title: Molecular characterisation of the tick Rhipicephalus microplus in Malaysia: new insights into the cryptic diversity and distinct genetic assemblages throughout the world.
abstract: BACKGROUND
  The morphotaxonomy of Rhipicephalus microplus complex has been challenged in the last few years and prompted many biologists to adopt a DNA-based method for distinguishing the members of this group. In the present study, we used a mitochondrial DNA analysis to characterise the genetic assemblages, population structure and dispersal pattern of R. microplus from Southeast Asia, the region where the species originated.
  
  
  METHODS
  A phylogeographic analysis inferred from the 16S rRNA and cytochrome oxidase subunit I (COI) genes was performed with five populations of R. microplus collected from cattle in Malaysia. Malaysian R. microplus sequences were compared with existing COI and 16S rRNA haplotypes reported globally in NCBI GenBank.
  
  
  RESULTS
  A total of seven and 12 unique haplotypes were recovered by the 16S rRNA and COI genes, respectively. The concatenated sequences of both 16S rRNA and COI revealed 18 haplotypes. Haplotype network and phylogenetic analyses based on COI+16S rRNA sequences revealed four genetically divergent groups among Malaysian R. microplus. The significantly low genetic differentiation and high gene flow among Malaysian R. microplus populations supports the occurrence of genetic admixture. In a broader context, the 16S rRNA phylogenetic tree assigned all isolates of Malaysian R. microplus into the previously described African/the Americas assemblage. However, the COI phylogenetic tree provides higher resolution of R. microplus with the identification of three main assemblages: clade A sensu Burger et al. (2014) comprises ticks from Southeast Asia, the Americas and China; clade B sensu Burger et al. (2014) is restricted to ticks that originated from China; and clade C sensu Low et al. (2015) is a new genetic assemblage discovered in this study comprising ticks from India and Malaysia.
  
  
  CONCLUSIONS
  We conclude that the R. microplus complex consisting of at least five taxa: R. australis, R. annulatus, R. microplus clade A sensu Burger et al. (2014), R. microplus clade B sensu Burger et al. (2014) and the new taxon, R. microplus clade C sensu Low et al. (2015). The use of COI as the standard genetic marker in discerning the genetic assemblages of R. microplus from a broad range of biogeographical regions is proposed.
authors.affiliation: Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia. lucaslow24@gmail.com.
authors.forename: Van Lun
authors.initials: VL
authors.lastname: Low
authors.affiliation: Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia. tayst@um.edu.my.
authors.forename: Sun Tee
authors.initials: ST
authors.lastname: Tay
authors.affiliation: Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia. khokailing@yahoo.com.
authors.forename: Kai Ling
authors.initials: KL
authors.lastname: Kho
authors.affiliation: Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia. fuixian@gmail.com.
authors.forename: Fui Xian
authors.initials: FX
authors.lastname: Koh
authors.affiliation: Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia. stanley.monas@gmail.com.
authors.forename: Tiong Kai
authors.initials: TK
authors.lastname: Tan
authors.affiliation: Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia. limailian@um.edu.my.
authors.forename: Yvonne Ai Lian
authors.initials: YA
authors.lastname: Lim
authors.affiliation: Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Kota Bharu, Kelantan, Malaysia. ong_beelee2010@yahoo.com.
authors.forename: Bee Lee
authors.initials: BL
authors.lastname: Ong
authors.affiliation: Veterinary Research Institute, Ipoh, Perak, Malaysia. chandra1959@gmail.com.
authors.forename: Chandrawathani
authors.initials: C
authors.lastname: Panchadcharam
authors.affiliation: Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia. ynorma@um.edu.my.
authors.forename: Yusoff
authors.initials: Y
authors.lastname: Norma-Rashid
authors.affiliation: Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia. sofian@um.edu.my.
authors.forename: Mohd
authors.initials: M
authors.lastname: Sofian-Azirun
mesh_terms: D000569:Americas; D000818:Animals; D002417:Cattle; D002418:Cattle Diseases / Q000469:parasitology*; D002681:China; D004272:DNA, Mitochondrial / Q000235:genetics; D005260:Female; D014644:Genetic Variation; D006239:Haplotypes; D007194:India; D008296:Malaysia; D008297:Male; D008969:Molecular Sequence Data; D010802:Phylogeny; D058974:Phylogeography; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D048494:Rhipicephalus / Q000145:classification* / Q000235:genetics*; D013984:Tick Infestations / Q000469:parasitology / Q000662:veterinary*
chemical_list: D004272:DNA, Mitochondrial; D012336:RNA, Ribosomal, 16S