title: A worldwide survey of genome sequence variation provides insight into the evolutionary history of the honeybee Apis mellifera.
abstract: The honeybee Apis mellifera has major ecological and economic importance. We analyze patterns of genetic variation at 8.3 million SNPs, identified by sequencing 140 honeybee genomes from a worldwide sample of 14 populations at a combined total depth of 634×. These data provide insight into the evolutionary history and genetic basis of local adaptation in this species. We find evidence that population sizes have fluctuated greatly, mirroring historical fluctuations in climate, although contemporary populations have high genetic diversity, indicating the absence of domestication bottlenecks. Levels of genetic variation are strongly shaped by natural selection and are highly correlated with patterns of gene expression and DNA methylation. We identify genomic signatures of local adaptation, which are enriched in genes expressed in workers and in immune system- and sperm motility-related genes that might underlie geographic variation in reproduction, dispersal and disease resistance. This study provides a framework for future investigations into responses to pathogens and climate change in honeybees.
authors.affiliation: Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
authors.forename: Andreas
authors.initials: A
authors.lastname: Wallberg
authors.affiliation: 1] Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden. [2].
authors.forename: Fan
authors.initials: F
authors.lastname: Han
authors.affiliation: 1] Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden. [2].
authors.forename: Gustaf
authors.initials: G
authors.lastname: Wellhagen
authors.affiliation: Norwegian Beekeepers Association, Kløfta, Norway.
authors.forename: Bjørn
authors.initials: B
authors.lastname: Dahle
authors.affiliation: Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Sendai, Japan.
authors.forename: Masakado
authors.identifier: 0000000187165438
authors.initials: M
authors.lastname: Kawata
authors.affiliation: Bee Research Department, National Center for Agricultural Research and Extension, Amman, Jordan.
authors.forename: Nizar
authors.initials: N
authors.lastname: Haddad
authors.affiliation: Department of Biology, University of São Paulo, São Paulo, Brazil.
authors.forename: Zilá Luz Paulino
authors.initials: ZL
authors.lastname: Simões
authors.affiliation: Plant Protection Research Institute, Agricultural Research Council, Stellenbosch, South Africa.
authors.forename: Mike H
authors.initials: MH
authors.lastname: Allsopp
authors.affiliation: Department of Biology, Ankara University, Ankara, Turkey.
authors.forename: Irfan
authors.initials: I
authors.lastname: Kandemir
authors.affiliation: Department of Zoology and Physical Anthropology, University of Murcia, Murcia, Spain.
authors.forename: Pilar
authors.identifier: 0000000200581402
authors.initials: P
authors.lastname: De la Rúa
authors.affiliation: Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa.
authors.forename: Christian W
authors.initials: CW
authors.lastname: Pirk
authors.affiliation: Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
authors.forename: Matthew T
authors.initials: MT
authors.lastname: Webster
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D000818:Animals; D001516:Bees / Q000145:classification / Q000235:genetics*; D016000:Cluster Analysis; D019175:DNA Methylation; D019143:Evolution, Molecular; D015870:Gene Expression; D017344:Genes, Insect / Q000235:genetics; D014644:Genetic Variation; D016678:Genome / Q000235:genetics*; D005838:Genotype; D005843:Geography; D019476:Insect Proteins / Q000235:genetics; D015810:Linkage Disequilibrium; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D019476:Insect Proteins