A parsimonious tree of complete mtDNA sequences from sheep.

<p>This tree was rooted by using the published argali (<i>O. ammon</i>) sequence (GenBank: HM236188). Mutations are shown on the branches and are numbered according to the sheep reference sequence (SRS, GenBank: NC_001941.1). Mutations are transitions unless a base is explicitly indicated. Suffixes indicate transversions (to A, G, C, or T), while “+ and d” denote insertions and deletions, respectively. Recurrent mutations are underlined. The samples are highlighted with different colors to identify their breed of origin. Control-region shared haplotypes (from np 15,452 to np 16,263; <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073712#pone-0073712-g003" target="_blank">Figure 3</a>) are indicated by dotted ovals. Additional information regarding each mtDNA is available in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073712#pone-0073712-t002" target="_blank">Table 2</a>.</p

PCo analysis.

<p>The plot is based on pairwise genetic distances among the eight breeds (indicated by different colors) and based on 291 control-region haplotypes. The IMd cluster is indicated by the oval.</p

Sources and haplogroup affiliation of the sheep complete mtDNA sequences.

a<p>Labeled as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073712#pone-0073712-g004" target="_blank">Figure 4</a>.</p

Plot of pairwise population genetic distances.

<p>Data were obtained by the concomitant analysis of all breeds subdivided into two groups: (1) SM, AP, SO, GP, MI; (2) SA, CO, LA.</p

Median-joining networks of the sheep control-region sequences.

<p>The top network was obtained from the entire dataset, while the bottom one was acquired by activating the haplotype frequency>1 option.</p

Estimates of genetic diversities ^a and haplogroup frequencies ^b for each sheep breed.

a<p>N = number of analyzed samples; π = nucleotide diversity; nh = number of unique haplotypes; Hd = haplotype diversity; <i>S</i> = number of polymorphic sites.</p>b<p>Relative frequencies are in parentheses.</p

Mitochondrial DNA variants of Podolian cattle breeds testify for a dual maternal origin

<div><p>Background</p><p>Over the past 15 years, 300 out of 6000 breeds of all farm animal species identified by the Food and Agriculture Organization of the United Nations (FAO) have gone extinct. Among cattle, many Podolian breeds are seriously endangered in various European areas. Podolian cattle include a group of very ancient European breeds, phenotypically close to the aurochs ancestors (<i>Bos primigenius</i>). The aim of the present study was to assess the genetic diversity of Podolian breeds and to reconstruct their origin.</p><p>Methodology</p><p>The mitochondrial DNA (mtDNA) control-regions of 18 Podolian breeds have been phylogenetically assessed. Nine non-Podolian breeds have been also included for comparison.</p><p>Conclusion</p><p>The overall analysis clearly highlights some peculiarities in the mtDNA gene pool of some Podolian breeds. In particular, a principal component analysis point to a genetic proximity between five breeds (<i>Chianina</i>, <i>Marchigiana</i>, <i>Maremmana</i>, <i>Podolica Italiana</i> and <i>Romagnola</i>) reared in Central Italy and the Turkish Grey. We here propose the suggestive hypothesis of a dual ancestral contribution to the present gene pool of Podolian breeds, one deriving from Eastern European cattle; the other arising from the arrival of Middle Eastern cattle into Central Italy through a different route, perhaps by sea, ferried by Etruscan boats. The historical migration of Podolian cattle from North Eastern Europe towards Italy has not cancelled the mtDNA footprints of this previous ancient migration.</p></div

Principal Component Analysis (PCA) of all Podolian breeds.

<p>Below is the plot of the contribution of each haplogroup to the first and second PC (projections of the axes of the original variables).</p

Sources and haplogroup affiliation for the Podolian and non-Podolian mtDNA sequences.

<p>Haplogroup frequencies (%) are in parentheses.</p

Analysis of molecular variance (AMOVA).

<p>Analysis of molecular variance (AMOVA).</p