title: Molecular evolution of regulatory genes in spruces from different species and continents: heterogeneous patterns of linkage disequilibrium and selection but correlated recent demographic changes.
abstract: Genes involved in transcription regulation may represent valuable targets in association genetics studies because of their key roles in plant development and potential selection at the molecular level. Selection and demographic signatures at the sequence level were investigated for five regulatory genes belonging to the knox-I family (KN1, KN2, KN3, KN4) and the HD-Zip III family (HB-3) in three Picea species affected by post-glacial recolonization in North America and Europe. To disentangle neutral and selective forces and estimate linkage disequilibrium (LD) on a gene basis, complete or nearly complete gene sequences were analysed. Nucleotide variation within species, haplotype structure, LD, and neutrality tests, in addition to coalescent simulations based on Tajima's D and Fay and Wu's H, were estimated. Nucleotide diversity was generally low in all species (average pi = 0.002-0.003) and much heterogeneity was seen in LD and selection signatures among genes and species. Most of the genes harboured an excess of both rare and frequent alleles in the three species. Simulations showed that this excess was significantly higher than that expected under neutrality and a bottleneck during the Last Glacial Maximum followed by population expansion at the Pleistocene/Holocene boundary or shortly after best explains the correlated sequence patterns. These results indicate that despite recent large demographic changes in the three boreal species from two continents, species-specific selection signatures could still be detected from the analysis of nearly complete regulatory gene sequences. Such different signatures indicate differential subfunctionalization of gene family members in the three congeneric species.
authors.affiliation: Arborea and Canada Research Chair in Forest and Environmental Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC G1V 0A6, Canada. marie-claire.namroud@sbf.ulaval.ca
authors.forename: Marie-Claire
authors.initials: MC
authors.lastname: Namroud
authors.forename: Carine
authors.initials: C
authors.lastname: Guillet-Claude
authors.forename: John
authors.initials: J
authors.lastname: Mackay
authors.forename: Nathalie
authors.initials: N
authors.lastname: Isabel
authors.forename: Jean
authors.initials: J
authors.lastname: Bousquet
mesh_terms: D019943:Amino Acid Substitution; D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D017343:Genes, Plant; D006239:Haplotypes; D018398:Homeodomain Proteins / Q000235:genetics; D054643:INDEL Mutation; D015810:Linkage Disequilibrium; D008969:Molecular Sequence Data; D009711:Nucleotides / Q000235:genetics; D028222:Picea / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics; D011110:Polymorphism, Genetic; D012639:Seeds; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D018398:Homeodomain Proteins; C405985:Knox1 protein, plant; D009711:Nucleotides; D010940:Plant Proteins