DNA barcoding of Vietnamese bent-toed geckos (Squamata: Gekkonidae: Cyrtodactylus) and the description of a new species

A new species of the Cyrtodactyluschauquangensis species group (Squamata, Gekkonidae) from Lao Cai Province, Vietnam

We describe a new species of the genus Cyrtodactylus based on five adult specimens from Bac Ha District, Lao Cai Province, northern Vietnam. Cyrtodactyluslucisp. nov. is distinguished from the remaining Indochinese bent-toed geckos by a combination of the following morphological characteristics: medium size (SVL up to 89.5 mm); dorsal tubercles in 17-19 irregular transverse rows; ventral scales in 32-34 longitudinal rows at midbody; precloacal pores present in both sexes, 9 or 10 in males, 8 or 9 in females; 12-15 enlarged femoral scales on each thigh; femoral pores 9-12 in males, 5-10 in females; postcloacal tubercles 2-4; lamellae under toe IV 21-23; dorsal pattern consisting of 5 or 6 irregular dark bands, a thin neckband without V-shape or triangle shape in the middle, top of head with dark brown blotches; subcaudal scales transversely enlarged. Molecular phylogenetic analyses recovered the new species as the sister taxon to C.gulinqingensis from Yunnan Province, China, with strong support from all analyses and the two taxa are separated by approximately 8.87-9.22% genetic divergence based on a fragment of the mitochondrial ND2 gene. This is the first representative of Cyrtodactylus known from Lao Cai Province.

A new species of Cyrtodactylus (Squamata: Gekkonidae) from Phu Yen Province, Vietnam

We describe a new species of the genus Cyrtodactylus based on six adult specimens from Lac Dao forests, Phu Yen Province, southern Vietnam. Cyrtodactylus tayhoaensis sp. nov. is distinguished from the remaining Indochinese bent-toed geckos by a combination of the following characters: medium size (SVL up to 94.2 mm); nasal scales 5-6; internasal single or double; ciliaria 29-34; dorsal tubercles in 20-22 irregular transverse rows; ventral scale in 37-41 longitudinal rows at midbody; ventrolateral folds present without interspersed tubercles; precloacal pores absent in females, precloacal pores 4 or 5 in males; 10 or 11 enlarged femoral scales on each thigh; femoral pores 3-7 in males, absent in females; postcloacal tubercles 3 or 4; lamellae under toe IV 22-24; dorsal pattern consisting of unclear transverse bands formed by irregularly shaped dark-brown blotches, a discontinuous neckband with V-shape or triangle shape in the middle, dorsal head surface with dark-brown blotches; subcaudal scales transversely enlarged. In the phylogenetic analyses, the new species is recovered as a sister taxon to C. kingsadai with approximately 4% genetic divergence between the two species based on a fragment of the COI gene. This is the second species of Cyrtodactylus known from Phu Yen Province located in southern Vietnam.

A new species of Cyrtodactylus Gray, 1827 (Squamata, Gekkonidae) from southwestern Yunnan, China

A new species of the Cyrtodactyluschauquangensis species group is described based on four specimens collected from the karst formations of Menglian County, Puer City, Yunnan Province, China. The new species can be separated from all other congeners by having a unique combination of morphological characters: a medium-sized body; ventrolateral folds present with interspersed small tubercles; seven precloacal pores in a continuous series in males, absent in females; enlarged femoral scales and femoral pores absent; two postcloacal tubercles on each side; and one or two rows of enlarged subcaudals. Genetically, the new species most closely related to C.wayakonei and the uncorrected sequence divergences of the ND2 gene and its flanking tRNAs between the new species and investigated congeners range from 7.2% to 18.4%.

A new species of Cyrtodactylus Gray, 1827 (Squamata, Gekkonidae) from Yunnan, China

A new species of Cyrtodactylus is described on the basis of five specimens collected from the karst formations of Zhenkang County, Yunnan Province, China. Cyrtodactyluszhenkangensissp. nov. is recognized by having a unique combination of morphological characters, the most diagnostic being: 12–15 enlarged femoral scales on each thigh; 2–5 femoral pores on each thigh in males, 0–3 pitted scales on each thigh in females; eight or nine precloacal pores in a continuous row or separated by one poreless scale in males, 7–9 pitted scales in females; subcaudals enlarged, arranged alternately as single and double on anterior and mostly single at middle and posterior; dorsal surface of head with obvious reticulations. Phylogenetic analyses show that the new species is a member of the C.wayakonei species group and a sister taxon to a clade consisting of C.wayakonei and C.martini based on Maximum Likelihood analyses and Bayesian Inference and differs from its congeners by at least 12.0% genetic divergence in a fragment of the COI gene.

Evolution of habitat preference in 243 species of Bent-toed geckos (Genus Cyrtodactylus Gray, 1827) with a discussion of karst habitat conservation

Understanding the processes that underpin adaptive evolutionary shifts within major taxonomic groups has long been a research directive among many evolutionary biologists. Such phenomena are best studied in large monophyletic groups that occupy a broad range of habitats where repeated exposure to novel ecological opportunities has happened independently over time in different lineages. The gekkonid genus Cyrtodactylus is just such a lineage with approximately 300 species that range from South Asia to Melanesia and occupy a vast array of habitats. Ancestral state reconstructions using a stochastic character mapping analysis of nine different habitat preferences were employed across a phylogeny composed of 76% of the known species of Cyrtodactylus. This was done in order to ascertain which habitat preference is the ancestral condition and from that condition, the transition frequency to more derived habitat preferences. The results indicate that a general habitat preference is the ancestral condition for Cyrtodactylus and the frequency of transitioning from a general habitat preference to anything more specialized occurs approximately four times more often than the reverse. Species showing extreme morphological and/or ecological specializations generally do not give rise to species bearing other habitat preferences. The evolution of different habitat preferences is generally restricted to clades that tend to occur in specific geographic regions. The largest radiations in the genus occur in rocky habitats (granite and karst), indicating that the transition from a general habitat preference to a granite or karst-dwelling life style may be ecologically uncomplicated. Two large, unrelated clades of karst-associated species are centered in northern Indochina and the largest clade of granite-associated species occurs on the Thai-Malay Peninsula. Smaller, independent radiations of clades bearing other habitat preferences occur throughout the tree and across the broad distribution of the genus. With the exception of a general habitat preference, the data show that karst-associated species far out-number all others (29.6% vs. 0.4%-10.2%, respectively) and the common reference to karstic regions as "imperiled arcs of biodiversity" is not only misleading but potentially dangerous. Karstic regions are not simply refugia harboring the remnants of local biodiversity but are foci of speciation that continue to generate the most speciose, independent, radiations across the genus. Unfortunately, karstic landscapes are some of the most imperiled and least protected habitats on the planet and these data continue to underscore the urgent need for their conservation.

A new species of Cyrtodactylus (Squamata, Gekkonidae) from Cambodia's Prey Lang Wildlife Sanctuary

Cyrtodactylusphnomchiensissp. nov. is described from Phnom Chi, an isolated mountain in Prey Lang Wildlife Sanctuary, Kampong Thom Province, Cambodia. The new species is recognized by having a unique combination of morphological characters, including snout-vent length 76.1–80.7 mm; paravertebral tubercles 31–36; ventral scales 45–54; enlarged femoral scales 0–8, without pores; enlarged precloacal scales 7–10, bearing pores 4–5 in males, pits 1–7 in females; the posterior border of nuchal loop unbroken and pointed, bordered anteriorly and posteriorly by a broad yellow or yellowish white band; and yellow spots on top of head. The new species also represents a divergent mitochondrial DNA lineage within the C.irregularis complex that is closely related to C.ziegleri, but the phylogenetic relationships among the new species and two divergent mitochondrial subclades within C.ziegleri are not resolved based on available sequence data. Cyrtodactylusphnomchiensissp. nov. is the only member of the C.irregularis complex known to occur west of the Mekong River. The new species may be endemic to Phnom Chi, and likely faces imminent conservation threats.

Cryptic diversity of limestone karst inhabiting land snails (Cyclophorus spp.) in northern Vietnam, their evolutionary history and the description of four new species

Limestone karsts can form terrestrial habitat islands for calcium-dependent organisms. In Vietnam, many karst habitats are threatened, while their rich biodiversity is still far from being thoroughly explored. Given that conservation of karst biota strongly relies on correct species identification, the presence of undetected cryptic species can pose severe problems. The present study focuses on cryptic diversity among karst-inhabiting land snails of the genus Cyclophorus in northern Vietnam, where specimens with a similar shell morphology have been reported from various regions. In order to examine the diversity and evolutionary history of this “widespread morphotype”, we generated a Bayesian phylogeny based on DNA sequence data. Automatic Barcode Gap Discovery (ABGD) and the Bayesian implementation of the Poisson tree processes model (bPTP) contributed to species delimitation and analyses of shell shape and size aided the morphological characterisation of individual species. We found that the examined specimens of the widespread morphotype did not form a single monophyletic group in the phylogeny but clustered into several different clades. We delimited nine different species that develop the widespread morphotype and described four of them as new. Processes of convergent evolution were probably involved in the origin of the delimited species, while their generally allopatric distribution could result from interspecific competition. Our findings indicate ongoing processes of speciation and a potential case of morphological character displacement. The high degree of morphological overlap found among the species underlines the importance of DNA sequence data for species delimitation and description in the genus Cyclophorus. Given the findings of the present study and the high potential that as yet undiscovered cryptic taxa have also evolved in other groups of karst-inhabiting organisms, we argue for a systematic and efficient detection and description of Vietnam’s karst biodiversity to provide a solid basis for future conservation planning.

Characterization of five complete Cyrtodactylus mitogenome structures reveals low structural diversity and conservation of repeated sequences in the lineage

Mitochondrial genomes (mitogenomes) of five Cyrtodactylus were determined. Their compositions and structures were similar to most of the available gecko lizard mitogenomes as 13 protein-coding, two rRNA and 22 tRNA genes. The non-coding control region (CR) of almost all Cyrtodactylus mitogenome structures contained a repeated sequence named the 75-bp box family, except for C. auribalteatus which contained the 225-bp box. Sequence similarities indicated that the 225-bp box resulted from the duplication event of 75-bp boxes, followed by homogenization and fixation in C. auribalteatus. The 75-bp box family was found in most gecko lizards with high conservation (55-75% similarities) and could form secondary structures, suggesting that this repeated sequence family played an important role under selective pressure and might involve mitogenome replication and the likelihood of rearrangements in CR. The 75-bp box family was acquired in the common ancestral genome of the gecko lizard, evolving gradually through each lineage by independent nucleotide mutation. Comparison of gecko lizard mitogenomes revealed low structural diversity with at least six types of mitochondrial gene rearrangements. Cyrtodactylus mitogenome structure showed the same gene rearrangement as found in most gecko lizards. Advanced mitogenome information will enable a better understanding of structure evolution mechanisms.

Reappraisal of the systematics of Microglanis cottoides (Siluriformes, Pseudopimelodidae), a catfish from southern Brazil

The southern region of Brazil is characterized by high species diversity and endemism of freshwater fishes distributed across geographically isolated river basins. Microglanis cottoides has a widespread range across these river basins and occurs in sympatry with other endemic species of the genus (e.g. M. cibelae, M. eurystoma, and M. malabarbai). Herein we tested the monophyly of M. cottoides and presented for the first time information about the molecular phylogeny of species in the genus. The results suggest that M. cottoides currently forms a non-monophyletic group which includes populations endemic to the Uruguay River basin that are more closely related to M. malabarbai, and excludes M. cibelae, found to be nested within M. cottoides. Based on an integrative approach using morphological and molecular data, we propose M. cibelae as a junior synonym of M. cottoides, and the populations of the Uruguay River basin previously assigned to M. cottoides in fact belong to M. malabarbai. Our molecular phylogeny shows that M. cottoides is sister to M. parahybae, which is also a coastal species, and M. malabarbai is sister of M. garavelloi, both endemic to inland river basins. The time-calibrated phylogeny indicates that the separation between inland and the coastal clades occurred in the Tertiary period, and that the species within the coastal basins diverged in the Pliocene, which overlaps with the diversification times estimated for the two inland species as well. This pattern of diversification corroborates some previous studies with other fishes from the same region.

A new species of the genus Theloderma Tschudi, 1838 (Amphibia: Anura: Rhacophoridae) from Tay Nguyen Plateau, central Vietnam

A new species of small tree frog from a primary montane tropical forest of central Vietnam, Tay Nguyen Plateau, is described based on morphological, molecular, and acoustic evidence. The Golden Bug-Eyed Frog, Theloderma auratum sp. nov., is distinguishable from its congeners and other small rhacophorid species based on a combination of the following morphological attributes: (1) bony ridges on head absent; (2) smooth skin completely lacking calcified warts or asperities; (3) pointed elongated tapering snout; (4) vocal opening in males absent; (5) vomerine teeth absent; (6) males of small body size (SVL 21.8-26.4 mm); (7) head longer than wide; ED/SVL ratio 13%-15%; ESL/SVL ratio 16%-20%; (8) small tympanum (TD/EL ratio 50%-60%) with few tiny tubercles; (9) supratympanic fold absent; (10) ventral surfaces completely smooth; (11) webbing between fingers absent; (12) outer and inner metacarpal tubercles present, supernumerary metacarpal tubercle single, medial, oval in shape; (13) toes half-webbed: I 2-2¼ II 1½-2¾ III 2-3¼ IV 3-1½ V; (14) inner metatarsal tubercle present, oval; outer metatarsal tubercle absent; (15) iris bicolored; (16) dorsal surfaces golden-yellow with sparse golden-orange speckling or reticulations and few small dark-brown spots; (17) lateral sides of head and body with wide dark reddish-brown to black lateral stripes, clearly separated from lighter dorsal coloration by straight contrasting edge; (18) ventral surfaces of body, throat, and chest greyish-blue with indistinct brown confluent blotches; (19) upper eyelids with few (3-5) very small flat reddish superciliary tubercles; (20) limbs dorsally reddish-brown, ventrally brown with small bluish-white speckles. The new species is also distinct from all congeners in 12S rRNA to 16S rRNA mitochondrial DNA fragment sequences (uncorrected genetic distance P>8.9%). Advertisement call and tadpole morphology of the new species are described. Our molecular data showed Theloderma auratum sp. nov. to be a sister species of Th. palliatum from Langbian Plateau in southern Vietnam.

A new karst-dwelling bent-toed gecko (Squamata: Gekkonidae: Cyrtodactylus) from Xiangkhoang Province, northeastern Laos

We describe a new karst-dwelling Cyrtodactylus from Ban Thathom, Xiangkhoang Province, northeastern Laos. The new species can be distinguished from other congeners by having four dark dorsal bands between limb insertions, a discontinuous nuchal loop, 10 precloacal pores in males or 10–12 precloacal pits (females) separated by a diastema from a series of enlarged femoral scales bearing 18 or 19 pores (male) or 8–10 pits (females) along each femur, 14–18 dorsal tubercle rows at midbody, no precloacal groove, 30–36 midbody scale rows across belly between ventrolateral skin folds, transversely enlarged subcaudal plates, and a maximal known snout-vent length of 75.5 mm. Our description brings to 22 the number of Cyrtodactylus species recorded from Laos.

Barcoding utility in a mega-diverse, cross-continental genus: keeping pace with Cyrtodactylus geckos

Over the past decade, DNA barcoding has become a staple of low-cost molecular systematic investigations. The availability of universal primers and subsidized sequencing projects (PolarBOL, SharkBOL, SpongeBOL) have driven this popularity, often without appropriate investigation into the utility of barcoding data for the taxonomic group of interest. Here, our primary aim is to determine the phylogenetic value of DNA barcoding (mitochondrial locus COI) within the gecko genus Cyrtodactylus. With >40 new species described since last systematic investigation, Cyrtodactylus represents one of the most diverse extant squamate genera, and their contemporary distribution spans the Indian subcontinent, eastward through Indochina, and into AustraloPapua. The complex biogeographic history of this group, and morphology-only designation of many species have complicated our phylogenetic understanding of Cyrtodactylus. To highlight the need for continued inclusive molecular assessment, we use Vietnamese Cyrtodactylus as a case study showing the geopolitically paraphyletic nature of their history. We compare COI to the legacy marker ND2, and discuss the value of COI as an interspecific marker, as well as its shortcomings at deeper evolutionary scales. We draw attention back to the Cold Code as a subsidized method for incorporating molecular methods into species descriptions in the effort to maintain accurate phylogenies.