Maintenance of quantitative genetic variance in complex, multitrait phenotypes: the contribution of rare, large effect variants in 2 Drosophila species

Emma Hine, Daniel E. Runcie, Scott L. Allen, Yiguan Wang, Stephen F. Chenoweth, Mark W. Blows, Katrina McGuigan

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

The interaction of evolutionary processes to determine quantitative genetic variation has implications for contemporary and future phenotypic evolution, as well as for our ability to detect causal genetic variants. While theoretical studies have provided robust predictions to discriminate among competing models, empirical assessment of these has been limited. In particular, theory highlights the importance of pleiotropy in resolving observations of selection and mutation, but empirical investigations have typically been limited to few traits. Here, we applied high-dimensional Bayesian Sparse Factor Genetic modeling to gene expression datasets in 2 species, Drosophila melanogaster and Drosophila serrata, to explore the distributions of genetic variance across high-dimensional phenotypic space. Surprisingly, most of the heritable trait covariation was due to few lines (genotypes) with extreme [>3 interquartile ranges (IQR) from the median] values. Intriguingly, while genotypes extreme for a multivariate factor also tended to have a higher proportion of individual traits that were extreme, we also observed genotypes that were extreme for multivariate factors but not for any individual trait. We observed other consistent differences between heritable multivariate factors with outlier lines vs those factors without extreme values, including differences in gene functions. We use these observations to identify further data required to advance our understanding of the evolutionary dynamics and nature of standing genetic variation for quantitative traits.

Original languageEnglish
Article numberiyac122
Number of pages17
JournalGenetics
Volume222
Issue number2
Early online date12 Aug 2022
DOIs
Publication statusPublished - 1 Oct 2022

Keywords / Materials (for Non-textual outputs)

  • drosophila melanogaster
  • drosophila serrata
  • gene expression
  • genetic covariance
  • house of cards
  • mutation–selection balance
  • sparse factor analysis
  • standing genetic variance

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