Ultraconserved elements-based phylogenomic systematics of the snake superfamily Elapoidea, with the description of a new Afro-Asian family.

The highly diverse snake superfamily Elapoidea is considered to be a classic example of ancient, rapid radiation. Such radiations are challenging to fully resolve phylogenetically, with the highly diverse Elapoidea a case in point. Previous attempts at inferring a phylogeny of elapoids produced highly incongruent estimates of their evolutionary relationships, often with very low statistical support. We sought to resolve this situation by sequencing over 4,500 ultraconserved element loci from multiple representatives of every elapoid family/subfamily level taxon and inferring their phylogenetic relationships with multiple methods. Concatenation and multispecies coalescent based species trees yielded largely congruent and well-supported topologies. Hypotheses of a hard polytomy were not retained for any deep branches. Our phylogenies recovered Cyclocoridae and Elapidae as diverging early within Elapoidea. The Afro-Malagasy radiation of elapoid snakes, classified as multiple subfamilies of an inclusive Lamprophiidae by some earlier authors, was found to be monophyletic in all analyses. The genus Micrelaps was consistently recovered as sister to Lamprophiidae. We establish a new family, Micrelapidae fam. nov., for Micrelaps and assign Brachyophis to this family based on cranial osteological synapomorphy. We estimate that Elapoidea originated in the early Eocene and rapidly diversified into all the major lineages during this epoch. Ecological opportunities presented by the post-Cretaceous-Paleogene mass extinction event may have promoted the explosive radiation of elapoid snakes.

Phylogeny and biogeography of the African burrowing snake subfamily Aparallactinae (Squamata: Lamprophiidae).

Members of the snake subfamily Aparallactinae occur in various habitats throughout sub-Saharan Africa. The monophyly of aparallactine snakes is well established, but relationships within the subfamily are poorly known. We sampled 158 individuals from six of eight aparallactine genera in sub-Saharan Africa. We employed concatenated gene-tree analyses, divergence dating approaches, and ancestral-area reconstructions to infer phylogenies and biogeographic patterns with a multi-locus data set consisting of three mitochondrial (16S, cyt b, and ND4) and two nuclear genes (c-mos and RAG1). As a result, we uncover several cryptic lineages and elevate a lineage of Polemon to full species status. Diversification occurred predominantly during the Miocene, with a few speciation events occurring subsequently in the Pliocene and Pleistocene. Biogeographic analyses suggested that the Zambezian biogeographic region, comprising grasslands and woodlands, facilitated radiations, vicariance, and dispersal for many aparallactines. Moreover, the geographic distributions of many forest species were fragmented during xeric and cooler conditions, which likely led to diversification events. Biogeographic patterns of aparallactine snakes are consistent with previous studies of other sub-Saharan herpetofauna.

Cyrtodactylus samroiyot, a new limestone-dwelling Bent-toed Gecko (Squamata: Gekkonidae) from Prachuap Khiri Khan Province, peninsular Thailand.

We describe Cyrtodactylus samroiyot sp. nov. from a limestone relief in Sam Roi Yot District, Prachuap Khiri Khan Province, peninsular Thailand. It is characterized by a maximal known SVL of 66.9 mm; 17-18 longitudinal rows of dorsal tubercles; 33-34 longitudinal rows of ventrals across the abdomen between the ventrolateral skin folds; a continuous series of seven precloacal pores in males (six shallow precloacal pits in females); a series of slightly enlarged, poreless and pitless femoral scales; no precloacal groove nor depression; median row of transversely enlarged subcaudal scales; a complete nuchal loop; and a dorsal pattern consisting of three long dark brown bands, one above shoulders and two above abdomen. 

Cyrtodactylus khelangensis, a new cave-dwelling Bent-toed Gecko (Squamata: Gekkonidae) from Lampang Province, northern Thailand.

We describe Cyrtodactylus khelangensis sp. nov. from a limestone cave in Pratu Pha, Mae Mo District, Lampang Province, northern Thailand. It is characterized by a maximal known SVL of 95.3 mm; 16-20 longitudinal rows of dorsal tubercles; a continuous series of 37-40 enlarged femoroprecloacal scales, including six-seven pitted or pore-bearing scales (males) or one or two pitted scales (females) on each femur separated by a diastema from 2-6 pore-bearing precloacal scales (males and females); no precloacal groove nor depression; transversely enlarged subcaudal scales; and four irregular brown dorsal bands between nuchal loop and hind limb insertions.

A new forest-dwelling Bent-toed Gecko (Squamata: Gekkonidae: Cyrtodactylus) from Doi Suthep, Chiang Mai Province, northern Thailand.

We describe a new forest-dwelling Cyrtodactylus from Doi Suthep, Chiang Mai Province, northern Thailand. Cyrtodactylus doisuthep sp. nov. is characterized by a maximal known SVL of 90.5 mm; 19 or 20 longitudinal rows of dorsal tubercles; a continuous series of 34 or 35 enlarged femoro-precloacal scales, including six or seven pitted scales on each femur (male and females) separated by a diastema from six pitted (females) or pore-bearing (male) precloacal scales; no precloacal groove or depression; transversely enlarged subcaudal scales; and six or seven irregular thin beige dorsal bands between limb insertions. 

Vertebral morphology and intracolumnar variation of the iconic African viperid snake Atheris (Serpentes, Viperidae).

We here provide a detailed description of the vertebral morphology of the African arboreal viperid snakes of the genus Atheris. Vertebrae of three different species of the genus, i.e., Atheris desaixi, Atheris hispida, and Atheris katangensis, were investigated via the aid of µCT (micro-computed tomography) scanning. We describe several vertebrae from different regions of the vertebral column for all three species, starting from the atlas-axis complex to the caudal tip, in order to demonstrate important differences regarding the intracolumnar variation. Comparison of these three species shows an overall similar general morphology of the trunk vertebrae among the Atheris species. We extensively compare Atheris with other known viperids. As the sole arboreal genus of Viperinae the prehensile nature of the tail of Atheris is reflected in its caudal vertebral morphology, which is characterized by a high number of caudal vertebrae but also robust and anteroventrally oriented pleurapophyses as a skeletal adaptation, linked with the myology of the tail, to an arboreal lifestyle. We anticipate that the extensive figuring of these viperid specimens will also aid identifications in paleontology.

Phylogenomics of Psammodynastes and Buhoma (Elapoidea: Serpentes), with the description of a new Asian snake family.

Asian mock vipers of the genus Psammodynastes and African forest snakes of the genus Buhoma are two genera belonging to the snake superfamily Elapoidea. The phylogenetic placements of Psammodynastes and Buhoma within Elapoidea has been extremely unstable which has resulted in their uncertain and debated taxonomy. We used ultraconserved elements and traditional nuclear and mitochondrial markers to infer the phylogenetic relationships of these two genera with other elapoids. Psammodynastes, for which a reference genome has been sequenced, were found, with strong branch support, to be a relatively early diverging split within Elapoidea that is sister to a clade consisting of Elapidae, Micrelapidae and Lamprophiidae. Hence, we allocate Psammodynastes to its own family, Psammodynastidae new family. However, the phylogenetic position of Buhoma could not be resolved with a high degree of confidence. Attempts to identify the possible sources of conflict in the rapid radiation of elapoid snakes suggest that both hybridisation/introgression during the rapid diversification, including possible ghost introgression, as well as incomplete lineage sorting likely have had a confounding role. The usual practice of combining mitochondrial loci with nuclear genomic data appears to mislead phylogeny reconstructions in rapid radiation scenarios, especially in the absence of genome scale data.

Cyrtodactylus sanook (Squamata: Gekkonidae), a new cave-dwelling gecko from Chumphon Province, southern Thailand.

We describe a new cave-dwelling species, Cyrtodactylus sanook sp. nov., from Tham Sanook, Chumphon Province, southern Thailand, characterized by a maximum SVL of 79.5 mm; 18-20 longitudinal rows of dorsal tubercles at midbody; a continuous series of enlarged femoral and precloacal scales, no femoral pores, three or four precloacal pores in males (no pores in females), no precloacal groove nor depression; 19-20 subdigital lamellae on 4th toe; transversally enlarged subcaudal plates; and 6-7 irregular pale narrow dorsal bands between limb insertions. It seems endemic to this cave and is the 7th Thai Cyrtodactylus species that is known only from a cave environment.

Morphological, acoustic and genetic identification of a reproducing population of the invasive African clawed frog Xenopuslaevis (Anura, Pipidae) recently discovered in Belgium.

Using external morphology of adults and tadpoles, osteology from high-resolution microcomputed tomography, vocalization analysis, and DNA sequence data, the identity of a reproducing Belgian population of invasive Xenopus at the current northernmost edge of the distribution of the genus in Europe was assessed. All data concur to an identification as Xenopus (Xenopus) laevis (Daudin, 1802). Genetically it is most closely related to populations of the Cape region in South Africa. No studies on the natural history of the Belgian Xenopus population and its impact on the local environment have been made to date.

Coluber korros Lesson, 1831 and Coluber korros Schlegel, 1837 (Reptilia: Squamata: Colubridae): there is a korros too many in the family.

The purpose of this paper is to solve an overlooked nomenclatural problem involving two taxa of Colubridae, both described as Coluber korros. The first one is Coluber korros Schlegel, 1837, now Ptyas korros, a well-known and widespread species in south-east Asia. Its senior homonym is Coluber korros Lesson, 1831, a long forgotten taxon. Furthermore, these taxa are undoubtedly non-conspecific. We tentatively identify the holotype of this latter taxon as a large specimen of Coelognathus radiatus (F. Boie, 1827) and we specify its type locality as "Region of Kolkata, West Bengal State, eastern India" (the same specification of type-locality can hence be applied to the elapid Naja kaouthia Lesson, 1831). Nevertheless, following the strict principle of priority, Coluber korros Lesson, 1831 has priority over Coluber korros Schlegel, 1837. Based on the Code, we use Article 23.9 on reversal of precedence in order to preserve the use of the well-known taxon Coluber korros Schlegel, 1837 (now Ptyas korros) against its senior primary homonym Coluber korros Lesson, 1831. Finally, we consider Coluber boncorage Lesson, 1831 to be a nomen dubium.

Rediscovery, range extension, phylogenetic relationships and updated diagnosis of the Ornate Long-tailed Lizard Latastia ornata Monard, 1940 (Squamata: Lacertidae).

The lacertid Latastia ornata was known to date only by its holotype collected in 1938 in Bafatá, central Guinea-Bissau. We report new specimens and localities from Guinea-Conakry, a new country record and major range extension of 700 km SE of the type-locality. We provide an updated diagnosis of the species, including the first genetic and osteological data, and confirm that Latastia ornata is closely related to, but distinct from, L. longicaudata based on external morphology, cranial osteology, DNA data and zoogeography.

Cranial osteology of Hypoptophis (Aparallactinae: Atractaspididae: Caenophidia), with a discussion on the evolution of its fossorial adaptations.

Fossoriality evolved early in snakes, and has left its signature on the cranial morphology of many extinct Mesozoic and early Caenozoic forms. Knowledge of the cranial osteology of extant snakes is indispensable for associating the crania of extinct lineages with a particular mode of life; this applies to fossorial taxa as well. In the present work, we provide a detailed description of the cranium of Hypoptophis wilsonii, a member of the subfamily Aparallactinae, using micro-computed tomography (CT). This is also the first thorough micro-CT-based description of any snake assigned to this African subfamily of predominantly mildly venomous, fossorial, and elusive snakes. The cranium of Hypoptophis is adapted for a fossorial lifestyle, with increased consolidation of skull bones. Aparallactines show a tendency toward reduction of maxillary length by bringing the rear fangs forward. This development attains its pinnacle in the sister subfamily Atractaspidinae, in which the rear fang has become the "front fang" by a loss of the part of the maxilla lying ahead of the fang. These dentitional changes likely reflect adaptation to subdue prey in snug burrows. An endocast of the inner ear of Hypoptophis shows that this genus has the inner ear typical of fossorial snakes, with a large, globular sacculus. A phylogenetic analysis based on morphology recovers Hypoptophis as a sister taxon to Aparallactus. We also discuss the implications of our observations on the burrowing origin hypothesis of snakes.

A new Four-clawed Gecko from limestone hills in Lopburi Province, central Thailand (Squamata, Gekkonidae: Gehyra).

We describe Gehyra wongchan sp. nov. from Tham Khao Chan (Khao Chan Cave), Tha Luang District, and Wat Khao Wong, Kok Samrong District, in Lopburi Province, central Thailand. The new species differs from all currently recognized Gehyra by the following combination of morphological characters and dorsal color pattern: maximal known snoutvent length of 52.4 mm, 810 supralabials, 7680 dorsal and 4850 ventral scale rows around midbody, absence of skin folds on limbs, 17 or 18 preanofemoral pores in males in a continuous series extending to mid-length of femur (pores absent in females), tail not- to moderately widened behind vent in adults, a single row of widened subcaudals, digits and toes unwebbed, 7 or 8 divided subdigital lamellae on 4th toe, and a dorsal pattern with white spots as large or larger than adjacent crescentic black markings on a beige to light-brown background.

On the distribution of Gonyosoma prasinum (Blyth, 1854) and Gonyosoma coeruleum Liu, Hou, Ye Htet Lwin, Wang amp; Rao, 2021, with a note on the status of Gonyosoma gramineum Gnther, 1864 (Squamata: Serpentes: Colubridae).

Based on 85 examined specimens, photographs of living specimens and illustrations published in the literature, we refine the distribution ranges of both Gonyosoma prasinum (Blyth, 1854) and of the recently described species Gonyosoma coeruleum Liu, Hou, Ye Htet Lwin, Wang Rao, 2021, which was not clearly addressed in its original description. We also redescribe the syntypes of Coluber prasinus Blyth, 1854 and the holotype of Gonyosoma gramineum Gnther, 1864, we discuss the status of this latter taxon, and we describe the hemipenial morphology of G. coeruleum.

Two new Kukri Snake species (Colubridae: Oligodon) from the Nakhon Si Thammarat Mountain Range, and addition of O. ocellatus to the fauna of Thailand.

We describe two new Kukri snakes of the genus Oligodon from the Nakhon Si Thammarat Mountain Range, southern peninsular Thailand. Oligodon phangan sp. nov., endemic to Pha-Ngan Island, Surat Thani Province, is characterized by a maximal known SVL of 369.1 mm; 12 maxillary teeth, the posterior three enlarged; 17-17-15 dorsal scale rows; 163-166 ventrals; 33-42 divided subcaudals; a single anal; dorsal color brown with a pair of discreet paravertebral and lateral stripes; no dorsal or supracaudal bands, blotches or crossbars; background color of belly pinkish-orange; underside of tail immaculate. Oligodon promsombuti sp. nov., whose type-locality is Khao Phanom Wang, Surat Thani Province, is also found in Trang Province, and is characterized by a maximal known SVL of 552.7 mm; 12 maxillary teeth, the posterior three enlarged; 17-17-15 dorsal scale rows; 177 ventrals; 40 divided subcaudals; a single anal; deeply forked hemipenes lacking spines; dorsal color blackish brown with nearly indistinct paravertebral stripes; no dorsal or supracaudal blotches or crossbars; background color of belly ivory, heavily speckled with subrectangular blackish blotches. We tentatively allocate both new species to the informal Oligodon-cyclurus-group. They are the 5th and 6th Oligodon species endemic to Thailand. We add Oligodon ocellatus, so far known only from Cambodia, southern Laos and southern Vietnam, to the Thai fauna, based on a specimen from Chong Mek, Ubon Ratchathani Province.

A new sandstone-dwelling leaf-toed gecko (Gekkonidae: Dixonius mekongensis) from the Thai-Lao border.

We describe Dixonius mekongensis sp. nov. from sandstone formations in Khong Chiam District, Ubon Ratchathani Province, in extreme eastern Thailand along the Laotian border. The new species differs from all currently recognized Dixonius by the following combination of morphological characters and pattern: maximal known snout-vent length of 51.2 mm; 16 longitudinal rows of dorsal tubercles; 32 to 34 paravertebral scales; 22 to 24 longitudinal rows of ventral scales across the abdomen; seven precloacal pores in males, no pores in females; a marked canthal stripe; and a spotted to uniform dorsal pattern. This description brings the number of Dixonius species to 13, with six species endemic to Thailand.

A new cave-dwelling Gekko (Gekko) from Lopburi Province, central Thailand (Squamata, Gekkonidae).

We describe Gekko pradapdao sp. nov. from Tham Khao Chan (Khao Chan Cave), Tha Luang District, Lopburi Province, in central Thailand. The new species, a member of the subgenus Gekko, differs from all currently recognized Gekko species by the following combination of morphological characters and pattern: maximal known snout-vent length of 127.1 mm, lack of contact between nostrils and rostral, 2428 interorbital scales between supraciliaries, 8991 scale rows around midbody, 1618 dorsal tubercle rows at midbody, 3034 ventral scale rows at midbody, 1113 precloacal pores in males, a single postcloacal tubercle on each side of the base of the tail, 1316 subdigital lamellae on 1st toe and 1719 on 4th toe, no Y-shaped mark on head, non-banded dorsal pattern on a dark chocolate brown to black background, and a dark brown iris. Urgent actions should be taken to evaluate the conservation status of the new species.

A revision of the dark-bellied, stream-dwelling snakes of the genus Hebius (Reptilia: Squamata: Natricidae) with the description of a new species from China, Vietnam and Thailand.

Species of the genus Hebius Thompson, 1913 with 17 or 19 dorsal scale rows at midbody and an overall dark venter are reviewed, including the two species previously known as Parahelicops annamensis Bourret, 1934 and Pararhabdophis chapaensis Bourret, 1934. Specimens with 17 scale rows are morphologically similar to Hebius venningi (Wall, 1910), which is here redefined based on external morphological characters such as scalation, and dorsal and ventral patterns. Consequently, Natrix nigriventer Wall, 1925 is resurrected from its synonymy with Hebius venningi, whereas Natrix taronensis Smith, 1940, previously considered a subspecies of H. venningi or a full species by some authors but without justification, is here confirmed to full species status. Another group of species, mostly similar in coloration and pattern to the H. venningi group but with 19 dorsal scale rows, includes H. modestus (Günther, 1875), H. deschauenseei (Taylor, 1934) and a new species which is described herein based on specimens from northern Vietnam, southern China and north-eastern Thailand due to distinct morphological differences. We also provide updated taxonomic accounts for the species of this group, including an identification key and distribution maps.

A new karst-dwelling, colorful pitviper (Viperidae: Trimeresurus) from northern Peninsular Thailand.

We describe a colorful and distinctively patterned, karst-dwelling pitviper, Trimeresurus kuiburi sp. nov., from the isolated, coastal massif of Khao Sam Roi Yot in Kui Buri District, Prachuap Khiri Khan Province, in northern Peninsular Thailand. The new species, member of the 'Cryptelytrops group' sensu Malhotra Thorpe (2004) and morphologically and genetically allied to Trimeresurus kanburiensis and T. venustus, differs from all pitviper taxa by a combination of red/purple bands on a green dorsum; a white concave suborbital stripe in males (straight and less visible in females); white, spaced vertebral dots in males (absent in females); pale green belly lacking dark dots or stripe on the lateral sides of the ventrals; partially fused first supralabial and nasal scale; 19 dorsal scale rows at midbody; 164171 ventrals; 6365 subcaudals in males, 5153 in females; maximal known SVL of 451 mm; and long, papillose hemipenes.

Night stalkers from above: A monograph of Toxicodryas/ tree snakes (Squamata: Colubridae) with descriptions of two new cryptic species from Central Africa.

The genus Toxicodryas, historically included with the renowned Australasian cat-eyed snakes of the colubrid genus Boiga, currently includes two widespread species (T. blandingii and T. pulverulenta) in western, central, and eastern Africa. We leverage findings from a recent phylogenomic and historical demographic analysis of this genus (based on 2848-4471 Rad-seq loci from across the genome), with robust sampling from throughout the ranges of both species, to define two additional taxonomic units, with species boundaries corresponding to river barriers. Additional morphometric data from scores of examined museum specimens and literature records bolster the recognition of these two new cryptic species. We hypothesize that T. blandingii occurs west of the confluence of the Congo and Ubangi rivers, whereas a cryptic new species that is found east of this biogeographic barrier has significantly higher numbers of ventral scale counts in both sexes, additional significant differences in several scale counts, and lower venom toxicity. Toxicodryas pulverulenta occurs west of the Niger Delta in West Africa, whereas a cryptic new species that is found east of this biogeographic barrier has significantly higher numbers of subcaudal scale counts in both sexes. A review of published information regarding morphological variation, ecology, natural history, habitat, and venom is summarized for these four Toxicodryas species.