Complete mitochondrial DNA sequences provide new insights into the Polynesian motif and the peopling of Madagascar

More than a decade of mitochondrial DNA (mtDNA) studies have given the 'Polynesian motif' renowned status as a marker for tracing the late-Holocene expansion of Austronesian speaking populations. Despite considerable research on the Polynesian motif in Oceania, there has been little equivalent work on the western edge of its expansion - leaving major issues unresolved regarding the motif's evolutionary history. This has also led to considerable uncertainty regarding the settlement of Madagascar. In this study, we assess mtDNA variation in 266 individuals from three Malagasy ethnic groups: the Mikea, Vezo, and Merina. Complete mtDNA genome sequencing reveals a new variant of the Polynesian motif in Madagascar; two coding region mutations define a Malagasy-specific sub-branch. This newly defined 'Malagasy motif' occurs at high frequency in all three ethnic groups (13-50%), and its phylogenetic position, geographic distribution, and estimated age all support a recent origin, but without conclusively identifying a specific source region. Nevertheless, the haplotype's limited diversity, similar to those of other mtDNA haplogroups found in our Malagasy groups, best supports a small number of initial settlers arriving to Madagascar through the same migratory process. Finally, the discovery of this lineage provides a set of new polymorphic positions to help localize the Austronesian ancestors of the Malagasy, as well as uncover the origin and evolution of the Polynesian motif itself

60,000 years of interactions between Central and Eastern Africa documented by major African mitochondrial haplogroup L2

Mitochondrial DNA (mtDNA) haplogroup L2 originated in Western Africa but is nowadays spread across the entire continent. L2 movements were previously postulated to be related to the Bantu expansion, but L2 expansions eastwards probably occurred much earlier. By reconstructing the phylogeny of L2 (44 new complete sequences) we provide insights on the complex net of within-African migrations in the last 60 thousand years (ka). Results show that lineages in Southern Africa cluster with Western/Central African lineages at a recent time scale, whereas, eastern lineages seem to be substantially more ancient. Three moments of expansion from a Central African source are associated to L2: (1) one migration at 70-50 ka into Eastern or Southern Africa, (2) postglacial movements (15-10 ka) into Eastern Africa; and (3) the southward Bantu Expansion in the last 5 ka. The complementary population and L0a phylogeography analyses indicate no strong evidence of mtDNA gene flow between eastern and southern populations during the later movement, suggesting low admixture between Eastern African populations and the Bantu migrants. This implies that, at least in the early stages, the Bantu expansion was mainly a demic diffusion with little incorporation of local populations.This research received support from the European project “A European Initial Training Network on the History, Archaeology, and New Genetics of the Trans-Atlantic Slave Trade (EUROTAST)” (EU project: 290344). PSo is supported by FCT (the Portuguese Foundation for Science and Technology), European Social Fund, Programa Operacional Potencial Humano and the FCT Investigator Programme (IF/01641/2013). IPATIMUP integrates the i3S Research Unit, which is partially supported by FCT. This work is funded by FEDER funds through the Operational Programme for Competitiveness FactorsCOMPETE and National Funds through FCT, under the project “PEst-C/SAU/LA0003/2013”. FCT/MEC supports CBMA through Portuguese funds (PIDDAC) - PEst-OE/BIA/UI4050/2014. NORTE-07-0162FEDER-00018 (Contributos para o reforço da capacidade do IPATIMUP enquanto actor do sistema regional de inovação) and NORTE-07-0162-FEDER-000067 (Reforço e consolidação da capacidade infraestrutural do IPATIMUP para o sistema regional de inovação), both supported by Programa Operacional Regional do Norte (ON.2 – O Novo Norte), through FEDER funds under the Quadro de Referência Estratégico Nacional (QREN)

Patterns of Passage into protected areas: drivers and outcomes of Fulani immigration, settlement and integration into the Kachia Grazing Reserve, Northwest Nigeria

Abstract Increasing land use and associated competition for natural resources in the wake of high human and livestock population pressures have been major challenges confronting pastoralists of West Africa. This is especially true in Nigeria where Fulani make up 4% of the national population and prevailing national insecurity issues are impacting on pastoral livelihoods, including violent conflicts over land and ethnic, religious and political disparities. This study examined the dynamics of immigration within the Kachia Grazing Reserve (KGR), an exclusively Fulani pastoralist community in Kaduna State, northwest Nigeria, prompted by concerns from both the farming communities and the authorities about mounting pressure on existing limited resources, particularly in regard to availability of cattle grazing resources. Drawing from a household census conducted in 2011 and employing a range of qualitative methods (focus group discussions and key informant interviews), this study explored the drivers and consequences of immigration and subsequent integration within the KGR community. The study revealed two types of immigration: a steady trickle of pastoralists migrating to the reserve to settle and acquire land, secure from the stresses of competition from cultivators, and the sudden influx of internally displaced persons fleeing violent clashes in their areas of origin. Population pressure within the reserve has risen steadily over the past three decades, such that it is severely overgrazed (as evidenced by reports from the KGR community that the animals run short of pasture even during the wet season due to desertification and the spread of non-edible weeds). The newer immigrants, fleeing conflict, tended to arrive in the reserve with significantly larger herds than those kept by established residents. Pastoralists in the reserve have been forced back into the practice of seasonal transhumance in both wet and dry seasons to support their herds, with all the attendant risks of theft, clashes with cultivators and increased disease transmission

A Genome-Wide Metabolic QTL Analysis in Europeans Implicates Two Loci Shaped by Recent Positive Selection

We have performed a metabolite quantitative trait locus (mQTL) study of the 1H nuclear magnetic resonance spectroscopy (1H NMR) metabolome in humans, building on recent targeted knowledge of genetic drivers of metabolic regulation. Urine and plasma samples were collected from two cohorts of individuals of European descent, with one cohort comprised of female twins donating samples longitudinally. Sample metabolite concentrations were quantified by 1H NMR and tested for association with genome-wide single-nucleotide polymorphisms (SNPs). Four metabolites' concentrations exhibited significant, replicable association with SNP variation (8.6×10−11<p<2.8×10−23). Three of these—trimethylamine, 3-amino-isobutyrate, and an N-acetylated compound—were measured in urine. The other—dimethylamine—was measured in plasma. Trimethylamine and dimethylamine mapped to a single genetic region (hence we report a total of three implicated genomic regions). Two of the three hit regions lie within haplotype blocks (at 2p13.1 and 10q24.2) that carry the genetic signature of strong, recent, positive selection in European populations. Genes NAT8 and PYROXD2, both with relatively uncharacterized functional roles, are good candidates for mediating the corresponding mQTL associations. The study's longitudinal twin design allowed detailed variance-components analysis of the sources of population variation in metabolite levels. The mQTLs explained 40%–64% of biological population variation in the corresponding metabolites' concentrations. These effect sizes are stronger than those reported in a recent, targeted mQTL study of metabolites in serum using the targeted-metabolomics Biocrates platform. By re-analysing our plasma samples using the Biocrates platform, we replicated the mQTL findings of the previous study and discovered a previously uncharacterized yet substantial familial component of variation in metabolite levels in addition to the heritability contribution from the corresponding mQTL effects

A Genome-Wide Metabolic QTL Analysis in Europeans Implicates Two Loci Shaped by Recent Positive Selection

We have performed a metabolite quantitative trait locus (mQTL) study of the 1H nuclear magnetic resonance spectroscopy (1H NMR) metabolome in humans, building on recent targeted knowledge of genetic drivers of metabolic regulation. Urine and plasma samples were collected from two cohorts of individuals of European descent, with one cohort comprised of female twins donating samples longitudinally. Sample metabolite concentrations were quantified by 1H NMR and tested for association with genome-wide single-nucleotide polymorphisms (SNPs). Four metabolites' concentrations exhibited significant, replicable association with SNP variation (8.6×10−11<p<2.8×10−23). Three of these—trimethylamine, 3-amino-isobutyrate, and an N-acetylated compound—were measured in urine. The other—dimethylamine—was measured in plasma. Trimethylamine and dimethylamine mapped to a single genetic region (hence we report a total of three implicated genomic regions). Two of the three hit regions lie within haplotype blocks (at 2p13.1 and 10q24.2) that carry the genetic signature of strong, recent, positive selection in European populations. Genes NAT8 and PYROXD2, both with relatively uncharacterized functional roles, are good candidates for mediating the corresponding mQTL associations. The study's longitudinal twin design allowed detailed variance-components analysis of the sources of population variation in metabolite levels. The mQTLs explained 40%–64% of biological population variation in the corresponding metabolites' concentrations. These effect sizes are stronger than those reported in a recent, targeted mQTL study of metabolites in serum using the targeted-metabolomics Biocrates platform. By re-analysing our plasma samples using the Biocrates platform, we replicated the mQTL findings of the previous study and discovered a previously uncharacterized yet substantial familial component of variation in metabolite levels in addition to the heritability contribution from the corresponding mQTL effects

Openness and archaeology's information ecosystem

The rise of the World Wide Web represents one of the most significant transitions in communicationssince the printing press or even since the origins of writing. To Open Access and Open Data advocates,the Web offers great opportunity for expanding the accessibility, scale, diversity, and quality ofarchaeological communications. Nevertheless, Open Access and Open Data face steep adoption barriers.Critics wrongfully see Open Access as a threat to peer review. Others see data transparency as naivelytechnocratic, and lacking in an appreciation of archaeology’s social and professional incentive structure.However, as argued in this paper, the Open Access and Open Data movements do not gloss oversustainability, quality and professional incentive concerns. Rather, these reform movements offer muchneeded and trenchant critiques of the Academy’s many dysfunctions. These dysfunctions, ranging fromthe expectations of tenure and review committees to the structure of the academic publishing industry, golargely unknown and unremarked by most archaeologists. At a time of cutting fiscal austerity, OpenAccess and Open Data offer desperately needed ways to expand research opportunities, reduce costs andexpand the equity and effectiveness of archaeological communication

Identifying darwinian selection acting on different human APOL1 variants among diverse African populations

Disease susceptibility can arise as a consequence of adaptation to infectious disease. Recent findings have suggested that higher rates of chronic kidney disease (CKD) in individuals with recent African ancestry might be attributed to two risk alleles (G1 and G2) at the serum-resistance-associated (SRA)-interacting-domain-encoding region of APOL1. These two alleles appear to have arisen adaptively, possibly as a result of their protective effects against human African trypanosomiasis (HAT), or African sleeping sickness. In order to explore the distribution of potential functional variation at APOL1, we studied nucleotide variation in 187 individuals across ten geographically and genetically diverse African ethnic groups with exposure to two Trypanosoma brucei subspecies that cause HAT. We observed unusually high levels of nonsynonymous polymorphism in the regions encoding the functional domains that are required for lysing parasites. Whereas allele frequencies of G2 were similar across all populations (3%-8%), the G1 allele was only common in the Yoruba (39%). Additionally, we identified a haplo type (termed G3) that contains a nonsynonymous change at the membrane-addressing-domain-encoding region of APOL1 and is present in all populations except for the Yoruba. Analyses of long-range patterns of linkage disequilibrium indicate evidence of recent selection acting on the G3 haplotype in Fulani from Cameroon. Our results indicate that the G1 and G2 variants in APOL1 are geographically restricted and that there might be other functional variants that could play a role in HAT resistance and CKD risk in African populations