A phylogenomic approach reveals a low somatic mutation rate in a long-lived plant

Abstract

Somatic mutations can have important effects on the life history, ecology, and evolution of plants, but the rate at which they accumulate is poorly understood and difficult to measure directly. Here, we develop a method to measure somatic mutations in individual plants and use it to estimate the somatic mutation rate in a large, long-lived, phenotypically mosaic Eucalyptus melliodora tree. Despite being 100 times larger than Arabidopsis, this tree has a per-generation mutation rate only ten times greater, which suggests that this species may have evolved mechanisms to reduce the mutation rate per unit of growth. This adds to a growing body of evidence that illuminates the correlated evolutionary shifts in mutation rate and life history in plants.

Keywords: bioinformatics; mutation rate; plants; somatic mutation.

Figure 1.

The Eucalyptus melliodora individual sequenced in this study. The eight branch tips sampled are shown by numbered green circles with internal nodes of the tree shown as letters in blue circles. Circles with dashed outlines are from the far side of the tree. Pink lines trace the physical branches that connect the sampled tips. The herbivore-resistant branch comprises samples 1–3.

Figure 2.

Phylogenetic trees reconstructed from somatic mutations resemble the physical structure of the tree more closely than expected by chance. (a) The PD between the physical tree (figure 1) and all 10 395 possible phylogenetic trees of eight taxa is shown as a histogram. A tree with the same topology as the physical tree will have a PD of 0. The solid red line represents the boundary of the smallest 5% of the distribution of PDs, such that a tree with a PD lower than this line is more similar to the physical tree than expected by chance. All of the maximum-parsimony trees (dashed red lines) and the one maximum-likelihood tree (solid blue line) are more similar to the physical tree than expected by chance. (b) A side-by-side comparison of the physical tree (left, branch lengths in metres) and the maximum-likelihood tree (right, branch lengths in substitutions per site) inferred with the JC model. Letters on the nodes of the physical tree (left) correspond to the same letters of internal nodes in figure 1. Numbers on the maximum-likelihood tree (right) are bootstrap percentages. There is a single difference between the two trees: the inferred tree groups samples M8 and M5 together with low bootstrap support (44%), which is a grouping that does not occur in the physical tree.