Range-Wide Phylogeography and Ecological Niche Modeling Provide Insights into the Evolutionary History of the Mongolian Racerunner (Eremias argus) in Northeast Asia

The Mongolian racerunner, Eremias argus, is a small lizard endemic to Northeast Asia that can serve as an excellent model for investigating how geography and past climate change have jointly influenced the evolution of biodiversity in this region. To elucidate the processes underlying its diversification and demography, we reconstructed the range-wide phylogeographic pattern and evolutionary trajectory, using phylogenetic, population genetic, landscape genetic, Bayesian phylogeographic reconstruction and ecological niche modeling approaches. Phylogenetic analyses of the mtDNA cyt b gene revealed eight lineages that were unbounded by geographic region. The genetic structure of E. argus was mainly determined by geographic distance. Divergence dating indicated that E. argus and E. brenchleyi diverged during the Mid-Pliocene Warm Period. E. argus was estimated to have coalesced at~0.4351 Ma (Marine Isotope Stage 19). Bayesian phylogeographic diffusion analysis revealed out-of-Inner Mongolia and rapid colonization events from the end of the Last Interglacial to the Last Glacial Maximum, which is consistent with the expanded suitable range of the Last Glacial Maximum. Pre-Last Glacial Maximum growth of population is presented for most lineages of E. argus. The Glacial Maximum contraction model and the previous multiple glacial refugia hypotheses are rejected. This may be due to an increase in the amount of climatically favorable habitats in Northeast Asia. Furthermore, E. argus barbouri most likely represents an invalid taxon. The present study is the first to report a range-wide phylogeography of reptiles over such a large region in Northeast Asia. Our results make a significant contribution towards understanding the biogeography of the entire Northeast Asia.

Osteoderm Development during the Regeneration Process in Eurylepis taeniolata Blyth, 1854 (Scincidae, Sauria, Squamata)

Osteoderms are bony structures that develop within the dermal layer of the skin in vertebrates and are very often found in different lizard families. Lizard osteoderms are diverse in topography, morphology, and microstructure. Of particular interest are the compound osteoderms of skinks, which are a complex of several bone elements known as osteodermites. We present new data on the development and regeneration of compound osteoderms based on the results of a histological and Computed Microtomography (micro-CT) study of a scincid lizard: Eurylepis taeniolata. The specimens studied are stored in the herpetological collections of the Saint-Petersburg State University and Zoological Institute of the Russian Academy of Sciences located in St. Petersburg, Russia. The topography of osteoderms in the integuments of the original tail area and its regenerated part was studied. A comparative histological description of the original and regenerated osteoderms of Eurylepis taeniolata is presented for the first time. The first description of the development of compound osteoderm microstructure in the process of caudal regeneration is also presented.

Four new species of the genus Diploderma Hallowell, 1861 (Squamata, Agamidae) from China

Four new species of Diploderma are described from Sichuan and Yunnan provinces, southwestern China, based on an integrative taxonomic approach, combining morphological and genetic data. The first new species from Danba County, Sichuan Province, is morphologically most similar and phylogenetically closely related to D. flaviceps, but it can be diagnosed from the latter by having a relatively much shorter tail and by a genetic distance of 4.4% in the ND2 gene; the second new species from Muli County, Sichuan Province, is phylogenetically closely related to D. daochengense, D. yongshengense, and D. yulongense, but it can be diagnosed from the latter three species by having a pale yellow gular spot and by genetic distances of 5.6–6.7% in the ND2 gene; the third new species from Jiulong County, Sichuan Province, is morphologically most similar and phylogenetically closely related to D. angustelinea, but it can be diagnosed from the latter by having a relatively much longer tail and by a genetic distance of 2.8% in the ND2 gene; and the last new species from Weixi County, Yunnan Province, is phylogenetically closely related to D. aorun, but it can be diagnosed from the latter by having a pale yellow gular spot and by a genetic distance of 2.9% in the ND2 gene. Our work brings the number of species within the genus Diploderma to 46.

Three new species of Diploderma Hallowell, 1861 (Squamata, Agamidae) from the Hengduan Mountain Region, south-western China

Three new species of Diploderma are described from the Hengduan Mountain Region in south-western China, based on morphological and genetic data. The first new species from Yulong County, Yunnan Province is morphologically most similar and phylogenetically closely related to D.brevicauda, but it can be diagnosed from the latter by having a relatively longer tail; the second new species from Xiangcheng County, Sichuan Province is phylogenetically closely related to D.bowoense, but it can be diagnosed from the latter by the absence of a distinct gular spot; and the third new species from Yongsheng County, Yunnan Province is phylogenetically closely related to D.yulongense, but it can be diagnosed from the latter by having different colourations of the ventral and ventrolateral surfaces of the body. Taxonomy and diversity survey are the basis of species conservation, our discoveries contributing to better conservation of the species of this genus.

Integrative Taxonomy Reveals a New Cryptic Species of <i>Xenopeltis</i> Gray, 1831 (Ophidia: Macrostomata: Pythonoidea: Xenopeltidae) from Central Highlands, Vietnam

Herein, we describe a new cryptic snake species of the genus Xenopeltis from Central Highlands of Vietnam: Kon Plông District, Kon Tum Province based both on morphological and molecular data. Xenopeltis intermedius sp. nov. is distinguished from the two known species by a combination of the following morphological characters. Xenopeltis intermedius sp. nov. differs from X. unicolor and X. hainanensis by the number of ventrals and subcaudals. The skull is less elongated than in X. unicolor and somewhat more elongate than in X. hainanensis. X. intermedius demonstrates differences in size, shape proportions and relief of the parietal bone and the number of teeth from X. hainanensis and X. unicolor. We provide a COI-based estimation of diversity of the genus Xenopeltis. Genetic divergence (p-distance) between Xenopeltis sp. nov. from Kon Tum Province, Central Highlands region of Vietnam, and two other congeners was 5.7% (for X. hainanensis) and 12.9% (for X. unicolor). The new species is currently known only from one locality from Central Highland and was recorded from 1500 to 2500 m a.s.l. in the evergreen polydominant forests in the mountainous regions of Kon Tum Province. This is the third species of Xenopeltis from Vietnam.

A global reptile assessment highlights shared conservation needs of tetrapods

Comprehensive assessments of species’ extinction risks have documented the extinction crisis¹ and underpinned strategies for reducing those risks². Global assessments reveal that, among tetrapods, 40.7% of amphibians, 25.4% of mammals and 13.6% of birds are threatened with extinction³. Because global assessments have been lacking, reptiles have been omitted from conservation-prioritization analyses that encompass other tetrapods^4–7. Reptiles are unusually diverse in arid regions, suggesting that they may have different conservation needs⁶. Here we provide a comprehensive extinction-risk assessment of reptiles and show that at least 1,829 out of 10,196 species (21.1%) are threatened—confirming a previous extrapolation⁸ and representing 15.6 billion years of phylogenetic diversity. Reptiles are threatened by the same major factors that threaten other tetrapods—agriculture, logging, urban development and invasive species—although the threat posed by climate change remains uncertain. Reptiles inhabiting forests, where these threats are strongest, are more threatened than those in arid habitats, contrary to our prediction. Birds, mammals and amphibians are unexpectedly good surrogates for the conservation of reptiles, although threatened reptiles with the smallest ranges tend to be isolated from other threatened tetrapods. Although some reptiles—including most species of crocodiles and turtles—require urgent, targeted action to prevent extinctions, efforts to protect other tetrapods, such as habitat preservation and control of trade and invasive species, will probably also benefit many reptiles.

An extinction-risk assessment of reptiles shows that at least 21.1% of species are threatened by factors such as agriculture, logging, urban development and invasive species, and that efforts to protect birds, mammals and amphibians probably also benefit many reptiles.

A New Species of Cyrtodactylus Gray, 1827 (Squamata, Gekkonidae) from Southern Yunnan, China

A new species of Cyrtodactylus is described based on five specimens collected from the karst formations of Maguan County, Wenshan Prefecture, Yunnan Province, China. The new species is recognized by having a unique combination of morphological characters: medium body size, ventrolateral folds present without interspersed tubercles, 7 – 9 precloacal pores in a continuous series, enlarged femoral scales present and continuous with pore-bearing precloacal scales, femoral pores on each enlarged femoral scale in males, 1 – 4 postcloacal tubercles on each side, subcaudals enlarged, a black postocular streak extending from posterior corner of eye rearwards to above tympanum, nuchal loop discontinuous, 6 – 7 black irregular dorsal bands between limbs, most bands discontinuous. Genetically, uncorrected sequence divergences of the ND2 gene and its flanking tRNAs between the new species and investigated congeners ranged from 12.5% to 18.2%.

A new record of odd-scaled snake (Serpentes, Xenodermidae) from Vietnam: expanded description of Parafimbrios vietnamensis based on integrative taxonomy

Based on the combination of molecular and morphological data, we herein report the second known finding of the xenodermid snake species Parafimbriosvietnamensis Ziegler, Ngo, Pham, Nguyen, Le & Nguyen, 2018. The male individual was found in the Yen Bai Province of northwestern Vietnam, more than 200 km from the type locality in Lai Chau Province. Genetic divergence between the newly-collected male and the holotype was low (1.7%), and is in agreement with morphological data that supports that they are conspecific. We give a detailed description of the morphological characters and coloration of the new record and provide an expanded diagnosis of P.vietnamensis. Parafimbrios is a poorly-understood genus, and our recent discovery brings the total number of known specimens of the genus to nine, 1/3 of them having been found in Vietnam (one specimen of P.lao and now two specimens of P.vietnamensis).

The Results of Four Recent Joint Expeditions to the Gobi Desert: Lacertids and Agamids

The National University of Mongolia, the Mongolian State University of Education, the University of Nebraska, and the University of Kansas conducted four collaborative expeditions between 2010 and 2014, resulting in accounts for all species of lacertid and agamid, except Phrynocephalus kulagini. These expeditions resulted in a range extension for Eremias arguta and the collection of specimens and tissues across 134 unique localities. In this paper we summarize the species of the Agamidae (Paralaudakia stoliczkana, Ph. hispidus, Ph. helioscopus, and Ph. versicolor) and Lacertidae (E. argus, E. arguta, E. dzungarica, E. multiocellata, E. przewalskii, and E. vermiculata) that were collected during these four expeditions. Further, we provide a summary of all species within these two families in Mongolia. Finally, we discuss issues of Wallacean and Linnaean shortfalls for the herpetofauna of the Mongolian Gobi Desert, and provide future directions for studies of community assemblages and population genetics of reptile species in the region.

Phylogenetic relationships and biogeographic range evolution in cat-eyed snakes, Boiga (Serpentes: Colubridae)

The genus Boiga includes 35, primarily arboreal snake species distributed from the Middle East to Australia and many islands in the western Pacific, with particularly high species diversity in South-East Asia. Despite including the iconic mangrove snakes (Boiga dendrophila complex) and the brown tree snake (Boiga irregularis; infamous for avian extinctions on small islands of the Pacific), species-level phylogenetic relationships and the biogeographic history of this ecologically and morphologically distinct clade are poorly understood. In this study, we sequenced mitochondrial and nuclear DNA for 24 Boiga species and used these data to estimate a robust phylogenetic inference, in order to (1) test the hypothesis that Boiga is monophyletic, (2) evaluate the validity of current species-level taxonomy and (3) examine whether geographic range evolution in Boiga is consistent with expectations concerning dispersal and colonization of vertebrates between continents and islands. Our results support the prevailing view that most dispersal events are downstream – from continents to oceanic islands – but we also identify a role for upstream dispersal from oceanic islands to continents. Additionally, the novel phylogeny of Boiga presented here is informative for updating species-level taxonomy within the genus.

New Record and Distribution of the Genus Goniurosaurus Barbour, 1908 (Eublapharidae, Sauria, Reptilia) in Vietnam

The paper described the distribution of the eublepharid lizards of the genus Goniurosaurus in Vietnam and a new first record of Goniurosaurus lichtenfelderi, which was made westwards of the Song Hong River.

An annotated type catalogue of amphibians and reptiles collected by Nikolay A. Zarudny in Iran and Middle Asia

A complete catalogue is provided for the type specimens of amphibians and reptiles collected by Nikolay A. Zarudny and stored mostly in the herpetological collection of the Zoological Institute, Russian Academy of Sciences, St. Petersburg, Russia (ZISP), as of August 2018. The collection contains 270 type specimens, representing 51 taxa (species and/or subspecies) of one family of turtles, one amphisbaenia family, five lizard families and four snake families from 74 type localities. As a result of studying Zarudny's collections, mainly from Iran, was the description by A. M. Nikolsky of two new genera, Microgecko and Diplometopon, and 42 species and subspecies (varieties). Twenty-two of these taxa are regarded currently as valid.

A molecular phylogenetic hypothesis for the Asian agamid lizard genus Phrynocephalus reveals discrete biogeographic clades implicated by plate tectonics

Phylogenetic relationships of the agamid lizard genus Phrynocephalus are described in the context of plate tectonics. A near comprehensive taxon sampling reports three data sets: (1) mitochondrial DNA from ND1 to COI (3' end of ND1, tRNAGln, tRNAIle, tRNAMet, ND2, tRNATrp, tRNAAla, tRNAAsn, tRNACys, tRNATyr, and the 5' end of COI) with 1761 aligned positional sites (1595 included, 839 informative), (2) nuclear RAG-1 DNA with 2760 aligned positional sites (342 informative), and (3) 25 informative allozyme loci with 213 alleles (107 informative when coded as presence/absence). It is hypothesized that Phrynocephalus phyletic patterns and speciation reflect fault lines of ancient plates now in Asia rejuvenated by the more recent Indian and Arabian plate collisions. Molecular estimates of lineage splits are highly congruent with geologic dates from the literature.  A southern origin for the genus in Southwest Asia is resolved in phylogenetic estimates and a northern origin is statistically rejected. On the basis of monophyly and molecular evidence several taxa previously recognized as subspecies are recognized as species: P. hongyuanensis, P. sogdianus, and P. strauchi as "Current Status"; Phrynocephalus bannikovi, Phrynocephalus longicaudatus, Phrynocephalus turcomanus, and Phrynocephalus vindumi are formally "New Status". Phylogenetic evaluation indicates a soft substrate habitat of sand for the shared ancestor of modern Phrynocephalus. Size diversity maximally overlaps in the Caspian Basin and northwestern Iranian Plateau. The greatest species numbers of six in sympatry and regional allopatry are found in the southern Caspian Basin and southern Helmand Basin, both from numerous phylogenetic lineages in close proximity attributed to tectonic induced events.

A Taxonomic Reevaluation of the Gekkonid Lizard Genus Teratoscincus in China

New collections of Teratoscincus from China and reexamination of type specimens in the Zoological Institute, St. Petersburg, Russia, reveal that T. roborowskii Bedriaga, «1905» (1906), is a valid species. The type locality given by Bedriaga is in error and is here corrected to the Turpan Depression, Xinjiang Uygur Autonomous Region, China where the species is endemic. Two additional species inhabit China, T. przewalskii (in the Taklimakan Desert, Hami Depression, Junggar Depression, and part of the Gobi Desert of Xinjiang Uygur Autonomous Region and adjacent provinces) and T. scincus (in the Ili River Valley of extreme western Xinjiang Uygur Autonomous Region).

SEM Study of Skin Sense Organs in Two <i>Uromastyx</i> Species (Sauria: Agamidae) and <i>Sphenodon punctatus</i> (Rhynchocephalia: Sphenodontidae)

External morphology and distribution of sense organs in the integument of Uromastyx assmussi and U. hardwickii and also of tuatara, Sphenodon punctatus were studied using SEM. Bristless skin organs in both species of Uromastyx and Sphenodon have large diameter (to 160 μm) and are few in the number (0 – 1 per scale) on cephalic and flank body scales. The reduction of sense organ number is discussed with respect of possible significance of this character in agamid system.

Phylogeny and divergence times of some racerunner lizards (Lacertidae: Eremias) inferred from mitochondrial 16S rRNA gene segments

Eremias, or racerunners, is a widespread lacertid genus occurring in China, Mongolia, Korea, Central Asia, Southwest Asia and Southeast Europe. It has been through a series of taxonomic revisions, but the phylogenetic relationships among the species and subgenera remain unclear. In this study, a frequently studied region of the mitochondrial 16S rRNA was used to (i) reassess the phylogenetic relationships of some Eremias species, (ii) test if the viviparous species form a monophyletic group, and (iii) estimate divergence time among lineages using a Bayesian relaxed molecular-clock approach. The resulting phylogeny supports monophyly of Eremias sensu Szczerbak and a clade comprising Eremias, Acanthodactylus and Latastia. An earlier finding demonstrating monophyly of the subgenus Pareremias is corroborated, with Eremias argus being the sister taxon to Eremias brenchleyi. We present the first evidence that viviparous species form a monophyletic group. In addition, Eremias przewalskii is nested within Eremias multiocellata, suggesting that the latter is likely a paraphyletic species or a species complex. Eremias acutirostris and Eremias persica form a clade that is closely related to the subgenus Pareremias. However, the subgenera Aspidorhinus, Scapteira, and Rhabderemias seem not to be monophyletic, respectively. The Bayesian divergence-time estimation suggests that Eremias originated at about 9.9 million years ago (with the 95% confidence interval ranging from 7.6 to 12 Ma), and diversified from Late Miocene to Pleistocene. Specifically, the divergence time of the subgenus Pareremias was dated to about 6.3 million years ago (with the 95% confidence interval ranging from 5.3 to 8.5 Ma), which suggests that the diversification of this subgenus might be correlated with the evolution of an East Asian monsoon climate triggered by the rapid uplift of the Tibetan Plateau approximately 8 Ma.

The impact of conservation on the status of the world's vertebrates

Using data for 25,780 species categorized on the International Union for Conservation of Nature Red List, we present an assessment of the status of the world's vertebrates. One-fifth of species are classified as Threatened, and we show that this figure is increasing: On average, 52 species of mammals, birds, and amphibians move one category closer to extinction each year. However, this overall pattern conceals the impact of conservation successes, and we show that the rate of deterioration would have been at least one-fifth again as much in the absence of these. Nonetheless, current conservation efforts remain insufficient to offset the main drivers of biodiversity loss in these groups: agricultural expansion, logging, overexploitation, and invasive alien species.

Historical biogeography, phylogenetic relationships and intraspecific diversity of agamid lizards in the Central Asian deserts of Kazakhstan and Uzbekistan

The Central Asian agamid lizards are ecologically and morphologically diverse, occurring across a broad range of desert environments in this biogeographically important region. It is probable that past climatic shifts have significantly influenced the diversification patterns and distributions of the agamid lizards of this region. To assess this within a phylogenetic framework we sequenced a approximately 1200 bp region of mitochondrial DNA and a approximately 1200 bp nuclear gene (RAG-1), incorporating both inter- and intraspecific sampling across Central Asian agamids. Our topology and divergence time estimates support an Eocene origin of the Agaminae subfamily on the Indian subcontinent, coinciding with the collision of India into Eurasia. The onset of aridification in Central Asia during the Late Oligocene, resulting from the retreat of the Paratethys Sea and the intensified uplift of the Tibetan-Himalayan complex, probably played an important role in the diversification of Phrynocephalus, one of the three genera studied. Intensification of aridity and geologic events in the Plio-Pleistocene and Quaternary glacial cycling probably had a significant influence on intraspecific diversification patterns within Phrynocephalus.

Assembly of the eastern North American herpetofauna: new evidence from lizards and frogs

Darwin first recognized the importance of episodic intercontinental dispersal in the establishment of worldwide biotic diversity. Faunal exchange across the Bering Land Bridge is a major example of such dispersal. Here, we demonstrate with mitochondrial DNA evidence that three independent dispersal events from Asia to North America are the source for almost all lizard taxa found in continental eastern North America. Two other dispersal events across Beringia account for observed diversity among North American ranid frogs, one of the most species-rich groups of frogs in eastern North America. The contribution of faunal elements from Asia via dispersal across Beringia is a dominant theme in the historical assembly of the eastern North American herpetofauna.

A phylogeny of Chinese species in the genus Phrynocephalus (Agamidae) inferred from mitochondrial DNA sequences

We investigated the phylogenetic relationships among most Chinese species of lizards in the genus Phrynocephalus (118 individuals collected from 56 populations of 14 well-defined species and several unidentified specimens) using four mitochondrial gene fragments (12S rRNA, 16S rRNA, cytochrome b, and ND4-tRNA(LEU)). The partition-homogeneity tests indicated that the combined dataset was homogeneous, and maximum-parsimony (MP), neighbor-joining (NJ), maximum-likelihood (ML) and Bayesian (BI) analyses were performed on this combined dataset (49 haplotypes including outgroups for 2058bp in total). The maximum-parsimony analysis resulted in 24 equally parsimonious trees, and their strict consensus tree shows that there are two major clades representing the Chinese Phrynocephalus species: the viviparous group (Clade A) and the oviparous group (Clade B). The trees derived from Bayesian, ML, and NJ analyses were topologically identical to the MP analysis except for the position of P. mystaceus. All analyses left the nodes for the oviparous group, the most basal clade within the oviparous group, and P. mystaceus unresolved. The phylogenies further suggest that the monophyly of the viviparous species may have resulted from vicariance, while recent dispersal may have been important in generating the pattern of variation among the oviparous species.

Evaluating trans-tethys migration: an example using acrodont lizard phylogenetics

A phylogenetic tree for acrodont lizards (Chamaeleonidae and Agamidae) is established based on 1434 bases (1041 informative) of aligned DNA positions from a 1685-1778 base pair region of the mitochondrial genome. Sequences from three protein-coding genes (ND1, ND2, and COI) are combined with sequences from eight intervening tRNA genes for samples of 70 acrodont taxa and two outgroups. Parsimony analysis of nucleotide sequences identifies eight major clades in the Acrodonta. Most agamid lizards are placed into three distinct clades. One clade is composed of all taxa occurring in Australia and New Guinea; Physignathus cocincinus from Southeast Asia is the sister taxon to the Australia-New Guinea clade. A second clade is composed of taxa occurring from Tibet and the Indian Subcontinent east through South and East Asia. A third clade is composed of taxa occurring from Africa east through Arabia and West Asia to Tibet and the Indian Subcontinent. These three clades contain all agamid lizards except Uromastyx, Leiolepis, and Hydrosaurus, which represent three additional clades of the Agamidae. The Chamaeleonidae forms another clade weakly supported as the sister taxon to the Agamidae. All eight clades of the Acrodonta contain members occurring on land masses derived from Gondwanaland. A hypothesis of agamid lizards rafting with Gondwanan plates is examined statistically. This hypothesis suggests that the African/West Asian clade is of African or Indian origin, and the South Asian clade is either of Indian or Southeast Asian origin. The shortest tree suggests a possible African origin for the former and an Indian origin for the latter, but this result is not statistically robust. The Australia-New Guinea clade rafted with the Australia-New Guinea plate and forms the sister group to a Southeast Asian taxon that occurs on plates that broke from northern Australia-New Guinea. Other acrodont taxa are inferred to be associated with the plates of Afro-Arabia and Madagascar (Chameleonidae), India (Uromastyx), or southeast Asia (Hydrosaurus and Leiolepis). Introduction of different biotic elements to Asia by way of separate Gondwanan plates may be a major theme of Asian biogeography. Three historical events may be responsible for the sharp faunal barrier between Southeast Asia and Australia-New Guinea, known as Wallace's line: (1) primary vicariance caused by plate separations; (2) secondary contact of Southeast Asian plates with Eurasia, leading to dispersal from Eurasia into Southeast Asia, and (3) dispersal of the Indian fauna (after collision of that subcontinent) to Southeast Asia. Acrodont lizards show the first and third of these biogeographic patterns and anguid lizards exhibit the second pattern. Modern faunal diversity may be influenced primarily by historical events such as tectonic collisions and land bridge connections, which are expected to promote episodic turnover of continental faunas by introducing new faunal elements into an area. Repeated tectonic collisions may be one of the most important phenomena promoting continental biodiversity. Phylogenetics is a powerful method for investigating these processes.

Vicariant patterns of fragmentation among gekkonid lizards of the genus Teratoscincus produced by the Indian collision: A molecular phylogenetic perspective and an area cladogram for Central Asia

A well-supported phylogenetic hypothesis is presented for gekkonid lizards of the genus Teratoscincus. Phylogenetic relationships of four of the five species are investigated using 1733 aligned bases of mitochondrial DNA sequence from the genes encoding ND1 (subunit one of NADH dehydrogenase), tRNA(Ile), tRNA(Gln), tRNA(Met), ND2, tRNA(Trp), tRNA(Ala), tRNA(Asn), tRNA(Cys), tRNA(Tyr), and COI (subunit I of cytochrome c oxidase). A single most parsimonious tree depicts T. przewalskii and T. roborowskii as a monophyletic group, with T. scincus as their sister taxon and T. microlepis as the sister taxon to the clade containing the first three species. The aligned sequences contain 341 phylogenetically informative characters. Each node is supported by a bootstrap value of 100% and the shortest suboptimal tree requires 29 additional steps. Allozymic variation is presented for proteins encoded by 19 loci but these data are largely uninformative phylogenetically. Teratoscincus species occur on tectonic plates of Gondwanan origin that were compressed by the impinging Indian Subcontinent, resulting in massive montane uplifting along plate boundaries. Taxa occurring in China (Tarim Block) form a monophyletic group showing vicariant separation from taxa in former Soviet Central Asia and northern Afghanistan (Farah Block); alternative biogeographic hypotheses are statistically rejected. This vicariant event involved the rise of the Tien Shan-Pamir and is well dated to 10 million years before present. Using this date for separation of taxa occurring on opposite sides of the Tien Shan-Pamir, an evolutionary rate of 0.57% divergence per lineage per million years is calculated. This rate is similar to estimates derived from fish, bufonid frogs, and agamid lizards for the same region of the mitochondrial genome ( approximately 0.65% divergence per lineage per million years). Evolutionary divergence of the mitochondrial genome has a surprisingly stable rate across vertebrates.

Phylogenetic relationships among Agamid lizards of the Laudakia caucasia species group: testing hypotheses of biogeographic fragmentation and an area cladogram for the Iranian Plateau

Phylogenetic relationships within the Laudakia caucasia species group on the Iranian Plateau were investigated using 1708 aligned bases of mitochondrial DNA sequence from the genes encoding ND1 (subunit one of NADH dehydrogenase), tRNAGln, tRNAIle, tRNAMet, ND2, tRNATrp, tRNAAla, tRNAAsn, tRNACys, tRNATyr, and COI (subunit I of cytochrome c oxidase). The aligned sequences contain 207 phylogenetically informative characters. Three hypotheses for historical fragmentation of Laudakia populations on the Iranian Plateau were tested. In two hypotheses, fragmentation of populations is suggested to have proceeded along continuous mountain belts that surround the Iranian Plateau. In another hypothesis, fragmentation is suggested to have resulted from a north-south split caused by uplifting of the Zagros Mountains in the late Miocene or early Pliocene [5-10 MYBP (million years before present)]. The shortest tree suggest the later hypothesis, and statistical tests reject the other two hypothesis. The phylogenetic tree is exceptional in that every branch is well supported. Geologic history provides dates for most branches of the tree. A plot of DNA substitutions against dates from geologic history refines the date for the north-south split across the Iranian Plateau to 9 MYBP (late Miocene). The rate of evolution for this segment of mtDNA is 0.65% (0.61-0.70%) change per lineage per million years. A hypothesis of area relationships for the biota of the Iranian Plateau is generated from the phylogenetic tree.

Evolutionary shifts in three major structural features of the mitochondrial genome among iguanian lizards

A phylogenetic tree for major lineages of iguanian lizards is estimated from 1,488 aligned base positions (858 informative) of newly reported mitochondrial DNA sequences representing coding regions for eight tRNAs, ND2, and portions of ND1 and COI. Two well-supported groups are defined, the Acrodonta and the Iguanidae (sensu lato). This phylogenetic hypothesis is used to investigate evolutionary shifts in mitochondrial gene order, origin for light-strand replication, and secondary structure of tRNACys. These three characters shift together on the branch leading to acrodont lizards. Plate tectonics and the fossil record indicate that these characters changed in the Jurassic. We propose that changes to the secondary structure of tRNACys may destroy function of the origin for light-strand replication which, in turn, may facilitate shifts in gene order.

Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome

Two novel mitochondrial gene arrangements are identified in an agamid lizard and a ranid frog. Statistical tests incorporating phylogeny indicate a link between novel vertebrate mitochondrial gene orders and movement of the origin of light-strand replication. A mechanism involving errors in light-strand replication and tandem duplication of genes is proposed for rearrangement of vertebrate mitochondrial genes. A second mechanism involving small direct repeats also is identified. These mechanisms implicate gene order as a reliable phylogenetic character. Shifts in gene order define major lineages without evidence of parallelism or reversal. The loss of the origin of light-strand replication from its typical vertebrate position evolves in parallel and, therefore, is a less reliable phylogenetic character. Gene junctions also evolve in parallel. Sequencing across multigenic regions, in particular transfer RNA genes, should be a major focus of future systematic studies to locate novel gene orders and to provide a better understanding of the evolution of the vertebrate mitochondrial genome.

Replication slippage may cause parallel evolution in the secondary structures of mitochondrial transfer RNAs

Presence of the dihydrouridine (D) stem in the mitochondrial cysteine tRNA is unusually variable among lepidosaurian reptiles. Phylogenetic and comparative analyses of cysteine tRNA gene sequences identify eight parallel losses of the D-stem, resulting in D-arm replacement loops. Sampling within the monophyletic Acrodonta provides no evidence for reversal. Slipped-strand mispairing of noncontiguous repeated sequences during replication or direct replication slippage can explain repeats observed within cysteine tRNAs that contain a D-arm replacement loop. These two mechanisms involving replication slippage can account for the loss of the cysteine tRNA D-stem in several lepidosaurian lineages, and may represent general mechanisms by which the secondary structures of mitochondrial tRNAs are altered.