title: Genome-wide analysis of signatures of selection in populations of African honey bees (Apis mellifera) using new web-based tools.
abstract: BACKGROUND
  With the development of inexpensive, high-throughput sequencing technologies, it has become feasible to examine questions related to population genetics and molecular evolution of non-model species in their ecological contexts on a genome-wide scale. Here, we employed a newly developed suite of integrated, web-based programs to examine population dynamics and signatures of selection across the genome using several well-established tests, including F ST, pN/pS, and McDonald-Kreitman. We applied these techniques to study populations of honey bees (Apis mellifera) in East Africa. In Kenya, there are several described A. mellifera subspecies, which are thought to be localized to distinct ecological regions.
  
  
  RESULTS
  We performed whole genome sequencing of 11 worker honey bees from apiaries distributed throughout Kenya and identified 3.6 million putative single-nucleotide polymorphisms. The dense coverage allowed us to apply several computational procedures to study population structure and the evolutionary relationships among the populations, and to detect signs of adaptive evolution across the genome. While there is considerable gene flow among the sampled populations, there are clear distinctions between populations from the northern desert region and those from the temperate, savannah region. We identified several genes showing population genetic patterns consistent with positive selection within African bee populations, and between these populations and European A. mellifera or Asian Apis florea.
  
  
  CONCLUSIONS
  These results lay the groundwork for future studies of adaptive ecological evolution in honey bees, and demonstrate the use of new, freely available web-based tools and workflows ( http://usegalaxy.org/r/kenyanbee ) that can be applied to any model system with genomic information.
authors.affiliation: Department of Biology, Pennsylvania State University, University Park, PA, USA. zlf105@psu.edu.
authors.forename: Zachary L
authors.initials: ZL
authors.lastname: Fuller
authors.affiliation: Department of Entomology, Center for Pollinator Research, Pennsylvania State University, University Park, PA, USA. elina.l.nino@gmail.com.
authors.forename: Elina L
authors.initials: EL
authors.lastname: Niño
authors.affiliation: Department of Entomology, Center for Pollinator Research, Pennsylvania State University, University Park, PA, USA. hmpatch@psu.edu.
authors.forename: Harland M
authors.initials: HM
authors.lastname: Patch
authors.affiliation: Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA, USA. oscar@bx.psu.edu.
authors.forename: Oscar C
authors.initials: OC
authors.lastname: Bedoya-Reina
authors.affiliation: Department of Entomology, Center for Pollinator Research, Pennsylvania State University, University Park, PA, USA. tlb60@psu.edu.
authors.forename: Tracey
authors.initials: T
authors.lastname: Baumgarten
authors.affiliation: Department of Biological Sciences, South Eastern Kenya University (SEKU), P.O. Box 170-90200, Kitui, Kenya. elliudmuli@gmail.com.
authors.forename: Elliud
authors.initials: E
authors.lastname: Muli
authors.affiliation: The International Center of Insect Physiology and Ecology (icipe), PO Box 30772-00100, Nairobi, Kenya. nelimafiona@yahoo.com.
authors.forename: Fiona
authors.initials: F
authors.lastname: Mumoki
authors.affiliation: Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA, USA. ar7jq@virgina.edu.
authors.forename: Aakrosh
authors.initials: A
authors.lastname: Ratan
authors.affiliation: Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA. jjm123@psu.edu.
authors.forename: John
authors.initials: J
authors.lastname: McGraw
authors.affiliation: Department of Entomology, Center for Pollinator Research, Pennsylvania State University, University Park, PA, USA. mxt15@psu.edu.
authors.forename: Maryann
authors.initials: M
authors.lastname: Frazier
authors.affiliation: The International Center of Insect Physiology and Ecology (icipe), PO Box 30772-00100, Nairobi, Kenya. dmasiga@icipe.org.
authors.forename: Daniel
authors.initials: D
authors.lastname: Masiga
authors.affiliation: Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA, USA. scs19@psu.edu.
authors.forename: Stephen
authors.initials: S
authors.lastname: Schuster
authors.affiliation: Department of Entomology, Center for Pollinator Research, Pennsylvania State University, University Park, PA, USA. cmgrozinger@psu.edu.
authors.forename: Christina M
authors.initials: CM
authors.lastname: Grozinger
authors.affiliation: Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA, USA.
authors.forename: Webb
authors.initials: W
authors.lastname: Miller
mesh_terms: D000818:Animals; D001516:Bees / Q000235:genetics*; D019143:Evolution, Molecular; D005828:Genetics, Population / Q000379:methods; D049750:Genome, Insect / Q000235:genetics*; D023281:Genomics / Q000379:methods; D007630:Kenya; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011157:Population Dynamics; D012641:Selection, Genetic / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*