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Background   Anopheles sinensis  is one of the most abundant vectors of malaria and other diseases in Asia. Vector control through the use of insecticides is the front line control method of vector-borne diseases. Pyrethroids are the most commonly used insecticides due to their low toxicity to vertebrates and low repellency. However, the extensive use of insecticides has imposed strong selection pressure on mosquito populations for resistance. High levels of resistance to pyrethroid insecticides and various mutations and haplotypes in the  para  sodium channel gene that confers knockdown resistance ( kdr ) have been detected in  An. sinensis . Despite the importance of  kdr  mutations in pyrethroid resistance, the evolutionary origin of the  kdr  mutations is unknown. This study aims to examine the evolutionary genetics of  kdr  mutations in relation to spatial population genetic structure of  An. sinensis .    Methods  Adults or larvae of  Anopheles sinensis  were collected from various geographic locations in China. DNA was extracted from individual mosquitoes. PCR amplification and DNA sequencing of the  para-type  sodium channel gene were conducted to analyse  kdr  allele frequency distribution,  kdr  codon upstream and downstream intron polymorphism, population genetic diversity and  kdr  codon evolution. The mitochondrial cytochrome  c  oxidase COI and COII genes were amplified and sequenced to examine population variations, genetic differentiation, spatial population structure, population expansion and gene flow patterns.    Results  Three non-synonymous mutations (L1014F, L1014C, and L1014S) were detected at the  kdr  codon L1014 of  para-type  sodium channel gene. A patchy distribution of  kdr  mutation allele frequencies from southern to central China was found. Near fixation of  kdr  mutation was detected in populations from central China, but no  kdr  mutations were found in populations from southwestern China. More than eight independent mutation events were detected in the three  kdr  alleles, and at least one of them evolved multiple times subsequent to their first divergence. Based on sequence analysis of the mitochondrial COI and COII genes, significant and large genetic differentiation was detected between populations from southwestern China and central China. The patchy distribution of  kdr  mutation frequencies is likely a consequence of geographic isolation in the mosquito populations and the long-term insecticide selection.    Conclusion  Our results indicate multiple origins of the  kdr  insecticide-resistant alleles in  An. sinensis  from southern and central China. Local selection related to intense and prolonged use of insecticide for agricultural purposes, as well as frequent migrations among populations are likely the explanations for the patchy distribution of  kdr  mutations in China. On the contrary, the lack of  kdr  mutations in Yunnan and Sichuan is likely a consequence of genetic isolation and absence of strong selection pressure. The present study compares the genetic patterns revealed by a functional gene with a neutral marker and demonstrates the combined impact of demographic and selection factors on population structure.    Electronic supplementary material  The online version of this article (doi:10.1186/s13071-016-1513-6) contains supplementary material, which is available to authorized users.

Landscape genetic structure and evolutionary genetics of insecticide resistance gene mutations in Anopheles sinensis