Reference genome of the rubber boa, Charina bottae (Serpentes: Boidae).

The rubber boa, Charina bottae is a semi-fossorial, cold-temperature adapted snake that ranges across the wetter and cooler ecoregions of the California Floristic Province. The rubber boa is 1 of 2 species in the family Boidae native to California and currently has 2 recognized subspecies, the Northern rubber boa C. bottae bottae and the Southern rubber boa C. bottae umbratica. Recent genomic work on C. bottae indicates that these 2 subspecies are collectively composed of 4 divergent lineages that separated during the late Miocene. Analysis of habitat suitability indicates that C. bottae umbratica montane sky-island populations from southern California will lose the majority of their habit over the next 70 yr, and is listed as Threatened under the California Endangered Species Act. Here, we report a new, chromosome-level assembly of C. bottae bottae as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genome strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises 289 scaffolds covering 1,804,944,895 bp, has a contig N50 of 37.3 Mb, a scaffold N50 of 97 Mb, and BUSCO completeness score of 96.3%, and represents the first reference genome for the Boidae snake family. This genome will enable studies of genetic differentiation and connectivity among C. bottae bottae and C. bottae umbratica populations across California and help manage locally endemic lineages as they confront challenges from human-induced climate warming, droughts, and wildfires across California.

Rivers of Indochina as potential drivers of lineage diversification in the spotted flying lizard (Draco maculatus) species complex.

Southeast Asia hosts a rich concentration of biodiversity within multiple biodiversity hotspots. Indochina, a region with remarkably high levels of in situ diversification, possesses five major rivers (Ayeyarwady, Chiang Mai, Mekong, Red, and Salween), several of which coincide with phylogenetic breaks of terrestrial taxa. Draco maculatus possesses a range that stretches across Indochina, which widespread geographic distribution along with potential discrete variation within subspecies alludes to the possibility of this taxon constituting multiple divergent lineages. Using sequence data from three mitochondrial (12S, 16S, and ND2) and three nuclear (BDNF, CMOS, and PNN) genes, we provide the first estimated phylogeny of this hypothesized species complex and examine its phylogeographic architecture with maximum likelihood and Bayes factor delimitation (BFD) approaches. Our results support multiple divergent lineages with phylogenetic breaks coincident with rivers, indicating that river barriers may be contributing to the elevated levels of in situ diversification of Indochina.

Species delimitation with gene flow: A methodological comparison and population genomics approach to elucidate cryptic species boundaries in Malaysian Torrent Frogs.

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 Fst  = 0.9) to differentiating populations involving recent gene flow (mean Fst  = 0.05; Nm  > 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 Eurasian invasion: phylogenomic data reveal multiple Southeast Asian origins for Indian Dragon Lizards.

BACKGROUND: The Indian Tectonic Plate split from Gondwanaland approximately 120 MYA and set the Indian subcontinent on a ~ 100 million year collision course with Eurasia. Many phylogenetic studies have demonstrated the Indian subcontinent brought with it an array of endemic faunas that evolved in situ during its journey, suggesting this isolated subcontinent served as a source of biodiversity subsequent to its collision with Eurasia. However, recent molecular studies suggest that Eurasia may have served as the faunal source for some of India's biodiversity, colonizing the subcontinent through land bridges between India and Eurasia during the early to middle Eocene (~35-40 MYA). In this study we investigate whether the Draconinae subfamily of the lizard family Agamidae is of Eurasian or Indian origin, using a multi locus Sanger dataset and a novel dataset of 4536 ultraconserved nuclear element loci. RESULTS: Results from our phylogenetic and biogeographic analyses revealed support for two independent colonizations of India from Eurasian ancestors during the early to late Eocene prior to the subcontinent's hard collision with Eurasia. CONCLUSION: These results are consistent with other faunal groups and new geologic models that suggest ephemeral Eocene land bridges may have allowed for dispersal and exchange of floras and faunas between India and Eurasia during the Eocene.

A new species of the Cyrtodactyluschauquangensis group (Squamata, Gekkonidae) from the borderlands of extreme northern Thailand.

Phylogenetic and morphological analyses delimit and diagnose, respectively, a new population of a karst-dwelling Cyrtodactylus from extreme northern Thailand. The new species, Cyrtodactylusphamiensis sp. nov., of the chauquangensis group inhabits karst caves and outcroppings and karst vegetation in the vicinity of Pha Mi Village in Chiang Rai Province, Thailand. Within the chauquangensis group, Cyrtodactylusphamiensis sp. nov. is the earliest diverging species of a strongly supported clade composed of the granite-dwelling C.doisuthep and the karst-dwelling sister species Cyrtodactylus sp. 6 and C.erythrops. The nearly continuous karstic habitat between the type locality of Cyrtodactylusphamiensis sp. nov. and its close relatives Cyrtodactylus sp. 6 and C.erythrops, extends for approximately 200 km along the border region of Thailand and the eastern limit of the Shan Plateau of Myanmar. Further exploration of this region, especially the entire eastern ~ 95% of the Shan Plateau, will undoubtably recover new populations whose species status will need evaluation. As in all other countries of Indochina and northern Sundaland, the continual discovery of new karst-dwelling populations of Cyrtodactylus shows no signs of tapering off, even in relatively well-collected areas. This only highlights the conservation priority that these unique karstic landscapes still lack on a large scale across all of Asia.

Two new species of Dixonius from Vietnam and Laos with a discussion of the taxonomy of Dixonius (Squamata, Gekkonidae).

Integrated analyses using maximum likelihood (ML), Bayesian inference (BI), principal component analysis (PCA), discriminate analysis of principal components (DAPC), multiple factor analysis (MFA), and analysis of variance (ANOVA) recovered two new diagnosable species of gekkonid lizards in the genus Dixonius, one from the Central Highlands, Gia Lai Province, Vietnam and another from the Vientiane Province, Laos. Phylogenetic analyses based on the mitochondrial NADH dehydrogenase subunit 2 gene (ND2) and adjacent tRNAs showed that Dixoniusgialaiensissp. nov. is the sister species of D.minhlei from Dong Nai Province, Vietnam and is nested within a clade that also includes the sister species D.siamensis and D.somchanhae. Dixoniusmuangfuangensissp. nov. is the sister species to D.lao from Khammouane Province, Laos and is embedded in a clade with D.vietnamensis, D.taoi, and undescribed species from Thailand. Multivariate (PCA, DAPC, and MFA) and univariate (ANOVA) analyses using combinations of 15 meristic (scale counts), six morphometric (measurements), and five categorical (color pattern and morphology) characters from 44 specimens encompassing all eight species of Dixonius from Vietnam and Laos clearly illustrate Dixoniusgialaiensissp. nov. and Dixoniusmuangfuangensissp. nov. are statistically different and discretely diagnosable from all closely related species of Dixonius. These integrative analyses also highlight additional taxonomic issues that remain unresolved within Dixonius and the need for additional studies. The discovery of these new species further emphasizes the underappreciated herpetological diversity of the genus Dixonius and illustrates the continued need for field work in these regions.

A new species of Hemiphyllodactylus (Squamata, Gekkonidae) from Ha Giang Province, Vietnam.

An integrative analysis recovered a new species of the Hemiphyllodactylustypus group from a karst formation in Lung Cu Commune, Dong Van District, Ha Giang Province, northeastern Vietnam. Hemiphyllodactyluslungcuensissp. nov. is embedded within clade 6 of the typus group, bearing an uncorrected pairwise sequence divergence of 4.6-20.2% from all other species based on a 1,038 base pair segment of the mitochondrial NADH dehydrogenase subunit 2 gene (ND2). It is diagnosable from other species in clade 6 by statistically significant mean differences in normalized morphometric, meristic, and categorical characters. A multiple factor analysis using the three aforementioned character types recovered its unique, non-overlapping placement in morphospace as statistically significantly different from that of all other species in clade 6. The description of this new Hemiphyllodactylus species contributes to a growing body of literature underscoring the high degree of herpetological diversity and endemism in karst landscapes in Vietnam as well as in the genus Hemiphyllodactylus.

The Fergana Valley Is an Isolate of Biodiversity: A Discussion of the Endemic Herpetofauna and Description of Two New Species of Alsophylax (Sauria: Gekkonidae) from Eastern Uzbekistan.

The high level of endemism in Fergana Valley has been well documented in numerous studies for various groups of animals and plants. In a relatively small area, there are 45 endemic plant species, five endemic insect species, and five endemic reptile species. In surveying this area for data on distribution, abundance, acoustics, and genetic samples for species of reptiles, we discovered two new species of gecko from the genus Alsophylax. Phylogenetic analyses of mitochondrial DNA sequences indicate the relatives of these new species are the even-fingered gecko, Alsophylax pipiens, and the southern even-fingered gecko, Alsophylax laevis, located hundreds of kilometers to the northwest and southwest of the Fergana Valley. The threats to these new endemic species are significant given the amount of continued agricultural development that involves new territories previously considered "unsuitable" for any species of significance that is leading to the further reduction in, fragmentation of, and degradation of the remaining natural ecosystems in the Fergana Valley. The conservation of these rare and locally endemic species depends directly on the readiness of the state to create areas with IUCN I and II protection. The many studies documenting levels of endemism, along with the data published in this study, are the basis for the justification for state-protected areas in the Fergana Valley.

The biogeography of bent-toed geckos, Cyrtodactylus (Squamata: Gekkonidae).

The gekkonid genus Cyrtodactylus is the third largest vertebrate genus on the planet with well over 300 species that range across at least eight biogeographic regions from South Asia to Melanesia. The ecological and morphological plasticity within the genus, has contributed to its ability to disperse across ephemeral seaways, river systems, basins, land bridges, and mountain ranges-followed by in situ diversification within specific geographic areas. Ancestral ranges were reconstructed on a mitochondrial phylogeny with 346 described and undescribed species from which it was inferred that Cyrtodactylus evolved in a proto-Himalaya region during the early Eocene. From there, it dispersed to what is currently Indoburma and Indochina during the mid-Eocene-the latter becoming the first major center of origin for the remainder of the genus that seeded dispersals to the Indian subcontinent, Papua, and Sundaland. Sundaland became a second major center of radiation during the Oligocene and gave rise to a large number of species that radiated further within Sundaland and dispersed to Wallacea, the Philippines, and back to Indochina. One Papuan lineage dispersed west to recolonize and radiate in Sundaland. Currently, Indochina and Sundaland still harbor the vast majority of species of Cyrtodactylus.

Description of two new species of Hemiphyllodactylus (Reptilia: Gekkonidae) from karst landscapes in Yunnan, China, highlights complex conservation needs.

Karst habitats are hotspots of diversity and endemism. Their naturally fragmented distributions across broad geographic landscapes have led to the complex array of smaller evolutionary ecosystems that present unique challenges from a conservation perspective. Comprehensive biodiversity assessments of karst habitats have revealed that these ecosystems contain an almost unparalleled level of endemism, and many site-restricted species remain undescribed, thus posing considerable challenges for effective conservation management. Small rock-dwelling species, such as geckos, may be particularly prone to such isolation. In this paper, we discuss one such genus, i.e., Hemiphyllodactylus, and explore its diversity across karst landforms in Yunnan Province, southwestern China. Based on morphological and genetic data, we describe two new species of Hemiphyllodactylus from karst habitats in Simao District and Yanshan County. A phylogenetic tree for Hemiphyllodactylus was constructed using 1 039 base pairs (bp) of the mitochondrial NADH dehydrogenase subunit 2 gene ( ND2). The Simao and Yanshan specimens can be distinguished from all other congeners within their respective subclades based on uncorrected genetic pairwise distances greater than 6.3% and 4.3% respectively, as well as significant morphological differences. The discovery and description of these two new species brings the total number of described Hemiphyllodactylus species in China to 14 and indicates many more undescribed species from unsurveyed karst regions await discovery. Our findings suggest that karst ecosystems in Yunnan support a higher diversity of Hemiphyllodactylus than previously known. This study also highlights the importance of karst ecosystems as refugia for site-specific endemic species and the need for heightened conservation efforts.

A new species of Hemiphyllodactylus Bleeker (Squamata: Gekkonidae) from Yunnan, China and its phylogenetic relationship to other congeners.

A new species of the gekkonid genus Hemiphyllodactylus is described from forested karst hills near Zhutangxiang town, Lancang Lahu Autonomous County, Yunnan, China. Hemiphyllodactylus zhutangxiangensis sp. nov. is distinguished from all other congeners in morphology and an uncorrected pairwise sequence divergence of greater than 14% based on 1039 base pairs of the mitochondrial NADH dehydrogenase subunit 2 gene (ND2). The new species is defined by the following characters: a maximum SVL of 44.42 mm; 79 chin scales; enlarged postmentals; five circumnasal scales; 24 internasal scales; 811 supralabial scales; 811 infralabial scales; subdigital lamellae on fingers IIV (35)-(46)-(4 or 5)-(4 or 5); subdigital lamellae on toes IIV (4 or 5)-(4 or 5)-(46)-(4 or 5); dorsal scales 1115; ventral scales 57; 2023 continuous femoroprecloacal pores; having pale-grey base color on the body with various darker transverse dorsal blotches; a dark postorbital stripe extending to at least to the base of the neck; no dark dorsolateral or ventrolateral stripe on trunk; and postsacral marking bearing a dark fork-like pattern with anteriorly projecting arms. The new species brings the species total of Hemiphyllodactylus in China to 11.

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 insular species of the Cyrtodactylus intermedius (Squamata: Gekkonidae) group from Cambodia with a discussion of habitat preference and ecomorphology.

An integrative taxonomic analysis based on mitochondrial and morphological data recovered the population of Cyrtodactylus on Koh Rong Island, Preah Sihanouk Province, Cambodiaa as an endemic insular species belonging to the Cyrtodactylus intermedius group. This brings the number of species in the C. intermedius group to at least 10 and the number of species in Cambodia to at least seven. Species of this relatively small group vary widely in habitat preference, occurring in general, terrestrial, karstic, or granitic habitats. Ancestral character state mapping recovered a general habitat preference as the ancestral condition from which all others independently evolved even though this did not covary with morphology. The description of another new species of reptile from Cambodia continues to underscore the potentially significant amount of unrealized biodiversity in Indochina and Southeast Asia and the continued need for field surveys in unexplored or poorly explored areas.

Geographic structure of genetic variation in the Parachute Gecko Ptychozoon lionotum Annandale, 1905 across Indochina and Sundaland with descriptions of three new species.

An integrative taxonomic analysis of the Ptychozoon lionotum group across its range in Indochina and Sundaland recovers P. lionotum sensu lato Annandale, 1905 as paraphyletic with respect to P. popaense Grismer, Wood, Thura, Grismer, Brown, Stuart, 2018a and composed of four allopatric, genetically divergent, ND2 mitochondrial lineages. Multivariate and univariate analyses of continuous and discrete morphological and color pattern characters statistically and discretely diagnose each lineage from one another and together, with maximum likelihood and Bayesian inference analyses, provide the foundation for the recognition of each lineage as a new species-hypotheses corroborated with a Generalized Mixed Yule Coalescent species delimitation analysis. Ptychozoon cicakterbang sp. nov. ranges throughout Peninsular Malaysia to Pulau Natuna Besar, Indonesia; P. kabkaebin sp. nov. is endemic to northern and central Laos; and P. tokehos sp. nov. ranges from southern Thailand south of the Isthmus of Kra northward to Chiang Mai, fringing the Chao Phraya Basin and ranging southward through Cambodia to southern Vietnam. Ptychozoon lionotum sensu stricto ranges from northwestern Laos through southern Myanmar to eastern India. The phylogeographic structure within each species varies considerably with P. lionotum s.s. showing no genetic divergence across its 1,100 km range compared to P. cicakterbang sp. nov. showing upwards of 8.2% sequence divergence between syntopic individuals. Significant phylogeographic structure exists within P. tokehos sp. nov. and increased sampling throughout Thailand may require additional taxonomic changes within this species.

Six new species of the Cyrtodactylus intermedius complex (Squamata: Gekkonidae) from the Cardamom Mountains and associated highlands of Southeast Asia.

An integrative taxonomic analysis using color pattern, morphology, and 1449 base pairs of the ND2 mitochondrial gene and its five flanking tRNAs demonstrated that eight species-level lineages occur within the Cyrtodactylus intermedius complex (Cyrtodactylus intermedius sensu stricto, C. phuquocensis and related populations) of the Cardamom mountains and associated highlands that have a sequence divergence ranging 3.4-8.9%. Additionally, each lineage is discretely diagnosable from one another based on morphology and color pattern and most occur in specific geographic regions (upland areas, karst formations or islands) that prevent or greatly restrict interpopulation gene flow. Six of these lineages were masquerading under the nomen C. intermedius and are described as the following: Cyrtodactylus auralensis sp. nov. endemic to Phnom Aural, the highest mountain in Cambodia; C. bokorensis sp. nov. endemic to the Bokor Plateau, Cambodia; C. cardamomensis sp. nov. from the main block of the Cardamom mountains; C. thylacodactylus sp. nov. endemic to Phnom Dalai the northernmost peak of the Cardamom mountains; C. laangensis sp. nov. endemic to the Phnom Laang karst formation, Cambodia; and C. septimontium sp. nov. from the Bay Núi Hills of southwest Vietnam.

Elevational size variation and two new species of torrent frogs from Peninsular Malaysia (Anura: Ranidae: Amolops Cope).

Previously, only one species of torrent frog (Amolops larutensis) was thought to occur throughout Peninsular Malaysia. However, genomic work has demonstrated that populations from eastern Peninsular Malaysia form two separate lineages that are genetically distinct from A. larutensis that is now restricted to the western half of Peninsular Malaysia. This study demonstrates that all three lineages can be morphologically distinguished from each other, thereby providing additional support for the recognition of the eastern lineages as two distinct species. These lineages are described herein as Amolops gerutu sp. nov. from the eastern states of Kelantan, Terengganu, and Pahang, and A. australis sp. nov. from the southern-most state of Johor. In general, these two new species form a clade that is sister to A. larutensis and can be readily distinguished from it by having: (1) considerably denser and more pronounced dorsal tubercles, and (2) the posterodorsal surface of thighs having dense, dark stippling as opposed to broad vermiculations. Although differences in other morphometric characters were detected, their utility as diagnostic characters should be applied with caution due to the large intraspecific variation that overlaps among different species in many of the characters we measured. As such, we advocate for the use of tuberculation and pattern of the posterodorsal portion of the thighs as primary diagnostic characters. These characters can readily distinguish A. larutensis from the two new species. To differentiate A. australis sp. nov. from A. gerutu sp. nov. and A. larutensis, body size can be a good diagnostic character as A. australis sp. nov. is significantly smaller in both males (mean = 31.04 ± 1.59 mm) and females (mean = 46.48 ± 3.2 mm). Additionally, we show a strong positive correlation between body size and elevation, with populations from montane forests (>900 m asl) being considerably larger than populations at lower elevations.

Dragons in the mist: three new species of Pseudocalotes Fitzinger (Squamata: Agamidae) from the sky island archipelago of Peninsular Malaysia.

An integrative taxonomic analysis is used to delimit and describe three new species of Pseudocalotoes from the sky island archipelago of the Banjaran (=mountain range) Titiwangsa of Peninsular Malaysia. Pseudocalotes drogon sp. nov., from Fraser's Hill, Pahang is basal to the sister species P. larutensis from Bukit Larut, Perak in the Banjaran Bintang and the new species P. rhaegal sp. nov. from Cameron Highlands, Pahang. Pseudocalotes drogon sp. nov. is differentiated from all other species of Psuedocalotes by having the combination of a flat rostrum; seven postrostrals; an interparietal; 11 circumorbitals; five canthals; 7-10 superciliaries; one scale between the rostral and nasal; nine supralabials; eight infralabials; 10 postnasal-suborbital scales; four postmentals; five or six sublabials; five or six chinshields; 47 smooth, wide, gular scales; weak transverse gular and antehumeral folds; two enlarged scales between the ear and eye; enlarged upper and lower posttemporals; a single enlarged supratympanic; no enlarged postrictals; three large scales bordering the dorsal margin of the ear opening; large pretympanic scales; eight scales in the nuchal crest not separated by a gap; enlarged vertebral scales extending to the tip of the tail; keeled and non-plate-like scales on flanks; 51 midbody scales; midventrals smaller than dorsals; 19 subdigital lamellae on the fourth finger; 23 subdigital lamellae on the fourth toe; preaxial scales on third toe enlarged and spinose; subdigital lamellae not unicarinate; HW/HL 0.52; HL/SVL 0.31; no elbow or knee patches; and a male dewlap color of lime-green bearing a central yellow spot. Pseudocalotes rhaegal sp. nov. is differentiated from all other Psuedocalotes by having the combination of a convex rostrum; 6-8 postrostrals; an interparietal; nine or 10 circumorbitals; five canthals; 7-10 superciliaries; one or two scales between the rostral and nasal scales; eight or nine supralabials; seven or eight infralabials; 11 or 12 postnasal-suborbital scales; four postmentals; four or five chinshields; 40-45 smooth, wide, gular scales; no transverse gular fold; a weak antehumeral fold; three or four enlarged scales between the ear and eye; an enlarged upper and lower posttemporal; an enlarged supratympanic; no enlarged postrictals; no large scales bordering the upper margin of the ear opening or in the pretympanic region; 6-8 enlarged nuchal crest scales not separated by a gap; enlarged vertebral scales extending to the base of the tail; weakly keeled, non-plate-like scales on the flanks; 52-58 midbody scales; midventrals smaller than dorsals; 19-21 subdigital lamellae on the fourth finger; 22-26 subdigital lamellae on the fourth toe; preaxial scales on the third enlarged and rounded; subdigital lamellae not unicarinate; HW/HL 0.50-0.54; HL/SVL 0.28-0.30; no elbow or knee patches; and female dewlap color yellow bearing a purple base. The analyses also indicated that the new species, P. viserion sp. nov. from Genting Highlands, Pahang in the southern section of the Banjaran Titiwangsa is the sister species of P. flavigula from Cameron Highlands 121 km to the north and can be separated from all other species of Psuedocalotes by having the combination of three postrostrals; 10 circumorbitals; four or five canthals; 5-7 superciliaries; rostral and nasals in contact; supralabials contacting the nasal; six or seven supralabials; six or seven infralabials; two or three postmentals; 47 or 48 smooth, flat, gular scales; three chinshields; weak transverse gular and antehumeral folds; two enlarged scales between the ear and eye; an enlarged upper and lower posttemporal; an enlarged supratympanic; no enlarged postrictals; 7-9 nuchal crest scales lacking gaps and not extending beyond midbody; weakly keeled and plate-like scales on the flanks; 35-38 midbody scales; ventrals smaller than dorsals; 22 or 23 subdigital lamellae on the fourth finger; 26 or 27 subdigital lamellae on the fourth toe; preaxial scales on the third toe not modified; subdigital scales not unicarinate; HW/HL 0.62; no white marking below the eye; dewlap in males yellow; and no elbow or knee patches. Pseudocalotes rhaegal sp. nov. most likely occurs in syntopy with P. flavigula in Tanah Rata at Cameron Highlands and its discovery adds to a growing body of literature detailing the recent descriptions of several new, upland, closely related, sympatric species in Peninsular Malaysia. Another new population referred to here as Pseudocalotes sp. nov. from the Hala-Bala Wildlife Sanctuary, Betong District, Yala Province, Thailand is discussed. The discovery and description of these three new Pseudocalotes from the upland regions of Peninsular Malaysia continues to underscore the remarkably high herpetological diversity and ecological complexity in this sky island archipelago that is still underestimated, unappreciated, and unprotected.

Systematics and natural history of Southeast Asian Rock Geckos (genus Cnemaspis Strauch, 1887) with descriptions of eight new species from Malaysia, Thailand, and Indonesia.

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. 

First record of Batrachochytrium dendrobatidis infecting four frog families from Peninsular Malaysia.

The fungal pathogen Batrachochytrium dendrobatidis (Bd) infects amphibians on every continent where they occur and is linked to the decline of over 200 amphibian species worldwide. At present, only three published Bd surveys exist for mainland Asia, and Bd has been detected in South Korea alone. In this article, we report the first survey for Bd in Peninsular Malaysia. We swabbed 127 individuals from the six amphibian families that occur on Peninsular Malaysia, including two orders, 27 genera, and 47 species. We detected Bd on 10 out of 127 individuals from four of five states and five of 11 localities, placing the 95% confidence interval for overall prevalence at 4-14%. We detected no variation in Bd prevalence among regions, elevations, or taxonomic groups. The infection intensity ranged from 1 to 157,000 genome equivalents. The presence of Bd infections in native species without clinical signs of disease suggests that Bd may be endemic to the region. Alternately, Bd may have been introduced from non-native amphibians because of the substantial amphibian food trade in Peninsular Malaysia. Under both scenarios, management efforts should be implemented to limit the spread of non-native Bd and protect the tremendous amphibian diversity in Peninsular Malaysia.