The Silk roads: phylogeography of Central Asian dice snakes (Serpentes: Natricidae) shaped by rivers in deserts and mountain valleys.

Influenced by rapid changes in climate and landscape features since the Miocene, widely distributed species provide suitable models to study the environmental impact on their evolution and current genetic diversity. The dice snake Natrix tessellata, widely distributed in the Western Palearctic is one such species. We aimed to resolve a detailed phylogeography of N. tessellata with a focus on the Central Asian clade with 4 and the Anatolia clade with 3 mitochondrial lineages, trace their origin, and correlate the environmental changes that affected their distribution through time. The expected time of divergence of both clades began at 3.7 Mya in the Pliocene, reaching lineage differentiation approximately 1 million years later. The genetic diversity in both clades is rich, suggesting different ancestral areas, glacial refugia, demographic changes, and colonization routes. The Caspian lineage is the most widespread lineage in Central Asia, distributed around the Caspian Sea and reaching the foothills of the Hindu Kush Mountains in Afghanistan, and Eastern European lowlands in the west. Its distribution is limited by deserts, mountains, and cold steppe environments. Similarly, Kazakhstan and Uzbekistan lineages followed the Amu Darya and the Syr Darya water systems in Central Asia, with ranges delimited by the large Kyzylkum and Karakum deserts. On the western side, there are several lineages within the Anatolia clade that converged in the central part of the peninsula with 2 being endemic to Western Asia. The distribution of both main clades was affected by expansion from their Pleistocene glacial refugia around the Caspian Sea and in the valleys of Central Asia as well as by environmental changes, mostly through aridification.

Kukri snakes Oligodon Fitzinger, 1826 of the Western Palearctic with the resurrection of Contia transcaspica Nikolsky, 1902 (Reptilia, Squamata, Colubridae).

The kukri snakes of the genus Oligodon Fitzinger, 1826 reach the westernmost limits of their distribution in Middle and Southwest Asia (Afghanistan, Iran, and Turkmenistan), and the Palearctic portions of Pakistan. In this article, we review the systematics and distribution of the two species native to this region, Oligodon arnensis (Shaw, 1802) and Oligodon taeniolatus (Jerdon, 1853) based on an integrative approach combining morphological, molecular, and species distribution modeling (SDM) data. Phylogenetic analyses recover O. taeniolatus populations from Iran and Turkmenistan in a clade with the O. arnensis species complex, rendering the former species paraphyletic relative to O. taeniolatus sensu stricto on the Indian subcontinent. To correct this, we resurrect the name Contia transcaspica Nikolsky, 1902 from the synonymy of O. taeniolatus and assign it to populations in Middle-Southwest Asia. So far, Oligodon transcaspicus comb. et stat. nov. is known only from the Köpet-Dag Mountain Range of northeast Iran and southern Turkmenistan, but SDM mapping suggests it may have a wider range. Genetic samples of O. "arnensis" from northern Pakistan are nested in a clade sister to the recently described Oligodon churahensis Mirza, Bhardwaj & Patel, 2021, and are phylogenetically separate from O. arnensis sensu stricto in south India and Sri Lanka. Based on morphological similarity, the Afghanistan and Pakistan populations are assigned to Oligodon russelius (Daudin, 1803) and we synonymize O. churahensis with this species. Our investigation leads us to remove O. taeniolatus from the snake fauna of Afghanistan, Iran, and Turkmenistan, with the consequence that only Oligodon transcaspicus comb. et stat. nov. and O. russelius are present in these countries. Additional studies are needed to resolve the taxonomy of the O. taeniolatus and O. arnensis species complexes on the Indian subcontinent, and an updated key for both groups is provided.

Global Protected Areas as refuges for amphibians and reptiles under climate change.

Protected Areas (PAs) are the cornerstone of biodiversity conservation. Here, we collated distributional data for >14,000 (~70% of) species of amphibians and reptiles (herpetofauna) to perform a global assessment of the conservation effectiveness of PAs using species distribution models. Our analyses reveal that >91% of herpetofauna species are currently distributed in PAs, and that this proportion will remain unaltered under future climate change. Indeed, loss of species' distributional ranges will be lower inside PAs than outside them. Therefore, the proportion of effectively protected species is predicted to increase. However, over 7.8% of species currently occur outside PAs, and large spatial conservation gaps remain, mainly across tropical and subtropical moist broadleaf forests, and across non-high-income countries. We also predict that more than 300 amphibian and 500 reptile species may go extinct under climate change over the course of the ongoing century. Our study highlights the importance of PAs in providing herpetofauna with refuge from climate change, and suggests ways to optimize PAs to better conserve biodiversity worldwide.

Appearances often deceive in racerunners: integrative approach reveals two new species of Eremias (Squamata: Lacertidae) from Pakistan.

Based on newly provided morphological and previously published genetic data, we describe two new distinctive sympatric lacertid lizards of the genus Eremias (subgenus Aspidorhinus) from the arid mountains of northwestern Balochistan Province, Pakistan. The new species, Eremias killasaifullahi sp. nov. and Eremias rafiqi sp. nov. are distinguished from all other species of the subgenus Aspidorhinus (E. afghanistanica, E. fahimii, E. isfahanica, E. kopetdaghica, E. lalezharica, E. montana, E. nikolskii, E. papenfussi, E. persica, E. regeli, E. roborowskii, E. strauchi, E. suphani, and E. velox) by unique morphological characters and genetic differentiation. In the molecular phylogeny of Aspidorhinus, both new taxa are well-supported lineages differentiated from other species of this subgenus by uncorrected p distances from 8.5% to 21.6%, respectively. Both new species belong to E. persica complex where E. rafiqi sp. nov. is partly similar in dorsal color pattern to E. persica but can be distinguished from this species by unique meristic and morphometric characters. Eremias rafiqi sp. nov. is found in Pakistan, Afghanistan, and eastern Iran. Eremias killasaifullahi sp. nov. can be differentiated from E. persica by its distant distribution, dorsal color and pattern, smaller size, and less number of gulars and ventral scales. Eremias killasaifullahi sp. nov. is only known from the type locality and represents the local microendemism, along with other endemic species of reptiles reported from this part of Pakistan. We, however, expect that E. killasaifullahi sp. nov. could have a broader range in northwestern Pakistan and southeastern Afghanistan, which should be an object of following investigations. Our data show that remote areas between Hindu Kush Mountains and Indus River need attention as they most probably represent possible sources of genetic and species diversity in the region.

The evolutionary history of an accidental model organism, the leopard gecko Eublepharis macularius (Squamata: Eublepharidae).

The leopard gecko, Eublepharis macularius, is a widely used model organism in laboratory and experimental studies. The high phenotypic diversity in the pet trade, the fact that the provenance of different breeding lines is unknown, and that distinct Eublepharis species are known to hybridize, implies that the continued use of E. macularius as a model requires clarity on the origin of the lineages in the pet trade. We combine multi-locus sequence data and the first range-wide sampling of the genus Eublepharis to reconstruct the evolutionary history of the Eublepharidae and Eublepharis, with an updated time-tree for the Eublepharidae. Our sampling includes five of the six recognized species and additional nominal taxa of uncertain status comprising 43 samples from 34 localities plus 48 pet-trade samples. The Eublepharidae began diversifying in the Cretaceous. Eublepharis split from its sister genera in Africa in the Palaeocene-Eocene, and began diversifying in the Oligocene-Miocene, with late Miocene-Pliocene cladogenesis giving rise to extant species. The current species diversity within this group is moderately underestimated. Our species delimitation suggests 10 species with four potentially unnamed divergent lineages in Iran, India and Pakistan. All 30 individuals of E. macularius that we sampled from the pet trade, which include diverse morphotypes, come from a few shallow E. macularius clades, confirming that lab and pet trade strains are part of a single taxon. One of the wild-caught haplotypes of E. macularius, from near Karachi, Pakistan, is identical to (10) pet-trade samples and all other captive populations are closely related to wild-caught animals from central/southern Pakistan (0.1-0.5 % minimum pairwise uncorrected ND2 sequence divergence).

Morphological and molecular data on tadpoles of the westernmost Himalayan spiny frog Allopaa hazarensis (Dubois & Khan, 1979).

Little is known about the life history, ecology, and distribution of the genus Allopaa (Dicroglossidae) and far less recent data are available about the larvae of this taxon. Here, we provide data on the larval stage of Allopaa hazarensis (Dubois & Khan, 1979) from northern Pakistan based on the examination of three tadpoles. Specimens were obtained from two sites in Buner, Khyber Pakhtunkhwa province, Pakistan. Morphological and genetic analysis (mtDNA and nDNA) confirmed the identity of the tadpoles as A. hazarensis. Tadpole characterizations were illustrated by detailed imagery. Basic measurements and details on oral apparatus provide relevant taxonomic characteristics to distinguish the tadpoles of this species from other spiny frogs. The illustration and description of the tadpole of A. hazarensis should facilitate the identification of this species in the field.

Relict groups of spiny frogs indicate Late Paleogene-Early Neogene trans-Tibet dispersal of thermophile faunal elements.

BACKGROUND: The Himalaya-Tibet orogen (HTO) presents an outstanding geologically active formation that contributed to, and fostered, modern Asian biodiversity. However, our concepts of the historical biogeography of its biota are far from conclusive, as are uplift scenarios for the different parts of the HTO. Here, we revisited our previously published data set of the tribe Paini extending it with sequence data from the most western Himalayan spiny frogs Allopaa and Chrysopaa and using them as an indirect indicator for the potential paleoecological development of Tibet. METHODS: We obtained sequence data of two mitochondrial loci (16S rRNA, COI) and one nuclear marker (Rag1) from Allopaa samples from Kashmir Himalaya as well as Chrysopaa sequence data from the Hindu Kush available from GenBank to complement our previous data set. A Maximum likelihood and dated Bayesian gene tree were generated based on the concatenated data set. To resolve the inconsistent placement of Allopaa, we performed different topology tests. RESULTS: Consistent with previous results, the Southeast Asian genus Quasipaa is sister to all other spiny frogs. The results further reveal a basal placement of Chrysopaa relative to Allopaa and Nanorana with an estimated age of ca. 26 Mya. Based on the topology tests, the phylogenetic position of Allopaa as a sister clade to Chaparana seems to be most likely, resulting in a paraphyletic genus Nanorana and a separation from the latter clade around 20 Mya, although a basal position of Allopaa to the genus Nanorana cannot be entirely excluded. Both, the placements of Chrysopaa and Allopaa support the presence of basal Paini lineages in the far northwestern part of the HTO, which is diametrically opposite end of the HTO with respect to the ancestral area of spiny frogs in Southeast Asia. These striking distributional patterns can be most parsimoniously explained by trans-Tibet dispersal during the late Oligocene (subtropical Chrysopaa) respectively early Miocene (warm temperate Allopaa). Within spiny frogs, only members of the monophyletic Nanorana+Paa clade are adapted to the colder temperate climates, indicating that high-altitude environments did not dominate in the HTO before ca. 15 Mya. Our results are consistent with fossil records suggesting that large parts of Tibet were characterized by subtropical to warm temperate climates at least until the early Miocene. They contradict prevalent geological models of a highly uplifted late Paleogene proto-Plateau.

Out of the blue: The first record of the genus Heremites Gray, 1845 (Squamata, Scincidae) from Pakistan.

The genus Heremites Gray, 1845 is endemic to the Western Palearctic region, containing morphologically similar species with a not well resolved taxonomy. The genus has a broad distribution from North Africa to Central Asia, with the only known record from northeastern Afghanistan. Three species are currently recognized in the genus with one, H. septemtaeniatus (Reuss, 1834), representing populations at the eastern edge of the genus range. During extensive fieldwork, we discovered H. septemtaeniatus from northwestern Pakistan and provisionally suggest that this population could be morphologically defined as H. septemtaeniatus transcaucasicus (Chernov, 1926). This important contribution to the knowledge regarding the family Scincidae in Pakistan, however, needs further investigation using an integrative approach.

A new species of Microgecko Nikolsky, 1907 (Squamata: Gekkonidae) from Pakistan.

Members of the dwarf geckos of the genus Microgecko Nikolsky, 1907 are distributed from western Iran to northwestern India, with seven currently recognized species. Three taxa have been reported from Pakistan, M. depressus, M. persicus persicus and M. p. euphorbiacola. The former is the only endemic species restricted to Pakistan. Herein, we describe a new species, Microgecko tanishpaensis sp. nov., on the basis of four specimens collected from the remote area of the Toba Kakar Range in northwestern Balochistan. The type locality lies in an isolated valley in mountainous terrain known for the occurrence of other endemic reptile species, including geckos. Microgecko tanishpaensis sp. nov. is differentiated from the morphologically similar species M. depressus by possessing larger size, five scales bordering the nostril, internasals (supranasals) scales in contact with nostril, two large pairs of postmentals, higher numbers of interorbitals (27-30), scales around midbody (76-84), ventral scales from the postmental to vent (144-156) and scales along dorsal midline from axilla to groin (75-86). A morphological comparison of M. tanishpaensis sp. nov. with other species of the genus and an updated identification key for the genus Microgecko are presented.

A new species of Eremias (Squamata: Lacertidae) from the arid mountains of Pakistan.

A new, morphologically distinctive lacertid lizard of the genus Eremias (Rhabderemias) is described from the arid mountains of northwestern Balochistan Province in Pakistan. Eremias kakari sp. nov. has an isolated distribution and can be easily distinguished from all other species of mainly desert subgenus Rhabderemias (E. andersoni, E. cholistanica, E. fasciata, E. lineolata, E. pleskei, E. scripta, E. vermiculata). Apart from other differences, E. kakari sp. nov. can be distinguished from geographically close members of the subgenus Rhabderemias (E. cholistanica, E. fasciata, and E. scripta) by having a single row of subdigital lamellae and a complete row of lateral scales and hence three scales around the penultimate phalanx of 4th toe. The new species is morphologically (dorsal pattern) very similar to E. fasciata but can be distinguished from this species for having 22-26 subdigital lamellae under 4th toe, 48-55 dorsal scales across midbody, ventrals in 11-14 oblique longitudinal series across the belly, 17-21 femoral pores and 17-21 scales in the 9th-10th annulus posterior to the postcloacal granules. The new species is currently known only from the type locality situated in the Toba Kakar Range, near to Tanishpa village. However, we expect that Eremias kakari sp. nov. would have a broader range in northwestern Pakistan and southeastern Afghanistan. An identification key for the Pakistani Eremias, together with other remarks to the new species, is presented.

The genus Microhyla (Anura: Microhylidae) in Pakistan: species status and origins.

The territory of Pakistan has been influenced by biota from different geographic directions, and is divided zoogeographically into the Palearctic and Oriental regions (Khan 2006; Masroor 2012). This makes Pakistan one of the important territories in Eurasia in the understanding of past biodiversity dynamics. Well-known examples of Oriental elements among its amphibian fauna are observed in all four families of toads and frogs currently known from Pakistan: Bufonidae, Microhylidae, Megophryidae, and Dicroglossidae. In this short contribution, we focused on the species status and the origins of the genus Microhyla (Microhylidae), known from the north-eastern part (Punjab, Islamabad, and Azad Jammu and Kashmir; Masroor 2012) of the country. However, Sarkar (1984), also reported Microhyla from Bhuj in Gujarat, India, very close to the southern Pakistani province of Sindh. This genus has not yet been reported from the Palearctic region of the country and all currently known localities are from the Oriental parts of Pakistan (i.e. eastward of the Indus River). The genus is represented in the country by M. ornata (Duméril Bibron, 1841), originally reported as Oxyglossus lima (Khan 1968). However, in view of the overall distribution and diversity of the genus based on genetic data (Garg et al. 2018, 2019; Gorin et al. 2020), it appears that populations from Pakistan could possibly have a different evolutionary history and be different taxon (see the currently scattered range of the genus between northern and western India and Pakistan; Fig. 1). Therefore, we tested this assumption using mitochondrial (mt) and nuclear (n) DNA data.

Fifteen shades of green: The evolution of Bufotes toads revisited.

The radiation of Palearctic green toads (Bufotes) holds great potential to evaluate the role of hybridization in phylogeography at multiple stages along the speciation continuum. With fifteen species representing three ploidy levels, this model system is particularly attractive to examine the causes and consequences of allopolyploidization, a prevalent yet enigmatic pathway towards hybrid speciation. Despite substantial efforts, the evolutionary history of this species complex remains largely blurred by the lack of consistency among the corresponding literature. To get a fresh, comprehensive view on Bufotes phylogeography, here we combined genome-wide multilocus analyses (RAD-seq) with an extensive compilation of mitochondrial, genome size, niche modelling, distribution and phenotypic (bioacoustics, morphometrics, toxin composition) datasets, representing hundreds of populations throughout Eurasia. We provide a fully resolved nuclear phylogeny for Bufotes and highlight exceptional cyto-nuclear discordances characteristic of complete mtDNA replacement (in 20% of species), mitochondrial surfing during post-glacial expansions, and the formation of homoploid hybrid populations. Moreover, we traced the origin of several allopolyploids down to species level, showing that all were exclusively fathered by the West Himalayan B. latastii but mothered by several diploid forms inhabiting Central Asian lowlands, an asymmetry consistent with hypotheses on mate choice and Dobzhansky-Muller incompatibilities. Their intermediate call phenotypes potentially allowed for rapid reproductive isolation, while toxin compositions converged towards the ecologically-closest parent. Across the radiation, we pinpoint a stepwise progression of reproductive isolation through time, with a threshold below which hybridizability is irrespective of divergence (<6My), above which species barely admix and eventually evolve different mating calls (6-10My), or can successfully cross-breed through allopolyploidization (>15My). Finally, we clarified the taxonomy of Bufotes (including genetic analyses of type series) and formally described two new species, B. cypriensis sp. nov. (endemic to Cyprus) and B. perrini sp. nov. (endemic to Central Asia). Embracing the genomic age, our framework marks the advent of a new exciting era for evolutionary research in these iconic amphibians.

The sparid fishes of Pakistan, with new distribution records.

The family sparidae is represented in Pakistan by 14 species belonging to eight genera: the genus Acanthopagrus with four species, A. berda, A. arabicus, A. sheim, and A. catenula; Rhabdosargus, Sparidentex and Diplodus are each represented by two species, R. sarba and R. haffara, Sparidentex hasta and S. jamalensis, and Diplodus capensis and D. omanensis, and the remaining four genera are represented by single species, Crenidens indicus, Argyrops spinifer, Pagellus affinis, and Cheimerius nufar. Five species, Acanthopagrus arabicus, A. sheim, A. catenula, Diplodus capensis and Rhabdosargus haffara are reported for the first time from Pakistani coastal waters. The Arabian Yellowfin Seabream Acanthopagrus arabicus and Spotted Yellowfin Seabream Acanthopagrus sheim have only recently been described from Pakistani waters, while Diplodus omanensis and Pagellus affinis are newly identified from Pakistan. Acanthopagrus catenula has long been incorrectly identified as A. bifasciatus, a species which has not been recorded from Pakistan. All species are briefly described and a key is provided for them. 

A preliminary phylogeny of the Palearctic naked-toed geckos (Reptilia: Squamata: Gekkonidae) with taxonomic implications.

Palearctic naked-toed geckos are a group of gekkonid geckos that range from North Africa to northern India and western China, with their greatest diversity in Iran and Pakistan. Relationships among the constituent genera remain incompletely resolved and the monophyly of key genera remains unverified. Further, competing classifications are in current use and many species have been allocated to different genera by different authors. We used both mitochondrial (ND2) and nuclear genes (RAG1, PDC) to explore relationships among representatives of all but one genus in the group (Rhinogecko), including four genera not previously included in phylogenetic analyses (Asiocolotes, Altigekko, Indogekko, and Siwaligekko). Siwaligekko (and presumably other Tibeto-Himalayan species often referred to Cyrtopodion) are more closely related to tropical Asian Cyrtodactylus than to Palearctic naked-toed geckos. Sampled species of Asiocolotes and Altigekko are sister taxa, but both genera are here considered junior subjective synonyms of Altiphylax. Cyrtopodion sensu lato is non-monophyletic; Mediodactylus and Tenuidactylus, which have variably been considered as subgenera or synonyms of Cyrtopodion are both valid genera. Indogekko is embedded within Cyrtopodion and is here treated as a subgenus. Bunopus and Crossobamon are closely related to one-another, and with Agamura are interdigitated among taxa previously assigned to Cyrtopodion. Our data confirm the previous identification of a Saharo-Arabian Stenodactylus/Tropiocolotes/Pseudoceramodactylus clade and verify that Microgecko and Alsophylax are not members of the main clade of Palearctic naked-toed geckos. Osteological differences between Tropiocolotes and Microgecko, formerly treated as congeneric, are discussed and illustrated. The divergence between Cyrtodactylus and the Palearctic naked-toed clade predates the initial collision of the Indian and Eurasian plates, but deeper divergences within both groups are consistent with mountain building in the Himalayas and adjacent ranges as promoting cladogenic events. Miocene divergences within Tenuidactylus are consistent with vicariant speciation caused by uplift events in the Iranian and Transcaspian regions. Taxonomic implications of our phylogenetic results are discussed and a preliminary allocation of all species of padless Palearctic gekkonids to genus is provided.