We hypothesize the phylogenetic relationships of the agamid genusPhrynocephalusto assess how past environmental changes shaped the evolutionary and biogeographic history of these lizards and especially the impact of paleogeography and climatic factors.Phrynocephalusis one of the most diverse and taxonomically confusing lizard genera. As a key element of Palearctic deserts, it serves as a promising model for studies of historical biogeography and formation of arid habitats in Eurasia. We used 51 samples representing 33 of 40 recognized species ofPhrynocephaluscovering all major areas of the genus. Molecular data included four mtDNA (COI,ND2,ND4,Cytb; 2,703 bp) and four nuDNA protein-coding genes (RAG1,BDNF,AKAP9,NKTR; 4,188 bp). AU-tests were implemented to test for significant differences between mtDNA- and nuDNA-based topologies. A time-calibrated phylogeny was estimated using a Bayesian relaxed molecular clock with nine fossil calibrations. We reconstructed the ancestral area of origin, biogeographic scenarios, body size, and the evolution of habitat preference. Phylogenetic analyses of nuDNA genes recovered a well-resolved and supported topology. Analyses detected significant discordance with the less-supported mtDNA genealogy. The position ofPhrynocephalus mystaceusconflicted greatly between the two datasets. MtDNA introgression due to ancient hybridization best explained this result. MonophyleticPhrynocephaluscontained three main clades: (I) oviparous species from south-western and Middle Asia; (II) viviparous species of Qinghai–Tibetan Plateau (QTP); and (III) oviparous species of the Caspian Basin, Middle and Central Asia.Phrynocephalusoriginated in late Oligocene (26.9 Ma) and modern species diversified during the middle Miocene (14.8–13.5 Ma). The reconstruction of ancestral areas indicated thatPhrynocephalusoriginated in Middle East–southern Middle Asia. Body size miniaturization likely occurred early in the history ofPhrynocephalus. The common ancestor ofPhrynocephalusprobably preferred sandy substrates with the inclusion of clay or gravel. The time of Agaminae radiation and origin ofPhrynocephalusin the late Oligocene significantly precedes the landbridge between Afro-Arabia and Eurasia in the Early Miocene. Diversification ofPhrynocephaluscoincides well with the mid-Miocene climatic transition when a rapid cooling of climate drove progressing aridification and the Paratethys salinity crisis. These factors likely triggered the spreading of desert habitats in Central Eurasia, whichPhrynocephalusoccupied. The origin of the viviparous Tibetan clade has been associated traditionally with uplifting of the QTP; however, further studies are needed to confirm this. Progressing late Miocene aridification, the decrease of the Paratethys Basin, orogenesis, and Plio–Pleistocene climate oscillations likely promoted further diversification withinPhrynocephalus. We discussPhrynocephalustaxonomy in scope of the new analyses.

We provide a diversity assessment of the agamid genus Phrynocephalus Kaup, 1825. We analyze COI mtDNA barcodes from 385 individuals sampled all over Phrynocephalus range. We apply the ABGD, ASAP, bGMYC, mlPTP and hsPTP species delimitation algorithms to analyze the COI gene fragment variation and assess the species diversity in Phrynocephalus. Nine species groups are revealed in Phrynocephalus in agreement with earlier studies on the phylogenetic relationships of the genus. We demonstrate that the present taxonomy likely underestimates the actual diversity of the genus. Alternative species delimitation algorithms provide a confusingly wide range of possible number of Phrynocephalus species—from 54 to 103 MOTUs (molecular operational taxonomic units). The ASAP species delimitation scheme recognizing 63 MOTUs likely most closely fits the currently recognized taxonomic framework of Phrynocephalus. We also report on 13 previously unknown Phrynocephalus lineages as unverified candidate species. We demonstrate that the ASAP and the ABGD algorithms likely most closely reflect the actual diversity of Phrynocephalus, while the mlPTP and hsPTP largely overestimate it. We argue that species delimitation in these lizards based exclusively on mtDNA markers is insufficient, and call for further integrative taxonomic studies joining the data from morphology, mtDNA and nuDNA markers to fully stabilize the taxonomy of Phrynocephalus lizards.

In the first half of the 20th century, four Swedish expeditions to Indochina contributed significantly to the knowledge on the herpetofauna of mainland Southeast Asia. The collected material was examined by L. G. Andersson in Stockholm, resulting in the description of seven new species and forms of amphibians and reptiles from Vietnam and Thailand. However, the taxonomic status of three enigmatic frog species described by Andersson, namely Rana scutigera, Oxyglossus laevis var. vittata, and Microhyla fusca, remained doubtful. All three taxa are only known from their type specimens and their short original descriptions. Though subsequent studies have doubted their validity or systematic assignment, they have been treated as valid species until today. We have examined the external morphology and coloration of the type specimens, what led to a taxonomic reallocation of these three species. We demonstrate that Rana scutigera Andersson, 1916 is a junior synonym of Polypedates megacephalus Hallowell, 1861, Oxyglossus laevis var. vittata Andersson, 1942 is synonymized with Occidozyga martensii (Peters, 1967), and Microhyla fusca Andersson, 1942 represents a junior synonym of Microhyla butleri Boulenger, 1900.

Lizards of the sunwatcher toad-headed agama species complex Phrynocephalus superspecies helioscopus, mostly distributed in Central Asia and Middle East, were examined using analysis of variation at the mitochondrial cytochrome oxidase c subunit I gene fragment and fingerprint analysis of nuclear DNA (inter-SINE PCR technique). A total of 86 individual tissue samples from 53 populations, to the full extent representing different parts of the species complex range, were subjected to molecular genetic examination, and surprisingly deep differentiation was revealed. The populations analyzed split into 12 isolated phylogroups, many of which were characterized by a narrow range and genetic isolation. Monophyly of sunwatcher (Ph. helioscopus) and Persian (Ph. persicus) toad-headed agamas was confirmed. However, both of these species probably represent the species complexes. Zoogeography of Central Asiais discussed.

There are evidences that the genus Pipistrellus (true pipistrelles) in its current understanding may be paraphyletic. We have studied for the first time the phylogenetic relationships between the majority of supraspecific taxa of the subtribe Pipistrellina based on the analysis of the sequences of three nuclear genes (RAG2, APOB, and DMP1). Our data support the monophyly of the subtribe itself, but definitely show that the genus Pipistrellus in the modern sense is paraphyletic with respect to noctules, Nyctalus, and thick thumb pipistrelles, Glischropus (which both are morphologically distinct taxa). Moreover, noctules are extremely close to the “western” clade of Pipistrellus. The latter genus should probably be divided into two or more separate genera, or Nyctalus and Glischropus should be treated as its subgenera.