title: Copy number variation in the speciation of pigs: a possible prominent role for olfactory receptors.
abstract: BACKGROUND
  Unraveling the genetic mechanisms associated with reduced gene flow between genetically differentiated populations is key to understand speciation. Different types of structural variations (SVs) have been found as a source of genetic diversity in a wide range of species. Previous studies provided detailed knowledge on the potential evolutionary role of SVs, especially copy number variations (CNVs), between well diverged species of e.g. primates. However, our understanding of their significance during ongoing speciation processes is limited due to the lack of CNV data from closely related species. The genus Sus (pig and its close relatives) which started to diverge ~4 Mya presents an excellent model for studying the role of CNVs during ongoing speciation.
  
  
  RESULTS
  In this study, we identified 1408 CNV regions (CNVRs) across the genus Sus. These CNVRs encompass 624 genes and were found to evolve ~2.5 times faster than single nucleotide polymorphisms (SNPs). The majority of these copy number variable genes are olfactory receptors (ORs) known to play a prominent role in food foraging and mate recognition in Sus. Phylogenetic analyses, including novel Bayesian analysis, based on CNVRs that overlap ORs retain the well-accepted topology of the genus Sus whereas CNVRs overlapping genes other than ORs show evidence for random drift and/or admixture.
  
  
  CONCLUSIONS
  We hypothesize that inter-specific variation in copy number of ORs provided the means for rapid adaptation to different environments during the diversification of the genus Sus in the Pliocene. Furthermore, these regions might have acted as barriers preventing massive gene flow between these species during the multiple hybridization events that took place later in the Pleistocene suggesting a possible prominent role of ORs in the ongoing Sus speciation.
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University, 6700 AH, Wageningen, The Netherlands. paudelyogesh@gmail.com.|Current address: Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070, Basel, Switzerland. paudelyogesh@gmail.com.
authors.forename: Yogesh
authors.initials: Y
authors.lastname: Paudel
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University, 6700 AH, Wageningen, The Netherlands. ole.madsen@wur.nl.
authors.forename: Ole
authors.initials: O
authors.lastname: Madsen
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University, 6700 AH, Wageningen, The Netherlands. hendrik-jan.magens@wur.nl.
authors.forename: Hendrik-Jan
authors.initials: HJ
authors.lastname: Megens
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University, 6700 AH, Wageningen, The Netherlands. laurent.frantz@wur.nl.
authors.forename: Laurent A F
authors.initials: LA
authors.lastname: Frantz
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University, 6700 AH, Wageningen, The Netherlands. mirte.bosse@wur.nl.
authors.forename: Mirte
authors.initials: M
authors.lastname: Bosse
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University, 6700 AH, Wageningen, The Netherlands. richard.crooijmans@wur.nl.
authors.forename: Richard P M A
authors.initials: RP
authors.lastname: Crooijmans
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University, 6700 AH, Wageningen, The Netherlands. martien.groenen@wur.nl.
authors.forename: Martien A M
authors.initials: MA
authors.lastname: Groenen
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D002874:Chromosome Mapping; D016000:Cluster Analysis; D056915:DNA Copy Number Variations / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D018035:Receptors, Odorant / Q000235:genetics* / Q000378:metabolism; D017422:Sequence Analysis, DNA; D013552:Swine / Q000145:classification / Q000235:genetics*
chemical_list: D018035:Receptors, Odorant