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BackgroundThe Sahelian Fulani are the largest nomadic pastoral ethnic group. Their origins are still largely unknown and their Eurasian genetic component is usually explained by recent admixture events with northern African groups. However, it has also been proposed that Fulani may be the descendants of ancient groups settled in the Sahara during its last Green phase (12000-5000 BP), as also suggested by Y chromosome results.ResultsWe produced 23 high-coverage (30 ×) whole genomes from Fulani individuals from 8 Sahelian countries, plus 17 samples from other African groups and 3 Europeans as controls, for a total of 43 new whole genome sequences. These data have been compared with 814 published modern whole genomes and analyzed together with relevant published ancient individuals (for a total of > 1800 samples). These analyses showed that the non-sub-Saharan genetic ancestry component of Fulani cannot be only explained by recent admixture events, but it could be shaped at least in part by older events by events more ancient than previously reported, possibly tracing its origin to the last Green Sahara.ConclusionsAccording to our results, Fulani may be the descendants of Saharan cattle herders settled in that area during the last Green Sahara. The exact ancestry composition of such ghost Saharan population(s) cannot be completely unveiled from modern genomes only, but the joint analysis with the available African ancient samples suggested a similarity between ancient Saharans and Late Neolithic Moroccans.

Open Access (OA) to research publications is a fundamental resource for the advancement of scientific research. To facilitate the transition to OA, publishers and institutions have begun negotiating the so-called transformative agreements, contracts combining access to subscription journals with the ability to publish OA. While the debate on transformative agreements is very much alive, little attention is being paid to the "green road," the practice of openly self-archiving manuscripts that have been accepted by journals but not yet typeset. Here we focus on medical literature, showing how the green road could outperform transformative agreements as a means of increasing the full and free availability of peer-reviewed scientific papers.

Since prehistoric times, Italy has represented a bridge between peoples, genes and cultures. Its peculiar geographical position explains why: it is located in the center of the Mediterranean Sea, flanked by the Balkans and the Hellenic Peninsula to the east, Iberia to the west and surrounded by North Africa to the south and central Europe to the north. This makes Italy of extraordinary interest for the study of some different aspects of human diversity. Here we overview current knowledge regarding the relationships between the structure of the genetic variation of Italian populations and the geographical, ecological and cultural factors that have characterized their evolutionary history. Human presence in Italian territory is deeply rooted in the past. Lithic artifacts produced by the genus Homo and remains of Homo sapiens are among the earliest to have been found on the continent, as shown by the lithic industry of Pirro Nord (between 1.3 and 1.6 Mya) and the dental remains of the "Grotta del Cavallo" (between 45 and 43 Kya). Genetic and genomic studies relating to existing and extinct human groups have shed light on the migrations from Europe, Africa and Asia that created the ancient layers of the genetic structure of today's Italian populations, especially before the Iron Age. The important role of isolation (genetic and cultural) in shaping genetic structure is clearly visible in the patterns of intra- and inter-population diversity observed among Italian ethno-linguistic minorities that settled on the peninsula and on the major islands until the 19th century. Finally, selective pressures have likely driven the distribution of originally adaptive variants and haplotypes that now confer protection or susceptibility to major diseases such as diabetes and cardiovascular disease (in northern Italy) and tuberculosis and leprosy (in the south). What emerges is a picture where the combined effects of migration, isolation and natural selection generated by the interplay of geography, environment and culture have shaped a complex pattern of human diversity that is unique in Europe and which goes hand in hand with today's rich animal and plant biodiversity. In a nutshell, scientific evidence and cultural heritage paint Italy as a place with extremely diverse environments where distant peoples have met since the deep past, bringing and sharing genes and ideas.

SummaryIn this manuscript, we present an analysis of open access (OA) rates of papers concerning COVID-19 and other important human diseases, whose results helped develop an evidence-based scalable strategy aimed at increasing the full and timely access to medical literature. We show that COVID-19 papers are much more openly available (OA rate of 89.5%) than those concerning the four most recent viral outbreaks (Avian influenza, Middle East Respiratory Syndrome, Severe Acute Respiratory Syndrome, Swine influenza; OA rates (from 26.2% to 51.3%) and the ten non COVID-19 disease categories responsible for the highest number of deaths worldwide (OA rates from 44.0% for “Maternal and neonatal disorders” to 58.9% for “Respiratory infections and tuberculosis”). This evidence confronts us with an inevitable question: how can we bridge the gap between OA rates for COVID-19 and other high-impact human diseases? Based on empirical data and projections, we show that it is possible to increase substantially immediate OA to publicly-funded research and complement more demanding initiatives for access to medical literature in developing countries working on the sharing of post-prints at individual, group and multi stakeholder partnership level. However, to make our plan effective in bringing us closer to the “health information for all” goal a more widespread culture of cooperation is fundamental. We argue that the lesson taught by COVID-19 is a unique opportunity to raise awareness among researchers and stakeholders about the importance of open science for human health and to demonstrate that a real change is now possible.

Y chromosome short tandem repeats (Y-STRs) are commonly used to identify male lineages for investigative and judicial purposes and could represent the only source of male-specific genetic information from unbalanced female-male mixtures. The Yfiler Plus multiplex, which includes twenty conventional and seven rapidly-mutating Y-STRs, represents the most discriminating patrilineal system commercially available to date. Over the past five years, this multiplex has been used to analyze several Eurasian populations, with a reported discrimination capacity (DC) approaching or corresponding to the highest possible value. However, despite the inclusion of rapidly mutating Y-STRs, extensive haplotype sharing was still reported for some African populations due to a number of different factors affecting the effective population size. In the present study, we analyzed 27 Y-STRs included in the Yfiler Plus multiplex and 82 Y-SNPs in central Sahel (northern Cameroon and western Chad), an African region characterized by a strong ethnic fragmentation and linguistic diversity. We evaluated the effects of population sub-structuring on genetic diversity by stratifying a sample composed of 431 males according to their ethnicity (44 different ethnic groups) and urbanization degree (four villages and four towns). Overall, we observed a low discrimination capacity (DC = 0.90), with 71 subjects (16.5 %) sharing 27 Y-STR haplotypes. Haplotype sharing was essentially limited to subjects with the same binary haplogroup, coming from the same location and belonging to the same ethnic group. Haplotype sharing was much higher in rural areas (average DC = 0.83) than urban settlements (average DC = 0.96) with a significant correlation between DC and census size (r = 0.89; p = 0.003). Notably, we found that genetic differentiation between villages from the same country ( Φ ST = 0.14) largely exceeded that found among countries ( Φ ST = 0.02). These findings have important implications for the choice of the appropriate reference population database to evaluate the statistical relevance of forensic Y-haplotype matches.

The characterization of the structure of southern African populations has been the subject of numerous genetic, medical, linguistic, archaeological, and anthropological investigations. Current diversity in the subcontinent is the result of complex events of genetic admixture and cultural contact between early inhabitants and migrants that arrived in the region over the last 2000 years. Here, we analyze 1856 individuals from 91 populations, comprising novel and published genotype data, to characterize the genetic ancestry profiles of 631 individuals from 51 southern African populations. Combining both local ancestry and allele frequency based analyses, we identify a tripartite, ancient, Khoesan-related genetic structure. This structure correlates neither with linguistic affiliation nor subsistence strategy, but with geography, revealing the importance of isolation-by-distance dynamics in the area. Fine-mapping of these components in southern African populations reveals admixture and cultural reversion involving several Khoesan groups, and highlights that Bantu speakers and Coloured individuals have different mixtures of these ancient ancestries.

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 ethno-linguistic 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.

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.

The study of geographically and/or linguistically isolated populations could represent a potential area of interaction between population and forensic genetics. These investigations may be useful to evaluate the suitability of loci which have been selected using forensic criteria for bio-anthropological studies. At the same time, they give us an opportunity to evaluate the efficiency of forensic tools for parentage testing in groups with peculiar allele frequency profiles. Within the frame of a long-term project concerning Italian linguistic isolates, we studied 15 microsatellite loci (Identifiler kit) comprising the CODIS panel in 11 populations from the north-eastern Italian Alps (Veneto, Trentino and Friuli Venezia Giulia regions). All our analyses of inter-population differentiation highlight the genetic distinctiveness of most Alpine populations comparing them either to each other or with large and non-isolated Italian populations. Interestingly, we brought to light some aspects of population genetic structure which cannot be detected using unilinear polymorphisms. In fact, the analysis of genotypic disequilibrium between loci detected signals of population substructure when all the individuals of Alpine populations are pooled in a single group. Furthermore, despite the relatively low number of loci analyzed, genetic differentiation among Alpine populations was detected at individual level using a Bayesian method to cluster multilocus genotypes. Among the various populations studied, the four linguistic minorities (Fassa Valley, Luserna, Sappada and Sauris) showed the most pronounced diversity and signatures of a peculiar genetic ancestry. Finally, we show that database replacement may affect estimates of probability of paternity even when the local database is replaced by another based on populations which share a common genetic background but which differ in their demographic history. These findings point to the importance of considering the demographic and cultural profile of populations in forensic applications, even in a context of substantial genetic homogeneity such as that of European populations.

Human populations are often dichotomized into “isolated” and “open” 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 interpopulation 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 significantly 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 turned out to be distributed along a sort of 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 fails to capture the actual relations among their genomic features.

Background: 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. Aim: To overcome the confounding effect of sample size when detecting signatures of genetic isolation. Subjects and methods: 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. Results: 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. Conclusion: 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.

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.

Numerous populations spread out across Central Africa have been named Pygmies by Western explorers, since the 19th century, in reference to the mythical Pygmy population from Homer (A people of short stature at war with migrating birds, Iliad, song 3, v. 1-6). For more than forty years, Pygmy populations have attracted the interest of biological anthropologists because they were seen as the lively example that the adaptation to the environment shapes the diversity of external physical or physiological characters (e.g. Froment 1993; Perry and Dominy 2009; Campbell and Tishkoff 2010). Some biological anthropologists and geneticists wrongly perceived Central African Pygmies as a homogeneous group with similar cultural, morphological and biological features, and somewhat opposed to Non-Pygmy populations (often designated as “Bantu populations”, though they do not necessarily speak Bantu languages which Pygmy populations often speak). This view may be seen as the consequence of two misleading notions widespread in the Western culture. First, the prevalent historical use of the single exogenous term “Pygmy” to designate more than twenty human groups from the Congo Basin, de facto suggests that common historical, cultural, and even biological or morphological features are shared by Central African Pygmies. Second, Pygmy populations are often viewed as being exclusively forest hunter-gatherers, isolated from Non-Pygmy farmers, and living in the same way as ancestral human populations did before the Neolithic revolution. Since the 1960's, such stereotypes have been repeatedly challenged by scientific research. For instance, cultural anthropologists observed that the various Pygmy populations do not share a common myth of origin. Most of them do not know each other and are unaware of a common designation as Pygmies from outsiders; in fact the various Aka, Baka, Bongo, Efe (...) Pygmy populations are not a federated group of populations (Bahuchet 1993; Hewlett 1996). Additionally, physical anthropologists have observed the wide diversity of average height across African Pygmy populations and found no height discontinuity between Pygmies and Non-Pygmies—some neighbouring Non-Pygmy populations being also of short stature (Hiernaux 1974, Froment 1993). Finally, it has been highlighted that Pygmies are not exclusive hunter-gatherers, as they often practice fishing and agriculture (e.g. Bahuchet et al. 1989; Bahuchet 1992; Hewlett 1996) and, further challenging stereotypes, Pygmies are not isolated from neighbouring Non-Pygmy populations since these groups of populations have close socioeconomic relationships including intermarriages (e.g. Turnbull 1965; Kazadi 1981; Bahuchet and Guillaume 1982; Hewlett 1996; Joiris 2003).

Summary HLA class I diversity (loci A, B and C) was analysed in four populations, two from North Cameroon (Podokwo and Uldeme) and two from South Cameroon (Ewondo and Bamileke). Northern and southern Cameroon populations show a substantial genetic diversity in terms of haplotype sharing and genetic distances, even despite the low percentage of variance due to differences among populations evidenced by analysis of molecular variance. The signals of differentiation among populations are consistent with their linguistic affiliation, and support previous evidence, based on autosomal microsatellites and protein loci, which has shown that the complex pattern of genetic variation of Cameroon can in part be described by contrasting the northern and southern part of the country. Looking at our results in the more general framework of HLA diversity in sub-Saharan Africa, it turns out that the Podokwo and Uldeme show some genetic links to populations of the southern western branch of the Sahel corridor, while their high frequency of A*02 and C*04 alleles is congruent with previously hypothesised introgression of non-sub-Saharan alleles. On the other hand, signals of shared ancestry between the Bamileke and Ewondo and the Bantu speakers from central and southern Africa were detected.

The current distribution of Bantu languages is commonly considered to be a consequence of a relatively recent population expansion (3–5 kya) in Central Western Africa. While there is a substantial consensus regarding the centre of origin of Bantu languages (the Benue River Valley, between South East Nigeria and Western Cameroon), the identification of the area from where the population expansion actually started, the relation between the processes leading to the spread of languages and peoples and the relevance of local migratory events remain controversial. In order to shed new light on these aspects, we studied Y chromosome variation in a broad dataset of populations encompassing Nigeria, Cameroon, Gabon and Congo. Our results evidence an evolutionary scenario which is more complex than had been previously thought, pointing to a marked differentiation of Cameroonian populations from the rest of the dataset. In fact, in contrast with the current view of Bantu speakers as a homogeneous group of populations, we observed an unexpectedly high level of interpopulation genetic heterogeneity and highlighted previously undetected diversity for lineages associated with the diffusion of Bantu languages (E1b1a (M2) sub-branches). We also detected substantial differences in local demographic histories, which concord with the hypotheses regarding an early diffusion of Bantu languages into the forest area and a subsequent demographic expansion and migration towards eastern and western Africa.

This study analyzes data sharing regarding mitochondrial, Y chromosomal and autosomal polymorphisms in a total of 162 papers on ancient human DNA published between 1988 and 2013. The estimated sharing rate was not far from totality (97.6% +/- 2.1%) and substantially higher than observed in other fields of genetic research (evolutionary, medical and forensic genetics). Both a questionnaire-based survey and the examination of Journals' editorial policies suggest that this high sharing rate cannot be simply explained by the need to comply with stakeholders requests. Most data were made available through body text, but the use of primary databases increased in coincidence with the introduction of complete mitochondrial and next-generation sequencing methods. Our study highlights three important aspects. First, our results imply that researchers' awareness of the importance of openness and transparency for scientific progress may complement stakeholders' policies in achieving very high sharing rates. Second, widespread data sharing does not necessarily coincide with a prevalent use of practices which maximize data findability, accessibility, useability and preservation. A detailed look at the different ways in which data are released can be very useful to detect failures to adopt the best sharing modalities and understand how to correct them. Third and finally, the case of human paleogenetics tells us that a widespread awareness of the importance of Open Science may be important to build reliable scientific practices even in the presence of complex experimental challenges.

The hypervariable region-1 and four nucleotide positions (10400, 10873, 12308, and 12705) of the coding region of mitochondrial DNA (mtDNA) were analyzed in 441 individuals belonging to eight populations (Daba, Fali, Fulbe, Mandara, Uldeme, Podokwo, Tali, and Tupuri) from North Cameroon and four populations (Bakaka, Bassa, Bamileke, and Ewondo) from South Cameroon. All mtDNAs were assigned to five haplogroups: three sub-Saharan (L1, L2, and L3), one northern African (U6), and one European (U5). Our results contrast with the observed high frequencies of a Y-chromosome haplogroup of probable Asian origin (R1*-M173) in North Cameroon. As a first step toward a better understanding of the evident discrepancy between mtDNA and Y-chromosome data, we propose two contrasting scenarios. The first one, here termed "migration and asymmetric admixture," implies a back migration from Asia to North Cameroon of a population group carrying the haplotype R1*-M173 at high frequency, and an admixture process restricted to migrant males. The second scenario, on the other hand, temed "divergent drift," implies that modern populations of North Cameroon originated from a small population group which migrated from Asia to Africa and in which, through genetic drift, Y-chromosome haplotype R1*-M173 became predominant, whereas the Asian mtDNA haplogroups were lost.

The levels of haplotype diversity within the lineages defined by two single-nucleotide polymorphisms (SNPs) (-13910 C/T and -22018 G/A) associated with human lactase persistence were assessed with four fast-evolving microsatellite loci in 794 chromosomes from Portugal, Italy, Fulbe from Cameroon, Sao Tome and Mozambique. Age estimates based on the intraallelic microsatellite variation indicate that the -13910*T allele, which is more tightly associated with lactase persistence, originated in Eurasia before the Neolithic and after the emergence of modern humans outside Africa. We detected significant departures from neutrality for the -13910*T variant in geographically and evolutionary distant populations from southern Europe (Portuguese and Italians) and Africa (Fulbe) by using a neutrality test based on the congruence between the frequency of the allele and the levels of intraallelic variability measured by the number of mutations in adjacent microsatellites. This result supports the role of selection in the evolution of lactase persistence, ruling out possible confounding effects from recombination suppression and population history. Reevaluation of the available evidence on variation of the -13910 and -22018 loci indicates that lactase persistence probably originated from different mutations in Europe and most of Africa, even if 13910*T is not the causal allele, suggesting that selective pressure could have promoted the convergent evolution of the trait. Our study shows that a limited number of microsatellite loci may provide sufficient resolution to reconstruct key aspects of the evolutionary history of lactase persistence, providing an alternative to approaches based on large numbers of SNPs.

To investigate associations between genetic, linguistic, and geographic variation in Africa, we type 50 Y chromosome SNPs in 1122 individuals from 40 populations representing African geographic and linguistic diversity. We compare these patterns of variation with those that emerge from a similar analysis of published mtDNA HVS1 sequences from 1918 individuals from 39 African populations. For the Y chromosome, Mantel tests reveal a strong partial correlation between genetic and linguistic distances (r=0.33, P=0.001) and no correlation between genetic and geographic distances (r=-0.08, P>0.10). In contrast, mtDNA variation is weakly correlated with both language (r=0.16, P=0.046) and geography (r=0.17, P=0.035). AMOVA indicates that the amount of paternal among-group variation is much higher when populations are grouped by linguistics (Phi(CT)=0.21) than by geography (Phi(CT)=0.06). Levels of maternal genetic among-group variation are low for both linguistics and geography (Phi(CT)=0.03 and 0.04, respectively). When Bantu speakers are removed from these analyses, the correlation with linguistic variation disappears for the Y chromosome and strengthens for mtDNA. These data suggest that patterns of differentiation and gene flow in Africa have differed for men and women in the recent evolutionary past. We infer that sex-biased rates of admixture and/or language borrowing between expanding Bantu farmers and local hunter-gatherers played an important role in influencing patterns of genetic variation during the spread of African agriculture in the last 4000 years.

Understanding the relations between social and biological factors in determining the evolution of human populations is one of the principal aims of bio-anthropological research. The recent introduction of unilinearly transmitted polymorphisms of mitochondrial DNA and Y-chromosome has disclosed new possibilities for the study of bio-cultural evolutionary processes. In this communication, I present a study on the relationships between social structure and genetic variation in sub-Saharan Africa based on published and unpublished mitochondrial and Y-chromosomal data relative to a total of 40 populations. The results obtained reveal a striking difference in the genetic structure of farming (Bantu speakers) and hunting-gathering (Pygmies and Bushmen) populations. To explain this difference, I propose that asymmetric gene flow, polyginy and patrilocality, and hence the socio-cultural factors underlying them, have had an important role in determining and differentiating the genetic structure of sub-Saharan populations. The limits and the implications of this study are discussed.

This study analyzes the variation of six binary polymorphisms and six microsatellites in the Mbenzele Pygmies from the Central African Republic. Five different haplogroups (B2b, E(xE3a), E3a, P and BR(xB2b,DE,P)) were observed, with frequencies ranging from 0.022 (haplogroup P) to 0.609 (haplogroup E3a). A comparison of haplogroup frequencies indicates a close genetic affinity between the Mbenzele and the Biaka Pygmies, a finding consistent with the common origin and the geographical proximity of the two populations. The haplogroups P, BR(xB2b,DE,P) and E(xE3a), which are rare in sub-Saharan Africa but common in western Eurasia, were observed with frequencies ranging from 0.022 (haplogroup P) to 0.087 (haplogroup E(xE3a)). Thirty different microsatellite haplotypes were detected, with frequencies ranging from 0.022 to 0.152. The Mbenzele share the highest percent of microsatellite haplotypes with the Biaka Pygmies. Five out seven haplotypes which are shared by the Mbenzele and Biaka Pygmies belong to haplogroup E3a, which suggests that they are of Bantu origin. The plot based on F(st) genetic distances calculated using microsatellite data provides a picture of population relationships which is in part congruent and in part complementary to that obtained using haplogroup frequencies. Finally, the Mbenzele and Biaka Pygmies were found to be markedly more genetically similar using Y-chromosomal than autosomal microsatellites. We suggest that this could be due to the higher phylogenetic stability of Y-chromosome and to the effect of the male-biased gene flow during the Bantu expansion.

We have studied the polymorphism of HLA class I in two West African Pygmy populations, namely, the Bakola from Cameroon and the Mbenzele from the Central African Republic. A unique number of HLA alleles and haplotypes showed specific patterns of these populations. In this study, we identify two alleles (B*37, B*41) and three haplotypes (A*30-B*37, A*66-B*41 and A*68-B*58) that appear to be 'private' or typical of Western Pygmies. These data reflect similarities with the AKA Pygmies from the Central African Republic. On the other hand, we failed to identify alleles that are found at high frequencies among other sub-Saharan populations (B*42, B*51). Allelic and haplotypic frequency distributions show differences between the two Pygmy groups, e.g. B*35 was very common in the Mbenzele but has been found to be absent in the Bakola. In contrast, B*53, which is found in the Bakola, has been found to be rare in the Mbenzele Pygmies. In order to analyse the genetic relationships of the Bakola and Mbenzele Pygmies with other sub-Saharan populations, HLA gene frequencies were subjected to the Neighbour-Joining tree analysis. The Mbenzele, Bakola and AKA were found to be relatively close to each other and isolated from other sub-African populations. However, both the genetic distances and the within-group variation suggests that the Bakola are more admixed with Bantu farmers than Mbenzele.

We investigated the occurrence and intra-allelic variability of the T(-13910) variant located upstream of the lactase gene in 965 individuals from 20 different locations of Italy and Greece. The T(-13910) frequency ranges from 0.072 (Sardinia) to 0.237 (North-East Italy), with a statistically significant difference between North-East Italians and other Italian populations. The comparison of the lactose tolerance predicted by T(-13910) and that assessed by other studies using physiological tests shows a one-way statistically significant discrepancy that could be due to sampling differences. However, the possible role of other genetic factors underlying lactase persistence is worth exploring. The time of the most recent common ancestor and departures from neutrality of the T(-13910) allele were assessed using three microsatellite loci. Time estimates were found to be congruent with the appearance of dairy farming in Southern Europe and the occurrence of a single introgression event. Robust signals of selection can be observed in North-East Italy only. We discuss the possible role of cultural traits and genetic history in determining these observed micro-evolutionary patterns. We investigated the occurrence and intra-allelic variability of the T-13910 variant located upstream of the lactase gene in 965 individuals from 20 different locations of Italy and Greece. The T-13910 frequency ranges from 0.072 (Sardinia) to 0.237 (North-East Italy), with a statistically significant difference between North-East Italians and other Italian populations. The comparison of the lactose tolerance predicted by T-13910 and that assessed by other studies using physiological tests shows a one-way statistically significant discrepancy that could be due to sampling differences. However, the possible role of other genetic factors underlying lactase persistence is worth exploring. The time of most recent common ancestor and departures from neutrality of the T-13910 allele were assessed using three micro- satellite loci. Time estimates were found to be congruent with the appearance of dairy farming in Southern Europe and the occurrence of a single introgression event. Robust signals of selection can be observed in North-East Italy only. We discuss the possible role of cultural traits and genetic history in determining these observed micro-evolutionary patterns

The Open Data philosophy has gained considerable momentum in recent years, both in society and the scientific community. The accessibility via web of open data from the public sector has remarkably increased in the last decade, although there are substantial differences among nations (http://datacatalogs.org/). The expectation of many citizens, organizations and pressure groups (the so called “open government” movement) is that the free release of data from public administrations may help increase government transparency and accountability. Reaching this target, however, is, without doubt, a complex task. Numbers should not only be easily discoverable and accessible to everyone, but also arranged in such a way as to make it possible to give a direct answer to simple but important questions (e.g. how economic resources coming from taxpayers are used), and in an available form that allows for further manipulation and mining. Plus, it is necessary to develop effective ways for informed citizens to collaborate with governments in order to have a real impact on public choices. Having gone through these steps, open data practices may actually help establish a connection between politics, bureaucracies and the public and, ultimately, achieve a truly participatory governance (Lathrop & Ruma, 2011).

Variation at the UDP-glucuronosyltransferase (UGT) 1A1 gene promoter is present in humans. Variable numbers of TA repeats in the TATA box of this gene are found which are inversely related to levels of gene expression. We investigated this polymorphism in 658 individuals from a worldwide sample of 15 aboriginal and two admixed human populations. This study shows that there is a great deal of variability across ethnic groups with regard to UGT1A1 allele frequencies, with the most common allele varying in frequency from 33% to 91%. Populations of African origin harbor four different alleles while non-African populations appear to have only two alleles. In addition, alleles associated with lower gene expression levels reach the highest frequencies in populations of African origin and lowest among Asians and Amerindians. Thus, more variability in the metabolism of drugs eliminated by UGT1A1 glucuronidation should be expected in populations of Sub-Saharan African origin. The sequence analysis of nine primate species shows that the number of TA repeats has increased during primate evolution achieving the largest number in humans. We suggest that the UGT1A1 promoter variability does not reflect historical relationships between populations and that it may be maintained by natural selection. Our findings are consistent with the proposal that the TA repeat variation is a balanced polymorphism.

A recent survey conducted on Vanuatu Island suggests that resistance to Plasmodium falciparum in alpha-thalassemic individuals may have an immunological basis. This study is important since it seems to undermine the current idea that red-cell genetic defects give protection against falciparum malaria by reducing intraerythrocytic growth and development of the parasite. However, the mechanisms underlying these clinical and genetic observations are not yet fully understood. Based on a review of the relevant literature, we first show that the model based on the interaction between hemoglobin (Hb) and membrane components may provide a molecular basis for the involvement of the immune response in genetic adaptation to malaria. Second, we discuss the main evolutionary implications of the model. Finally, we suggest two approaches by which anthropological studies could provide a useful way of testing the model: 1) analysis of the interactions of malaria-resistance genes with genetic polymorphisms which affect the erythrocyte redox status and 2) study of the antimalarial effects of natural products (introduced as a part of a diet or for traditional antimalarial therapy) capable of interfering with the Hb/membrane interaction.

Aim: To analyze the human genetic variation of glutathione peroxidases (GPX), estimating the functional differences among human populations and suggesting interethnic differences in predisposition to disease and drug response. Materials & methods: Using 1000 Genomes Project data, we analyzed 723 GPX variants in 1092 individuals belonging to 14 populations. Combining functional prediction analyses of coding and noncoding variants, we developed a method to estimate haplotype functionality. Results: GPX rare variants have a higher functional impact than common variants. The frequency among Asian patients of haplotypes associated with normal functionality is significantly higher for GPX1 and lower for GPX3 than for non-Asian patients; no adaptation signals in GPX1 and GPX3 were found in Asian patients. Conclusion: GPX1 and GPX3 differences may be associated with alterations in antioxidant capacity and redox regulation, which suggests diverse susceptibility to complex disease and diverse response to relevant drugs in Asians compared with individuals with other ethnic origins. Original submitted 7 February 2013; Revision submitted 16 May 2013

[Background] When studying the genetic structure of human populations, the role of cultural factors may be difficult to ascertain due to a lack of formal models. Linguistic diversity is a typical example of such a situation. Patrilocality, on the other hand, can be integrated into a biological framework, allowing the formulation of explicit working hypotheses. The present study is based on the assumption that patrilocal traditions make the hypervariable region I of the mtDNA a valuable tool for the exploration of migratory dynamics, offering the opportunity to explore the relationships between genetic and linguistic diversity. We studied 85 Niger-Congo-speaking patrilocal populations that cover regions from Senegal to Central African Republic. A total of 4175 individuals were included in the study., [Results] By combining a multivariate analysis aimed at investigating the population genetic structure, with a Bayesian approach used to test models and extent of migration, we were able to detect a stepping-stone migration model as the best descriptor of gene flow across the region, with the main discontinuities corresponding to forested areas., [Conclusions] Our analyses highlight an aspect of the influence of habitat variation on human genetic diversity that has yet to be understood. Rather than depending simply on geographic linear distances, patterns of female genetic variation vary substantially between savannah and rainforest environments. Our findings may be explained by the effects of recent gene flow constrained by environmental factors, which superimposes on a background shaped by pre-agricultural peopling., This research was partially supported by the Istituto Italiano di Antropologia and the University of Rome “La Sapienza” (funds to GDB). Sapienza Università di Roma Istituto Italiano di Antropologia (Italia)

We report on the allele distributions in a normal black African population at two microsatellite loci neighbouring the FRAXA locus and at the CGG repeat in the 5' end of the FMR-1 gene, which causes the fragile X syndrome. The CGG repeat distribution was found to be similar to that of other ethnic groups, as well as to that of other non-human primates, possibly predicting a comparable prevalence of fragile X in Africa. Significant linkage disequilibrium has been observed between fragile X mutations and alleles of the DXS548 and FRAXAC1 loci in European and Asian populations, and some founder chromosomes may be extremely old. Those associated with FRAXAC1-A and DXS548-2 alleles are not present in the Asian fragile X samples. We searched for these alleles and their frequency in the well defined Bamileke population of Cameroon. All previously described alleles and some new ones were found in this sample, supporting the hypothesis of their pre-existence and subsequent loss in Asian populations. Finally, the heterozygosity of the Bamileke sample was significantly higher at both marker loci and comparable to that of Europeans at the CGG repeat, confirming the notion that genetic diversity is greater in Africans than in other groups and supporting the view that evolution of modern man started in Africa.

This paper focuses on the interaction between oxidized hemoglobin and the erythrocyte membrane, and its relevance to some falciparum malaria-linked genetic traits. We first present the experimental evidence which suggests that the interaction between hemoglobin derivatives and membrane proteins is an important cellular mechanism for the erythrocytes carrying HbS, HbE, HbF, α- and β-thalassemia, and G6PD deficiency. Thereafter, we show how the Hb/membrane interaction might act as primum movens for diverse cellular mechanisms which 1) reduce invasion of erythrocytes by the falciparum parasite; 2) impair parasite survival and development within the cell; 3) accelerate infected erythrocyte clearance by phagocytosis. We claim that oxidative stress is the driving force of this process, since highly reactive species (like O2− and H2O2) mediate the gradual oxidation of Hb to irreversible hemichrome-containing Heinz bodies. We therefore suggest that positing the interaction between oxidized hemoglobin and cell membrane as a common basis for several falciparum malaria-linked genetic traits is not only consistent with experimental evidence gathered so far, but provides a new, clearer perspective: the molecular event on which these known protective traits rest. In the last part of the paper we will discuss two case studies which provide further support for the role played by hemoglobin derivatives and membrane proteins: 1) the influence of a cyanogen-rich diet on the distribution of Hbβ*S gene frequencies in Liberia (Jackson [1990] Am. J. Hum. Biol. 2:521–532); and 2) population data on polymorphisms at the Hbβ and GPXI loci (Destro-Bisol and Spedini [1989] Am. J. Phys. Anthropol. 79:217–224). © 1996 Wiley-Liss, Inc.

Due to its important effects on the ecological dynamics and the genetic structure of species, biologists have long been interested in gender-biased dispersal, a condition where one gender is more prone to move from the natal site. More recently, this topic has attracted a great attention from human evolutionary geneticists. Considering the close relations between residential rules and social structure, gender-biased dispersal is, in fact, regarded as an important case study concerning the effects of socio-cultural factors on human genetic variation. It all started with the seminal paper by Mark Seielstad, Erich Minch and Luigi Luca Cavalli Sforza from Stanford University (Seielstad et al. 1998). They observed a larger differentiation for Y-chromosome than mitochondrial DNA between extant human populations, purportedly a consequence of the prevalence of long-term patrilocality in human societies. Subsequent studies, however, have highlighted the need to consider geographically close and culturally homogeneous groups, disentangle signals due to different peopling events and obtain unbiased estimates of genetic diversity. In this issue of Molecular Ecology, not only do Marks et al. (2012) adopt an experimental design which addresses these concerns, but they also take a further and important step forward by integrating the genetic analysis of two distant populations, the Basotho and Spanish, with data regarding migration rates and matrimonial distances. Using both empirical evidence and simulations, the authors show that female-biased migration due to patrilocality might shape the genetic structure of human populations only at short ranges and under substantial differences in migration rates between genders. Providing a quantitative framework for future studies of the effects of residential rules on the human genome, this study paves the way for further developments in the field. On a wider perspective, Marks et al.'s work demonstrates the power of approaches which integrate biological, cultural and demographic lines of evidence in the study of relations between social and genetic structures of human populations.

The achievement of a robust, effective and responsible form of data sharing is currently regarded as a priority for biological and bio-medical research. Empirical evaluations of data sharing may be regarded as an indispensable first step in the identification of critical aspects and the development of strategies aimed at increasing availability of research data for the scientific community as a whole. Research concerning human genetic variation represents a potential forerunner in the establishment of widespread sharing of primary datasets. However, no specific analysis has been conducted to date in order to ascertain whether the sharing of primary datasets is common-practice in this research field. To this aim, we analyzed a total of 543 mitochondrial and Y chromosomal datasets reported in 508 papers indexed in the Pubmed database from 2008 to 2011. A substantial portion of datasets (21.9%) was found to have been withheld, while neither strong editorial policies nor high impact factor proved to be effective in increasing the sharing rate beyond the current figure of 80.5%. Disaggregating datasets for research fields, we could observe a substantially lower sharing in medical than evolutionary and forensic genetics, more evident for whole mtDNA sequences (15.0% vs 99.6%). The low rate of positive responses to e-mail requests sent to corresponding authors of withheld datasets (28.6%) suggests that sharing should be regarded as a prerequisite for final paper acceptance, while making authors deposit their results in open online databases which provide data quality control seems to provide the best-practice standard. Finally, we estimated that 29.8% to 32.9% of total resources are used to generate withheld datasets, implying that an important portion of research funding does not produce shared knowledge. By making the scientific community and the public aware of this important aspect, we may help popularize a more effective culture of data sharing.

Although essential for the fine-scale reconstruction of genetic structure, only a few micro-geographic studies have been carried out in European populations. This study analyzes mitochondrial variation (651 bp of the hypervariable region plus 17 single-nucleotide polymorphisms) in 393 samples from nine populations from Trentino (Eastern Italian Alps), a small area characterized by a complex geography and high linguistic diversity. A high level of genetic variation, comparable to geographically dispersed European groups, was observed. We found a difference in the intensity of peopling processes between two longitudinal areas, as populations from the west-central part of the region show stronger signatures of expansion, whereas those from the eastern area are closer to the expectations of a stationary demographic state. This may be explained by geomorphological factors and is also supported by archeological data. Finally, our results reveal a striking difference in the way in which the two linguistically isolated populations are genetically related to the neighboring groups. The Ladin speakers were found to be genetically close to the Italian-speaking populations and differentiated from the other Dolomitic Ladins, whereas the German-speaking Cimbri behave as an outlier, showing signatures of founder effects and low growth rate.