title: Expression Divergence Is Correlated with Sequence Evolution but Not Positive Selection in Conifers.
abstract: The evolutionary and genomic determinants of sequence evolution in conifers are poorly understood, and previous studies have found only limited evidence for positive selection. Using RNAseq data, we compared gene expression profiles to patterns of divergence and polymorphism in 44 seedlings of lodgepole pine (Pinus contorta) and 39 seedlings of interior spruce (Picea glauca × engelmannii) to elucidate the evolutionary forces that shape their genomes and their plastic responses to abiotic stress. We found that rapidly diverging genes tend to have greater expression divergence, lower expression levels, reduced levels of synonymous site diversity, and longer proteins than slowly diverging genes. Similar patterns were identified for the untranslated regions, but with some exceptions. We found evidence that genes with low expression levels had a larger fraction of nearly neutral sites, suggesting a primary role for negative selection in determining the association between evolutionary rate and expression level. There was limited evidence for differences in the rate of positive selection among genes with divergent versus conserved expression profiles and some evidence supporting relaxed selection in genes diverging in expression between the species. Finally, we identified a small number of genes that showed evidence of site-specific positive selection using divergence data alone. However, estimates of the proportion of sites fixed by positive selection (α) were in the range of other plant species with large effective population sizes suggesting relatively high rates of adaptive divergence among conifers.
authors.affiliation: School of Biological Sciences, Monash University, Melbourne, VIC, Australia kathryn.hodgins@monash.edu.
authors.forename: Kathryn A
authors.initials: KA
authors.lastname: Hodgins
authors.affiliation: Department of Botany, University of British Columbia, Vancouver, BC, Canada Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada Department of Biological Sciences, University of Calgary, Calgary, AB, Canada.
authors.forename: Sam
authors.initials: S
authors.lastname: Yeaman
authors.affiliation: School of Biological Sciences, Monash University, Melbourne, VIC, Australia.
authors.forename: Kristin A
authors.initials: KA
authors.lastname: Nurkowski
authors.affiliation: Department of Botany, University of British Columbia, Vancouver, BC, Canada.
authors.forename: Loren H
authors.initials: LH
authors.lastname: Rieseberg
authors.affiliation: Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada.
authors.forename: Sally N
authors.initials: SN
authors.lastname: Aitken
mesh_terms: D005075:Biological Evolution; D019143:Evolution, Molecular; D018506:Gene Expression Regulation, Plant; D014644:Genetic Variation; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D005810:Multigene Family; D059645:Mutation Rate; D028222:Picea / Q000235:genetics*; D028223:Pinus / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics; D012641:Selection, Genetic; D059467:Transcriptome
chemical_list: D010940:Plant Proteins
keywords: Engelmann spruce; RNAseq; climate.; gene expression; lodgepole pine; positive selection; white spruce