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Malaria is a global public health challenge, with drug resistance a major barrier to disease control and elimination. To meet the urgent need for better treatments and vaccines, a deeper knowledge of Plasmodium biology and malaria epidemiology is required. An improved understanding of the genomic variation of malaria parasites, especially the most virulent Plasmodium falciparum (Pf) species, has the potential to yield new insights in these areas. High-throughput sequencing and genotyping is generating large amounts of genomic data across multiple parasite populations. The resulting ability to identify informative variants, particularly single-nucleotide polymorphisms (SNPs), will lead to the discovery of intra- and inter-population differences and thus enable the development of genetic barcodes for diagnostic assays and clinical studies. Knowledge of genetic variability underlying drug resistance and other differential phenotypes will also facilitate the identification of novel mutations and contribute to surveillance and stratified medicine applications. The PlasmoView interactive web-browsing tool enables the research community to visualise genomic variation and annotation (eg, biological function) in a geographic setting. The first release contains over 600 000 high-quality SNPs in 631 Pf isolates from laboratory strains and four malaria-endemic regions (West Africa, East Africa, Southeast Asia and Oceania). [ABSTRACT FROM AUTHOR]

The oldest known shipwreck in southern Africa was found in Namibia in 2008. 1–4 Forty tons of cargo, including gold and silver coins, helped identify the ship as the Bom Jesus , a Portuguese nau (trading vessel) lost in 1533 while headed to India. 4–6 The cargo included >100 elephant tusks, 7 which we examined using paleogenomic and stable isotope analyses. Nuclear DNA identified the ivory source as African forest (Loxodonta cyclotis) rather than savanna (Loxodonta africana) elephants. Mitochondrial sequences traced them to West and not Central Africa and from ≥17 herds with distinct haplotypes. Four of the haplotypes are known from modern populations; others were potentially lost to subsequent hunting of elephants for ivory. Stable isotope analyses (δ13C and δ15N) indicated that the elephants were not from deep rainforests but from savanna and mixed habitats. Such habitats surround the Guinean forest block of West Africa 8 and accord with the locations of major historic Portuguese trading ports. 9,10 West African forest elephants currently range into savanna habitats; 11–13 our findings suggest that this was not consequent to regional decimation of savanna elephants for their ivory in the 19th and 20th centuries. During the time of the Bom Jesus , ivory was a central driver in the formation of maritime trading systems connecting Europe, Africa, and Asia. Our integration of paleogenomic, archeological, and historical methods to analyze the Bom Jesus ivory provides a framework for examining vast collections of archaeological ivories around the world, in shipwrecks and other contexts. • The largest 16th-century cargo of shipwreck ivory was analyzed using DNA and isotopes • The tusks derived from ≥17 different herds of forest elephants from West Africa • The formative stages of global trade relied on extensive West African networks • Historical habitat use and genetic diversity data provide conservation benchmarks de Flamingh et al. analyze ivory from a sixteenth-century shipwreck. DNA establishes that the tusks were from ≥17 different herds of West African forest elephants. Isotope analyses find that the elephants were from different habitats, but not deep rainforests. The data provide insights into global commodity circulation and historical elephant ecology. [ABSTRACT FROM AUTHOR]