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Climate change has essential effects on patterns of population persistence, connectivity, and divergence. We used mtDNA sequences and species distribution modeling to assess the impact of climatic changes in the past (Last Glacial Maximum [LGM: 21 Kya] and Mid-Holocene [6 Kya]), recent (1970–2000), and future (2070) on the phylogeography and spatial distribution of populations of the Hyrcanian wood frog, Rana pseudodalmatina, in northern Iran. Based on two mitochondrial genes (cytochrome b and 16S ribosomal RNA), we found evidence for two regional patterns that diverged in the Pleistocene (1.6 Mya) and are distributed in the eastern and western sections of the current species range. Biogeographic analyses support the hypothesis that both vicariance (an increase in the Caspian Sea water levels) and dispersal events have been involved in shaping the species' genetic structure. Reconstruction of the ancestral distribution of R. pseudodalmatina suggests the species' range contracted in two independent eastern and western glacial refugia during the LGM, expanding from the Mid-Holocene to the present to occupy Hyrcanian forests continuously. According to future climate projections, the species' range shows a tendency to shift to higher altitudes. Landscape connectivity analyses support higher population continuity in the central part of the current range, with isolated populations in the easternmost and westernmost extremes. Our integrative study of R. pseudodalmatina provides support for the “refugia-within-refugia” scenario in the Hyrcanian forests.

We investigated the phylogeographic structure of the genus Saara and studied whether the Zagros Mountain ranges influence the gene flow and dispersal at the landscape scale between the Iranian Saara species, including S. asmussi in the central Iranian plateau and S. loricata in the Mesopotamian lowlands. Phylogenetic analyses clearly show three well-supported species, including S. loricata, S. asmussi and S. hardwickii, that are distinct from Uromastyx species. The S-DIVA and BBM analyses demonstrate that species of Saara originated from an ancestor somewhere in the Iranian Plateau and then dispersed to its current geographical range. Our results indicate that the separation of S. loricata from S. asmussi coincides with the orogenic events of the Zagros Mountains during the Pliocene, and thus it may show a vicariance event. Diversification within populations of S. loricata and S. assmussi are estimated to have occurred during the Pleistocene. The haplotype network indicates one haplogroup for each of the Iranian Saara species. Population genetic analyses shows signals of demographic expansions at the beginning of the Holocene for S. loricata. Our results support the hypothesis that the Zagros Mountains act as a barrier for gene flow and Quaternary climatic oscillations affected intraspecific genetic divergences of S. loricata and S. asmussi.

The Persian squirrel (Sciurus anomalus) is limited to the Irano-Anatolian region of western Asia. The evolutionary history and phylogenetic status of the Persian squirrel are ambiguous. Here, we present a molecular phylogeny using mitochondrial and nuclear genes (D-loop noncoding region, Cyt b, COI, Cmyc, and Rag1) for S. anomalus and other Sciurus species. Our analyses revealed three major clades comprising (i) Sciurus species in North America, (ii) Sciurus vulgaris and Sciurus lis in Eurasia and (iii) S. anomalus in western Asia. For mitochondrial and nuclear genes, uncorrected genetic distances between S. anomalus and each of the two other clades were similar. We conclude that the divergence of S. anomalus from the ancestor of New World species occurred on the Eurasian continent during the Miocene period 10 Mya (HPD: 11-8 Mya), with the ancestral New World species then moving from Eurasia through Beringia to North America. During the Pleistocene period S. anomalus gradually became widespread in association with prevalent woodlands throughout the Irano-Anatolian terrain and the eastern coast of the Mediterranean Sea. Today we find this species in fragmented forests in and around the Mediterranean Sea, Anatolia (Turkey) and in the Zagros Mountains (western Iran).

Paradactylodon, a genus of Hynobiidae, is distributed in mountainous regions of the Middle East. This genus comprises three species, Paradactylodon mustersi (Afghanistan), Paradactylodon persicus, and Paradactylodon gorganensis (Iran). Initially, P. persicus was reported from Talysh Mountains, and afterward, P. gorganensis was described from the eastern Alborz Mountains. Although these two Iranian Paradactylodon species were distinguished based on morphological features, there are arguments about their systematic status. In this contribution, 30 samples of hynobiid salamanders were collected from Talysh and Alborz Mountains and the phylogenetic relationship between the two species was assessed using two mtDNA markers (COI and 16S). Additionally, in order to survey the potential habitat suitability for the species, Species Distribution Models (SDMs) were performed and projected on climate scenarios that reflect current and past (6 ky and 21 ky before present) conditions. Our results indicated that P. gorganensis is nested within P. persicus. Overall, both SDM and molecular analyses suggest that the Iranian Paradactylodon population was affected by the Quaternary glacial period, and according to haplotype networks, haplotype diversity was higher in the western part of the distribution range of the species. Given the low genetic distance among all samples, we suggest P. gorganensis be synonymized with P. persicus. Considering the conservational values and numerous threats that this endemic species is facing, we encourage a revision of the IUCN Red List category of the species immediately.

We describe a new species of Lacertid lizard of the genus Eremias from the border of the northeastern side of Markazi Province to the western side of Tehran Province in Iran. Eremias fahimii sp. nov. is part of the Eremias subgenus (or morphotype) by virtue of lacking lateral fringes on the fourth toe, having movable eyelids, a lower nasal shield that rests on two supralabials, and ventral plates arranged in oblique longitudinal rows. It can be further differentiated from previously described species assigned to this morphotype by the absence of distinctly keeled upper caudal scales, gular scales that do not extend to the second inframaxiallary scales, shape and relative size of frontoparietals, parietal and parietals, scale counts and absence of lateral color ocellus. In addition, the molecular phylogeny of the most common Iranian racerunners including Eremias fahimii sp. nov. was studied using mitochondrial Cytochrome b (Cyt b) and 12S ribosomal RNA (12S) genes. Our results support the validation of the new species which depicts a sister group relationship to E. persica. Of the 20 species of Eremias known from Iran, E. fahimii sp. nov. is the seventh endemic species along with E. andersoni, E. isfahanica, E. lalezharica, E. kavirensis, E. montana and E. papenfussi. Despite the fact that up to now E. fahimii sp. nov. is only known from the type locality, it is highly probable that it also occurs in Tehran, Alborz, Qom, Qazvin and Zanjan Provinces due to topological characteristics and habitat similarities in these areas.

The molluscan fauna of the Persian Gulf has recently been relatively well documented, yet there are few records of heterobranch sea slugs (opisthobranchs) from the Arabian parts and no report from the Iranian waters. Here we report for the first time the occurrence of one of these molluscs in the northern Persian Gulf (Bandar Abbas, Iran). Sacoglossan specimens were collected in association with the seaweed, Caulerpa sertularioides. Since morphological attributes were not adequately reliable for species identification, molecular approaches were carried out. Maximum-likelihood and Bayesian Inference analysis of partial DNA sequences of the mitochondrial cytochrome c oxidase subunit I (COI) locus were used for DNA barcoding of large-bodied specimens of Elysia. All Persian Gulf specimens were genetically confirmed as Elysia cf. tomentosa sp. 5, one of at least five morphologically similar but genetically distinct species in the taxonomically challenging and unresolved E. tomentosa complex. This species has previously been recorded only from Australia and Thailand and our finding adds another distant point to the geographic distribution of this species.

The Iranian Plateau is an area of highly complex landscape and incredibly diverse habitats, from salt deserts to temperate forests. Such a heterogeneous environment, at the crossroads of Asia, Europe, and Africa, fuels the high diversity and uniqueness of the Iranian fauna and flora. Nevertheless, our understanding of the historical processes that shaped the Iranian biodiversity remains limited. In this context, we revisit the evolutionary history of the two most widespread lizard species on the Iranian Plateau (Eremias persica and Mesalina watsonana) to explore whether these two taxa of similar ecology have been subjected to similar historical processes. To achieve that, we performed a series of phylogenetic analyses and thoroughly tested all possible alternative topologies based on available mitochondrial sequences (cytochrome b and 12S ribosomal RNA). Additionally, we estimated the number of mitochondrial clusters based on a novel single-locus delimitation method and the time of their divergence, using recently inferred evolutionary rates for lacertid species. The results indicate that the two taxa have been shaped by similar physiographic and climatic barriers since both phylogenies split into similar geographical clusters. However, E. persica has twice as long evolutionary time on the Iranian Plateau than M. watsonana. The first divergence of E. persica was estimated in the Middle Miocene (∼13 Mya), at the time of the major uplift of the Zagros mountain range. The Upper Miocene tectonic rearrangement that resulted in the uplift of the Alborz mountains coincides with the original split in M. watsonana (∼6.6 Mya) and several contemporaneous splits within E. persica.

The meadow lizard Darevskia praticola (Eversmann, 1834) displays a wide distribution range from the Western Balkans and Caucasus to the Hyrcanian forest in Iran. Based on previous studies, four subspecies have been described (D. p. praticola, D. p. pontica, D. p. hyrcanica and D. p. loriensis), but molecular evidence suggests two main phylogenetic lineages, Balkan and Caucasus. In this study we incorporated geographic records and analysed new samples from Alborz Mountains (Gilan Province, Iran), exploring their phylogenetic affinities using two mitochondrial markers (Cyt b and ND4). For the first time, Iranian samples are included in a molecular phylogeny. Our results meet the previous suggestions regarding the presence of a nuclear mitochondrial DNA fragment (numt) in Cyt b, causing misleading phylogenetic inferences since it renders the species paraphyletic. In contrast, the ND4 genealogy groups the species into a monophyletic clade, as expected. Samples attributed to D. p. hyrcanica (Azerbaijan and Iran) and D. p. loriensis (Armenia) are settled in a single clade with minute genetic distance, suggesting synonymisation.

The barnacle Amphibalanus eburneus (Gould, 1841), native to the northwest Atlantic Ocean, became nearly cosmopolitan due to extensive shipping activities. In the Caspian Sea, A. eburneus have been reported solely from Azerbaijan and Turkmenistan. The current study provides robust evidence of its occurrence in Iran. We observed that the previously vacant niche on the hard substrates bordering a shrimp farm in Gomishan Wetland, southern Caspian Sea, is now occupied by A. eburneus. The identity of the species was confirmed by both morphological and molecular approaches. Massive development of this (previously thought) brackish species in saline waters (33–57 psu) of the Gomishan Wetland demonstrates the high invasion potential of the species. Although it seems that this introduction has had no impact so far, it can be projected that the entire coastline of the southern Caspian Sea might be colonized by A. eburneus, which may outcompete the native fauna of the area in the future.

We report on a Euphrates softshell turtle (Rafetus euphraticus) nest and hatchlings that emerged from the nest that was constructed in a sand patch of the Dez River in southwestern Iran and discovered on 8 July 2012. Information on nest location and structure and hatchling morphology is presented.

A variety of different methods are available for investigating the effects of past climate fluctuation on biota. Among them, molecular phylogeography and species distribution modeling approaches have been shown to be especially useful tools to trace past climate induced modifications of species’ geographic distributions. The results of both analytical approaches are here combined to better understand the influences of past climate changes on the fragmented distribution pattern of the lizard genus Iranolacerta that currently occurs in the northwest and central Zagros Mountains of Iran. While Iranolacerta zagrosica is restricted to few localities and cannot be modeled, the potential distribution of Iranolacerta brandtii suggested a large region of unfavorable habitat between northwest and the central Zagros Mountains populations. From the phylogenetic perspective, both species display deep genetic separation likely predating the Pleistocene. However, limited genetic diversity across this divided range of I. brandtii implies that the current separation is recent. Deeper genetic divergences were, nevertheless, uncovered within the northwest population. Since no recent geological events explain these results, the most likely explanation for such a distribution pattern is due to past climate fluctuations. Both sources of evidence suggest that during the early Holocene the northwest and Zagros populations of I. brandtii were connected, and the current pattern was shaped with their disconnection in the early Holocene. Further studies may identify potential glacial refugia for other species in this biodiverse region.

Global warming is expected to cause several modifications to physical environments, and sea level rise is a certain outcome. However, assessment of the potential impacts caused by sea level rise on biodiversity is still emerging. Therefore, we assessed the combined impact of global warming and sea level rise on the potential distribution of 19 coastal lowland anurans in the biodiversity hotspot Atlantic Forest. We applied a correlative species distribution model (SDM) (BIOCLIM) and GIS-based spatial analyses. We evaluated the extent of changes of potential distributions under extreme and moderate global warming scenarios as well as two extreme sea level rise scenarios. Our results suggest wide areas of suitable habitat for most species in the future. However, for 15% of these species the SDMs predict massive losses of range extent as a result of a combination of global warming and sea level rise. Such observations highlight an immediate need to consider the potential effects of sea level rise in conservation action plans. Since the current potential distribution of these anuran species is likely underestimated, we also analyzed their environmental niche under current conditions in order to provide a baseline for further field surveys. Considering this current state of knowledge for such species, species distribution modeling to help gather further information on unknown species is desirable.

Timon, a small genus of lacertid lizards, includes four species distributed in two separate ranges in the western and eastern part of the Mediterranean Basin. Phylogenetic relationships between the two groups have not been resolved, and the taxonomic situation of the two subspecies of the eastern representative of the genus, Timon princeps, is not clear. To address these questions, partial DNA sequences of two nuclear (β-fibrinogen intron 7 and C-mos) and three mitochondrial (cytochrome b, 12S rRNA and 16S rRNA) genes were analyzed. Based on the high genetic distance between the two subspecies of T. princeps we promote their taxonomic status to full species, Timon princeps and Timon kurdistanicus. Divergence time estimates based on other lacertid species suggest that the separation of the green (Lacerta) and ocellated (Timon) lizards took place around 12 My ago, and that the Eastern group underwent speciation around 4-5 my ago, perhaps associated with the uplifting of the Zagros mountains. As expected given this ancient divergence and complex paleogeography, considerable levels of genetic diversity are recovered within both taxa, with geographically close individuals showing very divergent haplotypes.

One new Asaccus from the Anatolian plateau and three new Asaccus from the Iranian plateau are described as follows. (1) Asaccus barani sp. nov.: diagnosed by strongly heterogeneous dorsal tubercles; (2) Asaccus iranicus sp. nov.: diagnosed by small body size and digits (forelimbs) parallel joint to palm; (3) Asaccus tangestanensis sp. nov.: by having enlarged trihedral tubercles all over the dorsal body; (4) Asaccus zagrosicus sp. nov.: secondary postmentals are not in contact with lowerlabials (100% of specimens). Other important data on the new Asaccus are given in detail in the text.

In order to determine population variation in the Caspian Bent-toed Gecko, Cyrtopodion caspium, nine morphometric, six meristic and four ratios were assessed in 48 adult males from three populations in the northern part of Iran (Moghan Steppe, Damghan and Sari). The Moghan population proved to be the largest in most characters compared to the Damghan and Sari populations. Principal Components Analysis (PCA) discriminated the Moghan population in the northwest of Iran from the other two populations. Although all populations occupy different habitats, the lack of significant differences between two geographically close populations (Sari and Damghan) shows that habitat type on the larger scale is not the reason for separation. So it is inferred that the geographic isolation of the Moghan population and reduced gene flow are responsible for the incipient speciation occurring between these populations.

The Persian Lizard, Iranolacerta brandtii, was until recently considered to be restricted to north-western Iran (Azerbaijan and Esfahan provinces). However, two recent studies have revealed the existence of populations in Eastern Anatolia, extending the range of this species for about 230 km westwards. The fragmented distribution of this species has been considered to be a consequence of the climatic oscillations during the Pleistocene and Holocene, which created events of alternating contact and isolation of populations in distinct glacial refugia. According to our obtained genealogy derived from three mitochondrial fragments (12S rRNA, 16S rRNA and cytb), the Turkish specimens cluster together but form an independent clade, sister to the individuals from Tabriz in Iran. The separation of these two clades is concurrent with the cladogenesis between the Esfahan and Ardabil clades, estimated to have taken place during the late Holocene.

We describe a new species of the genus Cyrtopodion from the coastal area of Bushehr Province in southern Iran based on morphometric and pholidotic data. Cyrtopodion kiabii sp. nov. belongs to the agamuroides-group and the key characters to distinguish this species from all other members of the group are the lower number of ventrals and the extremely slender habitus with long and delicate legs. Resulting from pholidosis, the observed presence of sexual dimorphism, and distribution we suggest a close relationship with C. gastropholis, which is also reviewed herein.

A molecular phylogeny of the sphaerodactylid geckos of the genus Pristurus is inferred based on an alignment of 1845 base pairs (bp) of concatenated mitochondrial (12S) and nuclear (acm4, cmos, rag1 and rag2) genes for 80 individuals, representing 18 of the 23–26 species, and the three subspecies of P. rupestris. The results indicate that P. rupestris is polyphyletic and includes two highly divergent clades: the eastern clade, found in coastal Iran and throughout the Hajar Mountain range in northern Oman and eastern UAE; and the western clade, distributed from central coastal Oman, through Yemen, Saudi Arabia and north to southern Jordan. Inferred haplotype networks for the four nuclear genes show that the eastern and western clades of “P. rupestris” are highly differentiated and do not share any alleles. Moreover, although the two clades are differentiated by a morphological multivariate analysis, no one character or set of characters was found to be diagnostic. Based on the molecular analysis of specimens from the type locality of P. rupestris rupestris, the name P. rupestris is applied to the eastern clade. The name that should apply to the western clade cannot be clarified until morphological and genetic data for “P. rupestris” is available from the vicinity of Bosaso, Somalia, and therefore we refer to it as Pristurus sp. 1. The phylogenetic tree of Pristurus supports the hypothesis that P. celerrimus is sister to all the other species in the analyses and that the Socotra Archipelago was independently colonized a minimum of two times.

The genus Tropiocolotes comprises small, naked toed, ground dwelling and nocturnal desert geckos, ranging from Morocco and Mauritania in northern Africa to south and central Arabia as well as coastal Iran. Herein, we describe a new species of the genus Tropiocolotes from western Iran based on five specimens from Nayband region. This new taxon is described with a statistical approach based on 34 meristic, metric and qualitative morphological characters of more than 300 individuals of related species.

We describe a new species of Eremias lacertid from the Alborz Mountain range in northern Iran (Tehran Province). Eremias papenfussi n. sp. is part of the Eremias subgenus (or morphotype) by virtue of lacking lateral fringes on the fourth toe and color pattern. It can be further differentiated from previously described species assigned to this morphotype by the absence of distinctly keeled upper caudal scales, gular scales that do not extend to the second inframaxiallary scales, color pattern, and scale counts. Eremias papenfussi is found on rocky mountain slopes of the Alborz where it is presumed to have a much broader distribution than demonstrated by the available specimens. Of the 15 species of Eremias known from Iran, E. papenfussi is the fifth species known to inhabit rocky mountain slopes along with E. strauchi, E. lalezharica, E. montanus and E. novo.