Somatic mutation rates scale with time not growth rate in long-lived tropical trees
The rates of appearance of new mutations play a central role in evolution. However, mutational processes in natural environments and their relationship with growth rates are largely unknown, particular in tropical ecosystems with high biodiversity. Here, we examined the somatic mutation landscapes o...
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eLife Sciences Publications Ltd
2024-10-01
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| Online Access: | https://elifesciences.org/articles/88456 |
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| author | Akiko Satake Ryosuke Imai Takeshi Fujino Sou Tomimoto Kayoko Ohta Mohammad Na'iem Sapto Indrioko Widiyatno Widiyatno Susilo Purnomo Almudena Molla Morales Viktoria Nizhynska Naoki Tani Yoshihisa Suyama Eriko Sasaki Masahiro Kasahara |
| author_facet | Akiko Satake Ryosuke Imai Takeshi Fujino Sou Tomimoto Kayoko Ohta Mohammad Na'iem Sapto Indrioko Widiyatno Widiyatno Susilo Purnomo Almudena Molla Morales Viktoria Nizhynska Naoki Tani Yoshihisa Suyama Eriko Sasaki Masahiro Kasahara |
| author_sort | Akiko Satake |
| collection | DOAJ |
| description | The rates of appearance of new mutations play a central role in evolution. However, mutational processes in natural environments and their relationship with growth rates are largely unknown, particular in tropical ecosystems with high biodiversity. Here, we examined the somatic mutation landscapes of two tropical trees, Shorea laevis (slow-growing) and S. leprosula (fast-growing), in central Borneo, Indonesia. Using newly constructed genomes, we identified a greater number of somatic mutations in tropical trees than in temperate trees. In both species, we observed a linear increase in the number of somatic mutations with physical distance between branches. However, we found that the rate of somatic mutation accumulation per meter of growth was 3.7-fold higher in S. laevis than in S. leprosula. This difference in the somatic mutation rate was scaled with the slower growth rate of S. laevis compared to S. leprosula, resulting in a constant somatic mutation rate per year between the two species. We also found that somatic mutations are neutral within an individual, but those mutations transmitted to the next generation are subject to purifying selection. These findings suggest that somatic mutations accumulate with absolute time and older trees have a greater contribution towards generating genetic variation. |
| format | Article |
| id | doaj-art-7752b59b6a76409cbb9c4882bbecf05a |
| institution | OA Journals |
| issn | 2050-084X |
| language | English |
| publishDate | 2024-10-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj-art-7752b59b6a76409cbb9c4882bbecf05a2025-08-20T02:10:34ZengeLife Sciences Publications LtdeLife2050-084X2024-10-011210.7554/eLife.88456Somatic mutation rates scale with time not growth rate in long-lived tropical treesAkiko Satake0https://orcid.org/0000-0002-0831-8617Ryosuke Imai1Takeshi Fujino2Sou Tomimoto3https://orcid.org/0009-0005-8376-7104Kayoko Ohta4Mohammad Na'iem5Sapto Indrioko6Widiyatno Widiyatno7Susilo Purnomo8Almudena Molla Morales9Viktoria Nizhynska10Naoki Tani11Yoshihisa Suyama12Eriko Sasaki13https://orcid.org/0000-0002-0878-364XMasahiro Kasahara14Department of Biology, Faculty of Science, Kyushu University, Fukuoka, JapanDepartment of Biology, Faculty of Science, Kyushu University, Fukuoka, JapanDepartment of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, JapanDepartment of Biology, Faculty of Science, Kyushu University, Fukuoka, JapanDepartment of Biology, Faculty of Science, Kyushu University, Fukuoka, JapanFaculty of Forestry, Universitas Gadjah Mada, Sleman, IndonesiaFaculty of Forestry, Universitas Gadjah Mada, Sleman, IndonesiaFaculty of Forestry, Universitas Gadjah Mada, Sleman, IndonesiaPT. Sari Bumi Kusuma, Pontianak, IndonesiaGregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, AustriaGregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, AustriaForestry Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Japan; Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, JapanField Science Center, Graduate School of Agricultural Science, Tohoku University, Osaki, JapanDepartment of Biology, Faculty of Science, Kyushu University, Fukuoka, JapanDepartment of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, JapanThe rates of appearance of new mutations play a central role in evolution. However, mutational processes in natural environments and their relationship with growth rates are largely unknown, particular in tropical ecosystems with high biodiversity. Here, we examined the somatic mutation landscapes of two tropical trees, Shorea laevis (slow-growing) and S. leprosula (fast-growing), in central Borneo, Indonesia. Using newly constructed genomes, we identified a greater number of somatic mutations in tropical trees than in temperate trees. In both species, we observed a linear increase in the number of somatic mutations with physical distance between branches. However, we found that the rate of somatic mutation accumulation per meter of growth was 3.7-fold higher in S. laevis than in S. leprosula. This difference in the somatic mutation rate was scaled with the slower growth rate of S. laevis compared to S. leprosula, resulting in a constant somatic mutation rate per year between the two species. We also found that somatic mutations are neutral within an individual, but those mutations transmitted to the next generation are subject to purifying selection. These findings suggest that somatic mutations accumulate with absolute time and older trees have a greater contribution towards generating genetic variation.https://elifesciences.org/articles/88456somatic mutationmutational spectrumgenetic diversitytropical ecosystemsshorea |
| spellingShingle | Akiko Satake Ryosuke Imai Takeshi Fujino Sou Tomimoto Kayoko Ohta Mohammad Na'iem Sapto Indrioko Widiyatno Widiyatno Susilo Purnomo Almudena Molla Morales Viktoria Nizhynska Naoki Tani Yoshihisa Suyama Eriko Sasaki Masahiro Kasahara Somatic mutation rates scale with time not growth rate in long-lived tropical trees eLife somatic mutation mutational spectrum genetic diversity tropical ecosystems shorea |
| title | Somatic mutation rates scale with time not growth rate in long-lived tropical trees |
| title_full | Somatic mutation rates scale with time not growth rate in long-lived tropical trees |
| title_fullStr | Somatic mutation rates scale with time not growth rate in long-lived tropical trees |
| title_full_unstemmed | Somatic mutation rates scale with time not growth rate in long-lived tropical trees |
| title_short | Somatic mutation rates scale with time not growth rate in long-lived tropical trees |
| title_sort | somatic mutation rates scale with time not growth rate in long lived tropical trees |
| topic | somatic mutation mutational spectrum genetic diversity tropical ecosystems shorea |
| url | https://elifesciences.org/articles/88456 |
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