Semi-feral local livestock populations, like Maremmana cattle, are the object of renewed interest for the conservation of biological diversity and the preservation and exploitation of unique and potentially relevant genetic material. The aim of this study was to estimate genetic diversity parameters in semi-feral Maremmana cattle using both pedigree- and genomic-based approaches (FIS and FROH), and to detect regions of homozygosity (ROH) and heterozygosity (ROHet) in the genome. The average heterozygosity estimates were in the range reported for other cattle breeds (HE=0.261, HO=0.274). Pedigree-based average inbreeding (F) was estimated at 4.9%. The correlation was low between F and genomic-based approaches (r=0.03 with FIS, r=0.21 with FROH), while it was higher between FIS and FROH (r=0.78). The low correlation between F and FROH coefficients may be the result of the limited pedigree depth available for the animals involved in this study. The ROH islands identified in Maremmana cattle included candidate genes associated with climate adaptation, carcass traits or the regulation of body weight, fat and energy metabolism. The ROHet islands contained candidate genes associated with nematode resistance and reproduction traits in livestock. The results of this study confirm that genome-based measures like FROH may be useful estimators of individual autozygosity, and may provide insights on pedigree-based inbreeding estimates in cases when animals’ pedigree data are unavailable, thus providing a more detailed picture of the genetic diversity.

BackgroundThe current distribution of genetic diversity is the result of a vast array of microevolutionary processes, including short-term demographic and ecological mechanisms and long-term allopatric isolation in response to Quaternary climatic fluctuations. We investigated past processes that drove the population differentiation and spatial genetic distribution of the Italian wall lizard Podarcis siculus by means of sequences of mitochondrial cytb (n = 277 from 115 localities) and nuclear mc1r and β-fibint7genes (n = 262 and n = 91, respectively) from all its distribution range. The pattern emerging from the genetic data was compared with current and past (last glacial maximum) species distribution modeling (SDM).ResultsWe identified seven deeply divergent parapatric clades which presumably remained isolated in different refugia scattered mainly throughout the Tyrrhenian coast. Conversely, the Adriatic coast showed only two haplogroups with low genetic variability. These results appear to agree with the SDM prediction at the last glacial maximum (LGM) indicating a narrow area of habitat suitability along the Tyrrhenian coast and much lower suitability along the Adriatic one. However, the considerable land exposure of the Adriatic coastline favored a glacial colonization of the Balkan Peninsula.ConclusionsOur population-level historical demography showed a common trend consistent with glacial expansions and regional persistence during the last glacial maximum. This complex genetic signature appears to be inconsistent with the expectation of the expansion-contraction model and post-LGM (re)colonizations from southern refugia. Hence it is one of an increasing number of cases in which these assumptions are not met, indicating that long-term fragmentation and pre-LGM events such as glacial persistence were more prominent in shaping genetic variation in this temperate species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0847-1) contains supplementary material, which is available to authorized users.

Two Cordulegaster dragonflies present in Italy, the Palaearctic and northern distributed Cordulegaster boltonii and the endemic to the south of the peninsula Cordulegaster trinacriae, meet in central Italy and give rise to individuals of intermediate morphology. By means of mitochondrial and nuclear markers and of Geometric Morphometrics applied to sexual appendages, we defined i) the geographical boundaries between the two species in Italy and ii) we determined the presence, the extent, and the genetic characteristics of the hybridization. Genetic data evidenced asymmetric hybridization with the males of C. trinacriae able to mate both interspecifically and intraspecifically. The results contrast with expectations under neutral gene introgression and sexual selection. This data, along with the morphological evidence of significant differences in size and shape of sexual appendages between the males of the two species, seem indicative of the role of mechanical constraints in intraspecific matings. The origin of the two species is dated about to 1.32 Mya and the hybridization resulted related to range expansion of the two species after Last Glacial Maximum and this led to the secondary contact between the two taxa in central Italy. At last, our results indicate that the range of C. trinacriae, a threatened and protected species, has been moving northward probably driven by climate changes. As a result, the latter species is currently intruding into the range of C. boltonii. The hybrid area is quite extended and the hybrids seem well adapted to the environment. From a conservation point of view, even if C. trinacriae has a strong genetic identity, the discovery of hybridization between the two species should be considered in a future species management.

Coat color is among the most distinctive phenotypes in cattle. Worldwide, several breeds share peculiar coat color features such as the presence of a fawn pigmentation of the calf at birth, turning over time to grey, and sexual dichromatism. The aim of this study was to search for polymorphisms under differential selection by contrasting grey cattle breeds displaying the above phenotype with non-grey cattle breeds, and to identify the underlying genes. Using medium-density SNP array genotype data, a multi-cohort FST-outlier approach was adopted for a total of 60 pair-wise comparisons of the 15 grey with 4 non-grey cattle breeds (Angus, Limousin, Charolais, and Holstein), with the latter selected as representative of solid and piebald phenotypes, respectively. Overall, more than 50 candidate genes were detected; almost all were either directly or indirectly involved in pigmentation, and some of them were already known for their role in phenotypes related with hair graying in mammals. Notably, 17 relevant genes, including SDR16C5, MOS, SDCBP, and NSMAF, were located in a signal on BTA14 convergently observed in all the four considered scenarios. Overall, the key stages of pigmentation (melanocyte development, melanogenesis, and pigment trafficking/transfer) were all represented among the pleiotropic functions of the candidate genes, suggesting the complex nature of the grey phenotype in cattle.

Background: Assessment of genetic diversity and population structure provides important control metrics to avoid genetic erosion, inbreeding depression and crossbreeding between exotic and locally-adapted cattle breeds since these events can have deleterious consequences and eventually lead to extinction. Historically, the Alpine Arc represents an important pocket of cattle biodiversity with a large number of autochthonous breeds that provide a fundamental source of income for the entire regional economy. By using genotype data from medium-density single nucleotide polymorphism (SNP) arrays, we performed a genome-wide comparative study of 23 cattle populations from the Alpine Arc and three cosmopolitan breeds. Results: After filtering, we obtained a final genotyping dataset consisting of 30,176 SNPs for 711 individuals. The local breeds showed high or intermediate values of genetic diversity compared to the highly selected cosmopolitan breeds. Patterns of genetic differentiation, multidimensional scaling, admixture analysis and the constructed phylogenetic tree showed convergence, which indicates the presence of gene flow among the breeds according to both geographic origin and historical background. Among the most differentiated breeds, we identified the modern Brown cattle. In spite of admixture events, several local breeds have preserved distinctive characteristics, which is probably due to differences in genetic origin and geographic location. Conclusions: This study represents one of the most comprehensive genome-wide analysis of the Alpine cattle breeds to date. Using such a large dataset that includes the majority of the local breeds found in this region, allowed us to expand knowledge on the evaluation and status of Alpine cattle biodiversity. Our results indicate that although many of the analyzed local breeds are listed as endangered, they still harbor a large amount of genetic diversity, even when compared to some cosmopolitan breeds. This finding, together with the reconstruction of the phylogeny and the relationships between these Alpine Arc cattle breeds, provide crucial insights not only into the improvement of genetic stocks but also into the implementation of future conservation strategies.