Genome-wide single nucleotide polymorphisms reveal recurrent waves of speciation in niche-pockets, in Europe's most venomous snake.

Within the Balkan Peninsula, topographic and climatic agents have promoted biodiversity and shaped the speciation history of many ectotherms. Here, we targeted an iconic European reptile, the nose-horned viper species-complex (Vipera ammodytes), and explored its spatial and temporal evolution. We (i) utilized genome-wide single nucleotide polymorphisms to infer genetic structure and build a time-calibrated species-tree, and (ii) applied species distribution modelling with niche-divergence tests among major phylogenomic clades. Geographically structured genetic diversity was found. Cycles of recurrent isolation and expansion during glacial-interglacial periods led to allopatric speciation and to secondary contacts and formation of multiple hybrid zones throughout the Balkan Peninsula. Deep divergence is still detected among populations separated by old and imminent biogeographical barriers (Pindos Mountain Range, the Cyclades islands, etc.), but in most cases speciation is incomplete. At the other end of the speciation continuum, we recognize two well-differentiated lineages, currently lacking any evidence of gene flow; one is distributed in the Northwestern Balkans and the other in the Southeastern Balkans, further expanding into Asia. Despite their split 5 million years ago, there is no evidence of ecological divergence, as speciation probably occurred in niche-pockets of analogous environments. These two lineages probably represent different species, while V. transcaucasiana does not merit species status. By comparing the genomic phylogenies to an updated mitochondrial one, we propose an evolutionary scenario that resolves all mitonuclear conflicts, according to which the history of the V. ammodytes species-complex was shaped by complex processes, including a major event of introgressive hybridization with asymmetric mitochondrial capture.

Revising the taxonomy of Darevskia valentini (Boettger, 1892) and Darevskia rudis (Bedriaga, 1886) (Squamata, Lacertidae): a Morpho-Phylogenetic integrated study in a complex Anatolian scenario.

Revealing biodiversity allows the accurate determination of the underlying causes of many biological processes such as speciation and hybridization. These processes contain many complex patterns, especially in areas with high species diversity. As two of the prominent zoogeographic areas, Anatolia and Caucasus are also home to the genus Darevskia, which has a complex morphological structure and parthenogenetic speciation. Darevskia valentini and D. rudis are two largely distributed taxa of this genus, both of which have a controversial taxonomic delimitation. Here we performed both a highly detailed morphological comparison and a molecular evaluation for the populations in both species groups. The most comprehensive taxonomic revision of this complex was carried out to determine the cases where the data obtained were compatible or not with each approach. As a result of the obtained outputs, it seems that D. spitzenbergerae stat. nov., D. mirabilis stat. nov. and D. obscura stat. nov. should be accepted as the species level, this later with subspecies D. o. bischoffi comb. nov. and D. o. macromaculata comb. nov.. Also, we propose two new taxa: D. josefschmidtleri sp. nov. and D. spitzenbergerae wernermayeri ssp. nov.. It has also been shown that "lantzicyreni" subspecies belong to D. rudis instead of D. valentini. The extensive revision has contributed to subsequent studies to more accurately understand the past histories of species in the genus Darevskia.

The demise of a wonder: Evolutionary history and conservation assessments of the Wonder Gecko Teratoscincus keyserlingii (Gekkota, Sphaerodactylidae) in Arabia.

Effective biodiversity conservation planning starts with genetic characterization within and among focal populations, in order to understand the likely impact of threats for ensuring the long-term viability of a species. The Wonder Gecko, Teratoscincus keyserlingii, is one of nine members of the genus. This species is distributed in Iran, Afghanistan, and Pakistan, with a small isolated population in the United Arab Emirates (UAE), where it is classified nationally as Critically Endangered. Within its Arabian range, anthropogenic activity is directly linked to the species' decline, with highly localised and severely fragmented populations. Here we describe the evolutionary history of Teratoscincus, by reconstructing its phylogenetic relationships and estimating its divergence times and ancestral biogeography. For conservation implications of T. keyserlingii we evaluate the genetic structure of the Arabian population using genomic data. This study supports the monophyly of most species and reveals considerable intraspecific variability in T. microlepis and T. keyserlingii, which necessitate broad systematic revisions. The UAE population of T. keyserlingii likely arrived from southern Iran during the Pleistocene and no internal structure was recovered within, implying a single population status. Regional conservation of T. keyserlingii requires improved land management and natural habitat restoration in the species' present distribution, and expansion of current protected areas, or establishment of new areas with suitable habitat for the species, mostly in northern Abu Dhabi Emirate.

Genomic and mitochondrial evidence of ancient isolations and extreme introgression in the four-lined snake.

Comparing mitochondrial and genomic phylogenies is an essential tool for investigating speciation processes, because each genome carries different inheritance properties and evolutionary characteristics. Furthermore, mitonuclear discordance may arise from ecological adaptation, historic isolation, population size changes, and sex-biased dispersal. Closely related taxa are expected to experience gene flow; however, this may not be true for insular populations or populations isolated in refugia. The four-lined snake Elaphe quatuorlineata has a fragmented distribution, separating populations of the Italian and Balkan Peninsulas, whereas several insular Aegean populations of significantly smaller body size (Cyclades island group and Skyros Island, Greece) are currently considered distinct subspecies. We constructed the species-tree phylogeny of this species utilizing genome-wide single nucleotide polymorphisms and a gene-tree based on complete cytochrome b sequences, aiming to detect convergence and discrepancies between biparentally and maternally inherited genomes. Population structuring, phylogenetic patterns and migration events among geographically defined lineages supported our hypothesis of isolation in multiple sub-refugia. Where biogeographical barriers did not restrict subsequent dispersal, extensive genetic exchange occurred between mainland Balkan populations. This process has led to the mitochondrial sweep of an ancestral mitolineage that survived only in peripheral (East Greece) and insular populations (North Cyclades and Skyros). The Central Cyclades represent an ancient lineage for both molecular markers that emerged almost 3.3 Mya. Considering their distinct morphology, insular E. quatuorlineata populations should be the future focus of an extensive sampling, especially since the mitonuclear discordance observed in this species could be related to ecological adaptations, such as the island-dwarfism phenomenon.

Phylogeography of Aegean green toads (Bufo viridis subgroup): continental hybrid swarm vs. insular diversification with discovery of a new island endemic.

BACKGROUND: Debated aspects in speciation research concern the amount of gene flow between incipient species under secondary contact and the modes by which post-zygotic isolation accumulates. Secondary contact zones of allopatric lineages, involving varying levels of divergence, provide natural settings for comparative studies, for which the Aegean (Eastern Mediterranean) geography offers unique scenarios. In Palearctic green toads (Bufo viridis subgroup or Bufotes), Plio-Pleistocene (~ 2.6 Mya) diverged species show a sharp transition without contemporary gene flow, while younger lineages, diverged in the Lower-Pleistocene (~ 1.9 Mya), admix over tens of kilometers. Here, we conducted a fine-scale multilocus phylogeographic analysis of continental and insular green toads from the Aegean, where a third pair of taxa, involving Mid-Pleistocene diverged (~ 1.5 Mya) mitochondrial lineages, earlier tentatively named viridis and variabilis, (co-)occurs. RESULTS: We discovered a new lineage, endemic to Naxos (Central Cyclades), while coastal islands and Crete feature weak genetic differentiation from the continent. In continental Greece, both lineages, viridis and variabilis, form a hybrid swarm, involving massive mitochondrial and nuclear admixture over hundreds of kilometers, without obvious selection against hybrids. CONCLUSIONS: The genetic signatures of insular Aegean toads appear governed by bathymetry and Quaternary sea level changes, resulting in long-term isolation (Central Cyclades: Naxos) and recent land-bridges (coastal islands). Conversely, Crete has been isolated since the end of the Messinian salinity crisis (5.3 My) and Cretan populations thus likely result from human-mediated colonization, at least since Antiquity, from Peloponnese and Anatolia. Comparisons of green toad hybrid zones support the idea that post-zygotic hybrid incompatibilities accumulate gradually over the genome. In this radiation, only one million years of divergence separate a scenario of complete reproductive isolation, from a secondary contact resulting in near panmixia.

Next-generation sequencing yields the complete mitochondrial genome of the endangered Milos viper Macrovipera schweizeri (Reptilia, Viperidae).

The Milos viper, Macrovipera schweizeri, is an endangered viperid snake found on four Aegean islands (Greece). Its complete mitochondrial genome, the first reported for the genus Macrovipera, was assembled through next-generation sequencing. Its total length is 17,152 bp and includes 22 tRNAs, two ribosomal RNA genes, 13 protein-coding genes and two control regions, showing the typical gene-arrangement for Viperidae. Eight tRNAs and ND3 are encoded on the light strand, while all other genes are encoded on the heavy strand. A mitogenomic phylogeny that included Macrovipera schweizeri and 13 other viperid genera returned an unresolved relationship among the genera Macrovipera, Daboia and Vipera.

Taxonomic reassessment of Blanus strauchi (Bedriaga, 1884) (Squamata: Amphisbaenia: Blanidae), with the description of a new species from southeast Anatolia (Turkey).

The study of mitochondrial and nuclear DNA sequences reveals that the polytypic Blanus strauchi is a species complex including three well-defined allopatric clades, one of which consists of two sub-clades. Only the two sub-clades of the Western clade are morphologically diagnosable in the field, whereas obvious characters to distinguish the Central and the Eastern clades are lacking. However, all four clades show significant statistical differentiation on meristic traits, as well as in morphometric characters of the head when compared by means of the geometric morphometrics. The genetic distance between the three major mitochondrial clades is comparable to the p-distances for the same markers observed between Blanus species-pairs from Morocco and the Iberian Peninsula, respectively. The nuclear marker confirms the mitochondrial clades, and shows that the three major clades do not share any haplotypes, as an indication of restricted gene flow among them. On the basis of this evidence, the taxonomy of Blanus strauchi is re-assessed: the Western clade corresponds to B. strauchi, with two subspecies: B. s. strauchi and B. s. bedriagae. The Central clade corresponds to B. aporus, here elevated at the species rank. For the eastern clade there are no available names, and therefore it is described here as Blanus alexandri sp. nov.