Areas of sympatry and hybridization of closely related species can be difficult to assess through morphological differences alone. Species which coexist and are similar morphologically may be distinguished only with molecular techniques. The roe deer (Capreolus spp.) is a meso-mammal having a Palaearctic distribution, with two closely related species: the European C. capreolus and the Siberian C. pygargus. We analysed mtDNA sequences from 245 individuals, sampled through all the entire range of the genus, to investigate the distribution of genetic lineages and outline phylogeographical patterns. We found that: (1) a C. pygargus lineage occurs in Poland and Lithuania, much farther west than the area which so far was believed its westernmost limit; (2) no haplotype of this C. pygargus lineage matches any found in East Europe and Asia -this should rule out human introductions and may indicate Pleistocene-Holocene migrations from the east; (3) no geographical structuring of C. pygargus lineages occurs, questioning the existence of putative subspecies; (4) several genetic lineages of C. capreolus can be recognized, consistent with the existence of two subspecies, respectively in central-southern Italy and southern Spain. Coalescence times suggest that intraspecific variation in C. capreolus and C. pygargus developed approximately 100-10 kya. The extant mitochondrial lineages pre-dated the Last Glacial Maximum. Capreolus pygargus must have moved westward to Central Europe, where at least one genetic lineage still survives, coexisting with C. capreolus.

We re-sequenced 815 bp of the mtDNA of loggerhead turtles from a population nesting in Calabria (southern Italy), which was found recently. Non-invasive sampling was applied and information on deposition date and place was used to avoid possible resampling of nesting females. Among 38 nests laid by independent females, we found the common haplotype CC-A2.1 (57.9%) and two other haplotypes which have never been described in Mediterranean nesting grounds, CC-A20.1 (36.8%) and CC-A31.1 (5.3%). Calabria harbors the highest intra-population diversity among 11 Mediterranean nesting populations. Our findings narrow the gap between haplotypes recorded in feeding grounds and those found in nesting grounds. Analyses of population structure show a strong maternal isolation, with Calabria and east Turkey displaying far more diversity than expected considering their census size. These observations suggest that recurrent female founder effects from sources yet to be identified in the Atlantic or in the Mediterranean may have shaped the pattern of mtDNA diversity in this latter basin. Our results provide evidence that the Ionian Calabrian sites should be protected because of the high diversity found there

Molecular phylogeny and evolutionary history of Cervus, the most successful and widespread cervid genus, have been extensively addressed in Europe, fairly in eastern Asia, but scarcely in central Asia, where some populations have never been phylogenetically investigated with DNA-based methods. Here, we applied a coalescent Bayesian approach to most Cervus taxa using complete mitochondrial cytochrome b gene and control region to provide a temporal framework for species differentiation and dispersal, with special emphasis on the central Asian populations from the Tarim Basin (C. elaphus bactrianus, C. elaphus yarkandensis) and Indian Kashmir (C. elaphus hanglu) aiming at assessing their phylogenetic and phylogeographic patterns. Red deer (C. elaphus), wapiti (C. canadensis) and sika deer (C. nippon) are confirmed as highly differentiated taxa, with genetic distances, divergence times and phylogenetic positions compatible with the rank of species. Similarly, the red deer of the Tarim group, hitherto considered as subspecies of C. elaphus, showed a comparable pattern of genetic distinction in the phylogeny and, according to our results, are thus worthy of being raised to the species level. The systematic position of the endangered red deer from Indian Kashmir is assessed here for the first time, and implications for its conservation are also outlined. Based on phylogeny and divergence time estimates, we propose a novel evolutionary pattern for the genus Cervus during the Mio/Pliocene, in the light of palaeo-climatological information.

Traditional pastoralists survive in few places in the world. They can still be encountered in the African Sahel, where annual alternations of dry and wet seasons force them to continual mobility. Little is known about the genetic structure of these populations. We present here the population distribution of 312 hypervariable segment I mitochondrial DNA (mtDNA) and 364 Y-short tandem repeat haplotypes in both farmer and pastoralist groups from the Lake Chad Basin and the West African Sahel. We show that the majority of pastoral populations (represented in the African Sahel by the Fulani nomads) fail to show significant departure from neutrality for mtDNA as evidenced by Fu's Fs statistics and exhibit lower levels of intrapopulation diversity measures for mtDNA when contrasted with farmers. These differences were not observed for the Y chromosome. Furthermore, analyses of molecular variance and population distributions of the mtDNA haplotypes show more heterogeneity in the sedentary groups than in the pastoralists. On the other hand, pastoralists retain a signature of a wide phylogenetic distance contributing to their male gene pool, whereas in at least some of the farmer populations, a founder effect and/or drift might have led to the presence of a single major lineage. Interestingly, these observations are in contrast with those recorded in Central Asia, where similar comparisons of farmer and pastoral groups have recently been carried out. We can conclude that in Africa, there have been no substantial mating exchanges between the Fulani pastoralists coming to the Lake Chad Basin from the West African Sahel and their farmer neighbors. At the same time, we suggest that the emergence of pastoralism might be an earlier and/or a demographically more important event than the introduction of sedentary agriculture, at least in this part of Africa.

In migratory species female- and male-mediated gene flow are important for defining relevant Management Units, and for evaluating connectivity between these and their respective foraging grounds. The stock composition at five Mediterranean foraging areas was investigated by analysing variation in the mitochondrial D-loop and six microsatellite loci in a sample of 268 loggerhead turtles (Caretta caretta) stranded or accidentally caught by fisheries. This involved a comprehensive Mixed Stock Analysis which considers also recent data from major rookeries in Libya and Turkey, and the generation of a standardized nomenclature of allele sizes at the microsatellite loci. The results indicate: that the north Adriatic, the Tunisian continental shelf, the waters around Malta and the Italian Ionian Sea represent important areas for the conservation of rookeries in Greece, Libya and Turkey, respectively; that waters off the Italian peninsula and the islands of Lampedusa and Malta are mainly inhabited by individuals of Mediterranean origin, with a major contribution from the nearest and largest colonies, while Atlantic turtles are restricted to the western areas; that specific migratory routes exist from rookeries to foraging grounds; a poor bi-parental genetic structuring, which suggests a high male-mediated gene flow in the Mediterranean; mixing of small turtles in waters distant from natal rookeries, and recovery of structuring for large-sized individuals; and that uncommon mtDNA haplotypes are more powerful markers than microsatellite alleles in assessing an individual's origin, owing to their higher geographic specificity. © 2013 John Wiley & Sons, Ltd

BackgroundThe northern Adriatic Sea represents one of the most important neritic foraging grounds for the loggerhead sea turtle Caretta caretta L. in the Mediterranean Sea. Four genera of blood flukes with variable prevalence and pathogenic impact have been reported worldwide in this species. Hapalotrema Looss, 1899 and Amphiorchis Price, 1934 are the only two genera reported in Mediterranean waters; however, updated data describing spirorchiidiasis in the central and eastern Mediterranean and infection prevalence are still lacking. This work aimed to investigate the presence and pathology of spirorchiidiasis in C. caretta in the Mediterranean Sea.MethodsOne hundred sixty-eight animals stranded along the northwestern Adriatic coast between 2009 and 2015 were submitted to necropsy and subsequent analyses for the detection of adult flukes, detection of eggs in the faeces and spleen and histopathology. Molecular analyses were carried out on hosts (mitochondrial D-loop) and parasites (28S gene and ITS2 spacer) to trace the turtle origins and identify the fluke phylogenetic relationships.ResultsSpirorchiidiasis was detected in 16.7% of the animals. Hapalotrema mistroides (Monticelli, 1899) and Neospirorchis sp. were found in twenty-six and ten cases, respectively. Adult flukes were found in six cases, while eggs were detectable through copromicroscopic examination for all infected turtles, and the results for the detection of eggs in the spleen agreed with the copromicroscopic analysis. Only mild lesions were observed. Eggs of types 1 and 3 were grossly visible in the gastrointestinal mucosa, vasculitis was rarely observed in the heart and great vessels, and multifocal granulomas were widespread in the tissues. Molecular identification unambiguously assigned the spirorchiid samples to H. mistroides and Neospirorchis sp. Genetic characterization of loggerhead mtDNA pointed to a Mediterranean origin of the turtle hosts.ConclusionThis survey provides new data on the spread of spirorchiidiasis in the Mediterranean loggerhead sea turtle population and reports for the first time the presence of Neospirorchis spp. in this basin. The infections did not have a causal effect on the death nor a strong impact on the general health status of the animals.Electronic supplementary materialThe online version of this article (10.1186/s13071-017-2396-x) contains supplementary material, which is available to authorized users.

the genetic discrimination between phylogenetically close taxa can be challenging if their gene pools are not differentiated and there are many shared polymorphisms. The gene flow between wild boar (Sus scrofa) and domestic pig (S. s. domesticus) has never been interrupted from domestication onwards, due to non-stop natural and human-mediated crossbreeding. To date there are no individual genetic markers that are able to distinguish between the two forms, nor even to identify effectively their hybrids. We developed a combined molecular protocol based on multiplex porcine-specific STR-profiling system and new real time pcR-based assays of single polymorphisms in the NR6A1 and MC1R genes to gain high diagnostic power in the differentiation of wild boar, pig and hybrids for forensic purposes. The combined approach correctly assigned individuals to one or the other parental gene pool and identified admixed genotypes. Evidence was found for substantial reduction of false negative results by using multiple marker systems jointly, compared to their use individually. Our protocol is a powerful and costeffective diagnostic tool that can easily be adopted by most forensic laboratories to assist authorities contrast food adulteration, assure veterinary public health and fight against wildlife crimes, like poaching and illegal detention of wild animals.

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