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Nature ecology & evolution
06, 2022;6 (6): 738-749.

Evolution of coastal forests based on a full set of mangrove genomes.

Ziwen He, Xiao Feng, Qipian Chen, Liangwei Li, Sen Li, Kai Han, Zixiao Guo, Jiayan Wang, Min Liu, Chengcheng Shi, Shaohua Xu, Shao Shao, Xin Liu, Xiaomeng Mao, Wei Xie, Xinfeng Wang, Rufan Zhang, Guohong Li, Weihong Wu, Zheng Zheng, Cairong Zhong, Norman C Duke, David E Boufford, Guangyi Fan, Chung-I Wu, Robert E Ricklefs, Suhua Shi
Author Information
  1. Ziwen He: State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China.
  2. Xiao Feng: State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China. ORCID
  3. Qipian Chen: State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China.
  4. Liangwei Li: BGI-Qingdao, BGI-Shenzhen, Qingdao, China. ORCID
  5. Sen Li: State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China. ORCID
  6. Kai Han: BGI-Qingdao, BGI-Shenzhen, Qingdao, China.
  7. Zixiao Guo: State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China.
  8. Jiayan Wang: State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China.
  9. Min Liu: State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China.
  10. Chengcheng Shi: BGI-Qingdao, BGI-Shenzhen, Qingdao, China. ORCID
  11. Shaohua Xu: State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China.
  12. Shao Shao: State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China.
  13. Xin Liu: BGI-Qingdao, BGI-Shenzhen, Qingdao, China.
  14. Xiaomeng Mao: State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China. ORCID
  15. Wei Xie: State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China.
  16. Xinfeng Wang: State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China.
  17. Rufan Zhang: State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China.
  18. Guohong Li: State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China.
  19. Weihong Wu: State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China.
  20. Zheng Zheng: State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China.
  21. Cairong Zhong: Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, China.
  22. Norman C Duke: Centre for Tropical Water and Aquatic Ecosystem Research, James Cook University, Townsville, Queensland, Australia. ORCID
  23. David E Boufford: Harvard University Herbaria, Cambridge, MA, USA. ORCID
  24. Guangyi Fan: BGI-Qingdao, BGI-Shenzhen, Qingdao, China.
  25. Chung-I Wu: State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China.
  26. Robert E Ricklefs: Department of Biology, University of Missouri-St. Louis, St. Louis, MO, USA.
  27. Suhua Shi: State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China. lssssh@mail.sysu.edu.cn. ORCID
PMID: 35484219 DOI: 10.1038/s41559-022-01744-9

Abstract

Genomic studies are now poised to explore whole communities of species. The ~70 species of woody plants that anchor the coastal ecosystems of the tropics, collectively referred to as mangroves, are particularly suited to this exploration. In this study, we de novo sequenced the whole genomes of 32 mangroves, which we combined with other sequences of 30 additional species, comprising almost all mangroves globally. These community-wide genomic data will be valuable for ecology, evolution and biodiversity research. While the data revealed 27 independent origins of mangroves, the total phylogeny shows only modest increases in species number, even in coastal areas of active speciation, suggesting that mangrove extinction is common. A possible explanation for common extinction is the frequent sea-level rises and falls (SLRs and SLFs) documented in the geological record. Indeed, near-extinctions of species with extremely small population size (N) often happened during periods of rapid SLR, as revealed by the genome-wide heterozygosity of almost all mangroves. Reduction in N has possibly been further compounded by population fragmentation and the subsequent accumulation of deleterious mutations, thus pushing mangroves even closer to extinction. Crucially, the impact of the next SLR will be exacerbated by human encroachment into these mangrove habitats, potentially altering the ecosystems of tropical coasts irreversibly.

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MeSH Term

Ecosystem
Forests
Genome
Humans
Phylogeny
Plants
Journal Article Research Support, Non-U.S. Gov't
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