Genomic insights into rapid speciation within the world’s largest tree genus Syzygium

Yee Wen Low (), Sitaram Rajaraman, Crystal M. Tomlin, Joffre Ali Ahmad, Wisnu H. Ardi, Kate Armstrong, Parusuraman Athen, Ahmad Berhaman, Ruth E. Bone, Martin Cheek, Nicholas R. W. Cho, Le Min Choo, Ian D. Cowie, Darren Crayn, Steven J. Fleck, Andrew J. Ford, Paul I. Forster, Deden Girmansyah, David J. Goyder, Bruce Gray, Charlie D. Heatubun, Ali Ibrahim, Bazilah Ibrahim, Himesh D. Jayasinghe, Muhammad Ariffin Kalat, Hashendra S. Kathriarachchi, Endang Kintamani, Sin Lan Koh, Joseph T. K. Lai, Serena M. L. Lee, Paul K. F. Leong, Wei Hao Lim, Shawn K. Y. Lum, Ridha Mahyuni, William J. F. McDonald, Faizah Metali, Wendy A. Mustaqim, Akiyo Naiki, Kang Min Ngo, Matti Niissalo, Subhani Ranasinghe, Rimi Repin, Himmah Rustiami, Victor I. Simbiak, Rahayu S. Sukri, Siti Sunarti, Liam A. Trethowan, Anna Trias-Blasi, Thais N. C. Vasconcelos, Jimmy F. Wanma, Pudji Widodo, Douglas Siril A. Wijesundara, Stuart Worboys, Jing Wei Yap, Kien Thai Yong, Gillian S. W. Khew, Jarkko Salojärvi, Todd P. Michael, David J. Middleton, David F. R. P. Burslem, Charlotte Lindqvist (), Eve J. Lucas () and Victor A. Albert ()
Additional contact information
Yee Wen Low: National Parks Board
Sitaram Rajaraman: Nanyang Technological University
Crystal M. Tomlin: University at Buffalo
Joffre Ali Ahmad: Ministry of Primary Resources and Tourism
Wisnu H. Ardi: Bogor Botanical Garden
Kate Armstrong: New York Botanical Garden
Parusuraman Athen: National Parks Board
Ahmad Berhaman: Universiti Malaysia Sabah
Ruth E. Bone: Royal Botanic Gardens, Kew
Martin Cheek: Royal Botanic Gardens, Kew
Nicholas R. W. Cho: Nanyang Technological University
Le Min Choo: National Parks Board
Ian D. Cowie: Parks and Water Security
Darren Crayn: James Cook University
Steven J. Fleck: University at Buffalo
Andrew J. Ford: Tropical Forest Research Centre
Paul I. Forster: Brisbane Botanic Gardens
Deden Girmansyah: Herbarium Bogoriense
David J. Goyder: Royal Botanic Gardens, Kew
Bruce Gray: James Cook University
Charlie D. Heatubun: Royal Botanic Gardens, Kew
Ali Ibrahim: National Parks Board
Bazilah Ibrahim: National Parks Board
Himesh D. Jayasinghe: University of Colombo
Muhammad Ariffin Kalat: Ministry of Primary Resources and Tourism
Hashendra S. Kathriarachchi: University of Colombo
Endang Kintamani: Herbarium Bogoriense
Sin Lan Koh: National Parks Board
Joseph T. K. Lai: National Parks Board
Serena M. L. Lee: National Parks Board
Paul K. F. Leong: National Parks Board
Wei Hao Lim: National Parks Board
Shawn K. Y. Lum: Nanyang Technological University
Ridha Mahyuni: Herbarium Bogoriense
William J. F. McDonald: Brisbane Botanic Gardens
Faizah Metali: Universiti Brunei Darussalam
Wendy A. Mustaqim: Universitas Samudra
Akiyo Naiki: University of the Ryukyus
Kang Min Ngo: Nanyang Technological University
Matti Niissalo: National Parks Board
Subhani Ranasinghe: Department of National Botanic Gardens
Rimi Repin: Sabah Parks
Himmah Rustiami: Herbarium Bogoriense
Victor I. Simbiak: Universitas Papua
Rahayu S. Sukri: Universiti Brunei Darussalam
Siti Sunarti: Herbarium Bogoriense
Liam A. Trethowan: Royal Botanic Gardens, Kew
Anna Trias-Blasi: Royal Botanic Gardens, Kew
Thais N. C. Vasconcelos: Royal Botanic Gardens, Kew
Jimmy F. Wanma: Universitas Papua
Pudji Widodo: Universitas Jenderal Soedirman
Douglas Siril A. Wijesundara: National Institute of Fundamental Studies
Stuart Worboys: James Cook University
Jing Wei Yap: Universiti Tun Hussein Onn Malaysia
Kien Thai Yong: Universiti Malaya
Gillian S. W. Khew: National Parks Board
Jarkko Salojärvi: Nanyang Technological University
Todd P. Michael: Salk Institute for Biological Studies
David J. Middleton: National Parks Board
David F. R. P. Burslem: University of Aberdeen
Charlotte Lindqvist: Nanyang Technological University
Eve J. Lucas: Royal Botanic Gardens, Kew
Victor A. Albert: Nanyang Technological University

Nature Communications, 2022, vol. 13, issue 1, 1-15

Abstract: Abstract Species radiations, despite immense phenotypic variation, can be difficult to resolve phylogenetically when genetic change poorly matches the rapidity of diversification. Genomic potential furnished by palaeopolyploidy, and relative roles for adaptation, random drift and hybridisation in the apportionment of genetic variation, remain poorly understood factors. Here, we study these aspects in a model radiation, Syzygium, the most species-rich tree genus worldwide. Genomes of 182 distinct species and 58 unidentified taxa are compared against a chromosome-level reference genome of the sea apple, Syzygium grande. We show that while Syzygium shares an ancient genome doubling event with other Myrtales, little evidence exists for recent polyploidy events. Phylogenomics confirms that Syzygium originated in Australia-New Guinea and diversified in multiple migrations, eastward to the Pacific and westward to India and Africa, in bursts of speciation visible as poorly resolved branches on phylogenies. Furthermore, some sublineages demonstrate genomic clines that recapitulate cladogenetic events, suggesting that stepwise geographic speciation, a neutral process, has been important in Syzygium diversification.

Date: 2022
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DOI: 10.1038/s41467-022-32637-x

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