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While traditionally species recognition has been based solely on morphological differences either typological or quantitative, several newly developed methods can be used for a more objective and integrative approach on species delimitation. This may be especially relevant when dealing with cryptic species or species complexes, where high overallresemblance between species is coupled with comparatively high morphological variation within populations. Rock lizards, genus Darevskia, are such an example, as many of its members offer few diagnostic morphological features. Herein, we use a combination of genetic, morphological and ecological criteria to delimit cryptic species within two species complexes, D. chlorogaster and D. defilippii, both distributed in northern Iran. Our analyses are based on molecular information from two nuclear and two mitochondrial genes, morphological data (15 morphometric, 16 meristic and four categorical characters) and eleven newly calculated spatial environmental predictors. The phylogeny inferred for Darevskia confirmed monophyly of each species complex, with each of them comprising several highly divergent clades, especially when compared to other congeners. We identified seven candidate species within each complex, of which three and four species were supported by Bayesian species delimitation within D. chlorogaster and D. defilippii, respectively. Trained with genetically determined clades, Ecological Niche Modeling provided additional support for these cryptic species. Especially those within the D. defilippii-complex exhibit well-differentiated niches. Due to overall morphological resemblance, in a first approach PCA with mixed variables only showed the separation between the two complexes. However, MANCOVA and subsequent Discriminant Analysis performed separately for both complexes allowed for distinction of the species when sample size was large enough, namely within the D. chlorogaster-complex. In conclusion, the results support four new species, which are described herein.

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Considering all costs associated to sex, sexual reproduction could be expected to be rare. However, we find sexual reproduction to be pervasive in nature, and only a reduced number of taxa are completely asexual. In fact, the variety of sex reproductive systems, mating techniques and traits, reveals that the organisms’ reproduction has been an expressive target of selection and adaptation throughout evolution. Sex is selected because it facilitates adaptation in complex and changing environments (Weismann, 1889), and this has been already shown empirically in several models. However, studies and theories developed concerning the paradox of sex will not be able to clarify the current distribution and abundance of asexual lineages in nature. The understanding of rates of origin and extinction of asexual lineages, together with the putative differential evolution rates in organisms with sexual or asexual reproduction, should be considered in the main “origin of sex” question. The model used here, the genus Darevskia, is the first true parthenogenetic vertebrate described. It is a highly speciose genus, currently including 27 species, of which seven are parthenogenetic and of hybrid origin. Only a few of the sexual species contributed for the hybridization events which originated the parthenogens clonal lineages, and these were directional: the maternal species were always Darevskia raddei or D. mixta, and the paternal always D. valentini or D. portshinskii. Using a set of microsatellite and mtDNA markers, we first start to study the role of hybridization in the origin of vertebrate parthenogens, the extent of gene flow with sexual relatives and the relation between hybridization, asexuality and polyploidy, in the context of the main theories of asexual evolution proposed to date. We focus on the D. unisexualis, D. uzzelli and D. armeniaca parthenogens and polyploid backcrosses found in sympatric locations between the parthenogens and its sexual parentals. We find that only specific parental pairs are responsible for the origin of vertebrate parthenogenesis, regardless of their phylogenetic distance. Despite the recurrent hybridization presently reported in Darevskia, asexuality originated multiple times but only in a single temporal event the past. Parthenogenetic females are capable of backcrossing with sexual males, but can only produce polyploid individuals with reduced fertility that do not contribute for gene flow between parthenogens and sexuals. The sexual reproduction machinery can be lost with time in the parthenogenetic hybrids, which are most likely the result of a post-zygotic reproductive barrier to gene flow in the speciation continuum of Darevskia sexual species. In order to reconstruct the phylogenetic inference of this group, a set of capture sequence probes were designed from a transcriptome de novo assembly. Phylogenetic inference reconstruction has been extensively used to ask several evolutionary biology questions. However, despite the exponential use of high-throughput sequencing technologies and its promising applications in phylogenetics, next generation sequencing (NGS) techniques are still far from being as widely used in this field as in other areas of evolutionary genetics. The workflow developed in this thesis has proved to be not only cost-effective, but also to produce a very high number of cross genome phylogenetically informative markers in this non-model species. Finally, taking advantage of the hundreds of cross genome markers developed, a species tree was constructed and within genus relationships evaluated. Introgression tests showed a widespread pattern of gene flow across the genus, not only recent between recently diverged clades, but also both recent and ancient gene flow between early diverging Darevskia clades. Several evidences of hybridization with gene flow between diverging clades have been found in other systems. However, such widespread patterns where introgression has happened between all major clades, and in a very high number of species pairs, are not frequently found. It is also found that gene flow is completely absent between parthenogens sexual parental pairs. In groups with sexual-parthenogenetic reproducing species, pre- or post-zygotic reproductive barriers could be more difficult to attain and hybrid asexuality can, thus, effectively create reproductive barriers between diverging sexual taxa, that were likely faced with recurrent secondary contact. The work presented in this thesis shows that only a few sexual species pairs were responsible for the origin of the parthenogens, that some species acted always as the maternal species and others always as the paternal, that the phylogenetic distances between each pair are included in a wide range interval, and that introgression is found widespread across the genus but absent between the parental pairs. Regardless of the reproduction type, this study also shows the relevance and depth of hybridization during divergence. As has been shown intensively, gene flow is common during speciation and clades divergence. However, it would be interesting to analyse other groups together and test if deep branch gene flow is found only in some exclusive groups (such as sexual-asexual genera) or if it is something more widespread. This work presented here moves Darevskia towards providing a model that can be used to understand the origin of asexuality in vertebrates. Here the basis for future studies about sex and asexuality is provided, so that a focus on the differential evolution rates genomes of both reproduction mode can be analysed.

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Ecological pressure is the major driver of morphological adaptation. Different habitat preferences even among closely related spe cies, often result in the evolution of different body shapes. In the present study, we employed geometric morphometric and principal component analyses (PCA) to compare body shape and head plate morphology among seven species in the genus Darevskia Arribas, 1999 from the Elburz Mountains, Iran that occur in either rocky or forested habitats. The geometric morphometric analysis and the PCA of meristic characters recovered a wide degree of overlap between the rock and forest dwelling species. The PCA of the morphometric characters showed wide separation among the rock and forest dwelling species as well as among some of the rock dwelling species. These results strongly suggest that body shape is correlated with the habitat type whereas head plate morphology and scale meristics are not. Furthermore, the results suggest that the rock dwelling species may be occupying and navigating their microhabitat in different ways. Ecological observations are needed to test this hypothesis.

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Little is known about altitudinal distribution of lizards in Iran. In the present study we studied distribution pattern of members of family Lacertidae along the eleveatinal gradient in Iran. To determine environmental drivers of distribution pattern of 48 lizard species, all known valid members of family Lacertidae, along elevational gradient in Iran. Firstly, we classified Iran digital elevation model (DEM) based on 100m intervals, that resulted in 56 altitudinal bands and number of species in each band was recorded. Secondly, we extracted mean value of following variables; altitude, slop, area, solar radiation index (SRI), normalized differences vegetation index (NDVI), annual precipitation, precipitation of wettest month, precipitation of driest month precipitation, precipitation of wettest quarter, precipitation of driest quarter, and precipitation of warmest quarter, and using VIF measure correlated variables were removed. Finally, we performed a multiple regression and found that area and precipitation of warmest quarter are the most important drivers of distribution pattern of family Lacertidae along elevational gradient in Iran. General distribution pattern of family Lacertidae was unimodal and maximum number of species living from 1475 m to 1675 m.

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The study of genome size variation in cells of vertebrates using the DNA flow cytometry makes it possible to precisely determine polyploid individuals, which is extremely important when studying the processes of reticulate speciation. In addition, in many groups of vertebrates, closely related species often differ in the nuclear DNA content. Therefore, the purpose of our study was to explore the variability of genome size and ploidy in populations of 29 species and subspecies of mountain lizards of the genus Darevskia, as well as their hybrids. As a result of the study, the range of variability in individuals of different ploidy (91% of diploid and 9% of triploid individuals) was established not to overlap. Among diploid species, no correlation was found between the nuclear DNA content and phylogenetic relationships, geographic coordinates, altitude, average annual temperatures and precipitation. Representatives of all studied species complexes (with the exception of D. adjarica) had approximately the same limits of variability. Two species (D. derjugini and D. saxicola) show significant intraspecific variability. Comparisons of the genome size of parthenogenetic and bisexual species generally revealed no noticeable differences between them. Studies of triploid hybrids have shown that their genome size as a whole roughly corresponds to the sum of the average size of the diploid genome of the maternal parthenogenetic species and the haploid genome of the paternal species. The variability of genome sizes within samples of triploid hybrids was on average slightly higher than in most parthenogenetic species, but some lower than in bisexual species. The paper discusses peculiarities of reticulate speciation in this group of animals.

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The global struggle to conserve as many species as possible with limited resources requires an improvement of our knowledge on the distribution of biodiversity. In Iran, the state of knowledge is poor for most groups of organisms, except few vertebrate groups and vascular plants. Reptiles are one of the best known, most diverse vertebrate groups in Iran, with a high rate of endemism (ca. 29%), but distribution patterns and related environmental drivers remain poorly understood. In the present study, based on a large publicly available dataset, we use general additive modelling (GAM) to identify explanatory variables for species richness of reptiles in Iran. Results indicate heterogeneity parameters (range +entropy) as the variables with the highest explanatory values. Based on the grid cells of the predicted environmental richness, using hotspot analysis, we suggest seven hotspots of reptile diversity (HRDs) across the country. Our results corroborate the previously recognized HRDs and detect three additional ones, located alongside the major mountain ranges around the central deserts plateau, particularly in the Zagros Mountains. Four of the largest HRDs (ca. 90%) situate within the Irano-Anatolian and Caucasus global biodiversity hotspot. In addition, our results reveal a large gap between identified HRDs and the current network of protected areas (PAs) in the country. While three of the detected HRDs in this study are partially touched (ca. 18%) by the PA network, overall, these areas are only covered by less than 10%. Therefore, the effectiveness of the current PAs for the protection of the reptile diversity of Iran is questionable.

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We present an annotated checklist for a total 241 reptiles and 22 amphibians including 5 frogs, 9 toads, 7 newts and salamanders, 1 crocodile, 1 worm lizard, 148 lizards, 79 snakes and 12 turtles and tortoises, includes the most scientific literature up to August 2014 and also based on several field surveys conducted in different Provinces of Iran from 2009 to 2014. We present an up-to-dated checklist of reptiles and amphibians in Iran. We provide a comprehensive listing of taxonomy, names, distribution and conservation status of all amphibians and reptiles of Iran. This checklist includes all recognized named taxa, English names for classes, orders, families, species, subspecies along with Persian names for species, including indication of native and introduced species. For the first time we report two non-native introduced reptiles from natural habitats of Iran. Of the total 22 species of amphibians in Iran, 6 (27.2%) are endemic and of the total 241 species of reptiles, 55 (22.8%) are endemic. Of the 22 amphibians species in Iran, 3 (13%) are Critically Endangered, 2 (9%) are Vulnerable and of the 241 reptile species 3 (1.2%) are Critically Endangered, 4 (1.6%) are Endangered and 10 (4.1%) are Vulnerable. Accordingly, this paper combines significant aspects of taxonomy, common names, conservation status and distribution of the Iranian herpetofauna.

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We present a comprehensive summary of the distribution of the lizards of Iran accompanied by an annotated checklist. The updated maps of distribution of all 146 species of 41 genera of 11 families are based on all available bibliographic records, catalogues of museum collections and our own field observations. The final dataset used for the distribution maps contains 8525 georeferenced records and cover 41% of the country when plotted on a grid of 0.25° × 0.25° resolution. The dataset is publicly accessible through GBIF portal (http://www.gbif.org/dataset/7db4f705-61ae-4c6e-9de2-06674e7d46b2). Following the latest biogeographic division of the country, ~53% of the species (76 species) inhabit the Iranian Province, ~41% (60 species) the Western Asian mountain transition zone, ~9% (13 species) the Turanian Province, and ~18% (27 species) the Arabian Province. In addition, ~2% (3 species) reach Iran from the Indo-Malay biogeographic region and ~2% (3 species) are believed to have been introduced to Iran by humans. Endemic species (46) represent ~32% of the known species diversity. The most species-rich family of lizards in Iran is Lacertidae with 47 species, followed by Gekkonidae (41), Agamidae (18), Scincidae (15), Phyllodactylidae (10), Sphaerodactylidae (4), Eublepharidae and Uromastycidae (3), Anguidae and Varanidae (2), and Trogonophidae with one representative.