title: Genomic signatures of population decline in the malaria mosquito Anopheles gambiae.
abstract: BACKGROUND
  Population genomic features such as nucleotide diversity and linkage disequilibrium are expected to be strongly shaped by changes in population size, and might therefore be useful for monitoring the success of a control campaign. In the Kilifi district of Kenya, there has been a marked decline in the abundance of the malaria vector Anopheles gambiae subsequent to the rollout of insecticide-treated bed nets.
  
  
  METHODS
  To investigate whether this decline left a detectable population genomic signature, simulations were performed to compare the effect of population crashes on nucleotide diversity, Tajima's D, and linkage disequilibrium (as measured by the population recombination parameter ρ). Linkage disequilibrium and ρ were estimated for An. gambiae from Kilifi, and compared them to values for Anopheles arabiensis and Anopheles merus at the same location, and for An. gambiae in a location 200 km from Kilifi.
  
  
  RESULTS
  In the first simulations ρ changed more rapidly after a population crash than the other statistics, and therefore is a more sensitive indicator of recent population decline. In the empirical data, linkage disequilibrium extends 100-1000 times further, and ρ is 100-1000 times smaller, for the Kilifi population of An. gambiae than for any of the other populations. There were also significant runs of homozygosity in many of the individual An. gambiae mosquitoes from Kilifi.
  
  
  CONCLUSIONS
  These results support the hypothesis that the recent decline in An. gambiae was driven by the rollout of bed nets. Measuring population genomic parameters in a small sample of individuals before, during and after vector or pest control may be a valuable method of tracking the effectiveness of interventions.
authors.affiliation: Department of Life Sciences, Imperial College London, Silwood Park, Ascot, SL5 7PY, UK. s.oloughlin@imperial.ac.uk.
authors.forename: Samantha M
authors.initials: SM
authors.lastname: O'Loughlin
authors.affiliation: NIMR Amani Research Centre, P.O. Box 81, Muheza, Tanzania.|Global Health Division, RTI International, Dar es Salaam, Tanzania.
authors.forename: Stephen M
authors.initials: SM
authors.lastname: Magesa
authors.affiliation: Centre for Geographic Medicine Research Coast, Kenya Medical Research Institute, P.O. Box 428, Kilifi, Kenya.|Malaria Public Health Department, Centre for Geographic Medicine, KEMRI-Wellcome Trust Research Programme, Kenyatta National Hospital Grounds, P.O. Box 43640-00100, Nairobi, Kenya.
authors.forename: Charles
authors.initials: C
authors.lastname: Mbogo
authors.affiliation: Kilimanjaro Christian Medical University College, Moshi, Tanzania.
authors.forename: Franklin
authors.initials: F
authors.lastname: Mosha
authors.affiliation: Centre for Geographic Medicine Research Coast, Kenya Medical Research Institute, P.O. Box 428, Kilifi, Kenya.|Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK.|Wellcome Trust Centre for Human Genetics, Oxford, OX3 7BN, UK.
authors.forename: Janet
authors.initials: J
authors.lastname: Midega
authors.affiliation: Department of Life Sciences, Imperial College London, Silwood Park, Ascot, SL5 7PY, UK.
authors.forename: Austin
authors.initials: A
authors.lastname: Burt
mesh_terms: D000818:Animals; D000852:Anopheles / Q000145:classification / Q000235:genetics* / Q000254:growth & development*; D003198:Computer Simulation; D014644:Genetic Variation; D005828:Genetics, Population; D023281:Genomics; D007303:Insect Vectors; D007630:Kenya; D057147:Mosquito Nets / Q000706:statistics & numerical data
keywords: Anopheles gambiae; Kilifi; Linkage disequilibrium; Pest management; Population control; Population recombination