Quantifying natural seasonal variation in mutation parameters with mutation accumulation lines

Abstract

Mutations create novel genetic variants, but their contribution to variation in fitness and other phenotypes may depend on environmental conditions. Furthermore, natural environments may be highly heterogeneous. We assessed phenotypes associated with survival and reproductive success in over 30,000 plants representing 100 mutation accumulation lines of Arabidopsis thaliana across four temporal environments at a single field site. In each of the four assays, environmental variance was substantially larger than mutational variance. For some traits, whether mutational variance was significantly varied between seasons. The founder genotype had mean trait values near the mean of the distribution of the mutation accumulation lines in all field experiments. New mutations also contributed more phenotypic variation than would be predicted, given phenotypic and sequence‐level divergence among natural populations of A. thaliana. The combination of large environmental variance with a mean effect of mutation near zero suggests that mutations could contribute substantially to standing genetic variation.

Direct inference of the distribution of fitness effects of spontaneous mutations inChlamydomonas reinhardtii

“…Why are we seeing a high proportion of positive-effect mutations? One possibility is that mutations that increase fitness are common in natural populations, and this is reflected in MA experiments (Shaw et al 2003;Rutter et al 2018). An alternative view is that deleterious mutations predominate in nature, principally because organisms are well adapted to the environments they typically…”

Distributed phenomics with the unPAK project reveals the effects of mutations

“…For example, even a bivariate analysis (fruit number and inflorescence height; Figure c) reveals more lines that produce extreme phenotypes than either of the univariate analyses summarized in Figure (a,b). It is noteworthy that many of the T‐DNA mutant lines produce more fruits or larger inflorescences than Columbia, as seen in a previous phenotypic survey of these mutants (Rutter et al ., ), and is consistent with a relatively high frequency of mutant lines in A. thaliana with higher fitness than non‐mutant genotypes (Rutter et al ., , ). Figure (c) also suggests that with respect to fruit number and inflorescence size, morphospace is well explored by the phytometer lines included in each experimental replicate.…”

Rapid evolution by spontaneous mutation increases genetic diversity facilitating plant population survival

“…After the propagation of a set of MA lines through multiple generations, the genetic differences among the MA lines and between those lines and the founder reflect the input of mutation. Significant MA line effects for multiple traits, including performance and trait measures, were found under both field and greenhouse conditions (Rutter et al 2010; Roles et al 2016, Rutter et al 2018). Each of the MA lines in our experiment is fixed for an average of 20 different sequence level mutations, single nucleotide mutations (SNMs) and indels combined (Ossowski et al 2010, Rutter et al 2012, Weng et al 2019).…”

“…We used survival and seed set data of A. thaliana MA lines and the founder as assessed in field experiments in 2004 and 2005 from Rutter et al (2010, 2012 and 2018) planted in a randomized design (Fig. 1).…”

“…Therefore, we aim to investigate the link between evolutionary genetics and spatial ecological interactions of mutation accumulation lines (MA lines) in the model plant organism Arabidopsis thaliana (Brassicaceae) to advance our understanding of the genetic origins of population and community dynamics, contributing to a fuller understanding of the maintenance of biodiversity. We take advantage of 25th generation A. thaliana mutation accumulation (MA) lines that were planted under field conditions in years 2004 and 2005 with spatial records of each individual each year (e.g., Rutter et al 2010; 2012, Rutter et al 2018) (Fig. 1).…”