Single-nucleotide polymorphism, linkage disequilibrium and geographic structure in the malaria parasite Plasmodium vivax: prospects for genome-wide association studies

Background: The ideal malaria parasite populations for initial mapping of genomic regions contributing to phenotypes such as drug resistance and virulence, through genome-wide association studies, are those with high genetic diversity, allowing for numerous informative markers, and rare meiotic recombination, allowing for strong linkage disequilibrium (LD) between markers and phenotype-determining loci. However, levels of genetic diversity and LD in field populations of the major human malaria parasite P. vivax remain little characterized. Results: We examined single-nucleotide polymorphisms (SNPs) and LD patterns across a 100-kb chromosome segment of P. vivax in 238 field isolates from areas of low to moderate malaria endemicity in South America and Asia, where LD tends to be more extensive than in holoendemic populations, and in two monkey-adapted strains (Salvador-I, from El Salvador, and Belem, from Brazil). We found varying levels of SNP diversity and LD across populations, with the highest diversity and strongest LD in the area of lowest malaria transmission. We found several clusters of contiguous markers with rare meiotic recombination and characterized a relatively conserved haplotype structure among populations, suggesting the existence of recombination hotspots in the genome region analyzed. Both silent and nonsynonymous SNPs revealed substantial between-population differentiation, which accounted for similar to 40% of the overall genetic diversity observed. Although parasites clustered according to their continental origin, we found evidence for substructure within the Brazilian population of P. vivax. We also explored between-population differentiation patterns revealed by loci putatively affected by natural selection and found marked geographic variation in frequencies of nucleotide substitutions at the pvmdr-1 locus, putatively associated with drug resistance. Conclusion: These findings support the feasibility of genome-wide association studies in carefully selected populations of P. vivax, using relatively low densities of markers, but underscore the risk of false positives caused by population structure at both local and regional levels.

Traditional architecture in the Pacific

Architecture of the Pacific covers a region of more than third of the earth’s surface. The sparse Pacific population spreads over some 30 000 islands, which graduate in size from small atolls to the largest island, Australia, a continent. Pacific architecture can be studied as four cultural units: Micronesia, Polynesia, Melanesia, and Australasia (Australia and New Zealand). While many of the islands of Micronesia lie above the Equator, the remaining Pacific islands are in the southern hemisphere. With the exception of Australia, most of the islands have a warm and humid tropical climate with high rainfalls and lush vegetation. Some islands lie in the cyclonic and earthquake belts. Two distinct racial groups settled the region. The indigenous people, the Micronesians, Melanesians, Polynesians, Australian Aborigines and New Zealand Maoris, migrated from Asia thousands of years ago. The second group, the recent immigrants, were Europeans, who occupied the region during the last two centuries, and pockets of Asians brought in by colonial administrations as labourers during the early twentieth century.

A Century of Change in Coral Reef Status in Southeast and Central Pacific: Polynesia Mana Node, Cook Islands, French Polynesia, Kiribati, Niue, Tokelau, Tonga, Wallis and Futuna

The Polynesia Mana Node of the southeast and central Pacific contains 7 independent or autonomous countries or territories with only 6,000 km2 of land on 347 islands, but surrounded by 12 million km2 of EEZ. These seas contain 13,000 km2 of coral reefs as the main natural ecosystem providing food resources and opportunities for development, especially for tourism and pearl culture for 500,000 inhabitants. During the 19th and first half of the 20th centuries, there was major exploitation by the colonial powers of mother-of-pearl oysters for the button industry, as well as guano, sandalwood and trepang. The Polynesian people were largely involved in a subsistence economy and all coral reefs and lagoons were healthy. During the last two decades of the 20th, all countries experienced rapid development and urbanization, rising populations, and some increased agriculture. These developments were limited to a few islands of each country (i.e. 15 islands amongst the 347) with resulting degradation of the coral reefs around these sites. The other islands remained mostly uninhabited and pristine, and continued with a subsistence economy. Generally, there was more damage to the coral reefs through natural events such as cyclones and coral bleaching, than by human activities. There is however, an urgent need to combat the threats on some islands from increased sedimentation, over-fishing, dredging and nutrient pollution.

China and Southeast Asia

In the new millennium, no issue in international relations will be more important than how to accommodate the rising power of China. Many analysts, especially in the United States, see China as a significant threat to American interests in Asia. Washington has treaty commitments in both Northeast and Southeast Asia and retains a substantial military presence in the region. Beijing claims it does not seek to replace the United States reigning global hegemony, but seeks to promote a multi-polar world in which six states (the US, China, the EU, Russia, Japan, and India) would have pre-eminent status.