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 today as a Reviewed Preprint in eLife, provides what the editors describe as compelling evidence that tree species acquire mutations at a similar annual rate, regardless of cell division and regardless of their growth rate.
Findings can be used to inform ecosystem conservation strategies, particularly in Southeast Asian tropical forests, which are threatened by climate change and deforestation.
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Biodiversity ultimately results from mutations that provide genetic variations to 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, how and when these mutations occur in natural environments is poorly understood.
Somatic mutations are spontaneous changes in an organism’s DNA that occur during its lifetime. They can arise due to external factors such as ultraviolet radiation or internal factors such as DNA replication errors. It is unclear which of these factors causes more frequent mutations, particularly in tropical ecosystems and trees, which are not as well characterized as their more temperate counterparts.
To better understand this, Satake and colleagues examined the rates and patterns of somatic mutations in two tropical tree species native to central Borneo, Indonesia: the slow-growing plant Shorea laevis (S. laevis)and growing rapidly S. leprosula. The species S. leprosula grows more than three times faster than S. laevis.
Comparing the somatic mutations of the two tree species allowed the team to gain insights into the impact of growth rate on the accumulation of these mutations and its potential role in driving evolution and species diversity. They collected seven DNA samples from leaves at the topmost level of tree branches, as well as samples from the trunk of each tree, for a total of 32 samples. The length and diameter of trees at breast height were used to determine the mean age of each species in the sampling area. S. laevis the trees were on average 256 years old, while S. leprosula the trees were on average 66 years old.
To identify the mutations present, the team constructed a reference genetic dataset for each tree species, using DNA collected from the leaves. The genome sequence was determined using a technique called PacBio RS II long-read and Illumina short-read sequencing. The team extracted DNA twice from each sample, allowing them to detect single nucleotide variants (SNVs) within the same individual by identifying which ones were identical between the two samples. Most of the mutations were found to be present within a single branch of a tree. However, some mutations were found across multiple branches, implying that they had been transmitted between branches at some point during the growth of the trees.
In both species, the team noted a linear increase in the number of mutations with physical distance between branches. The mutation rate per meter was on average 3.7 times higher in slow growth S. leaves which is growing rapidly S. leprosula, suggesting that slow-growing trees accumulate more somatic mutations. However, when accounting for differences in growth rates and calculating the mutation rate per year, the two species had equal rates. This finding suggests that somatic mutations accumulate in a clock-like fashion as a tree ages, independent of DNA replication and growth rate.
We also found that somatic mutations are neutral within an individual, i.e. they are neither beneficial nor detrimental to survival. However, those mutations passed on to the next generation are subject to strong natural selection during seed germination and growth, says co-lead author Ryosuke Imai, postdoctoral fellow in the Department of Biology, Faculty of Science, Kyushu University . This suggests that somatic mutations accumulate over time and that older trees contribute more to generating genetic variation and adapting to their environment, thereby increasing their species’ chances of survival.
Imai and colleagues encourage further research in this area. In particular, they state that mathematical modeling would be needed to account for asymmetric cell division during elongation and branching in order to further validate the results.
In trees, somatic mutations can be passed on to seeds, resulting in rich genetic variation within successive generations, says one of the authors Masahiro Kasahara, an associate professor in the department of computational biology and medical sciences at the University of Tokyo, Japan . As Southeast Asian tropical rainforests face the threats of climate change and deforestation, our study suggests that long-lived trees may play a crucial role in maintaining and increasing the genetic variation of these tropical systems.
Reference: Ryosuke Imai Takeshi Fujino Sou Tomimoto Kayoko Ohta Mohammad Naiem Sapto Indrioko undefined Widiyatno Susilo Purnomo Almudena Moll-Morales Viktoria Nizhynska Naoki Tani Yoshihisa Suyama Eriko Sasaki Masahiro Kasahara Akiko Satake. The molecular clock in long-lived tropical trees is independent of growth rate. and Life 2023 doi: 10.7554/eLife.88456.1
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