A new species of limestone karst-adapted gecko of the Cyrtodactylus pulchellus complex, C. dayangbuntingensis sp. nov., is described from Dayang Bunting Island of the Langkawi Archipelago off the northwest coast of Peninsular Malaysia. It is the third species of the group to be described from the archipelago after C. langkawiensis and C. macrotuberculatus. The new species can be distinguished from all other species of Cyrtodactylus based on molecular evidence from the mitochondrial gene ND2 and its flanking tRNAs as well as having unique combinations of morphological and color pattern characteristics. This discovery underscores the need for continued surveys of the many islands in the archipelago to properly ascertain its true herpetological diversity.
An integrative taxonomic analysis of Subdoluseps herberti from southern Thailand and Peninsular Malaysia and S. samajaya from Sarawak, East Malaysia (Borneo) recovers the former as paraphyletic with respect to the latter. The analyses recover the three southernmost populations of S. herberti in Peninsular Malaysia as conspecific and the sister lineage of S. samajaya, whereas S. herberti from Thailand and northern Peninsular Malaysia constitute the sister species to S. samajaya plus the southern three Peninsular Malaysian populations. As such, the southern populations are described herein as S. malayana sp. nov. and all three species are referred to as the S. herberti group. Clade boundaries and breaks within this group on the Thai-Malay Peninsula occurring at the Isthmus of Kra, across the Kangar-Pattani line, and between the Thai-Malay Peninsula and Borneo are consistent with phylogeographic patterns of other Sundaic taxa. The discovery of S. malayana sp. nov. continues to underscore the fact that, despite the well-studied nature of the lizard fauna of Peninsular Malaysia, much of it still remains unrealized and for conservation efforts to move forward, field research followed by expeditiously revised taxonomies must continue.
A review of the taxonomic status of the Smooth Slug Snake (Asthenodipsas laevis) in Borneo resulted in the discovery of two previously unrecognised species from the highlands of Sabah, East Malaysia. Asthenodipsas jamilinaisi sp. nov. and A. stuebingi sp. nov. are presumed to be closely related to A. laevis based on similarities in pholidosis and patterning but can be separated from A. laevis by their dorsal scale rows of 15/15/15 vs 15/15/13 and the presence of a sharp vertebral keel. Asthenodipsas jamilinaisi sp. nov. can be further differentiated from A. stuebingi sp. nov. by the greatly enlarged size of the vertebral scales, higher number of ventrals in males (173-175 vs 165), higher number of subcaudals (53 vs 35-47) and colour pattern (dark overall with indistinct bands vs lighter head and body with clear, distinct bands and a dark neck patch). The discovery highlights the need for more careful examination of much of the herpetofauna of Borneo that still remains underestimated and understudied. There is an urgent need for continued surveys into its diversity and the collection of genetic material for integrated taxonomic revisions.
A new species of Ansonia is described from the Shan Plateau of Myanmar based on an integrative taxonomic analysis that differentiates it from all other congeners. Molecular phylogenetic analyses based on the mitochondrial genes 12S and 16S rRNA and tRNA-val recover A. kyaiktiyoensis sp. nov. as the sister species to A. inthanon from Thailand but differs from it and other congeners by at least a 5.0% sequence divergence. It is further differentiated by the following combination of morphological characters: (1) maximum SVL 24 mm in males and females; (2) first finger shorter than second; (3) absence of interorbital and tarsal ridges; (4) presence of light-coloured interscapular spot; (5) presence of yellow rictal tubercle; (6) absence of wide, light-coloured patch below eye; (7) presence of large, discrete, bright-yellow submandibular spots along the underside of lower jaw; (8) iris yellow-gold; (9) presence of markings on the snout consisting of streaks below the eye to the lip, and on the canthus rostralis to the nostril; (10) dorsum grey-brown with orange-beige spots, a dark-brown X-shaped marking on the back surrounding the interscapular spot, and dark-coloured markings on rump; (11) fore- and hind limbs with orange-beige cross-bars; and (12) venter light-gray with yellow spotting, especially near flanks and underside of hind limbs. Ansonia kyaiktiyoensis sp. nov. is the westernmost known record for the genus and the only species west of the Salween Basin. Its discovery echoes the increasing number of herpetological discoveries being made in upland regions fringing the Ayeyarwady and Salween Basins.
A survey of a limestone forest at Gunung Baling, Kedah, West Malaysia lead to the discovery of an undescribed species of Bent-toed Gecko from the Cyrtodactylus pulchellus complex. Cyrtodactylus evanquahi sp. nov. can be distinguished from all other species in the C. pulchellus complex by a suite of morphological and color pattern characteristics: prominent tuberculation, higher number of dark body bands, and a smaller maximum SVL. It is further differentiated from all other species as follows; no tubercles on the ventral surface of the forelimbs, gular region, or in the ventrolateral folds; 31-34 paravetebral dorsal tubercles; 18-23 longitudinal rows of tubercles; 29-33 ventral scales; 22-23 subdigital lamellae on the fourth toe; 32-36 femoroprecloacal pores; a shallow precloacal groove in males; body bands and nuchal loop edged with a thin white line bearing tubercles; no scattered white spots on the dorsum; six or seven dark body bands much thinner than interspaces; 9-11 dark caudal bands on original tail; bands on the original tail separated by immaculate white caudal bands. It is further differentiated by an uncorrected pairwise genetic divergence of 6.50-15.67% from all other congeners in the C. pulchellus complex. It is most closely related to C. pulchellus from Penang Island ∼76 km to the southwest. In addition to the new samples from Gunung Baling, we added four samples of C. bintangrendah from the new locality of Belukar Semang, Perak. The discovery of yet another new species of the C. pulchellus complex from a limestone habitat continues to underscore the high degree of endemism and the importance of these unique habitats for biodiversity, and the continued need for their conservation.
A reappraisal of the taxonomic status of the Dark-necked Slug Snake (Asthenodipsas malaccana Peters, 1864) across its range revealed that populations from Borneo are not conspecific with true A. malaccana from the Thai-Malay Peninsula and Sumatra, and is therefore described herein as new. Asthenodipsas borneensis sp. nov. can be distinguished from A. malaccana and other congeners by the absence of a preocular and suboculars, seven or eight supralabials with 3rd and 4th in contact with orbit, 4-7 infralabials with 2nd or 3rd pair in contact, two pairs of posterior inframaxillaries, 15/15/15 rows of dorsal scales, presence of sharp vertebral keel, divided subcaudals, maximum recorded SVL=441 mm, 166-179 ventrals, 35-48 subcaudals, head white to greyish brown and dorsum beige to orange-brown with a conspicuous dark-brown or black patch on the neck followed by multiple, narrow, vertical, dark bands along the rest of the body and tail. This discovery adds to a growing number of new slug snake species recently described from Southeast Asia and highlights the underestimated diversity in this family, especially in Borneo. Taxonomic revisions of the reptiles and amphibians of Borneo are still needed before the true diversity of the island and the relationships of the various taxa can be fully understood.
Most new cryptic species are described using conventional tree- and distance-based species delimitation methods (SDMs), which rely on phylogenetic arrangements and measures of genetic divergence. However, although numerous factors such as population structure and gene flow are known to confound phylogenetic inference and species delimitation, the influence of these processes is not frequently evaluated. Using large numbers of exons, introns, and ultraconserved elements obtained using the FrogCap sequence-capture protocol, we compared conventional SDMs with more robust genomic analyses that assess population structure and gene flow to characterize species boundaries in a Southeast Asian frog complex (Pulchrana picturata). Our results showed that gene flow and introgression can produce phylogenetic patterns and levels of divergence that resemble distinct species (up to 10% divergence in mitochondrial DNA). Hybrid populations were inferred as independent (singleton) clades that were highly divergent from adjacent populations (7%-10%) and unusually similar (<3%) to allopatric populations. Such anomalous patterns are not uncommon in Southeast Asian amphibians, which brings into question whether the high levels of cryptic diversity observed in other amphibian groups reflect distinct cryptic species-or, instead, highly admixed and structured metapopulation lineages. Our results also provide an alternative explanation to the conundrum of divergent (sometimes nonsister) sympatric lineages-a pattern that has been celebrated as indicative of true cryptic speciation. Based on these findings, we recommend that species delimitation of continuously distributed "cryptic" groups should not rely solely on conventional SDMs, but should necessarily examine population structure and gene flow to avoid taxonomic inflation.
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.
Phylogenetic analyses based on the mitochondrial gene ND2 and its flanking tRNAs indicate the diminutive upland and insular species Sphenomorphus bukitensis, S. butleri, S. langkawiensis, S. perhentianensis, and S. temengorensis form a monophyletic group that is phylogenetically embedded within the Southeast Asian genus Tytthoscincus. The analyses also indicate that a new swamp-dwelling skink from the Bukit Panchor State Park, Pulau Pinang, Peninsular Malaysia is the sister species to the swamp-dwelling species S. sibuensis from Pulau Sibu, Johor and Singapore and that these two are also embedded in the genus Tytthoscincus. By transferring the two Peninsular Malaysian clades of Sphenomorphus into the genus Tytthoscincus, the monophyly of the latter is maintained. The new species T. panchorensis sp. nov. can be distinguished from all other species of Tytthoscincus by having a unique combination of morphological and color pattern characteristics.
An integrative taxonomic analysis based on the mitochondrial gene ND2 and its flanking tRNAs, morphology, and color pattern indicates that a newly discovered gecko described herein as Hemiphyllodactylus cicak sp. nov. from Penang Hill on the Island of Penang, Peninsular Malaysia is a member of the H. harterti group. Hemiphyllodactylus cicak sp. nov. is most closely related to the clade composed of the sister species H. harterti from Bukit Larut, Perak in the Bintang Mountain Range and H. bintik from Gunung Tebu, Terengganu from the Timur Mountain Range. These three allopatric species form a monophyletic group that extends approximately 270 km across three isolated mountain ranges in northern Peninsular Malaysia. The molecular analysis also indicates that H. titiwangsaensis from the Titiwangsa Mountain Range is composed of three genetically distinct allopatric populations. The southern two populations from Fraser's Hill and Genting Highlands, Pahang have an uncorrected pairwise sequence divergence of 3.5% whereas these two populations have 12.4 and 12.8 % sequence divergences, respectively, from the northern population at Cameron Highlands, Pahang. Although the high sequence divergence clearly distinguishes the southern two populations from the former as a different species, all three populations are morphologically indistinguishable, leading to the hypothesis of a true, cryptic speciation event.
A new species of Bent-toed Gecko, Cyrtodactylus gunungsenyumensis sp. nov. of the sworderi complex, is described from Hutan Lipur Gunung Senyum, Pahang, Peninsular Malaysia and is differentiated from all other species in the sworderi complex by having a unique combination of characters including a maximum SVL of 74.7 mm; low, rounded, weakly keeled, body tubercles; 34-40 paravertebral tubercles; weak ventrolateral body fold lacking tubercles; 38-41 ventral scales; an abrupt transition between the posterior and ventral femoral scales; 20-23 subdigital lamellae on the fourth toe; enlarged femoral scales; no femoral or precloacal pores; no precloacal groove; wide caudal bands; and an evenly banded dorsal pattern. Cyrtodactylus gunungsenyumensis sp. nov. is a scansorial, karst forest-adapted specialist endemic to the karst ecosystem surrounding Gunung Senyum and occurs on the vertical walls of the limestone towers as well as the branches, trunks, and leaves of the vegetation in the associated karst forest. Cyrtodactylus gunungsenyumensis sp. nov. is the seventh species of karst forest-adapted Cyrtodactylus and the sixteenth endemic species of karst ecosystem reptile discovered in Peninsular Malaysia in the last seven years from only 12 different karst forests. This is a clear indication that many species remain to be discovered in the approximately 558 isolated karst ecosystems in Peninsular Malaysia not yet surveyed. These data continue to underscore the importance of karst ecosystems as reservoirs of biodiversity and microendemism and that they constitute an important component of Peninsular Malaysia's natural heritage and should be protected from the quarrying interests of foreign industrial companies.
An integrative taxonomic analysis used to identify a new population of Bronchocela from Phuket Island, Thailand indicates it is conspecific with B. rayaensis from the Langkawi Archipelago of northwestern Peninsular Malaysia. An additional specimen photographed from Khura Buri District, Phang-nga Province is also considered to be B. rayaensis and represents a northern range extension of 295 km from the Langkawi Archipelago.
A herpetological survey was conducted at Pulau Besar, Melaka from 10 to 12 June 2008, resulting in the discovery of five species of amphibians, nine species of lizards (including one new species of the gekkonid Cyrtodactylus) and one snake species. This report constitutes the first checklist of the herpetofauna of Pulau Besar and the Water Islands Archipelago.
A new species of scincid lizard, Lipinia sekayuensis sp. nov. from Hutan Lipur Sekayu, Terengganu State in northeastern Peninsular Malaysia is most similar to L. surda (Boulenger) but differentiated from it and all other species of Lipinia by having the combination of an adult SVL of 42.3 mm; six supralabials; five infralabials; four supraoculars; prefrontals widely separated; two loreals; fused frontoparietals; lower eyelids bearing a large, transparent disc; 21 midbody scale rows; 56 paravertertebral scale rows; 65 ventral scale rows; enlarged, precloacal scales; 10 subdigital lamellae on the third finger; 11, 15, and seven lamellae on the third, fourth, and fifth toes, respectively; distal subdigital lamellae keeled; a median row of slightly enlarged, subcaudal scales present; a generally unicolor, dark-brown dorsum bearing nine very faint, diffuse, darker stripes; and an external ear opening replaced by a scaly, auditory depression.
A newly discovered, diminutive, cave-dwelling, lowland species of the colubrid snake genus Lycodon Boie is described from a limestone cave along the Thai-Malaysian border in the state of Perlis, northwestern Peninsular Malaysia. Lycodon cavernicolus sp. nov. is most closely related to L. butleri Boulenger, an endemic, upland, forest-dwelling species from Peninsular Malaysia of the fasciatus group but is separated from L. butleri and all other species of the L. fasciatus group and the closely related L. ruhstrati group by having the combination of 245 (male) and 232 (female) ventral scales; 113 (male) and 92 (female) paired, subcaudal scales; a single precloacal plate; nine or 10 supralabials; 10 or 11 infralabials; a maximum total length of 508 mm (female); a relative tail length of 0.25-0.27; an immaculate venter in juveniles and dark-brown, posterior, ventral scale margins in adults; and dorsal and caudal bands in juveniles white. The discovery of L. cavernicolus sp. nov. adds to a rapidly growing list of newly discovered reptiles from karst regions and limestone forests of Peninsular Malaysia, underscoring the fact that these areas should be studied before they are quarried as they harbor a significant portion of the Peninsular Malaysia's herpetological diversity.
A new species of Bent-toed Gecko Cyrtodactylus guakanthanensis sp. nov. of the C. sworderi complex is described from a limestone forest in Perak, Peninsular Malaysia whose karst formations at the type locality are within an active quarry. Cyrtodactylus guakanthanensis sp. nov. can be distinguished from all other Sundaland species by having the following suite of character states: adult SVL 77.7-82.2 mm; moderately sized, conical, weakly keeled, body tubercles; tubercles present on occiput, nape, and limbs, and extend posteriorly beyond base of tail; 37-44 ventral scales; no transversely enlarged, median, subcaudal scales; proximal subdigital lamellae transversely expanded; 19-21 subdigital lamellae on fourth toe; abrupt transition between posterior and ventral femoral scales; enlarged femoral scales; no femoral or precloacal pores; precloacal groove absent; wide, dark postorbital stripes from each eye extending posteriorly to the anterior margin of the shoulder region thence forming a transverse band across the anterior margin of the shoulder region; and body bearing five (rarely four) wide, bold, dark bands. Destruction of the karst microhabitat and surrounding limestone forest will extirpate this new species from the type locality and perhaps drive it to complete extinction given that it appears to be restricted to the particular microhabitat structure of the type locality and is not widely distributed throughout the karst formations. As with plants and invertebrates, limestone forests are proving to be significant areas of high herpetological endemism and should be afforded special conservation status rather than turned into cement.
Cyrtodactylus metropolis sp. nov. from Batu Caves massif, Selangor, Peninsular Malaysia is differentiated from all congeners by having a unique suite of morphological and color pattern characteristics. Remarkably, this species has been overlooked despite a plethora of field studies at Batu Caves from 1898 to the present and no specimens had ever been examined until now. As with all other limestone forest-adapted Cyrtodactylus in Peninsular Malaysia, C. metropolis sp. nov. is not a cave-adapted species but is far more common on the exterior surfaces of the Batu Caves limestone massif and its surrounding limestone vegetation. We suggest that researchers devote time exploring the exterior surfaces of limestone massifs as well the interiors of their caves.
A review of the taxonomic status of the Asian Slug Snake, Asthenodipsas vertebralis (Boulenger, 1900) based on an integrative taxonomic approach using molecular, morphological, color pattern, and ecological data indicate it is composed of three well supported monophyletic lineages: (1) Pulau Tioman and Fraser's Hill, Pahang and Bukit Larut, Perak; Peninsular Malaysia; (2) its sister lineage from Northern Sumatra; and (3) the remaining basal lineage from Peninsular Malaysia. Furthermore, we consider the high sequence divergence (6.3%-10.2%) between these lineages (especially in areas of sympatry) and discrete differences in their morphology, color pattern, and microhabitat preference as evidence they are not conspecific. As such, we resurrect the name A. tropidonotus (Lidth de Jeude, 1923) for the Sumatra populations, restrict the name A. vertebralis to the populations from Pulau Tioman, Genting Highlands, Fraser's Hill, Gunung Benom, and Bukit Larut that contain terrestrial, banded adults; and consider A. lasgalenensis sp. nov. to be restricted to the populations from Fraser's Hill, Cameron Highlands, and Bukit Larut that contain arboreal, unbanded adults.
Molecular and morphological analyses indicate that a new upland species of the Cyrtodactylus sworderi complex, C. tebuensis sp. nov. from Gunung Tebu, Terengganu, Malaysia is most closely related to C. sworderi and together they form the sister lineage to C. quadrivirgatus. Cyrtodactylus tebuensis sp. nov. is differentiated from all other species of Sundaland Cyrtodactylus on the basis of having the unique combination of large, conical, keeled body tubercles; tubercles present on top of head, occiput, nape, and limbs, and extending posteriorly beyond base of tail; 43-51 ventral scales; no transversely enlarged, median subcaudal scales; proximal, subdigital lamellae transversely expanded; 17-21 subdigital lamellae on fourth toe; an abrupt transition between posterior and ventral femoral scales; enlarged femoral scales; no femoral or precloacal pores; no precloacal groove; body bearing four wide, bold, dark brown stripes (lateral stripe on each flank and a pair of paravertebral stripes); and a pairwise sequence divergence of 13.0% from its closest relative C. sworderi based on the mitochondrial gene ND2. Cyrtodactylus tebuensis sp. nov. is the first endemic upland species of gekkonid from northeastern Peninsular Malaysia and underscores the necessity for additional field work in all upland systems.
We sequenced the complete mitochondrial genome of the Tioman Island rock gecko, Cnemaspis limi, which is known as an endemic species to Malaysia. The complete mitogenome is 16,680 bp in size, consisting of 37 genes coding for 13 proteins, 22 transfer RNAs, two ribosomal RNAs and one control region. The A + T content of the overall base composition of H-strand is 53.09% (T: 23.20%, C: 32.48%, A: 29.89% and G: 14.43%). The major non-coding region (control region) is 1254 bp in length with the A + T content of 55.09% and four replicates of a 76-bp repeat within this region.