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      Phylogenetic Relationships of Three Italian Merino-Derived Sheep Breeds Evaluated through a Complete Mitogenome Analysis

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          Abstract

          In Italy, the crisis of the wool industry triggered the necessity to reconvert the two traditional Merino-derived breeds, Gentile di Puglia and Sopravissana, to meat production, by creating the Merinizzata Italiana. The aim of the present study was to assess the genetic diversity of these three Italian Merino-derived (IMd) breeds by examining the molecular information encoded in the maternally-inherited mitochondrial DNA (mtDNA). A parallel molecular investigation was performed on the putative paternal and maternal breeds, the Merino from Spain and the Appenninica from Italy, respectively, as well as on three unrelated dairy breeds (Sarda and Comisana from Italy, and Lacaune from France). Firstly, the mtDNA control region of 291 samples was analyzed. When comparing the overall genetic distances among the eight stocks, the three IMd breeds clustered together close to the Appenninica, thus confirming its parental role. Among the 90 IMd samples, 82 different haplotypes were observed, almost all belonging to haplogroup B, and only one to A. For 23 mtDNAs, including nine IMd, the analysis was then brought to the level of entire mitogenomes. Three distinct sub-haplogroups within B were found to encompass the IMd samples, with one clade (B1a2a1) apparently restricted to those sheep. Thus, despite experiencing a drastic reduction in number (mainly due to changes in breeding practices driven by the economy), the IMd breeds still represent a reservoir of distinctive mitochondrial variants, which could potentially contribute to the development of conservation and management programs of Italian sheep breeds.

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          Arlequin (version 3.0): An integrated software package for population genetics data analysis

          Arlequin ver 3.0 is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework. Arlequin 3 introduces a completely new graphical interface written in C++, a more robust semantic analysis of input files, and two new methods: a Bayesian estimation of gametic phase from multi-locus genotypes, and an estimation of the parameters of an instantaneous spatial expansion from DNA sequence polymorphism. Arlequin can handle several data types like DNA sequences, microsatellite data, or standard multi-locus genotypes. A Windows version of the software is freely available on http://cmpg.unibe.ch/software/arlequin3.
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            DNA markers reveal the complexity of livestock domestication.

            A series of recent genetic studies has revealed the remarkably complex picture of domestication in both New World and Old World livestock. By comparing mitochondrial and nuclear DNA sequences of modern breeds with their potential wild and domestic ancestors, we have gained new insights into the timing and location of domestication events that produced the farm animals of today. The real surprise has been the high number of domestication events and the diverse locations in which they took place - factors which could radically change our approach to conserving livestock biodiversity resources in the future.
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              The molecular dissection of mtDNA haplogroup H confirms that the Franco-Cantabrian glacial refuge was a major source for the European gene pool.

              Complete sequencing of 62 mitochondrial DNAs (mtDNAs) belonging (or very closely related) to haplogroup H revealed that this mtDNA haplogroup--by far the most common in Europe--is subdivided into numerous subhaplogroups, with at least 15 of them (H1-H15) identifiable by characteristic mutations. All the haplogroup H mtDNAs found in 5,743 subjects from 43 populations were then screened for diagnostic markers of subhaplogroups H1 and H3. This survey showed that both subhaplogroups display frequency peaks, centered in Iberia and surrounding areas, with distributions declining toward the northeast and southeast--a pattern extremely similar to that previously reported for mtDNA haplogroup V. Furthermore, the coalescence ages of H1 and H3 (~11,000 years) are close to that previously reported for V. These findings have major implications for the origin of Europeans, since they attest that the Franco-Cantabrian refuge area was indeed the source of late-glacial expansions of hunter-gatherers that repopulated much of Central and Northern Europe from ~15,000 years ago. This has also some implications for disease studies. For instance, the high occurrence of H1 and H3 in Iberia led us to re-evaluate the haplogroup distribution in 50 Spanish families affected by nonsyndromic sensorineural deafness due to the A1555G mutation. The survey revealed that the previously reported excess of H among these families is caused entirely by H3 and is due to a major, probably nonrecent, founder event.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2013
                9 September 2013
                : 8
                : 9
                : e73712
                Affiliations
                [1 ]Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia, Italy
                [2 ]Dipartimento di Biologia Applicata, Università degli Studi di Perugia, Perugia, Italy
                [3 ]Dipartimento di Agronomia Animali Alimenti risorse Naturali e Ambiente, Università degli Studi di Padova, Padova, Italy
                [4 ]Dipartimento di Patologia, Diagnostica e Clinica Veterinaria, Università degli Studi di Perugia, Perugia, Italy
                [5 ]Departamento de Génetica, Universidad de Córdoba, Cordoba, Spain
                University of Florence, Italy
                Author notes

                Competing Interests: The authors confirm that Alessandro Achilli is a PLOS ONE Editorial Board member. After having carefully read the journal’s policy, the authors confirm that this does not alter their adherence to all the PLOS ONE policies on sharing data and materials.

                Conceived and designed the experiments: HL FMS EL AA. Performed the experiments: HL PDL SC AM. Analyzed the data: HL UAP EL AA. Contributed reagents/materials/analysis tools: VL MTA FMS EL AA. Performed the collection of biological samples: AM VL MTA EL. Wrote the manuscript with contributions from the other authors: HL UAP EL AA.

                Article
                PONE-D-13-14582
                10.1371/journal.pone.0073712
                3767607
                24040036
                f11ceec0-9cbc-4123-9e06-6b0c4ad2a4cf
                Copyright @ 2013

                This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 10 April 2013
                : 28 July 2013
                Page count
                Pages: 10
                Funding
                This research received support from the Italian Ministry of the University: Progetti Ricerca Interesse Nazionale 2009 (to AA) and FIRB-Futuro in Ricerca 2008 and 2012 (Italian Ministry of the University) (to AA). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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