunglessness.
[Show abstract][Hide abstract] ABSTRACT: The phylogenetic relationships of many taxa remain poorly known because of a lack of appropriate data and/or analyses. Despite substantial recent advances, amphibian phylogeny remains poorly resolved in many instances. The phylogenetic relationships of the Ethiopian endemic monotypic genus Ericabatrachus has been addressed thus far only with phenotypic data and remains contentious.
We obtained fresh samples of the now rare and Critically Endangered Ericabatrachus baleensis and generated DNA sequences for two mitochondrial and four nuclear genes. Analyses of these new data using de novo and constrained-tree phylogenetic reconstructions strongly support a close relationship between Ericabatrachus and Petropedetes, and allow us to reject previously proposed alternative hypotheses of a close relationship with cacosternines or Phrynobatrachus.
We discuss the implications of our results for the taxonomy, biogeography and conservation of E. baleensis, and suggest a two-tiered approach to the inclusion and analyses of new data in order to assess the phylogenetic relationships of previously unsampled taxa. Such approaches will be important in the future given the increasing availability of relevant mega-alignments and potential framework phylogenies.
[Show abstract][Hide abstract] ABSTRACT: We analyze mitochondrial genomes to reconstruct a robust phylogenetic framework for caecilian amphibians and use this to investigate life-history evolution within the group. Our study comprises 45 caecilian mitochondrial genomes (19 of them newly reported), representing all families and 27 of 32 currently recognized genera, including some for which molecular data had never been reported. Support for all relationships in the inferred phylogenetic tree is high to maximal, and topology tests reject all investigated alternatives, indicating an exceptionally robust molecular phylogenetic framework of caecilian evolution consistent with current morphology-based supraspecific classification. We used the mitogenomic phylogenetic framework to infer ancestral character states and to assess correlation among three life-history traits (free-living larvae, viviparity, specialized pre-adult or vernal teeth), each of which occurs only in some caecilian species. Our results provide evidence that an ancestor of the Seychelles caecilians abandoned direct development and re-evolved a free-living larval stage. This study yields insights into the concurrent evolution of direct development and of vernal teeth in an ancestor of Teresomata that likely gave rise to skin-feeding (maternal dermatophagy) behavior and subsequently enabled evolution of viviparity, with skin feeding possibly a homologous precursor of oviduct feeding in viviparous caecilians.