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      A note on measuring natural selection on principal component scores

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          Abstract

          Measuring natural selection through the use of multiple regression has transformed our understanding of selection, although the methods used remain sensitive to the effects of multicollinearity due to highly correlated traits. While measuring selection on principal component (PC) scores is an apparent solution to this challenge, this approach has been heavily criticized due to difficulties in interpretation and relating PC axes back to the original traits. We describe and illustrate how to transform selection gradients for PC scores back into selection gradients for the original traits, addressing issues of multicollinearity and biological interpretation. In addition to reducing multicollinearity, we suggest that this method may have promise for measuring selection on high‐dimensional data such as volatiles or gene expression traits. We demonstrate this approach with empirical data and examples from the literature, highlighting how selection estimates for PC scores can be interpreted while reducing the consequences of multicollinearity

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          Most cited references31

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          Visualizing and quantifying natural selection.

          Modern methods of analysis are enabling researchers to study natural selection at a new level of detail. Multivariate statistical techniques can Identify specific targets of selection and provide parameter estimates that fit into equations for evolutionary change. A more Intuitive understanding of the form of selection can be provided through graphical representation of selection surfaces. Combinations of quantitative and visual analyses are providing researchers with new insights into the details of natural selection in the wild.
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            Role of FRIGIDA and FLOWERING LOCUS C in determining variation in flowering time of Arabidopsis.

            Arabidopsis (Arabidopsis thaliana) accessions provide an excellent resource to dissect the molecular basis of adaptation. We have selected 192 Arabidopsis accessions collected to represent worldwide and local variation and analyzed two adaptively important traits, flowering time and vernalization response. There was huge variation in the flowering habit of the different accessions, with no simple relationship to latitude of collection site and considerable diversity occurring within local regions. We explored the contribution to this variation from the two genes FRIGIDA (FRI) and FLOWERING LOCUS C (FLC), previously shown to be important determinants in natural variation of flowering time. A correlation of FLC expression with flowering time and vernalization was observed, but it was not as strong as anticipated due to many late-flowering/vernalization-requiring accessions being associated with low FLC expression and early-flowering accessions with high FLC expression. Sequence analysis of FRI revealed which accessions were likely to carry functional alleles, and, from comparison of flowering time with allelic type, we estimate that approximately 70% of flowering time variation can be accounted for by allelic variation of FRI. The maintenance and propagation of 20 independent nonfunctional FRI haplotypes suggest that the loss-of-function mutations can confer a strong selective advantage. Accessions with a common FRI haplotype were, in some cases, associated with very different FLC levels and wide variation in flowering time, suggesting additional variation at FLC itself or other genes regulating FLC. These data reveal how useful these Arabidopsis accessions will be in dissecting the complex molecular variation that has led to the adaptive phenotypic variation in flowering time.
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              Epistatic interaction between Arabidopsis FRI and FLC flowering time genes generates a latitudinal cline in a life history trait.

              Epistatic gene interactions are believed to be a major factor in the genetic architecture of evolutionary diversification. In Arabidopsis thaliana, the FRI and FLC genes mechanistically interact to control flowering time, and here we show that this epistatic interaction also contributes to a latitudinal cline in this life history trait within the species. Two major FLC haplogroups (FLC(A) and FLC(B)) are associated with flowering time variation in A. thaliana in field conditions, but only in the presence of putatively functional FRI alleles. Significant differences in latitudinal distribution of FLC haplogroups in Eurasia and North Africa also depend on the FRI genotype. There is significant linkage disequilibrium between FRI and FLC despite their location on separate chromosomes. Although no nonsynonymous polymorphisms differentiate FLC(A) and FLC(B), vernalization induces the expression of an alternatively spliced FLC transcript that encodes a variant protein with a radical amino acid replacement associated with the two FLC haplogroups. Numerous polymorphisms differentiating the FLC haplogroups also occur in intronic regions implicated in the regulation of FLC expression. The features of the regulatory gene interaction between FRI and FLC in contributing to the latitudinal cline in A. thaliana flowering time are consistent with the maintenance of this interaction by epistatic selection. These results suggest that developmental genetic pathways and networks provide the molecular basis for epistasis, contributing to ecologically important phenotypic variation in natural populations and to the process of evolutionary diversification.
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                Author and article information

                Contributors
                john.stinchcombe@utoronto.ca
                Journal
                Evol Lett
                Evol Lett
                10.1002/(ISSN)2056-3744
                EVL3
                Evolution Letters
                John Wiley and Sons Inc. (Hoboken )
                2056-3744
                21 June 2018
                August 2018
                : 2
                : 4 ( doiID: 10.1002/evl3.2018.2.issue-4 )
                : 272-280
                Affiliations
                [ 1 ] Department of Ecology and Evolutionary Biology University of Toronto Toronto Ontario Canada
                [ 2 ] Koffler Scientific Reserve University of Toronto Toronto Ontario Canada
                Author information
                http://orcid.org/0000-0003-3349-2964
                Article
                EVL363
                10.1002/evl3.63
                6121829
                30283681
                ae882bd9-7e22-4d27-8dc4-25634aeb9264
                © 2018 The Author(s). Evolution Letters published by Wiley Periodicals, Inc. on behalf of Society for the Study of Evolution (SSE) and European Society for Evolutionary Biology (ESEB).

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 08 November 2017
                : 18 May 2018
                : 25 May 2018
                Page count
                Figures: 2, Tables: 2, Pages: 9, Words: 6744
                Funding
                Funded by: NSERC Canada
                Categories
                Comment and Opinion
                Comments and Opinions
                Custom metadata
                2.0
                evl363
                August 2018
                Converter:WILEY_ML3GV2_TO_NLMPMC version:version=5.4.7.1 mode:remove_FC converted:04.09.2018

                flowering time,life history,multicollinearity,principal component analysis,principal component regression,selection gradients,trade‐offs

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