Molecular data in conjunction with morphology help resolve the Hemidactylus brookii complex (Squamata: Gekkonidae)

Differential Mitochondrial Genome Expression of Three Sympatric Lizards in Response to Low-Temperature Stress

Ecological factors related to climate extremes have a significant influence on the adaptability of organisms, especially for ectotherms such as reptiles that are sensitive to temperature change. Climate extremes can seriously affect the survival and internal physiology of lizards, sometimes even resulting in the loss of local populations or even complete extinction. Indeed, studies have shown that the expression levels of the nuclear genes and mitochondrial genomes of reptiles change under low-temperature stress. At present, the temperature adaptability of reptiles has rarely been studied at the mitochondrial genome level. In the present study, the mitochondrial genomes of three species of lizards, Calotes versicolor, Ateuchosaurus chinensis, and Hemidactylus bowringii, which live in regions of sympatry, were sequenced. We used RT-qPCR to explore the level of mitochondrial gene expression under low-temperature stress, as compared to a control temperature. Among the 13 protein-coding genes (PCGs), the steady-state transcript levels of ND4L, ND1, ATP6, and COII were reduced to levels of 0.61 ± 0.06, 0.50 ± 0.08, 0.44 ± 0.16, and 0.41 ± 0.09 in C. versicolor, respectively, compared with controls. The transcript levels of the ND3 and ND6 genes fell to levels of just 0.72 ± 0.05 and 0.67 ± 0.05 in H. bowringii, compared with controls. However, the transcript levels of ND3, ND5, ND6, ATP6, ATP8, Cytb, and COIII genes increased to 1.97 ± 0.15, 2.94 ± 0.43, 1.66 ± 0.07, 1.59 ± 0.17, 1.46 ± 0.04, 1.70 ± 0.16, and 1.83 ± 0.07 in A. chinensis. Therefore, the differences in mitochondrial gene expression may be internally related to the adaptative strategy of the three species under low-temperature stress, indicating that low-temperature environments have a greater impact on A. chinensis, with a small distribution area. In extreme environments, the regulatory trend of mitochondrial gene expression in reptiles is associated with their ability to adapt to extreme climates, which means differential mitochondrial genome expression can be used to explore the response of different lizards in the same region to low temperatures. Our experiment aims to provide one new research method to evaluate the potential extinction of reptile species in warm winter climates.

Singapore's herpetofauna: updated and annotated checklist, history, conservation, and distribution

Given Singapore's location at the confluence of important maritime trading routes, and that it was established as a British East India Company trading post in 1819, it is unsurprising that Singapore has become one of the centres of natural history collecting and research in Southeast Asia. Despite its small size, Singapore is home to a diverse herpetofauna assemblage and boasts a rich herpetological history. The first systematic studies of Singapore's herpetofauna (within the Linnaean binomial framework) date back to Stamford Raffles and the naturalists hired by him who first came to the island in 1819. Specimens that were collected during and after this time were deposited in museums worldwide. Over time, 39 species from Singapore were described as new to science. Due to the entrepôt nature of Singapore with its associated purchasing and trading of specimens (both alive and dead), poor record-keeping, and human introductions, numerous extraneous species from outside of Singapore were reported to occur on the island. Such issues have left a complicated legacy of ambiguous records and taxonomic complications concerning the identity of Singapore's species-rich herpetofauna, many of which were only resolved in the past 30-40 years. By compiling a comprehensive collection of records and publications relating to the herpetofauna of Singapore, we construct an updated and more accurate listing of the herpetofauna of Singapore. Our investigation culminated in the evaluation of 309 species, in which we compiled a final species checklist recognising 166 species (149 native and 17 non-native established species). Among the 149 native species are two caecilians, 24 frogs, one crocodilian, 13 turtles (three visitors), 34 lizards, and 75 snakes. Of the 17 non-native species are five frogs, four turtles, six lizards, and two snakes. The remaining 143 species represent species to be excluded from Singapore's herpetofauna species checklist. For each of the 309 species examined, we provide species accounts and explanatory annotations. Furthermore, we discuss Singapore's herpetofauna from a historical and conservation perspective. Immediate deforestation and nationwide urbanisation following colonisation completely eliminated many species from throughout much of the country and restricted them to small, degraded forest patches. We hope this publication highlights the importance of publishing observations and serves as a valuable resource to future researchers, naturalists, biological consultants, and policy makers in initiating studies on species ecology, distribution, status, and promoting conservation efforts to safeguard Singapore's herpetofauna.

Role of paleoclimatic and paleohydrological processes in lineage divergence in freshwater organisms: A snippet from lentic genus Pila

The Indian subcontinent is extremely diverse in terms of its flora and fauna. However, only a handful of studies have aimed to understand the diversity of freshwater invertebrates using multiple lines of evidence in recent times. Here we aimed to estimate the cryptic diversity of two widespread freshwater snail species within the genus Pila (Röding, 1798) and uncover the processes behind lineage diversification in these species. We sequenced mitochondrial and nuclear markers from a comprehensive sampling of specimens from different river basins in India. We implemented an integrative taxonomy approach to delimit the lineages in these groups, employing phylogenetic, geometric morphometric and niche modelling-based methods. Then, we investigated the drivers of lineage divergence in these species using population genetic tools in conjunction with divergence time estimation. We found that both species consist of several genetically and ecologically distinct lineages. The genetic data showed that several of these lineages are restricted to a single or a few river basins. The divergence time estimation analyses indicated that the time frame of divergence within the species coincided with paleohydrological and paleoclimatic events in the Miocene. The diversification was primarily driven by allopatric isolation into different river basins. To conclude, the study sheds light on the complex interaction between the habitat preference of the species and the environment in shaping the diversification patterns in this group.

New Morphological and Molecular Data Reveal an Underestimation of Species Diversity of Mites of the Genus Geckobia (Acariformes: Pterygosomatidae) in India

Mites of the genus Geckobia (Acariformes: Pterygosomatidae) are permanent and highly specialised ectoparasites of geckos (Gekkota). We conducted a local study on Geckobia mites associated with the geckos of the family Gekkonidae found mainly in the territory of the Indian Institute of Science’s campus (Bangalore, India). In total, we examined 208 lizards belonging to two genera: Hemidactylus and Cnemaspis. We assessed the prevalence of the mites and identified the preferred site for their infestation. We extended the standard morphological identification of the mite species by using DNA barcode markers, partial sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene and nuclear ribosomal gene sequences: 18S rRNA and hypervariable region D2 of nuclear 28S rRNA. We checked the suitability of COI and nuclear (D2 of 28S rRNA) markers for species delimitations and identification purposes of the genus. The distance- and phylogeny-based approaches were applied: (i) to test the presence of a barcoding gap, we used the automated barcoding gap discovery tool (ABGD) and investigated intra- and interspecific genetic distances, and (ii) to reconstruct evolutionary relationships within the species, we performed maximum likelihood (ML) and Bayesian inference with Markov-Chain Monte Carlo (BI) analyses. As a result, we described five new species—Geckobia gigantea sp. n., G. treutleri sp. n., G. unica sp. n. and G. brevicephala sp. n.—from four Hemidactylus species: H. giganteus, H. treutleri, H. parvimaculatus and H. frenatus, respectively, and G. mysoriensis sp. n. from Cnemaspis mysoriensis. Additionally, we found three already described species: Geckobia indica Hirst, 1917 on H. treutleri (new host), Geckobia bataviensis Vitzhum, 1926 on H. parvimaculatus (new host) and H. frenatus (new locality) and Geckobia phillipinensis Lawrence, 1953 on H. frenatus (new locality). The diagnoses of G. indica and G. phillipinensis were improved and supplemented by descriptions of the males and juveniles. Both topologies of the BI and ML phylogenetic trees, as well as genetic distances, supported the species boundaries in the mite population shown by the morphological data. Hemidactylus frenatus was the most infected gecko species (61% prevalence), with the highest number of mite species (three spp.). The scale-mite richness was higher than expected; therefore, further research is required to evaluate the true diversity of Geckobia mites.

Evaluating the drivers and engines of morphological diversification in the invasive gecko Hemidactylus mabouia (Moreau de Jonnès, 1818) (Squamata: Gekkonidae)

Development determines the range of possible phenotypes that can be produced and exposed to selection and has a major role in the evolutionary trajectories of species. Nevertheless, development is itself subject to evolutionary forces. Here, we describe differences at the ontogenetic and population levels in head and limb proportions of the invasive gecko Hemidactylus mabouia, to assess the developmental mechanisms and extrinsic forces associated with morphological diversification during colonization of novel habitats. We have found that allometric trajectories of most skeletal traits remain constant throughout postnatal development. Linear morphometric analysis did not find multivariate differences between ontogenetic stages or sexes. When comparing populations, our results showed that the divergence of the corresponding external measures was explained by shifts in the intercept of static allometry curves, indicating that differences arose early in development. Populations aggregated into two morphological groups that did not correspond to the groups formed on the basis of genetic structure. Using two different approaches, we found support for an adaptive hypothesis when comparing observed patterns of morphological variation with that expected under neutral evolutionary models.

A checklist of herpetofauna of Telangana state, India

A checklist of herpetofauna of Telangana, India including accepted English name, scientific name along with authority, Telugu and vernacular name, IUCN, Indian Wildlife Protection Act and CITES status, and endemicity is presented in this paper. The herpetofauna diversity of Telangana is represented by 98 species including 16 species of amphibians belonging to four families, one species of crocodile, six species of testudines, 35 species of saurians and 40 species of snakes. Three species—Hemidactylus flavicaudus, H. xericolus, and H. aemulus—are endemic to Telangana.

Occurrence patterns of herpetofauna in different habitat types of western Terai Arc Landscape, India

The Terai Arc Landscape (TAL) is an important region of biodiversity in India. Situated in the foothills of the Himalaya, it is spread across India and Nepal. We describe the herpetofauna of the western part of TAL encompassing Ramnagar Forest Division, which falls in Uttarakhand state of India. We primarily used visual encounter survey method for sampling. A total of 47 species of herpetofauna belonging to three orders, 17 families and 36 genera were recorded from 10 habitat types (6 terrestrial and 4 aquatic). Highest species richness (n=32) was recorded from the human settlement and least (n=4) species richness was reported from pond habitat.  In this paper, the diversity of amphibians and reptiles in each habitat type is discussed.

How the African house gecko (Hemidactylus mabouia) conquered the world

Alien species are among the greatest threats to biodiversity, but the evolutionary origins of invasiveness remain obscure. We conducted the first range-wide sampling of Hemidactylus mabouia from more than 120 localities across Africa, Madagascar and the Neotropics to understand the evolutionary history of one of the most widely distributed, invasive vertebrates in the world. We used a multi-locus phylogeny, species delimitation, fossil-calibrated timetree, ancestral area reconstruction and species distribution models (SDMs) to determine how many putative species-level lineages are contained within H. mabouia, the timing and tempo of diversification, and the origins of commensality-providing insights into the evolutionary origins of invasiveness. Our analyses suggest 'H. mabouia' originated in the Miocene in the Zambezian biogeographic region and includes as many as 20 putative species-level lineages, of which only Hemidactylus mabouia sensu stricto is invasive and widely distributed, including all Neotropical records. Zambezia is the hotspot for diversity within the group with 14 species in southeastern Zambezia. SDMs suggest that H. mabouia was able to establish in the Neotropics due to habitat suitability, and globalization and the slave trade probably allowed it to cross the Atlantic. Distribution models for the H. mabouia complex overpredict the range of the invasive H. mabouia sensu stricto-highlighting the importance of taxonomy in invasive species management.

Phylogenetic analyses of distantly related clades of bent-toed geckos (genus Cyrtodactylus) reveal an unprecedented amount of cryptic diversity in northern and western Thailand

Cyrtodactylus species are the most diverse of the geckos and are widely distributed in Southeast Asia, including Thailand. However, their patterns of distribution, especially in northern and western parts of Thailand, remain unknown because few Cyrtodactylus species in these regions have been described. Thus, a data set of mitochondrial NADH dehydrogenase 2 (ND2) gene and flanking tRNAs from Cyrtodactylus found in northern and western Thailand, including contiguous areas, was assembled to elucidate phylogenetic relationships and identify the distribution patterns of these geckos. The results showed four well-supported clades, a northwestern clade (A), a northern clade (B), a western clade (C), and a special clade characterized by specific morphological features (D). Clades A-C were grouped with strong support by the geography of their localities from northern Thailand (Mae Hong Son and Chiang Mai Provinces) along the Tenasserim mountain ranges to Phang-Nga Province, Thailand. Clade D is a distinct clade of Cyrtodactylus species characterized by a tuberculate and prehensile tail and distributed widely in mainland Southeast Asia. Overall, the results suggest a pattern of geographic separation and distribution of Cyrtodactylus in northern and western Thailand. Additionally, this study provides evidence of a hidden biodiversity of Cyrtodactylus in these regions.

B, P. Karthik, Babu Rao, S. Babu. Catalogue of herpetological specimens from peninsular India at the Sálim Ali Centre for Ornithology & Natural History (SACON), India

We list the herpetological voucher specimens in the holdings of the Sálim Ali Centre for Ornithology & Natural History (SACON), a wildlife research institute in India.  Most of the collections are the fruition of fieldwork by SACON’s herpetologist and a coauthor of this work—late Dr. Subramanian Bhupathy (1963–2014).  Taxonomically, the collection represents 125 species, comprising 29 amphibian species belonging to eight families and 96 reptilian species belonging to 17 families.  Geographically, the material in this collection originates from the Western Ghats, the Eastern Ghats, the Deccan Plateau, and the Coromandel Coast, comprehensively covering all ecoregions of peninsular India.  A total of 15 taxa (three amphibians, 12 reptiles) remain to be fully identified and are provisionally referred to most-resembling taxa, with cf. prefix.  All the specimens in this collection are non-types as on date.              

Into-India or out-of-India? Historical biogeography of the freshwater gastropod genus Pila (Caenogastropoda: Ampullariidae)

The biota of the Indian subcontinent was assembled through multiple associations with various landmasses during a period spanning the Late Cretaceous to the present. It consists of Gondwanan elements that subsequently dispersed ‘out-of-India’ and biota that dispersed ‘into-India’ after the subcontinent collided with Asia. However, the relative contribution of these connections to the current biotic assembly of the subcontinent has been under-explored. Our aim here was to understand the relative importance of these various routes of biotic assembly in India by studying the historical biogeography of the tropical Old World freshwater snail genus Pila. We reconstructed a near-complete phylogeny, based on nuclear and mitochondrial markers, of Ampullariidae including all the described Pila species from India and Ampullariids worldwide. Thereafter, molecular dating and ancestral range estimation analyses were carried out to ascertain the time frame and route of colonization of India by Pila. The results showed that Pila dispersed into India as well as other parts of tropical Asia from Africa after both India and Africa collided with Eurasia. Furthermore, multiple dispersals took place between Southeast Asia and India. These findings corroborate increasing evidence that much of the current Indian assemblage of biota actually dispersed ‘into-India’ after it collided with Asia.

The out-of-India hypothesis: evidence from an ancient centipede genus, Rhysida (Chilopoda: Scolopendromorpha) from the Oriental Region, and systematics of Indian species

The Oriental Region has been a focus of biogeographical research for more than two centuries. We examined systematics and biogeography of the centipede genus Rhysida in this region. A robust species hypothesis for the Indian subcontinental and Southeast Asian Rhysida clade uses molecular, morphological and distribution data. Twelve species are recognized in two monophyletic species complexes, eight belonging to the Rhysida immarginata and four to the Rhysida longipes species complex. They include Rhysida aspinosa, Rhysida crassispina, R. immarginata, R. longipes and seven new species, five of which are formally named in this paper: Rhysida ikhalama, Rhysida konda, Rhysida lewisi, Rhysida pazhuthara and Rhysida sada The nine Rhysida species are documented taxonomically and their morphological variation is reviewed. An integrative systematic approach reveals that diversity of Rhysida in the Indian subcontinent has been underestimated. Both species complexes started to diversify in the Early to Late Cretaceous in the Indian subcontinent. The out-of-India hypothesis is supported in both clades, because Southeast Asian species are nested in Indian subcontinental clades. Historical biogeographical analyses suggest two independent post-collision dispersal events, one in the immarginata clade and another where R. longipes expanded its range into Southeast Asia.

Repeated evolution of terrestrial lineages in a continental lizard radiation

The "early-burst" model of adaptive radiation predicts an early increase in phenotypic disparity concurrent with lineage diversification. Although most studies report a lack of this coupled pattern, the underlying processes are not identified. The continental radiation of Hemidactylus geckos from Peninsular India includes morphologically diverse species that occupy various microhabitats. This radiation began diversifying ~36 Mya with an early increase in lineage diversification. Here, we test the "early-burst" hypothesis by investigating the presence of ecomorphs and examining the pattern of morphological diversification in a phylogenetic framework. Two ecomorphs-terrestrial and scansorial species-that vary significantly in body size and toepad size were identified. Unlike the prediction of the "early-burst" model, we find that disparity in toepad morphology accumulated more recently ~14 Mya and fit the Ornstein-Ulhenbeck model. Ancestral state reconstruction of the two ecomorphs demonstrates that terrestrial lineages evolved independently at least five times from scansorial ancestors, with the earliest diversification in terrestrial lineages 19-12 Mya. Our study demonstrates a delayed increase in morphological disparity as a result of the evolution of terrestrial ecomorphs. The diversification of terrestrial lineages is concurrent with the establishment of open habitat and grasslands in Peninsular India, suggesting that the appearance of this novel resource led to the adaptive diversification.

A check list and population trends of invasive amphibians and reptiles in Taiwan

Invasive species have impacted biodiversity all around the world. Among various ecosystems, islands are most vulnerable to these impacts due to their high ratio of endemism, highly specialized adaptation, and isolated and unique fauna. As with other subtropical islands, Taiwan faces constant risk of biological invasions and is currently ranked as one of the countries most affected by invasive amphibians and reptiles. In this paper, a comprehensive checklist of all known exotic amphibians and reptiles is provided, including twelve species which have successfully colonized Taiwan and six species with a controversial status. We provide an update on the knowledge of all these species including their distribution, colonization history, threats to native animals, and population trends based on literature records, fauna surveys, and data collected during invasive species eradication and control programs. A list of species with high invasive potentials is also provided. This study reports, for the first time, a comprehensive survey of invasive herpetofauna in Taiwan, which should provide a valuable reference to other regions which might suffer from similar invasion risk.

First appearance deceives many: disentangling the Hemidactylus triedrus species complex using an integrated approach

The gekkonid lizard genus Hemidactylus Oken is the second most species-rich genus of geckos with greatest diversity in the tropical regions of the world. Some species of the genus are commensal and widespread; however, there are several endemic lineages with restricted distribution. India is home to at least 35 species, with 20 endemic species and the number is steadily increasing with exploration of new habitats and integrated taxonomic approach including molecular data. We made investigations into the molecular and morphological variation throughout the distribution of Hemidactylus triedrus Daudin, 1802 based on fresh specimens, literature review, museum material and molecular data. Results from morphological, molecular and micro-CT based anatomical data are unequivocal and show that H. triedrus is a species complex represented by three species, H. triedrus sensu stricto and two undescribed taxa. H. subtriedrus Jerdon, 1854 syn. nov. was found to be morphologically similar to the type specimen of H. triedrus, and genetically embedded in a clade containing H. triedrus sensu stricto and is here treated as a junior synonym of H. triedrus, whereas H. lankae Deraniyagala is referred to as nomen dubium given that the types are presently not traceable and the original description is inadequate in diagnosing the taxon. The populations from western-central India and parts of Pakistan, and from southern Karnataka are distinct and diagnosable, and are herein described as two new species, respectively. Morphological and molecular data support the distinctiveness of the new species. The present work resolves a taxonomic turmoil that lasted over two centuries highlighting the need for studies that integrate morphological and molecular data.

A new large species of gecko of the genus Hemidactylus Oken, 1817 (Reptilia: Sauria: Gekkonidae) from the Eastern Ghats, India

A new large species of gecko superficially resembling Hemidactylus maculatus Duméril & Bibron and its allied large Hemidactylus is described from Eastern Ghats. The new species, Hemidactylus kangerensis sp. nov. can be easily distinguished from members of the H. maculatus complex based on the number of femoral pores, i.e. 18-21 on each side, separated medially by 4 non-pored scales. A phylogenetic analysis based on partial sequence of mitochondrial gene cytochrome b shows that the gecko is a member of the "H. prashadi" clade and is sister to H. maculatus, from which it differs in an uncorrected pairwise sequence divergence of 10%. The discovery of a new large gecko from Eastern Ghats advocates the need for biodiversity assessment across the neglected Eastern Ghats.