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

Frequencies of sharing modalities in the four genetic research fields analyzed.

<p>Rates of usage of different sharing modalities based on the inspection of papers indexed in Medline from 01/01/2008 to 31/12/2011. The total number of scrutinized datasets for each field of research is reported in parentheses. It should be noted that the modality “will provide on request” was observed only by Milia et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0121409#pone.0121409.ref032" target="_blank">32</a>].</p

Results of the questionnaire-based survey.

<p>Rates of responses to the question “What is the contribution of the following factors to the higher rate of data sharing in DNA studies of ancient compared to extant humans?”. The absolute values are given in parentheses. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0121409#sec002" target="_blank">Materials and Methods</a> for complete statements.</p

Sharing rates in papers concerning mitochondrial and Y chromosomal polymorphisms in humans.

<p>Vertical bars indicate 95% confidence intervals. The total number of scrutinized datasets for each field of research is reported in parentheses. All papers were indexed in Medline from 1/1/2008 to 31/12/2011.</p

Data sharing modalities in human paleogenetics.

<p>Absolute counts are in parentheses.</p><p>Data sharing modalities in human paleogenetics.</p

Capocasa et al - Research biobanks Providing information and sharing resources Isita Conference presentation 19-05-2015

<p>Biobanks hold human biological samples and/or data giving a crucial contribution to the progress of<br>biomedical research. However, the effective and efficient exploitation of these resources depends on their accessibility. In fact, making bioresources promptly accessible to all, collaboration among research groups and multidisciplinarity are encouraged. Although this has become a rather common belief, several laboratories still apply secrecy and withholding of samples and data. In this study we conducted a questionnaire based survey in order to investigate sample and data accessibility in research biobanks operating all over the world. 46 out of the 238 contacted biobanks have decided to participate. Most of them provide permission to access their samples (95.7%) and data (85.4%), but free and unconditioned accessibility seems not to be a common practice. Three aspects are mainly considered in the biobanks guidelines as information needed in order to gain access to their resources: (i) request for applicants to explain what they would like to do with the required resources; (ii) the role of origin of research funds in the establishment of fruitful collaborations between biobanks and research labs; (iii) request of coauthorship in order to give access to their data. These results suggest that economic and academic aspects are involved in determining the extent of sharing of samples and data stored in biobanks. As a second step of this study, we investigated the reasons for the observed high heterogeneity of the requirements for the access to the biobanks’ resources. The analysis of informative answers suggested that the different<br>modalities of resource accessibility seem to be highly influenced by social context and legislations of the<br>countries where biobanks operate.</p

Cumulative distributions of papers on ancient human DNA from 1988 to 2013 according to the genetic system investigated.

<p>Cumulative distributions of papers on ancient human DNA from 1988 to 2013 according to the genetic system investigated.</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