Melanesian and Asian origins of Polynesians: mtDNA and Y chromosome gradients across the Pacific

The human settlement of the Pacific Islands represents one of the most recent major migration events of mankind. Polynesians originated in Asia according to linguistic evidence or in Melanesia according to archaeological evidence. To shed light on the genetic origins of Polynesians, we investigated over 400 Polynesians from 8 island groups, in comparison with over 900 individuals from potential parental populations of Melanesia, Southeast and East Asia, and Australia, by means of Y chromosome (NRY) and mitochondrial DNA (mtDNA) markers. Overall, we classified 94.1% of Polynesian Y chromosomes and 99.8% of Polynesian mtDNAs as of either Melanesian (NRY-DNA: 65.8%, mtDNA: 6%) or Asian (NRY-DNA: 28.3%, mtDNA: 93.8%) origin, suggesting a dual genetic origin of Polynesians in agreement with the "Slow Boat" hypothesis. Our data suggest a pronounced admixture bias in Polynesians toward more Melanesian men than women, perhaps as a result of matrilocal residence in the ancestral Polynesian society. Although dating methods are consistent with somewhat similar entries of NRY/mtDNA haplogroups into Polynesia, haplotype sharing suggests an earlier appearance of Melanesian haplogroups than those from Asia. Surprisingly, we identified gradients in the frequency distribution of some NRY/mtDNA haplogroups across Polynesia and a gradual west-to-east decrease of overall NRY/mtDNA diversity, not only providing evidence for a west-to-east direction of Polynesian settlements but also suggesting that Pacific voyaging was regular rather than haphazard. We also demonstrate that Fiji played a pivotal role in the history of Polynesia: humans probably first migrated to Fiji, and subsequent settlement of Polynesia probably came from Fiji

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Erratum to: Genetic analysis of over 1 million people identifies 535 new loci associated with blood pressure traits

In the version of this article originally published, the name of author Martin H. de Borst was coded incorrectly in the XML. The error has now been corrected in the HTML version of the paper

Evidence for three genetic loci involved in both anorexia nervosa risk and variation of body mass index

The maintenance of normal body weight is disrupted in patients with anorexia nervosa (AN) for prolonged periods of time. Prior to the onset of AN, premorbid body mass index (BMI) spans the entire range from underweight to obese. After recovery, patients have reduced rates of overweight and obesity. As such, loci involved in body weight regulation may also be relevant for AN and vice versa. Our primary analysis comprised a cross-trait analysis of the 1000 single-nucleotide polymorphisms (SNPs) with the lowest P-values in a genome-wide association meta-analysis (GWAMA) of AN (GCAN) for evidence of association in the largest published GWAMA for BMI (GIANT). Subsequently we performed sex-stratified analyses for these 1000 SNPs. Functional ex vivo studies on four genes ensued. Lastly, a look-up of GWAMA-derived BMI-related loci was performed in the AN GWAMA. We detected significant associations (P-values <5 × 10-5, Bonferroni-corrected P<0.05) for nine SNP alleles at three independent loci. Interestingly, all AN susceptibility alleles were consistently associated with increased BMI. None of the genes (chr. 10: CTBP2, chr. 19: CCNE1, chr. 2: CARF and NBEAL1; the latter is a region with high linkage disequilibrium) nearest to these SNPs has previously been associated with AN or obesity. Sex-stratified analyses revealed that the strongest BMI signal originated predominantly from females (chr. 10 rs1561589; Poverall: 2.47 × 10-06/Pfemales: 3.45 × 10-07/Pmales: 0.043). Functional ex vivo studies in mice revealed reduced hypothalamic expression of Ctbp2 and Nbeal1 after fasting. Hypothalamic expression of Ctbp2 was increased in diet-induced obese (DIO) mice as compared with age-matched lean controls. We observed no evidence for associations for the look-up of BMI-related loci in the AN GWAMA. A cross-trait analysis of AN and BMI loci revealed variants at three chromosomal loci with potential joint impact. The chromosome 10 locus is particularly promising given that the association with obesity was primarily driven by females. In addition, the detected altered hypothalamic expression patterns of Ctbp2 and Nbeal1 as a result of fasting and DIO implicate these genes in weight regulation

Observation of the Bc+→J/ψπ+π0B_c^+ \to J/\psi \pi^+ \pi^0 decay

The first observation of the $B_c^+ \to J/\psi \pi^+ \pi^0$ decay is reported with high significance using proton-proton collision data, corresponding to an integrated luminosity of 9 fb$^{-1}$, collected with the LHCb detector at centre-of-mass energies of 7, 8, and 13 TeV. The ratio of its branching fraction relative to the $B_c^+ \to J/\psi \pi^+$ channel is measured to be $$\frac{ {\cal{B}}_{( B_c^+ \to J/\psi \pi^+\pi^0 ) }} { {\cal{B}}_{( B_c^+ \to J/\psi \pi^+ ) }} = 2.80 \pm 0.15 \pm 0.11 \pm 0.16 \,,$$ where the first uncertainty is statistical, the second systematic and the third related to imprecise knowledge of the branching fractions for $B^+ \to J/\psi K^{*+}$ and $B^+ \to J/\psi K^+$ decays, which are used to determine the $\pi^0$ detection efficiency. The $\pi^+\pi^0$ mass spectrum is found to be consistent with the dominance of an intermediate $\rho^+$ contribution in accordance with a model based on QCD factorisation.The first observation of the ${B}_c^{+}\to J/\psi {\pi}^{+}{\pi}^0$ decay is reported with high significance using proton-proton collision data, corresponding to an integrated luminosity of 9 fb$^{−1}$, collected with the LHCb detector at centre-of-mass energies of 7, 8, and 13 TeV. The ratio of its branching fraction relative to the ${B}_c^{+}\to J/\psi {\pi}^{+}$ channel is measured to be$\frac{{\mathcal{B}}_{B_c^{+}\to J/\psi {\pi}^{+}{\pi}^0}}{{\mathcal{B}}_{B_c^{+}\to J/\psi {\pi}^{+}}}=2.80\pm 0.15\pm 0.11\pm 0.16,$where the first uncertainty is statistical, the second systematic and the third related to imprecise knowledge of the branching fractions for B$^{+}$ → J/ψK$^{*+}$ and ${B}_c^{+}\to J/\psi {\pi}^{+}$ decays, which are used to determine the π$^{0}$ detection efficiency. The π$^{+}$π$^{0}$ mass spectrum is found to be consistent with the dominance of an intermediate ρ$^{+}$ contribution in accordance with a model based on QCD factorisation.[graphic not available: see fulltext]The first observation of the $B_c^+ \to J/\psi \pi^+ \pi^0$ decay is reported with high significance using proton-proton collision data, corresponding to an integrated luminosity of 9fb$^{-1}$, collected with the LHCb detector at centre-of-mass energies of 7, 8, and 13 TeV. The ratio of its branching fraction relative to the $B_c^+ \to J/\psi \pi^+$ channel is measured to be $$\frac{ {\cal{B}}( B_c^+ \to J/\psi \pi^+\pi^0 ) } { {\cal{B}}( B_c^+ \to J/\psi \pi^+ ) } = 2.80 \pm 0.15 \pm 0.11 \pm 0.16 \,,$$ where the first uncertainty is statistical, the second systematic and the third related to imprecise knowledge of the branching fractions for $B^+ \to J/\psi K^{*+}$ and $B^+ \to J/\psi K^+$ decays, which are used to determine the $\pi^0$ detection efficiency. The $\pi^+\pi^0$ mass spectrum is found to be consistent with the dominance of an intermediate $\rho^+$ contribution in accordance with a model based on QCD factorisation

Study of Bc+→χcπ+B_c^+ \rightarrow \chi_c \pi^+ decays

International audienceA study of $B_c^+ \rightarrow \chi_c \pi^+$ decays is reported using proton-proton collision data, collected with the LHCb detector at centre-of-mass energies of 7, 8, and 13 TeV, corresponding to an integrated luminosity of 9fb$^{-1}$. The decay $B_c^+ \rightarrow \chi_{c2} \pi^+$ is observed for the first time, with a significance exceeding seven standard deviations. The relative branching fraction with respect to the $B_c^+ \rightarrow J/\psi \pi^+$ decay is measured to be $$\frac{\mathcal{B}_{B_c^+ \rightarrow \chi_{c2} \pi^+}} {\mathcal{B}_{B_c^+ \rightarrow J/\psi \pi^+}} = 0.37 \pm 0.06 \pm 0.02 \pm 0.01 ,$$ where the first uncertainty is statistical, the second is systematic, and the third is due to the knowledge of the $\chi_c \rightarrow J/\psi \gamma$ branching fraction. No significant $B_c^+ \rightarrow \chi_{c1} \pi^+$ signal is observed and an upper limit for the relative branching fraction for the $B_c^+ \rightarrow \chi_{c1} \pi^+$ and $B_c^+ \rightarrow \chi_{c2} \pi^+$ decays of $$\frac{\mathcal{B}_{B_c^+ \rightarrow \chi_{c1} \pi^+}} {\mathcal{B}_{B_c^+ \rightarrow \chi_{c2} \pi^+}} < 0.49$$ is set at the 90% confidence level