Impact of prior specifications in a shrinkage-inducing Bayesian model for quantitative trait mapping and genomic prediction

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Local adaptation in Scots pine (Pinus sylvestris) survival and growth in relation to timing of bud set

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Adaptive potential of northernmost tree populations to climate change, with emphasis on Scots pine (Pinus sylvestris L.).

The Journal of hereditySavolainen, OutiKujala, Sonja TSokol, CatherinaPyhajarvi, TanjaAvia, KomlanKnurr, TimoKarkkainen, KatriHicks, SheilaResearch Support, Non-U.S. Gov'tUnited StatesJ Hered. 2011 Sep-Oct;102(5):526-36. doi: 10.1093/jhered/esr056. Epub 2011 Jun 29.The adaptive potential of the northernmost Pinus sylvestris L. (and other northern tree) populations is considered by examining first the current patterns of quantitative genetic adaptive traits, which show high population differentiation and clines. We then consider the postglacial history of the populations using both paleobiological and genetic data. The current patterns of diversity at nuclear genes suggest that the traces of admixture are mostly visible in mitochondrial DNA variation patterns. There is little evidence of increased diversity due to admixture between an eastern and western colonization lineage, but no signal of reduced diversity (due to sequential bottlenecks) either. Quantitative trait variation in the north is not associated with the colonizing lineages. The current clines arose rapidly and may be based on standing genetic variation. The initial phenotypic response of Scots pine in the north is predicted to be increased survival and growth. The genetic responses are examined based on quantitative genetic predictions of sustained selection response and compared with earlier simulation results that have aimed at more ecological realism. The phenotypic responses of increased growth and survival reduce the opportunity for selection and delay the evolutionary responses. The lengthening of the thermal growing period also causes selection on the critical photoperiod in the different populations. Future studies should aim at including multiple ecological and genetic factors in evaluating potential responses

Data from: Genetic heterogeneity underlying variation in a locally adaptive clinal trait in Pinus sylvestris revealed by a Bayesian multipopulation analysis

Local adaptation is a common feature of plant and animal populations. Adaptive phenotypic traits are genetically differentiated along environmental gradients, but the genetic basis of such adaptation is still poorly known. Genetic association studies of local adaptation combine data over populations. Correcting for population structure in these studies can be problematic since both selection and neutral demographic events can create similar allele frequency differences between populations. Correcting for demography with traditional methods may lead to eliminating some true associations. We developed a new Bayesian approach for identifying the loci underlying an adaptive trait in a multipopulation situation in the presence of possible double confounding due to population stratification and adaptation. With this method we studied the genetic basis of timing of bud set, a surrogate trait for timing of yearly growth cessation that confers local adaptation to the populations of Scots pine (Pinus sylvestris). Population means of timing of bud set were highly correlated with latitude. Most effects at individual loci were small. Interestingly, we found genetic heterogeneity (i.e., different sets of loci associated with the trait) between the northern and central European parts of the cline. We also found indications of stronger stabilizing selection towards the northern part of the range. The harsh northern conditions may impose greater selective pressure on timing of growth cessation, and the relative importance of different environmental cues used for tracking the seasons might differ depending on latitude of origin

R script

R script to run MCMC simulation for the association analysis

Gibbs sampler

Gibbs sampler in a C-language module implemented as an extension to R

Data from: Genetic heterogeneity underlying variation in a locally adaptive clinal trait in Pinus sylvestris revealed by a Bayesian multipopulation analysis

Local adaptation is a common feature of plant and animal populations. Adaptive phenotypic traits are genetically differentiated along environmental gradients, but the genetic basis of such adaptation is still poorly known. Genetic association studies of local adaptation combine data over populations. Correcting for population structure in these studies can be problematic since both selection and neutral demographic events can create similar allele frequency differences between populations. Correcting for demography with traditional methods may lead to eliminating some true associations. We developed a new Bayesian approach for identifying the loci underlying an adaptive trait in a multipopulation situation in the presence of possible double confounding due to population stratification and adaptation. With this method we studied the genetic basis of timing of bud set, a surrogate trait for timing of yearly growth cessation that confers local adaptation to the populations of Scots pine (Pinus sylvestris). Population means of timing of bud set were highly correlated with latitude. Most effects at individual loci were small. Interestingly, we found genetic heterogeneity (that is, different sets of loci associated with the trait) between the northern and central European parts of the cline. We also found indications of stronger stabilizing selection toward the northern part of the range. The harsh northern conditions may impose greater selective pressure on timing of growth cessation, and the relative importance of different environmental cues used for tracking the seasons might differ depending on latitude of origin

Phenotype data

Phenotype data for 274 half-sib families used in association analysis (except entries 137,161,196; see Gibbs sampler file). Includes the following columns: a. TREE: identifier for individual mother trees b. METLA: alternative identifier c. POP: population identifier d. BUDSET: BLUP-estimate of breeding value of TREE (from mixed model) e. LATITUDE: latitude of origin f. POPMEAN: estimate of population mean (from mixed model)