A study of the relationship between the growth rate of tropical trees and the frequency of genetic mutations they accumulate suggests that older, long-lived trees play a greater role in generating and maintaining genetic diversity than short-lived trees.
The study, published as a Reviewed Preprint in eLife, provides what the editors describe as “convincing evidence” that tree species acquire mutations at a similar yearly rate, independent of cell division and growth rate. The findings could be used to inform ecosystem conservation strategies, particularly in Southeast Asia’s tropical forests, which are under threat from climate change and deforestation.
“Biodiversity ultimately results from mutations that provide genetic variation for organisms to adapt to their environment,” explains co-lead author Akiko Satake, a Professor in the Department of Biology, Faculty of Science, Kyushu University, Japan. “However, it is unclear how and when these mutations occur in natural environments.”
Biodiversity ultimately results from mutations that provide genetic variation for organisms to adapt to their environment. However, it is unclear how and when these mutations occur in natural environments.
Akiko Satake
Somatic mutations are changes in an organism’s DNA that occur spontaneously during its lifetime. They can be caused by external factors such as ultraviolet radiation or internal factors such as DNA replication errors. It is unclear which of these factors causes mutations more frequently, particularly in tropical ecosystems and trees, which are less well characterised than their temperate counterparts.
To understand this better, Satake and colleagues examined the rates and patterns of somatic mutations in two species of tropical trees native to central Borneo, Indonesia: the slow-growing Shorea laevis (S. laevis), and the fast-growing S. leprosula. The species S. leprosula grows more than three times faster than S. laevis.
The team gained insights into the impact of growth rate on the accumulation of these mutations, as well as its potential role in driving evolution and species diversity, by comparing the somatic mutations of the two tree species. They collected seven DNA samples from the highest level of the tree branches, as well as samples from each tree’s trunk, for a total of 32 samples. The average age of each species in the sampling area was determined by measuring the length and diameter of the trees at breast height. S. laevis trees were 256 years old on average, whereas S. leprosula trees were 66 years old on average.
To identify the mutations, the researchers created a reference genetic dataset for each tree species using DNA extracted from the leaves. Long-read PacBio RS II and short-read Illumina sequencing were used to determine the genome sequence. The researchers extracted DNA from each sample twice, which allowed them to identify single nucleotide variants (SNVs) within the same individual by identifying those that were identical between the two samples. The vast majority of mutations were discovered within a single tree branch. Some mutations, on the other hand, were found across multiple branches, implying that they were transmitted between branches at some point during the tree’s growth.
The team discovered a linear increase in the number of mutations with physical distance between branches in both species. The rate of mutations per metre in slow-growing S. leavis was 3.7 times higher than in fast-growing S. leprosula, implying that slow-growing trees accumulate more somatic mutations. When the differences in growth rates were taken into account and the rate of mutations per year was calculated, the two species had equal rates. This finding suggests that as a tree ages, somatic mutations accumulate in a clock-like fashion, independent of DNA replication and growth rate.
“We also found that somatic mutations are neutral within an individual — that is, they are neither beneficial nor detrimental to survival. However, those mutations transmitted to the next generation are subject to strong natural selection during seed germination and growth,” says co-lead author Ryosuke Imai, Post-doctoral Fellow in the Department of Biology, Faculty of Science, Kyushu University. “This suggests that somatic mutations accumulate with time, and older trees contribute more towards generating genetic variation and adaptation to their environment, thereby increasing the chances of their species’ survival.”
Imai and colleagues advocate for more research in this area. In particular, they claim that mathematical modeling would be required to account for asymmetric cell division during elongation and branching in order to validate the findings further.
“In trees, somatic mutations can be transmitted to seeds, resulting in rich genetic variations within subsequent generations,” says Masahiro Kasahara, Associate Professor at the University of Tokyo’s department of computational biology and medical sciences. “As Southeast Asia’s tropical rainforests face threats from climate change and deforestation, our research suggests that long-lived trees may play an important role in maintaining and increasing the genetic diversity of these tropical systems.”
