×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.
