Resolving the ancestry of Austronesian-speaking populations

There are two very different interpretations of the prehistory of Island Southeast Asia (ISEA), with genetic evidence invoked in support of both. The “out-of-Taiwan” model proposes a major Late Holocene expansion of Neolithic Austronesian speakers from Taiwan. An alternative, proposing that Late Glacial/postglacial sea-level rises triggered largely autochthonous dispersals, accounts for some otherwise enigmatic genetic patterns, but fails to explain the Austronesian language dispersal. Combining mitochondrial DNA (mtDNA), Y-chromosome and genome-wide data, we performed the most comprehensive analysis of the region to date, obtaining highly consistent results across all three systems and allowing us to reconcile the models. We infer a primarily common ancestry for Taiwan/ISEA populations established before the Neolithic, but also detected clear signals of two minor Late Holocene migrations, probably representing Neolithic input from both Mainland Southeast Asia and South China, via Taiwan. This latter may therefore have mediated the Austronesian language dispersal, implying small-scale migration and language shift rather than large-scale expansion

Early leaf removal impact on volatile composition of Tempranillo wines

Early defoliation is a very innovative technique in viticulture used for yield management. The effects of early leaf removal performed manually and mechanically at two different phenological stages, pre-bloom and fruit set, on the volatile composition of Tempranillo (Vitis vinifera L.) wines were studied. Volatiles were identified and quantified by gas chromatography Early leaf removal only modified the total concentrations of C6 compounds and acetates, whereas total alcohols, esters, volatile acids and terpenes remained generally unaffected. Early defoliation induced a significant reduction in C6 compounds and increased the concentrations of acetates in Tempranillo wines. An effect of timing (pre-bloom vs fruit set) alone was observed for all acetates analysed. Regarding the method of defoliation (manual vs mechanical), significant differences in some ethyl ester (ethyl-2-methylbutyrate and ethyl octanoate) and volatile acid concentrations were observed among treatments. Ethyl octanoate, 2-phenylethyl acetate, 3-methylbutyl acetate and hexanoic acid, with OAV (odour activity value) > 1 and mainly fruity and floral odour descriptors, showed higher levels after early defoliation treatments compared with non-defoliated vines. Principal component analysis illustrated the difference in wines from defoliated and non-defoliated treatments based on their volatile composition. It can be concluded that early leaf removal significantly modified the wine aroma compounds, increasing or decreasing several of these compounds.We thank the Agencia de Desarrollo Economico de La Rioja (ADER) and the Ministerio de Ciencia e Innovacion for their financial support (ADER-2006-I-ID-00157 and AGL2007-60378 respectively). We would also like to thank the Agrupacion de Bodegas Centenarias y Tradicionales de Rioja (ABC) and New Holland for their assistance and help. Dr Vilanova is grateful to the 'Isidro Parga Pondal' programme financed by the Xunta de Galicia (Spain)

Multiplexed SNP Typing of Ancient DNA Clarifies the Origin of Andaman mtDNA Haplogroups amongst South Asian Tribal Populations

The issue of errors in genetic data sets is of growing concern, particularly in population genetics where whole genome mtDNA sequence data is coming under increased scrutiny. Multiplexed PCR reactions, combined with SNP typing, are currently under-exploited in this context, but have the potential to genotype whole populations rapidly and accurately, significantly reducing the amount of errors appearing in published data sets. To show the sensitivity of this technique for screening mtDNA genomic sequence data, 20 historic samples of the enigmatic Andaman Islanders and 12 modern samples from three Indian tribal populations (Chenchu, Lambadi and Lodha) were genotyped for 20 coding region sites after provisional haplogroup assignment with control region sequences. The genotype data from the historic samples significantly revise the topologies for the Andaman M31 and M32 mtDNA lineages by rectifying conflicts in published data sets. The new Indian data extend the distribution of the M31a lineage to South Asia, challenging previous interpretations of mtDNA phylogeography. This genetic connection between the ancestors of the Andamanese and South Asian tribal groups ∼30 kya has important implications for the debate concerning migration routes and settlement patterns of humans leaving Africa during the late Pleistocene, and indicates the need for more detailed genotyping strategies. The methodology serves as a low-cost, high-throughput model for the production and authentication of data from modern or ancient DNA, and demonstrates the value of museum collections as important records of human genetic diversity

The Druze: A Population Genetic Refugium of the Near East

BACKGROUND: Phylogenetic mitochondrial DNA haplogroups are highly partitioned across global geographic regions. A unique exception is the X haplogroup, which has a widespread global distribution without major regions of distinct localization. PRINCIPAL FINDINGS: We have examined mitochondrial DNA sequence variation together with Y-chromosome-based haplogroup structure among the Druze, a religious minority with a unique socio-demographic history residing in the Near East. We observed a striking overall pattern of heterogeneous parental origins, consistent with Druze oral tradition, together with both a high frequency and a high diversity of the mitochondrial DNA (mtDNA) X haplogroup within a confined regional subpopulation. Furthermore demographic modeling indicated low migration rates with nearby populations. CONCLUSIONS: These findings were enabled through the use of a paternal kindred based sampling approach, and suggest that the Galilee Druze represent a population isolate, and that the combination of a high frequency and diversity of the mtDNA X haplogroup signifies a phylogenetic refugium, providing a sample snapshot of the genetic landscape of the Near East prior to the modern age

Intriguing Balancing Selection on the Intron 5 Region of LMBR1 in Human Population

Background: The intron 5 of gene LMBR1 is the cis-acting regulatory module for the sonic hedgehog (SHH) gene. Mutation in this non-coding region is associated with preaxial polydactyly, and may play crucial roles in the evolution of limb and skeletal system. Methodology/Principal Findings: We sequenced a region of the LMBR1 gene intron 5 in East Asian human population, and found a significant deviation of Tajima’s D statistics from neutrality taking human population growth into account. Data from HapMap also demonstrated extended linkage disequilibrium in the region in East Asian and European population, and significantly low degree of genetic differentiation among human populations. Conclusion/Significance: We proposed that the intron 5 of LMBR1 was presumably subject to balancing selection during the evolution of modern human

Ancient DNA from Hunter-Gatherer and Farmer Groups from Northern Spain Supports a Random Dispersion Model for the Neolithic Expansion into Europe

Background/Principal Findings: The phenomenon of Neolithisation refers to the transition of prehistoric populations from a hunter-gatherer to an agro-pastoralist lifestyle. Traditionally, the spread of an agro-pastoralist economy into Europe has been framed within a dichotomy based either on an acculturation phenomenon or on a demic diffusion. However, the nature and speed of this transition is a matter of continuing scientific debate in archaeology, anthropology, and human population genetics. In the present study, we have analyzed the mitochondrial DNA diversity in hunter-gatherers and first farmers from Northern Spain, in relation to the debate surrounding the phenomenon of Neolithisation in Europe. Methodology/Significance: Analysis of mitochondrial DNA was carried out on 54 individuals from Upper Paleolithic and Early Neolithic, which were recovered from nine archaeological sites from Northern Spain (Basque Country, Navarre and Cantabria). In addition, to take all necessary precautions to avoid contamination, different authentication criteria were applied in this study, including: DNA quantification, cloning, duplication (51 % of the samples) and replication of the results (43 % of the samples) by two independent laboratories. Statistical and multivariate analyses of the mitochondrial variability suggest that the genetic influence of Neolithisation did not spread uniformly throughout Europe, producing heterogeneous genetic consequences in different geographical regions, rejecting the traditional models that explain the Neolithisation in Europe

From social ties to embedded competencies: The case of business groups

Our current views of economic competition are still rooted in the imagery of the isolated firm that transacts with its buyers, suppliers, and competitors via largely anonymous factor and product markets. Yet this view is fundamentally at odds with the growing importance of business groups in the global economy. We thus need a reconceptualized version of our idea of economic competition, which is capable of explaining competitive advantage at the group-versus-group rather than firm-versus-firm level of analysis. In the present paper we build on insights derived from organizational sociology and organizational economics to develop a business group-level theory of competition and competitive advantage based on embedded competencies

Study protocol of European Fans in Training (EuroFIT):a four-country randomised controlled trial of a lifestyle program for men delivered in elite football clubs

Background: Lifestyle interventions targeting physical activity, sedentary time and dietary behaviours have the potential to initiate and support behavioural change and result in public health gain. Although men have often been reluctant to engage in such lifestyle programs, many are at high risk of several chronic conditions. We have developed an evidence and theory-based, gender sensitised, health and lifestyle program (European Fans in Training (EuroFIT)), which is designed to attract men through the loyalty they feel to the football club they support. This paper describes the study protocol to evaluate the effectiveness and cost-effectiveness of the EuroFIT program in supporting men to improve their level of physical activity and reduce sedentary behaviour over 12 months. Methods: The EuroFIT study is a pragmatic, two-arm, randomised controlled trial conducted in 15 football clubs in the Netherlands, Norway, Portugal and the UK (England). One-thousand men, aged 30 to 65 years, with a self-reported Body Mass Index (BMI) ≥27 kg/m2 will be recruited and individually randomised. The primary outcomes are objectively-assessed changes in total physical activity (steps per day) and total sedentary time (minutes per day) at 12 months after baseline assessment. Secondary outcomes are weight, BMI, waist circumference, resting systolic and diastolic blood pressure, cardio-metabolic blood biomarkers, food intake, self-reported physical activity and sedentary time, wellbeing, self-esteem, vitality and quality of life. Cost-effectiveness will be assessed and a process evaluation conducted. The EuroFIT program will be delivered over 12 weekly, 90-minute sessions that combine classroom discussion with graded physical activity in the setting of the football club. Classroom sessions provide participants with a toolbox of behaviour change techniques to initiate and sustain long-term lifestyle changes. The coaches will receive two days of training to enable them to create a positive social environment that supports men in engaging in sustained behaviour change. Discussion: The EuroFIT trial will provide evidence on the effectiveness and cost-effectiveness of the EuroFIT program delivered by football clubs to their male fans, and will offer insight into factors associated with success in making sustained changes to physical activity, sedentary behaviour, and secondary outcomes, such as diet.Trial registration: ISRCTN: 81935608. Registered 16 June 2015.<br/

The Influence of Natural Barriers in Shaping the Genetic Structure of Maharashtra Populations

BACKGROUND: The geographical position of Maharashtra state makes it rather essential to study the dispersal of modern humans in South Asia. Several hypotheses have been proposed to explain the cultural, linguistic and geographical affinity of the populations living in Maharashtra state with other South Asian populations. The genetic origin of populations living in this state is poorly understood and hitherto been described at low molecular resolution level. METHODOLOGY/PRINCIPAL FINDINGS: To address this issue, we have analyzed the mitochondrial DNA (mtDNA) of 185 individuals and NRY (non-recombining region of Y chromosome) of 98 individuals belonging to two major tribal populations of Maharashtra, and compared their molecular variations with that of 54 South Asian contemporary populations of adjacent states. Inter and intra population comparisons reveal that the maternal gene pool of Maharashtra state populations is composed of mainly South Asian haplogroups with traces of east and west Eurasian haplogroups, while the paternal haplogroups comprise the South Asian as well as signature of near eastern specific haplogroup J2a. CONCLUSIONS/SIGNIFICANCE: Our analysis suggests that Indian populations, including Maharashtra state, are largely derived from Paleolithic ancient settlers; however, a more recent (∼10 Ky older) detectable paternal gene flow from west Asia is well reflected in the present study. These findings reveal movement of populations to Maharashtra through the western coast rather than mainland where Western Ghats-Vindhya Mountains and Narmada-Tapti rivers might have acted as a natural barrier. Comparing the Maharastrian populations with other South Asian populations reveals that they have a closer affinity with the South Indian than with the Central Indian populations

The Western and Eastern Roots of the Saami - The Story of Genetic "Outliers" Told by Mitochondrial DNA and Y Chromosomes

Funding Information: We thank Tatyana Karafet and Boris Malyarchuk, for useful information; Henry Harpending, for the program POPSTR; Vincent Macaulay, for the program SAMPLING; Ille Hilpus and Jaan Lind, for technical assistance; and Charles Kurland and Thomas Gilbert, for helpful discussion and comments. We are grateful to two anonymous reviewers for their suggestions and advice. The research of R.V. was supported by Estonian basic research grant 514 and European Commission Directorate General Research grant ICA1CT20070006. The research of T.K. was supported by Estonian basic research grant 5574. The work of E.K. was supported by the Russian Foundation for Basic Research (project number 01-04-48487a) and the Ministry of Sciences and Technology of Russia. M.G., S.Z., and L.O. received support from expedition grants from the Siberian Branch of the Russian Academy of Sciences (1992–1997) and the Russian Foundation of Basic Research (project number 02-06-80524-a), and the research of P.R. received support from project number 0196005 of the Ministry of Science and Technology of the Republic of Croatia.The Saami are regarded as extreme genetic outliers among European populations. In this study, a high-resolution phylogenetic analysis of Saami genetic heritage was undertaken in a comprehensive context, through use of maternally inherited mitochondrial DNA (mtDNA) and paternally inherited Y-chromosomal variation. DNA variants present in the Saami were compared with those found in Europe and Siberia, through use of both new and previously published data from 445 Saami and 17,096 western Eurasian and Siberian mtDNA samples, as well as 127 Saami and 2,840 western Eurasian and Siberian Y-chromosome samples. It was shown that the "Saami motif" variant of mtDNA haplogroup U5b is present in a large area outside Scandinavia. A detailed phylogeographic analysis of one of the predominant Saami mtDNA haplogroups, U5b1b, which also includes the lineages of the "Saami motif," was undertaken in 31 populations. The results indicate that the origin of U5b1b, as for the other predominant Saami haplogroup, V, is most likely in western, rather than eastern, Europe. Furthermore, an additional haplogroup (H1) spread among the Saami was virtually absent in 781 Samoyed and Ob-Ugric Siberians but was present in western and central European populations. The Y-chromosomal variety in the Saami is also consistent with their European ancestry. It suggests that the large genetic separation of the Saami from other Europeans is best explained by assuming that the Saami are descendants of a narrow, distinctive subset of Europeans. In particular, no evidence of a significant directional gene flow from extant aboriginal Siberian populations into the haploid gene pools of the Saami was found.Peer reviewe