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A New Spotted Species of the Cyrtodactylus (Geckoella) collegalensis (Beddome, 1870) (Reptilia: Squamata) Complex from Coastal Kerala, Southwestern India
Abstract
We describe a new spotted species of ground-dwelling gecko of the genus Cyrtodactylus (Geckoella) from coastal Kerala, southwestern India, by using an integrative taxonomic approach. The new species is a member of the C. collegalensis species complex, with 10.0-13.5% uncorrected mitochondrial sequence divergence from the other six members of the C. collegalensis complex. The new species is also recognized in tree-based delimitation methods and can be morphologically diagnosed by a spotted dorsal pattern of four to six pairs of spots (occasionally fused into figure 8-shaped markings) from the banded species C. speciosus, C. rishivalleyensis, and C. yakhuna and from the spotted C. collegalensis, C. srilekhae, and C. varadgirii by the presence of a few scattered enlarged dorsal scales. This is the only Indian member of the C. collegalensis complex with a relatively broad distribution at low elevations, other than C. varadgirii from western India (distributed in Maharashtra, southern Gujarat, and western Madhya Pradesh). The sister species to the new species is the Sri Lankan C. yakhuna, which is a banded form from low elevations. The new species is the second gecko to have been described from Chengodumala and endemic to northern and central Kerala, highlighting the importance of this area, which is under increasing anthropogenic pressure. We also provide notes on the dorsal pholidosis of C. rishivalleyensis, which was overlooked in its original description.
... The vast majority of species in the genus are scansorial, with one major terrestrial radiation, the subgenus Geckoella Gray, 1867 (Agarwal and Karanth 2015) that corresponds to the triedrus clade within the triedrus group ). Cyrtodactylus (Geckoella) includes 10 species that are endemic to peninsular India and four to Sri Lanka (Smith 1935;Agarwal 2016;Agarwal et al. 2016;Amarasinghe et al. 2022;Narayanan et al. 2022;Agarwal et al. 2023). ...
... Phylogenetic relationships within Geckoella are well understood, the Sri Lankan C. triedrus (Günther, 1864) complex forming the sister taxon to the remaining species; which are split into a wet zone subclade that includes the C. albofasciatus (Boulenger, 1885) and C. deccanensis (Günther, 1864) complexes; and a dry zone subclade which includes C. jeyporensis (Beddome, 1878) as the sister taxon to the C. nebulosus (Beddome, 1870) complex; and the C. collegalensis (Beddome, 1870) complex with seven species in India and one in Sri Lanka (Smith 1935;Somaweera and Somaweera 2009;Agarwal and Karanth 2015;Agarwal 2016;Agarwal et al. 2016;Narayanan et al. 2022;Agarwal et al. 2023). ...
... The only treatment of any of these colour morphs was by Deraniyagala (1945), who described C. yakhuna (Deraniyagala, 1945) from Sri Lanka. The C. collegalensis complex has long been suspected to include multiple taxa in India (Mirza and Pal 2010) and besides the recognition of C. speciosus as a distinct form (Agarwal and Karanth 2015), five species have been described since 2016 (Agarwal 2016;Agarwal et al. 2016;Narayanan et al. 2022;Agarwal et al. 2023). These include C. varadgirii Agarwal et al., 2016 from central and western India, C. rishivalleyensis Agarwal, 2016 andC. ...
We describe two new spotted species of ground-dwelling gecko of the genus Cyrtodactylus (Geckoella) from southeastern India in an integrative taxonomic framework. The new species are recovered as sister taxa within the C. collegalensis species complex, with 13.0-16.7% uncorrected mitochondrial sequence divergence from the other eight members of the C. collegalensis complex and 10.4% from one another. The new species are morphologically diagnosed by a spotted dorsal pattern of four pairs of spots (occasion-ally fused into figure 8-shaped markings) from the banded species C. aravindi, C. speciosus, C. rishivalleyensis and C. yakhuna; and from the spotted species with three or fewer pairs of spots in C. collegalensis and C. srilekhae; and from C. chengodumalaensis by the absence of any enlarged dorsal scales and from C. varadgirii by the absence of a patch of enlarged roughly hexagonal scales on the canthus rostralis and beneath the angle of the lower jaw. The two new species can only be differentiated from each other based on slight differences in body size, relative body width and other statistically significant, size-corrected morphometric characters. These are among the first endemic lizards from Tropical Dry Evergreen habitats along the southeast coast of India.
Two new species of geckos of the genus Cnemaspis Strauch, 1887 are described from the Western Ghats of Kerala using an integrated taxonomic approach employing phylogenetic and multivariate morphometric methods. We provide a preliminary 16S rRNA tree of the Indian Cnemaspis and ascertain the phylogenetic placement of the two new species within the wynadensis clade. Our morphometric analysis indicates that, although there was overlap in the morphospace across species, the morphospace occupied by the two new species were considerably different from most other species within the wynadensis clade. Both the species Viz. C. zacharyi sp. nov. and C. chengodumalaensis
sp. nov. are medium to large-sized Cnemaspis and are genetically and morphologically distinct from other Indian congeners. Both species are predominantly found in rocky outcrops within forested patches outside protected areas in north Kerala, which are currently under threat from illegal quarrying and other unplanned developmental activities. The discovery of these novel species outside protected areas highlights the conservation value of rocky outcrops outside Wildlife Sanctuaries and National Parks and calls for urgent need to document species across protected and non-protected areas of the Western Ghats as well as the midland hillocks of Kerala.
We examined the amphibian and squamate reptilian species richness of Southern Eastern Ghats based on a long term-field survey with nearly two years of field days. We surveyed high elevation slopes (>900 m a.s.l.) of four select hill ranges namely Jawadi, Shevaroys, Kolli, and Sirumalai hills which comprehensively represented full geographical and spatial coverage. We present a descriptive species-account with basic morphological data supported by voucher photographs. We summarize the history of herpetological explorations in this landscape and also comment on some of the major previous works in the region. Our study revealed the presence of 62 species in the montane zones, including 32 (51%) new records involving all the three target taxa (frogs, lizards and snakes) and all the four hill ranges that testify the poor knowledge on the region's herpetofauna till date. Lastly, we remark on the unresolved taxonomic status of some species recorded in the present study. We recommend specimen-based revisionary works in the nearby Western Ghats, where such taxa are much more diverse, to enable taxonomic studies in this region.
Motivation:
In recent years, molecular species delimitation has become a routine approach for quantifying and classifying biodiversity. Barcoding methods are of particular importance in large-scale surveys as they promote fast species discovery and biodiversity estimates. Among those, distance-based methods are the most common choice as they scale well with large datasets; however, they are sensitive to similarity threshold parameters and they ignore evolutionary relationships. The recently introduced "Poisson Tree Processes" (PTP) method is a phylogeny-aware approach that does not rely on such thresholds. Yet, two weaknesses of PTP impact its accuracy and practicality when applied to large datasets; it does not account for divergent intraspecific variation and is slow for a large number of sequences.
Results:
We introduce the multi-rate PTP (mPTP), an improved method that alleviates the theoretical and technical shortcomings of PTP. It incorporates different levels of intraspecific genetic diversity deriving from differences in either the evolutionary history or sampling of each species. Results on empirical data suggest that mPTP is superior to PTP and popular distance-based methods as it, consistently yields more accurate delimitations with respect to the taxonomy (i.e., identifies more taxonomic species, infers species numbers closer to the taxonomy). Moreover, mPTP does not require any similarity threshold as input. The novel dynamic programming algorithm attains a speedup of at least five orders of magnitude compared to PTP, allowing it to delimit species in large (meta-) barcoding data. In addition, Markov Chain Monte Carlo sampling provides a comprehensive evaluation of the inferred delimitation in just a few seconds for millions of steps, independently of tree size.
Availability and implementation:
mPTP is implemented in C and is available for download at http://github.com/Pas-Kapli/mptp under the GNU Affero 3 license. A web-service is available at http://mptp.h-its.org .
Contact:
: paschalia.kapli@h-its.org or alexandros.stamatakis@h-its.org or tomas.flouri@h-its.org.
Supplementary information:
Supplementary data are available at Bioinformatics online.
PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and models of evolution for phylogenetic analyses. PartitionFinder 2 is substantially faster and more efficient than version 1, and incorporates many new methods and features. These include the ability to analyze morphological datasets, new methods to analyze genome-scale datasets, new output formats to facilitate interoperability with downstream software, and many new models of molecular evolution. PartitionFinder 2 is freely available under an open source license and works on Windows, OSX, and Linux operating systems. It can be downloaded from www.robertlanfear.com/partitionfinder The source code is available at https://github.com/brettc/partitionfinder.
Two new species of ground-dwelling geckos of the genus Cyrtodactylus (Geckoella) are described from the Mysore Pla-Teau, in southern India. The new species are members of the C. collegalensis species complex, with 8.7 % uncorrected ND2 sequence divergence from each other and greater than 10 % divergence from described members of the C. collega-lensis complex, from which they differ in subtle aspects of colour pattern and morphometric ratios. The type localities of the new species are ~ 130 km apart, and 100 km and 225 km from the type locality of C. collegalensis in the Biligiriranga Hills. The discovery of these new species in isolated mountains within a small area suggests other high elevation areas in the region may have undescribed species, and a redefinition of biodiversity patterns in peninsular India.
A new species of Cyrtodactylus (Geckoella) from the C. collegalensis complex is described based on a series of specimens from western and central India. Morphological and molecular data support the distinctiveness of the new form, which can be diagnosed from other Cyrtodactylus (including other Geckoella) species by its small body size (snout to vent length to 56 mm), the absence of precloacal and femoral pores, no enlarged preanal or femoral scales, and a dorsal scalation consisting wholly of small, granular scales. The new species is most closely related to C. collegalensis, C. speciosus and C. yakhuna, from which it differs by the presence of a patch of enlarged roughly hexagonal scales on the canthus rostralis and beneath the angle of jaw, its relatively long limbs and narrow body, and a dorsal colour pattern of 4-6 pairs of dark spots.
Sequence-based methods to delimit species are central to DNA taxonomy, microbial community surveys, and DNA meta-barcoding studies. Current approaches either rely on simple sequence similarity thresholds (OTU-picking) or on complex and compute-intensive evolutionary models. OTU-picking methods scale well on large data sets, but the results are highly sensitive to the similarity threshold. Coalescent-based species delimitation approaches often rely on Bayesian statistics and MCMC sampling, and can therefore only be applied to small data sets.
We introduce the Poisson Tree Processes (PTP) model to infer putative species boundaries on a given phylogenetic input tree. We also integrate PTP with our Evolutionary Placement Algorithm (EPA-PTP) to count the number of species in phylogenetic placements. We compare our approaches to popular OTU-picking methods and the General Mixed Yule Coalescent (GMYC) model. For de novo species delimitation, the stand-alone PTP model generally outperforms GMYC as well as OTU-picking methods when evolutionary distances between species are small. PTP neither requires an ultrametric input tree, nor a sequence similarity threshold as input. In the open reference species delimitation approach, EPA-PTP yields more accurate results than de novo species delimitation methods. Finally, EPA-PTP scales on large datasets because it relies on the parallel implementations of the EPA and RAxML, thereby allowing to delimit species in high-throughput sequencing data.
The code is freely available at www.exelixis-lab.org/software.html.
Alexandros.Stamatakis@h-its.org SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics on-line.
Understanding the evolutionary history of living organisms is a central problem in biology. Until recently the ability to infer evolutionary relationships was limited by the amount of DNA sequence data available, but new DNA sequencing technologies have largely removed this limitation. As a result, DNA sequence data are readily available or obtainable for a wide spectrum of organisms, thus creating an unprecedented opportunity to explore evolutionary relationships broadly and deeply across the Tree of Life. Unfortunately, the algorithms used to infer evolutionary relationships are NP-hard, so the dramatic increase in available DNA sequence data has created a commensurate increase in the need for access to powerful computational resources. Local laptop or desktop machines are no longer viable for analysis of the larger data sets available today, and progress in the field relies upon access to large, scalable high-performance computing resources. This paper describes development of the CIPRES Science Gateway, a web portal designed to provide researchers with transparent access to the fastest available community codes for inference of phylogenetic relationships, and implementation of these codes on scalable computational resources. Meeting the needs of the community has included developing infrastructure to provide access, working with the community to improve existing community codes, developing infrastructure to insure the portal is scalable to the entire systematics community, and adopting strategies that make the project sustainable by the community. The CIPRES Science Gateway has allowed more than 1800 unique users to run jobs that required 2.5 million Service Units since its release in December 2009. (A Service Unit is a CPU-hour at unit priority).
Specimens of Geckoella cf. collegalensis observed at Goregaon (Aarey Milk Colony, Mumbai, Maharashtra) from November 2007 to January 2009; provide new insights into the natural history and habitat of this poorly known gecko. Earlier regarded as a rare species restricted to low elevation area of south India, in fact appear to be widespread and terrestrial after a through review of museum specimens, published literature and our own observations.
Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net.
Two novel mitochondrial gene arrangements are identified in an agamid lizard and a ranid frog. Statistical tests incorporating
phylogeny indicate a link between novel vertebrate mitochondrial gene orders and movement of the origin of light-strand replication.
A mechanism involving errors in light-strand replication and tandem duplication of genes is proposed for rearrangement of
vertebrate mitochondrial genes. A second mechanism involving small direct repeats also is identified. These mechanisms implicate
gene order as a reliable phylogenetic character. Shifts in gene order define major lineages without evidence of parallelism
or reversal. The loss of the origin of light-strand replication from its typical vertebrate position evolves in parallel and,
therefore, is a less reliable phylogenetic character. Gene junctions also evolve in parallel. Sequencing across multigenic
regions, in particular transfer RNA genes, should be a major focus of future systematic studies to locate novel gene orders
and to provide a better understanding of the evolution of the vertebrate mitochondrial genome.
MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types—e.g. morphological, nucleotide, and protein—and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters.
Availability: http://morphbank.ebc.uu.se/mrbayes
Contact: fredrik.ronquist@ebc.uu.se
*
To whom correspondence should be addressed.
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