The area of the Aegean can be described as one of nature’s most active laboratories. The contemporary geomorphology of the Aegean is a result of diverse and still ongoing geological events, which coupled with climate changes, have created mountains and thousands of islands. The Aegean bridges three continents, where human activity has been recorded for at least 10,000 years. Herpetofauna diversity offered early researchers the possibility of describing patterns in the Aegean, especially as the distributional limit for several species and faunal elements. The patterns initially described at a rather coarse scale formed the frame on which the application of new techniques opened new views and permitted finer analyses. Here, we assess recent works on the Aegean’s herpetofauna, outlining the role of sea barriers, especially the Mid Aegean Trench (MAT). We propose four basic patterns (pre-MAT, post-MAT, newcomers, and that of an outlier) and discuss exceptions to these patterns, to interpret the diversity recorded. The interdisciplinary study of taxonomy helps explaining the observed diversity and provides powerful arguments for how exploring diversity can be used to explain more than biological processes.

Background: The evolutionary history of the biota of North Africa and Arabia is inextricably tied to the complex geological and climatic evolution that gave rise to the prevalent deserts of these areas. Reptiles constitute an exemplary group in the study of the arid environments with numerous well-adapted members, while recent studies using reptiles as models have unveiled interesting biogeographical and diversification patterns. In this study, we include 207 specimens belonging to all 12 recognized species of the genusStenodactylus. Molecular phylogenies inferred using two mitochondrial (12S rRNA and 16S rRNA) and two nuclear (c-mosandRAG-2) markers are employed to obtain a robust time-calibrated phylogeny, as the base to investigate the inter- and intraspecific relationships and to elucidate the biogeographical history ofStenodactylus, a genus with a large distribution range including the arid and hyper-arid areas of North Africa and Arabia.Results: The phylogenetic analyses of molecular data reveal the existence of three major clades within the genusStenodactylus, which is supported by previous studies based on morphology. Estimated divergence times between clades and sub-clades are shown to correlate with major geological events of the region, the most important of which is the opening of the Red Sea, while climatic instability in the Miocene is hypothesized to have triggered diversification. High genetic variability is observed in some species, suggesting the existence of some undescribed species. TheS. petrii-S. stenurusspecies complex is in need of a thorough taxonomic revision. New data is presented on the distribution of the sister speciesS. sthenodactylusandS. mauritanicus.Conclusions: The phylogenetic hypothesis for the genusStenodactyluspresented in this work permits the reconstruction of the biogeographical history of these common desert dwellers and confirms the importance of the opening of the Red Sea and the climatic oscillations of the Miocene as major factors in the diversification of the biota of North Africa and Arabia. Moreover, this study traces the evolution of this widely distributed and highly specialized group, investigates the patterns of its high intraspecific diversity and elucidates its systematics.

The current extensive use of the domestic goat (Capra hircus) is the result of its medium size and high adaptability as multiple breeds. The extent to which its genetic variability was influenced by early domestication practices is largely unknown. A common standard by which to analyze maternally-inherited variability of livestock species is through complete sequencing of the entire mitogenome (mitochondrial DNA, mtDNA). We present the first extensive survey of goat mitogenomic variability based on 84 complete sequences selected from an initial collection of 758 samples that represent 60 different breeds of C. hircus, as well as its wild sister species, bezoar (Capra aegagrus) from Iran. Our phylogenetic analyses dated the most recent common ancestor of C. hircus to ~460,000 years (ka) ago and identified five distinctive domestic haplogroups (A, B1, C1a, D1 and G). More than 90 % of goats examined were in haplogroup A. These domestic lineages are predominantly nested within C. aegagrus branches, diverged concomitantly at the interface between the Epipaleolithic and early Neolithic periods, and underwent a dramatic expansion starting from ~12–10 ka ago. Domestic goat mitogenomes descended from a small number of founding haplotypes that underwent domestication after surviving the last glacial maximum in the Near Eastern refuges. All modern haplotypes A probably descended from a single (or at most a few closely related) female C. aegagrus. Zooarchaelogical data indicate that domestication first occurred in Southeastern Anatolia. Goats accompanying the first Neolithic migration waves into the Mediterranean were already characterized by two ancestral A and C variants. The ancient separation of the C branch (~130 ka ago) suggests a genetically distinct population that could have been involved in a second event of domestication. The novel diagnostic mutational motifs defined here, which distinguish wild and domestic haplogroups, could be used to understand phylogenetic relationships among modern breeds and ancient remains and to evaluate whether selection differentially affected mitochondrial genome variants during the development of economically important breeds.

Recently, several works have focused on the lacertid lizards of the genus Podarcis, revealing cases of hidden diversity and paraphyly, and offering evidence that suggests the revision of the extant taxonomical arrangements within the genus. Hidden diversity and paraphyly have been shown to exist in the relationships between the Balkan species P. peloponnesiaca and P. erhardii as well. Here we couple a molecular (mtDNA) dataset with a corresponding morphological one, consisting of morphometric and pholidotic characters, to check for concordance between the two. Phylogenetic analyses reinforced previous suggestions for paraphyly of P. erhardii with respect to P. peloponnesiaca. We found the variation of certain pholidotic characters concordant with the relationships inferred from partial mtDNA sequences, whereas morphometric characters were not. The latter is possibly due to greater influence of morphometric characters by environmental factors. To avoid the observed paraphyly we proceed with the description of the populations from Crete and the islet of Pori, until now designated as P. erhardii, as separate taxa at the species level.