The widespread distribution and relapsing nature of Plasmodium vivax infection present major challenges for malaria elimination. To characterise the genetic diversity of this parasite within individual infections and across the population, we performed deep genome sequencing of >200 clinical samples collected across the Asia-Pacific region, and analysed data on >300,000 SNPs and 9 regions of the genome with large copy number variations. Individual infections showed complex patterns of genetic structure, with variation not only in the number of dominant clones but also in their level of relatedness and inbreeding. At the population level, we observed strong signals of recent evolutionary selection both in known drug resistance genes and at novel loci, and these varied markedly between geographical locations. These findings reveal a dynamic landscape of local evolutionary adaptation in P. vivax populations, and provide a foundation for genomic surveillance to guide effective strategies for control and elimination.

Testing models of macroevolution, and especially the sufficiency of microevolutionary processes, requires good collaboration between molecular biologists and paleontologists. We report such a test for events around the Late Cretaceous by describing the earliest penguin fossils, analyzing complete mitochondrial genomes from an albatross, a petrel, and a loon, and describe the gradual decline of pterosaurs at the same time modern birds radiate. The penguin fossils comprise four naturally associated skeletons from the New Zealand Waipara Greensand, a Paleocene (early Tertiary) formation just above a well-known Cretaceous/Tertiary boundary site. The fossils, in a new genus (Waimanu), provide a lower estimate of 61-62 Ma for the divergence between penguins and other birds and thus establish a reliable calibration point for avian evolution. Combining fossil calibration points, DNA sequences, maximum likelihood, and Bayesian analysis, the penguin calibrations imply a radiation of modern (crown group) birds in the Late Cretaceous. This includes a conservative estimate that modern sea and shorebird lineages diverged at least by the Late Cretaceous about 74 +/- 3 Ma (Campanian). It is clear that modern birds from at least the latest Cretaceous lived at the same time as archaic birds including Hesperornis, Ichthyornis, and the diverse Enantiornithiformes. Pterosaurs, which also coexisted with early crown birds, show notable changes through the Late Cretaceous. There was a decrease in taxonomic diversity, and small- to medium-sized species disappeared well before the end of the Cretaceous. A simple reading of the fossil record might suggest competitive interactions with birds, but much more needs to be understood about pterosaur life histories. Additional fossils and molecular data are still required to help understand the role of biotic interactions in the evolution of Late Cretaceous birds and thus to test that the mechanisms of microevolution are sufficient to explain macroevolution.

Good phylogenetic trees are required to test hypotheses about evolutionary processes. We report four new avian mitochondrial genomes, which together with an improved method of phylogenetic analysis for vertebrate mt genomes give results for three questions in avian evolution. The new mt genomes are: magpie goose (Anseranas semipalmata), an owl (morepork, Ninox novaeseelandiae); a basal passerine (rifleman, or New Zealand wren, Acanthisitta chloris); and a parrot (kakapo or owl-parrot, Strigops habroptilus). The magpie goose provides an important new calibration point for avian evolution because the well-studied Presbyornis fossils are on the lineage to ducks and geese, after the separation of the magpie goose. We find, as with other animal mitochondrial genomes, that RY-coding is helpful in adjusting for biases between pyrimidines and between purines. When RY-coding is used at third positions of the codon, the root occurs between paleognath and neognath birds (as expected from morphological and nuclear data). In addition, passerines form a relatively old group in Neoaves, and many modern avian lineages diverged during the Cretaceous. Although many aspects of the avian tree are stable, additional taxon sampling is required.