title: Population genomic structure and adaptation in the zoonotic malaria parasite Plasmodium knowlesi.
abstract: Malaria cases caused by the zoonotic parasite Plasmodium knowlesi are being increasingly reported throughout Southeast Asia and in travelers returning from the region. To test for evidence of signatures of selection or unusual population structure in this parasite, we surveyed genome sequence diversity in 48 clinical isolates recently sampled from Malaysian Borneo and in five lines maintained in laboratory rhesus macaques after isolation in the 1960s from Peninsular Malaysia and the Philippines. Overall genomewide nucleotide diversity (π = 6.03 × 10(-3)) was much higher than has been seen in worldwide samples of either of the major endemic malaria parasite species Plasmodium falciparum and Plasmodium vivax. A remarkable substructure is revealed within P. knowlesi, consisting of two major sympatric clusters of the clinical isolates and a third cluster comprising the laboratory isolates. There was deep differentiation between the two clusters of clinical isolates [mean genomewide fixation index (FST) = 0.21, with 9,293 SNPs having fixed differences of FST = 1.0]. This differentiation showed marked heterogeneity across the genome, with mean FST values of different chromosomes ranging from 0.08 to 0.34 and with further significant variation across regions within several chromosomes. Analysis of the largest cluster (cluster 1, 38 isolates) indicated long-term population growth, with negatively skewed allele frequency distributions (genomewide average Tajima's D = -1.35). Against this background there was evidence of balancing selection on particular genes, including the circumsporozoite protein (csp) gene, which had the top Tajima's D value (1.57), and scans of haplotype homozygosity implicate several genomic regions as being under recent positive selection.
authors.affiliation: Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, London, WC1E 7HT United Kingdom;
authors.forename: Samuel
authors.initials: S
authors.lastname: Assefa
authors.affiliation: Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115;
authors.forename: Caeul
authors.initials: C
authors.lastname: Lim
authors.affiliation: Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, London, WC1E 7HT United Kingdom;
authors.forename: Mark D
authors.initials: MD
authors.lastname: Preston
authors.affiliation: Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, London, WC1E 7HT United Kingdom;
authors.forename: Craig W
authors.identifier: http://orcid.org/0000-0001-9359-4888
authors.initials: CW
authors.lastname: Duffy
authors.affiliation: Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Jeddah, Kingdom of Saudi Arabia;
authors.forename: Mridul B
authors.initials: MB
authors.lastname: Nair
authors.affiliation: Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Jeddah, Kingdom of Saudi Arabia;
authors.forename: Sabir A
authors.initials: SA
authors.lastname: Adroub
authors.affiliation: Malaria Research Centre, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia;
authors.forename: Khamisah A
authors.initials: KA
authors.lastname: Kadir
authors.affiliation: Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115;
authors.forename: Jonathan M
authors.initials: JM
authors.lastname: Goldberg
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142;
authors.forename: Daniel E
authors.initials: DE
authors.lastname: Neafsey
authors.affiliation: Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, London, WC1E 7HT United Kingdom; Malaria Research Centre, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia;
authors.forename: Paul
authors.initials: P
authors.lastname: Divis
authors.affiliation: Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, London, WC1E 7HT United Kingdom;
authors.forename: Taane G
authors.initials: TG
authors.lastname: Clark
authors.affiliation: Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115; Malaria Research Centre, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia;
authors.forename: Manoj T
authors.initials: MT
authors.lastname: Duraisingh
authors.affiliation: Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, London, WC1E 7HT United Kingdom; Malaria Research Centre, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia; david.conway@lshtm.ac.uk arnab.pain@kaust.edu.sa bskhaira55@gmail.com.
authors.forename: David J
authors.initials: DJ
authors.lastname: Conway
authors.affiliation: Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Jeddah, Kingdom of Saudi Arabia; Malaria Research Centre, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia; Center for Zoonosis Control, Global Institution for Collaborative Research and Education, Hokkaido University, N20 W10 Kita-ku, Sapporo, Japan david.conway@lshtm.ac.uk arnab.pain@kaust.edu.sa bskhaira55@gmail.com.
authors.forename: Arnab
authors.initials: A
authors.lastname: Pain
authors.affiliation: Malaria Research Centre, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia; david.conway@lshtm.ac.uk arnab.pain@kaust.edu.sa bskhaira55@gmail.com.
authors.forename: Balbir
authors.initials: B
authors.lastname: Singh
mesh_terms: D000222:Adaptation, Physiological; D000818:Animals; D005828:Genetics, Population; D018503:Genome, Protozoan; D016790:Plasmodium knowlesi / Q000235:genetics* / Q000502:physiology; D020641:Polymorphism, Single Nucleotide
keywords: Plasmodium diversity; adaptation; population genomics; reproductive isolation; zoonosis