Evaluating mtDNA patterns of genetic isolation using a re-sampling procedure: A case study on Italian populations

<p><b>Background:</b> A number of studies which have investigated isolation patterns in human populations rely on the analysis of intra- and inter-population genetic statistics of mtDNA polymorphisms. However, this approach makes it difficult to differentiate between the effects of long-term genetic isolation and the random fluctuations of statistics due to reduced sample size.</p> <p><b>Aim:</b> To overcome the confounding effect of sample size when detecting signatures of genetic isolation.</p> <p><b>Subjects and methods:</b> A re-sampling based procedure was employed to evaluate reduction in intra-population diversity, departure from surrounding genetic background and demographic stationarity in 34 Italian populations subject to isolation factors.</p> <p><b>Results:</b> Signatures of genetic isolation were detected for all three statistics in seven populations: Pusteria valley, Sappada, Sauris, Timau settled in the eastern Italian Alps and Cappadocia, Filettino and Vallepietra settled in the Appenines. However, this study was unable to find signals for any of the statistics analysed in 19 populations. Finally, eight populations showing signals of isolation were found for one or two statistics.</p> <p><b>Conclusion:</b> The analysis revealed that the use of population genetic statistics combined with re-sampling procedure can help detect signatures of genetic isolation in human populations, even using a single, although highly informative, locus like mtDNA.</p

Procedure used to analyze data sharing in papers regarding human genetic variation.

<p>We retrieved a total of 1187 papers indexed between 1^st January 2008 and 31^st December 2011 in the PubMed using the key words “mtDNA human populations” and “Y chromosome human populations”. We set the following limits: “humans” for species and “English” for language. The procedure used for data request by email is described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037552#pone-0037552-g002" target="_blank">figure 2</a>. E-mails “will provide on request” were sent to the corresponding authors to request information from papers where data availability upon request is explicitly declared; E-mails “all authors” were sent to all corresponding authors who withheld datasets.</p

Data sharing rates in studies of genetic variation of mitochondrial and Y-chromosomal variation in human populations.

<p>Data sharing rates in studies of genetic variation of mitochondrial and Y-chromosomal variation in human populations.</p

Geographic location of the populations analysed in this study.

<p>Population labels: (1) Lessinia; (2) Sappada; (3) Sauris; (4) Timau.</p

Analysis of Molecular Variance (AMOVA) in four groups of linguistic population isolates.

<p>Population acronyms and references: LES Lessinia, SAP Sappada, SAU Sauris and TIM Timau (This study); LVB Val Badia and LVG Val Gardena <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056371#pone.0056371-Thomas1" target="_blank">[10]</a>, LUS Luserna and LVF Val di Fassa (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056371#pone.0056371-Coia1" target="_blank">[66]</a>, Coia V. unpublished data); AAP Andon Poci, ADU Dukasi, AKR Krusevo and AST Stip <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056371#pone.0056371-Bosch2" target="_blank">[67]</a>.</p

Posterior densities of Fst genetic distances for three micro-evolutionary scenarios.

<p>Frame A and B show mtDNA and Y chromosome diversity, respectively. Frames C and D show the proportion of mtDNA and Y chromosome simulations, respectively, with Fst values falling within different ranges around the observed Fst values (5%, 10%, 15%, 20%, and 25%, from left to right).</p

Ratios of effective population size and estimates of gene flow.

<p>Abbreviations: N1/N2, effective population size ratio between population 1 and population 2; m1-2, effective number of haplotypes migrating from population 1 to population 2 per year; m2-1, effective number of haplotypes migrating from population 2 to population 1 per year. 95% credibility intervals in brackets.</p

Multi-dimensional scaling plots of Fst genetic distances among European populations.

<p>(a) Plot based on mtDNA HVR1 and HVR2 sequences (stress value = 0.067). Population acronyms: BOL, Bologna; BOS, Bosnia; BUD, Budapest; ITC, Central Italy; CZE, Czech Republic; FRA, France; LES, Lessinia; GNE, North-East Germany; POR, Portugal; SAP, Sappada; SAU, Sauris; SLO, Slovenia; GRS, South Germany; SWI, South-West Switzerland; SPA, Spain; TIM, Timau; VOJ, Vojvodina; AUW, West Austria; GRW, West Germany; SLW, West Slovakia (References in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056371#pone.0056371.s002" target="_blank">Table S1</a>); (b) Plot based on mtDNA HVR1 sequences only (stress value = 0.173). Populations acronyms as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056371#pone.0056371.s003" target="_blank">Table S2</a>. Linguistic and/or geographic isolates are marked in red.</p