Human populations are often dichotomized into “isolated” and “open” categories using cultural and/or geographical barriers to gene flow as differential criteria. Although widespread, the use of these alternative categories could obscure further heterogeneity due to inter-population differences in effective size, growth rate, and timing or amount of gene flow. We compared intra and inter-population variation measures combining novel and literature data relative to 87,818 autosomal SNPs in 14 open populations and 10 geographic and/or linguistic European isolates. Patterns of intra-population diversity were found to vary considerably more among isolates, probably due to differential levels of drift and inbreeding. The relatively large effective size estimated for some population isolates challenges the generalized view that they originate from small founding groups. Principal component scores based on measures of intra-population variation of isolated and open populations were found to be distributed along a continuum, with an area of intersection between the two groups. Patterns of inter-population diversity were even closer, as we were able to detect some differences between population groups only for a few multidimensional scaling dimensions. Therefore, different lines of evidence suggest that dichotomizing human populations into open and isolated groups fails to capture the actual relations among their genomic features.
Biobanks, which contain human biological samples and/or data, provide a crucial contribution to the progress of biomedical research. However, the effective and efficient use of biobank resources depends on their accessibility. In fact, making bio-resources promptly accessible to everybody may increase the benefits for society. Furthermore, optimizing their use and ensuring their quality will promote scientific creativity and, in general, contribute to the progress of bio-medical research. Although this has become a rather common belief, several laboratories are still secretive and continue to withhold 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. The survey involved a total of 46 biobanks. Most of them gave permission to access their samples (95.7%) and data (85.4%), but free and unconditioned accessibility seemed not to be common practice. The analysis of the guidelines regarding the accessibility to resources of the biobanks that responded to the survey highlights three issues: (i) the request for applicants to explain what they would like to do with the resources requested; (ii) the role of funding, public or private, in the establishment of fruitful collaborations between biobanks and research labs; (iii) the request of co-authorship in order to give access to their data. These results suggest that economic and academic aspects are involved in determining the extent of sample and data sharing stored in biobanks. As a second step of this study, we investigated the reasons behind the high diversity of requirements to access biobank resources. The analysis of informative answers suggested that the different modalities of resource accessibility seem to be largely influenced by both social context and legislation of the countries where the biobanks operate.
Objectives: Tunisia has been a crossroads for people from Africa, Europe, and the Middle East since prehistoric times. At present, it is inhabited by two main ethnic groups, Arabs and Berbers, and several minorities. This study aims to advance knowledge regarding their genetic structure using new population samplings and a genome-wide approach. Materials and Methods: We investigated genomic variation, estimated ancestry components and dated admixture events in three Berber and two Arab populations from Southern Tunisia, mining a dataset including Middle Eastern, sub-Saharan, and European populations. Results: Differences in the proportion of North African, Arabian, and European ancestries and the varying impact of admixture and isolation determined significant heterogeneity in the genetic structure of Southern Tunisian populations. Admixture time estimates show a multilayer pattern of admixture events, involving both ethnolinguistic groups, which started around the mid XI century and lasted for nearly five centuries. Discussion: Our study provides evidence that the relationships between genetic and cultural diversity of old and new inhabitants of North Africa in southern Tunisia follow different patterns. The Berbers seem to have preserved a significant part of their common genomic heritage despite Islamization, Arab cultural influence, and linguistic diversity. Compared to Morocco and Algeria, southern Tunisian Arabs have retained a higher level of Arabian ancestry. This is more evident in the semi-nomad R'Baya, who have kept their original Bedouin lifestyle, than in the population from Douz, who have undergone multiple events of stratification and admixture.
1Biobanks hold human biological samples and/or data giving a crucial contribution to the progress 2 of biomedical research. However, the effective and efficient exploitation of these resources 3 depends on their accessibility. In fact, making bio-resources promptly accessible to all, can 4 favour collaboration among research groups as well as multidisciplinarity. Although this has 5 become a rather common belief, several laboratories still apply secrecy and withholding of 6 samples and data. In this study we conducted a questionnaire based survey in order to investigate 7 sample and data accessibility in research biobanks operating all over the world. 46 out of the 238 8 contacted biobanks have decided to participate. Most of them provide permission to access their 9 samples (95.7%) and data (85.4%), but free and unconditioned accessibility seems not to be a 10 common practice. The analysis of the biobanks guidelines regarding the accessibility of their 11 resources reveal the importance of three aspects: (i) request for applicants to explain what they 12 would like to do with the required resources; (ii) the role of funding, public or private, in the 13 establishment of fruitful collaborations between biobanks and research labs; (iii) request of co-14 authorship in order to give access to their data. These results suggest that economic and academic 15 aspects are involved in determining the extent of sharing of samples and data stored in biobanks. 16As a second step of this study, we investigated the reasons behind the high diversity of the 17 requirements for accessing to biobanks' resources. The analysis of informative answers suggested 18 that the different modalities of resource accessibility seem to be largely influenced by both social 19 context and legislation of the countries where biobanks operate. 20 21Keywords: open science, data sharing, human subjects, research ethics, biorepository. 22 23PeerJ PrePrints | https://dx.doi.org/10.7287/peerj.preprints.1212v1 | CC-BY 4.0 Open Access |
A number of studies carried out since the early ‘70s has investigated the effects of isolation on genetic variation within and among human populations in diverse geographical contexts. However, no extensive analysis has been carried out on the heterogeneity among genomes within isolated populations. This issue is worth exploring since events of recent admixture and/or subdivision could potentially disrupt the genetic homogeneity which is to be expected when isolation is prolonged and constant over time. Here, we analyze literature data relative to 87,815 autosomal single-nucleotide polymorphisms, which were obtained from a total of 28 European populations. Our results challenge the traditional paradigm of population isolates as structured as genetically (and genomically) uniform entities. In fact, focusing on the distribution of variance of intra-population diversity measures across individuals, we show that the inter-individual heterogeneity of isolated populations is at least comparable to the open ones. More in particular, three small and highly inbred isolates (Sappada, Sauris and Timau in Northeastern Italy) were found to be characterized by levels of inter-individual heterogeneity largely exceeding that of all other populations, possibly due to relatively recent events of genetic introgression. Finally, we propose a way to monitor the effects of inter-individual heterogeneity in disease-gene association studies.
Biobanks hold human biological samples and/or data giving a crucial contribution to the progress of biomedical research. However, the effective and efficient exploitation of these resources depends on their accessibility. In fact, making bio-resources promptly accessible to all, can favour collaboration among research groups as well as multidisciplinarity. 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. The analysis of the biobanks guidelines regarding the accessibility of their resources reveal the importance of three aspects: (i) request for applicants to explain what they would like to do with the required resources; (ii) the role of funding, public or private, in the establishment of fruitful collaborations between biobanks and research labs; (iii) request of co-authorship 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 behind the high diversity of the requirements for accessing to biobanks’ resources. The analysis of informative answers suggested that the different modalities of resource accessibility seem to be largely influenced by both social context and legislation of the countries where biobanks operate.
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.
28A number of studies carried out since the early '70s has investigated the effects of isolation on genetic 29 variation within and among human populations in diverse geographical contexts. However, no extensive 30 analysis has been carried out on the heterogeneity among genomes within isolated populations. This issue 31 is worth exploring since events of recent admixture and/or subdivision could potentially disrupt the 32 genetic homogeneity which is to be expected when isolation is prolonged and constant over time. Here, 33 we analyze literature data relative to 87,818 autosomal single-nucleotide polymorphisms, which were 34 obtained from a total of 28 European populations. Our results challenge the traditional paradigm of 35 population isolates as genetically (and genomically) uniform entities. In fact, focusing on the distribution 36 of variance of intra-population diversity measures across individuals, we show that the inter-individual 37 heterogeneity of isolated populations is at least comparable to the open ones. More in particular, three 38 small and highly inbred isolates (Sappada, Sauris and Timau in Northeastern Italy) were found to be 39 characterized by levels of this parameter largely exceeding that of all other populations, possibly due to 40 relatively recent events of genetic introgression. Finally, we propose a way to monitor the effects of inter-41 individual heterogeneity in disease-gene association studies. 42 43 the Cimbrians since it lacked consistent signatures of genetic isolation. Despite its limits [15], we maintain
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