Studio della variabilità genetica nel Grifone Sardo (<i>Gyps fulvus</i>) attraverso l’analisi del DNA mitocondriale

In Italy, the Griffon Vulture (Gyps fulvus) lives and nests exclusively in Sardinia. During the last century it has suffered the consequences of a drastic decline and currently there are only thirty territorial couples. It is therefore included in the category of Critically Endangered (CR) species. The aim of this work was to increase the understanding of genetic and evolutionary history of the Sardinian Griffon Vulture, useful to the preservation of this species. The first step was to obtain the complete sequence of Gyps fulvus mtDNA, so far known only for the 25%. Phylogenetic results from D-loop sequences analysis indicated the presence of a unique cluster, split into two groups, characterized by a high statistical support. Additional analysis were performed to validate the structure of the obtained tree, in order to identify the number and the diversity of haplotypes (Hap), pairwise differences and, by using Bayesian model-based clustering, a possible genetic structure. Our results indicate the presence of three different Hap within the sampled Gyps fulvus which are probably typical of the Mediterranean area. Phylogenetic analysis were also performed according to the molecular clock theory and divergence times were estimated by using the ND2 aminoacid sequences. The extant genetic diversity within Gyps resulted from a rapid adaptive radiation at about 1.62 million years ago (MYA), whereas the split G. fulvus/G. tenuirostris-G. indicus-G. coprotheres was dated at 0.54 MYA

Troubles phonético-phonologiques: traitement des aspects expressifs et réceptifs.

Sheep are thought to have been one of the first livestock to be domesticated in the Near East, thus playing an important role in human history. The current whole mitochondrial genome phylogeny for the genus Ovis is based on: the five main domestic haplogroups occurring among sheep (O. aries), along with molecular data from two wild European mouflons, three urials, and one argali. With the aim to shed some further light on the phylogenetic relationship within this genus, the first complete mitochondrial genome sequence of a Cypriot mouflon (O. gmelini ophion) is here reported. Phylogenetic analyses were performed using a dataset of whole Ovis mitogenomes as well as D-loop sequences. The concatenated sequence of 28 mitochondrial genes of one Cypriot mouflon, and the D-loop sequence of three Cypriot mouflons were compared to sequences obtained from samples representatives of the five domestic sheep haplogroups along with samples of the extant wild and feral sheep. The sample included also individuals from the Mediterranean islands of Sardinia and Corsica hosting remnants of the first wave of domestication that likely went then back to feral life. The divergence time between branches in the phylogenetic tree has been calculated using seven different calibration points by means of Bayesian and Maximum Likelihood inferences. Results suggest that urial (O. vignei) and argali (O. ammon) diverged from domestic sheep about 0.89 and 1.11 million years ago (MYA), respectively; and dates the earliest radiation of domestic sheep common ancestor at around 0.3 MYA. Additionally, our data suggest that the rise of the modern sheep haplogroups happened in the span of time between six and 32 thousand years ago (KYA). A close phylogenetic relationship between the Cypriot and the Anatolian mouflon carrying the X haplotype was detected. The genetic distance between this group and the other ovine haplogroups supports the hypothesis that it may be a new haplogroup never described before. Furthermore, the updated phylogenetic tree presented in this study determines a finer classification of ovine species and may help to classify more accurately new mitogenomes within the established haplogroups so far identified

Rooted tree obtained by Bayesian inference for <i>28H</i> dataset showing two clusters of sheep haplogroups.

<p>Nodal supports are indicated below the nodes (posterior probability for <i>BI</i> / bootstrap values for <i>ML</i>). Molecular dating in million years are indicated above the nodes. Sample codes are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144257#pone.0144257.t001" target="_blank">Table 1</a>.</p

Genetic diversity estimates obtained for whole genome (<i>28H</i>) (a) and <i>D-loop</i> (b) datasets.

<p>Genetic diversity estimates obtained for whole genome (<i>28H</i>) (a) and <i>D-loop</i> (b) datasets.</p

Structural organization of Cyprus mouflon mitogenome.

<p>Arrows indicate the reading frame orientation of each strand.</p

Rooted tree obtained by Bayesian inference for <i>D-loop</i> region and the corresponding 95% statistical parsimony networks.

<p>Bayesian groups inferred by the Bayesian assignment test are also represented through coloured boxes (G 1 in yellow, G 2 in blue, G 3 in red, G 4 in green). Nodal supports are indicated above the nodes (posterior probability for <i>BI</i> / bootstrap values for <i>ML</i>). Groups retrieved using the 95% statistical parsimony networks are shown on the right. Each black dot in the networks represents a point mutation. Haplotypes in the network are coloured according to the groups of individuals analyzed (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144257#pone.0144257.t001" target="_blank">Table 1</a> for details). Sample codes are given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144257#pone.0144257.t001" target="_blank">Table 1</a>.</p

Sampling plan.

<p>World map with enlargement on the Mediterranean basin, indicating the geographical distribution of samples used in the present study.</p

A median-joining network superimposed on the sample map.

<p>It highlights the geographic distribution of <i>D-loop</i> haplotypes. N1, N2 and N3 indicate the three main groups evidenced in this analysis. <i>CCA</i> indicate the likely common ancestor. The capital letters (A, B, C, D and E) inside white spots on the network correspond to the five sheep haplogroups used as references. Small red plots on the nodes, correspond to median vectors representing hypothetic connecting sequences, calculated with a maximum parsimony method. The long branches leading to isolated haplotypes were shortened and indicated with ‘‘\\”. The numbers of mutations between haplotypes that are greater than one are reported on the network branches. Sample codes are given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144257#pone.0144257.t001" target="_blank">Table 1</a>.</p

List of the species and the sequences included in phylogenetic analyses.

<p>List of the species and the sequences included in phylogenetic analyses.</p

Molecular dating in million years obtained in the present study for the main splitting events within <i>Ovis</i> genus based seven calibration points (<i>CP</i>).

<p>Molecular dating in million years obtained in the present study for the main splitting events within <i>Ovis</i> genus based seven calibration points (<i>CP</i>).</p