A well-supported and well-resolved phylogeny based on a concatenated data set from one mitochondrial and two nuclear genes, six morphological characters, and nine color pattern characters for 44 of the 50 species of the Southeast Asian Rock Geckos (genus Cnemaspis Strauch, 1887) is consistent with the previous taxonomy of Cnemaspis based solely on morphology and color pattern. Cnemaspis is partitioned into four major clades that collectively contain six species groups. The monophyly of all clades and species groups is strongly supported and they are parapatrically distributed across well-established, biogeographical regions ranging from southern Vietnam westward through southern Indochina, southward through the Thai-Malay Peninsula, then eastward to Borneo. Eight new species (Cnemaspis omari sp. nov. from the Thai-Malaysian border; C. temiah sp. nov. from Cameron Highlands, Pahang, Malaysia; C. stongensis sp. nov. from Gunung Stong, Kelantan, Malaysia; C. hangus sp. nov. from Bukit Hangus, Pahang, Malaysia; C. sundagekko sp. nov. from Pulau Siantan, Indonesia; C. peninsularis sp. nov. from southern Peninsular Malaysia and Singapore, and C. mumpuniae sp. nov. and C. sundainsula sp. nov. from Pulau Natuna Besar, Indonesia) are described based on morphology and color pattern and all but C. sundagekko sp. nov. are included in the phylogenetic analyses. Cnemaspis kendallii is polyphyletic and a composite of six species. An updated taxonomy consistent with the phylogeny is proposed for all 50 species and is based on 25 morphological and 53 color pattern characters scored across 594 specimens. Cladogenetic events and biogeographical relationships within Cnemaspis were likely influenced by this group's low vagility and the cyclical patterns of geographical and environmental changes in Sundaland over the last 25 million years and especially within the last 2.5 million years. The phylogeny indicates that nocturnality, diurnality, substrate preferences, and the presence of ocelli in the shoulder regions have evolved independently multiple times.
This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
Accurately delimiting species boundaries is a nontrivial undertaking that can have significant effects on downstream inferences. We compared the efficacy of commonly used species delimitation methods (SDMs) and a population genomics approach based on genomewide single-nucleotide polymorphisms (SNPs) to assess lineage separation in the Malaysian Torrent Frog Complex currently recognized as a single species (Amolops larutensis). First, we used morphological, mitochondrial DNA and genomewide SNPs to identify putative species boundaries by implementing noncoalescent and coalescent-based SDMs (mPTP, iBPP, BFD*). We then tested the validity of putative boundaries by estimating spatiotemporal gene flow (fastsimcoal2, ABBA-BABA) to assess the extent of genetic isolation among putative species. Our results show that the A. larutensis complex runs the gamut of the speciation continuum from highly divergent, genetically isolated lineages (mean F = 0.9) to differentiating populations involving recent gene flow (mean F = 0.05; N > 5). As expected, SDMs were effective at delimiting divergent lineages in the absence of gene flow but overestimated species in the presence of marked population structure and gene flow. However, using a population genomics approach and the concept of species as separately evolving metapopulation lineages as the only necessary property of a species, we were able to objectively elucidate cryptic species boundaries in the presence of past and present gene flow. This study does not discount the utility of SDMs but highlights the danger of violating model assumptions and the importance of carefully considering methods that appropriately fit the diversification history of a particular system.
The gekkonid genus Cyrtodactylus is the third most speciose vertebrate genus in the world, containing well over 300 species that collectively range from South Asia to Melanesia across some of the most diverse landscapes and imperiled habitats on the planet. A genus-wide phylogeny of the group has never been presented because researchers working on different groups were using different genetic markers to construct phylogenies that could not be integrated. We present here Maximum likelihood and Bayesian inference mitochondrial and mito-nuclear phylogenies incorporating of 310 species that include dozens of species that had never been included in a genus-wide analysis. Based on the mitochondrial phylogeny, we partition Cyrtodactylus into 31 well-supported monophyletic species groups which, if used as recommended herein, will increase the information content of future integrative taxonomic analyses that continue to add new species to this genus at an ever-increasing annual rate. Data presented here reiterate the outcome of several previous studies indicating that Cyrtodactylus comprises an unprecedented number of narrow-range endemics restricted to single mountain tops, small islands, or karst formations that still remain unprotected. This phylogeny can provide a platform for various comparative ecological studies that can be integrated with conservation management programs across the broad diversity of landscapes and habitats occupied by this genus. Additionally, these data indicate that the true number of Cyrtodactylus remains substantially underrepresented.
Since the book-formatted, monographic treatment of the lizards of Peninsular Malaysia, Singapore, and their adjacent islands by Grismer (2011), 47 additional species have been added to that fauna bringing the total to 174. One species, Cyrtodactylus stresemanni, was removed from the lizard fauna based on its likely mislabeled type locality; 44 species were described as new—29 gekkonids, 11 scincids, five agamids, and one dibamid; and three others, Cnemaspis narathiwatensis, Cyrtodactylus brevipalmatus, and Scincella melanosticta were recently discovered in northern Peninsular Malaysia. Taxonomic changes for seven previously described species occurring after 2011 are noted and significant, new locality records are documented here for additional species. The intent of this review is to provide an up to date peer-reviewed checklist for the lizard species of this region prior to a pending updated book monograph.
Conserving the planet's biodiversity is greatly handicapped, in that only a small fraction of it (∼14-75%) has been described so far. Integrative taxonomy is making significant inroads in light of this challenge by incorporating multiple data sets across a wide range of disciplines that simultaneously elucidate phylogenetic structure and delimit species-level lineages within a unified species concept. An integrative taxonomic approach to the classification of the gekkonid genus Hemiphyllodactylus Bleeker, 1860 reveals that it is far more diverse than posited by a recent taxonomic revision based solely on morphology, and that it is composed of at least 19 species, most of which are montane upland or insular endemics. Three new species (Hemiphyllodactylus dushanensis sp. nov., Hemiphyllodactylus jinpingensis sp. nov., and Hemiphyllodactylus longlingensis sp. nov.) from southern China previously considered to be subspecies of Hemiphyllodactylus yunnanensis (Boulenger, 1903) are elevated to full species status, and 10 new species-level lineages ranging from Vietnam, Laos, Thailand, Myanmar, Peninsular Malaysia, the Philippines, and Indonesia are identified. One new species, Hemiphyllodactylus tehtarik sp. nov. from Gunung Tebu, Terengganu, Peninsular Malaysia, is described herein, and is differentiated from all other species of Hemiphyllodactylus on the basis of morphology, colour pattern, and an 18.1-31.5% sequence divergence from all other congeners. Hemiphyllodactylus larutensis (Boulenger, 1900) is removed from the synonymy of H. harterti (Werner, 1900). Using an integrative taxonomic approach imbues the revised classification of 849 Hemiphyllodactylus with more objectivity, stability, and phylogenetic history, while identifying undescribed species-level lineages in potential need of conservation.
Karstic landscapes are immense reservoirs of biodiversity and range-restricted endemism. Nowhere is this more evident than in the world’s third-largest vertebrate genus Cyrtodactylus (Gekkonidae) which contains well over 300 species. A stochastic character mapping analysis of 10 different habitat preferences across a phylogeny containing 345 described and undescribed species recovered a karst habitat preference occurring in 25.0% of the species, whereas that of the other eight specific habitat preferences occurred in only 0.2–11.0% of the species. The tenth category—general habitat preference—occurred in 38.7% of the species and was the ancestral habitat preference for Cyrtodactylus and the ultimate origin of all other habitat preferences. This study echoes the results of a previous study illustrating that karstic landscapes are generators of species diversity within Cyrtodactylus and not simply “imperiled arks of biodiversity” serving as refugia for relics. Unfortunately, the immense financial returns of mineral extraction to developing nations largely outweighs concerns for biodiversity conservation, leaving approximately 99% of karstic landscapes with no legal protection. This study continues to underscore the urgent need for their appropriate management and conservation. Additionally, this analysis supports the monophyly of the recently proposed 31 species groups and adds one additional species group.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.