Molecular Phylogenetics of Saw-scaled Viper (Echis carinatus) from Pakistan (original) (raw)
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Zoology in the Middle East, 2016
The Saw-scaled vipers of the species Echis carinatus range from Sri Lanka and India westwards to Iraq, including the eastern Arabian Peninsula. We collected the species in southern Iraq and compared two mtDNA genes (16S and Cyt b) with other populations of this species and with other species of the genus. Analyses of both Maximum Likelihood and Bayesian Inference confirmed E. carinatus as a monophyletic species. The samples from Iraq cluster with populations of the species from Pakistan and UAE. Populations from India, however, are situated in a separate phylogenetic lineage. This can be explained by the geographic barriers between western (Iraq, Pakistan and UAE) and eastern (India) populations of the species. Soleyman Mountain in southern Pakistan is the main barrier between them and its role is reflected in the genetic distance between populations.
Amphibia-Reptilia, 2009
Phylogenetic analysis of 1117 bp of mitochondrial DNA sequences (731 bp of cytochrome b and 386 bp of 16S rRNA) indicate that Echis consists of four main clades: E. ocellatus, and the E. coloratus, E. pyramidum, and E. carinatus groups. In the E. coloratus group, E. coloratus itself shows substantial genetic divergence from E. omanensis, corroborating their separate species status. In the E. pyramidum clade, E. pyramidum from Egypt and E. leucogaster from West Africa are genetically very similar, even though samples are separated by 4000 km. South Arabian populations of the E. pyramidum group are much better differentiated from these and two species may be present, animals from Dhofar, southern Oman probably being referable to E. khosatzkii. In the E. carinatus group, specimens of E. carinatus sochureki and E. multisquamatus are very similar in their DNA. The phylogeny indicates that the split between the main groups of Echis was followed by separation of African and Arabian members...
Molecular phylogenetics and evolution, 2009
We analyze the phylogeny of the medically important and taxonomically unresolved viper genus Echis using four mitochondrial gene fragments. The results show that the populations of the genus fall into four main clades: the Echis carinatus, E. coloratus, E. ocellatus and E. pyramidum groups. The E. pyramidum and E. coloratus groups are sister taxa but the interrelationships of this clade and the E. ocellatus and E. carinatus groups are unresolved. The initial divergence of the genus appears to coincide with the collision between Afro-Arabia and Eurasia, and that between the E. coloratus and E. pyramidum clades appears to be associated with the opening of the Red Sea. Later land connections between Africa and Arabia may have contributed to shaping the distribution of the E. pyramidum complex. The present distribution of E. carinatus may be the result of range expansion from southern India. Taxonomically, our results provide molecular evidence for the validity of Echis omanensis, E. kh...
Recent advances in phylogeny and taxonomy of Near and Middle Eastern vipers–an update
2009
Th e number of recognized viper species in the Near and Middle East has been raised signifi cantly in the last 25 years (Table 1). While some smaller genera remained more or less stable, the genus Vipera has been subdivided into four genera on the basis of molecular genetic data. Of these genera, Daboia contains the former Vipera palaestinae and D. russelii, Macrovipera the species M. lebetina, M. schweizeri and an un-described, basal species from Iran, and Montivipera the former Vipera xanthina and V. raddei complexes. While the genetic diversity in the M. raddei complex is fairly low, it is high in the M. xanthina complex. Th is may give reason to synonymize several taxa in the M. raddei complex, while new taxa can be described in the Turkish M. xanthina complex. Th e number of known species in the Middle Eastern Saw-scaled vipers (genus Echis) must be raised from 2 to 6. Th ese species belong to 3 diff erent species complexes (an Asian, an African and an Arabian complex). A parti...
Molecular phylogenetics and evolution, 2009
We analyze the phylogeny of the medically important and taxonomically unresolved viper genus Echis using four mitochondrial gene fragments. The results show that the populations of the genus fall into four main clades: the Echis carinatus, E. coloratus, E. ocellatus and E. pyramidum groups. The E. pyramidum and E. coloratus groups are sister taxa but the interrelationships of this clade and the E. ocellatus and E. carinatus groups are unresolved. The initial divergence of the genus appears to coincide with the collision between Afro-Arabia and Eurasia, and that between the E. coloratus and E. pyramidum clades appears to be associated with the opening of the Red Sea. Later land connections between Africa and Arabia may have contributed to shaping the distribution of the E. pyramidum complex. The present distribution of E. carinatus may be the result of range expansion from southern India. Taxonomically, our results provide molecular evidence for the validity of Echis omanensis, E. khosatzkii, E. borkini and E. jogeri, for the presence of unsuspected genetic diversity within the E. pyramidum complex in eastern Africa, and for the conspecificity of E. carinatus and E. multisquamatus. The status of E. leucogaster remains to be confirmed.
Molecular Phylogenetics and Evolution, 2001
Nucleotide sequences of mitochondrial cytochrome b and 16S rRNA genes, totaling 946 bp, were used to reconstruct a molecular phylogeny of 42 species of the subfamily Viperinae representing 12 of the 13 recognized genera. Maximum-parsimony and maximum-likelihood were used as methods for phylogeny reconstruction with and without a posteriori weighting. When representatives of the Causinae were taken as outgroup, five major monophyletic groups were consistently identified: Bitis, Cerastes, Echis, the Atherini (Atheris s.l.), and the Eurasian viperines. Proatheris was affiliated with Atheris, and Adenorhinos clustered within Atheris. The African Bitis consisted of at least three monophyletic groups: i) the B. gabonica group, (ii) the B. caudalis group, and (iii) the B. cornuta group. B. worthingtoni and B. arietans are not included in any of these lineages. Eurasian viperines could be unambiguously devided into four monophyletic groups: (i) Pseudocerastes and Eristicophis, (ii) European vipers (Vipera s.str.), (iii) Middle East Macrovipera plus Montivipera (Vipera xanthina group), and (iv) North African Macrovipera plus Vipera palaestinae and Daboia russelii. These evolutionary lineages are consistent with historical biogeographical patterns. According to our analyses, the viperines originated in the Oligocene in Africa and successively underwent a first radiation leading to the five basal groups. The radiation might have been driven by the possession of an effective venom apparatus and a foraging startegy (sit-wait-strike) superior in most African biomes and might have been adaptive. The next diversifications led to the Proatheris-Atheris furcation, the basal Bitis splitting, and the emergence of the basal lineages within the Eurasian stock. Thereafter, lineages within Echis, Atheris, and Cerastes evolved. The emergence of three groups within Vipera s.l. might have been forced by the existence of three land masses during the early Miocene in the area of the Paratethys and the Med-iterranean Seas. Taxonomic consequences of these findings are discussed.
A Phylogeny of the< i> Trimeresurus Group of Pit Vipers: New Evidence from a Mitochondrial Gene Tree
Molecular Phylogenetics and Evolution, 2000
The Trimeresurus group is an important radiation of over 40 Asian pit viper species. Once considered congeneric, four genera are generally currently recognized (Trimeresurus sensu stricto, Ovophis, Protobothrops, and Tropidolaemus) but relationships within and between these are still unclear. This study, based on mitochondrial cytochrome b sequences, is the first to include a large number of species (21) and demonstrates that the current taxonomy does not adequately represent either the relationships or the genetic diversity present in the complex. Although many deeper nodes are not strongly supported, the following novel conclusions are all well supported: (1) the paraphyly of Trimeresurus sensu stricto, (2) the presence of several divergent clades within Trimeresurus sensu stricto, (3) the paraphyly of some widespread, medically significant, species, (4) the nonmonophyly of Ovophis, and (5) the monophyly of Protobothrops. Mapping of morphological characters onto the mitochondrial tree further supports the four groups proposed for Trimeresurus sensu stricto.
2020
The Arabian Horned Viper, <i>Cerastes gasperettii</i>, is distributed along the eastern edge of the Sinai Peninsula south and east across the Arabian Peninsula to Iraq, Kuwait and western Iran comprising two subspecies: <i>Cerastes. g. mendelssohni</i> in the Arava valley (Israel and Jordan) and <i>C. g. gasperettii</i> in the Arabian Peninsula and southwestern Iran. Phylogenetic relationships based on Maximum Likelihood, Bayesian Inference, haplotype networks, and genetic divergence among different populations of <i>C. gasperettii</i> are analysed in this study. Two mitochondrial (<i>12S</i> and <i>Cytb</i>) and two nuclear partial genes (<i>C-mos</i> and <i>MC1R</i>) with uneven distribution among the individuals were used to infer phylogenetic relationships. Bayesian inference (BI) phylogenetic tree indicates a dichotomy separating a southern (Oman, UAE, Yemen) from a northern clade (I...
Molecular phylogenetics of Black Cobra (Naja naja) in Pakistan
Electronic Journal of Biotechnology, 2019
Background: Snakes are found on every continent in the world except Antarctica, and on smaller land masses. Being ecologically important, they also cause a large number of bites, leading to millions of deaths. Mitochondrial and nuclear gene sequences are being used to identify, characterize, and infer genetic biodiversity among different snake species. Furthermore, phylogenetics helps in inferring the relationships and evolutionary histories among these species. Black cobra is one of the four most venomous snakes in Pakistan. Four mitochondrial (ND4, Cytochrome b, 12S rRNA, and 16S rRNA) and four nuclear (C-mos, RAG-1, BDNF, and NT3) genes were used to trace diversity and infer the phylogenetic relationship of black cobra in Pakistan. Results: Almost similar phylogenies were obtained through maximum likelihood and Bayesian inference, showing two species of cobra in Pakistan, namely, black cobra (Naja naja) and brown cobra (Naja oxiana). All Naja species were divided into three clades: black cobra (N. naja) and brown cobra (N. oxiana) cladding with different species of Naja; N. naja (Pakistan) cladding with N. naja from Nepal; and N. oxiana showed close relationship with Naja kaouthia from Thailand and Naja siamensis from Thailand. Conclusion: It was confirmed genetically that there are two cobra species in Pakistan, i.e., black and brown cobras. This study will help in not only genetic conservation but also developing anti-venom against snake species.
Scientific Reports
Iran is a mountainous country with more than half of its mainland covered by mountains 8. The Alborz encompasses a series of mountain ranges extending from northwestern to northeastern Iran 9. The formation of the Alborz Mountains was first initiated during the Paleocene and the rugged landscape of the Alborz took shape during the early Cenozoic. This uplift was the outcome of an expansive movement throughout Iran as well as the Caucasian Mountains 10,11. In addition, the Hyrcanian forests along the northern slopes of the Alborz Mountains and southern coasts of the Caspian Sea rank among the most important forest remnants in western Eurasia and are characterized by having one of the most ecologically valuable biodiversity hotspots in the Middle East 8. Recent research indicates that continental glaciers in Iran during the Pleistocene 12,13 , as well as the current climate change in northern Iran 14 , could have, respectively, led to latitudinal and altitudinal distribution shifts in a number of species, particularly poikilothermic animals, which are noted for their sensitivity to changes in temperature 15. The Caucasian pit viper Gloydius halys caucasicus (Nikolsky, 1916) is distributed throughout southeastern Azerbaijan, southern Turkmenistan (Kopet Dagh Mountains), from northeastern to northwestern Iran, and northwestern Afghanistan, and is relatively common across the Alborz Mountains. This viper is a member of the G. halys/G. intermedius species complex, which represents a group of closely related vipers of the Crotalinae subfamily (Viperidae), including a total of nine taxa: G. halys halys, G. h. caucasicus, G. caraganus, G. cognatus, G. stejnegeri, G. rickmersi, G. shedaoensis, G. changdaoensis, and G. intermedius 16-19. With a widespread range in the Palearctic, they inhabit a spectrum of various biotopes distributed across an extensive territory from Azerbaijan and Iran through several countries of Central Asia to eastern Siberia, Mongolia, and China 17,20-22. Although this complex has been the focus of numerous phylogenetic 16,17,20,23-28 , morphological 24,29 , ecological 30,31 , and captive-breeding studies 32 , it remains an enigmatic species group. The intricacy arises out of a recent discovery of a morphologically and genetically distinct species 17 , evincing the fact that the diversity within this complex is most likely underestimated. Additionally, Wagner et al. 17 proposed the elevation of the Caucasian pit viper from subspecies to species rank. This was later accepted by Shi et al. (2016, 2017). Moreover, Shi et al. 19 argued for elevation of two other subspecies G. h. cognatus and G. h. stejnegeri, to the full species rank, which was later reaffirmed by Shi et al. 18. The Caucasian pit viper occupies a diverse range of habitat types, from 30 m to about 3,000 m above sea level, within northern and southern slopes of the Alborz Mountains, thus serving as an ideal example to evaluate phylogenetic and phylogeographic patterns of a terrestrial poikilothermic species in northern Iran. Even though this species has been under intensive exploitation for venom milking by the Razi Vaccine and Serum Research Institute since 1924 26 , the details of its evolutionary history and population structure have remained poorly understood to this day 17,33,34. Developments in molecular taxonomy and barcoding techniques allow rapid detection of cryptic diversity 35. It has been demonstrated that combining molecular, morphological, ecological, and biological data is a crucial key to detecting cryptic species, especially in less well-known areas. Moreover, the growing concern toward conservation of genetic diversity calls for accurately defining evolutionary significant units (ESUs) based on evolutionary histories of relevant taxa 36 (see 37 for a review of ESU definitions), as species-based units cannot always prove applicable to all conservation strategies 38. Thus, phylogenetic and phylogeographic inferences are applied to conservation planning below the species level 13,39. In this study, we sought to better understand the phylogeny, phylogeography, and taxonomic reassessment of G. h. caucasicus across its entire distribution range in Iran and Azerbaijan, using partial mtDNA sequences of the Cytochrome b (cyt b) and NADH dehydrogenase subunit 4 (ND4) genes, as well as the nuclear proto oncogene c-mos. We (i) delineated the entire geographically defined evolutionary lineages of this viper and their spatial distribution from northeastern to northwestern Iran and southern Azerbaijan. We (ii) performed coalescent simulations to compare several historical biogeographical hypotheses (single refugium or multiple refugia, along with one-way or two-way gene flows) that involve lineage diversification within this viper. Then, we (iii) used statistical phylogenetic methods to evaluate the taxonomic status of this subspecies within the G. halys/G. intermedius species complex. Finally, (iv) we used our analyses to uncover patterns of historical migration of the species to Transcaucasia and to define ESUs of this viper. Given the genetic structure and distribution of the Iranian lineages, we proposed some recommendations for effective conservation of all phylogenetically significant lineages of the Caucasian pit viper in Iran.