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

Author

Listed:
  • Yee Wen Low

    (National Parks Board
    Royal Botanic Gardens, Kew
    University of Aberdeen)

  • Sitaram Rajaraman

    (Nanyang Technological University
    University of Helsinki)

  • 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
    BALITBANGDA Papua Barat
    Universitas Papua)

  • Ali Ibrahim

    (National Parks Board)

  • Bazilah Ibrahim

    (National Parks Board)

  • Himesh D. Jayasinghe

    (University of Colombo
    National Institute of Fundamental Studies)

  • 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
    University of Michigan)

  • 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
    Nanyang Technological University)

  • Jarkko Salojärvi

    (Nanyang Technological University
    University of Helsinki)

  • 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
    University at Buffalo)

  • Eve J. Lucas

    (Royal Botanic Gardens, Kew)

  • Victor A. Albert

    (Nanyang Technological University
    University at Buffalo)

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.

Suggested Citation

  • 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, 2022. "Genomic insights into rapid speciation within the world’s largest tree genus Syzygium," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-32637-x
    DOI: 10.1038/s41467-022-32637-x
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    References listed on IDEAS

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    1. Alexander A. Myburg & Dario Grattapaglia & Gerald A. Tuskan & Uffe Hellsten & Richard D. Hayes & Jane Grimwood & Jerry Jenkins & Erika Lindquist & Hope Tice & Diane Bauer & David M. Goodstein & Inna D, 2014. "The genome of Eucalyptus grandis," Nature, Nature, vol. 510(7505), pages 356-362, June.
    2. Todd P. Michael & Florian Jupe & Felix Bemm & S. Timothy Motley & Justin P. Sandoval & Christa Lanz & Olivier Loudet & Detlef Weigel & Joseph R. Ecker, 2018. "High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell," Nature Communications, Nature, vol. 9(1), pages 1-8, December.
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    Cited by:

    1. Crystal M. Tomlin & Sitaram Rajaraman & Jeanne Theresa Sebesta & Anne-Cathrine Scheen & Mika Bendiksby & Yee Wen Low & Jarkko Salojärvi & Todd P. Michael & Victor A. Albert & Charlotte Lindqvist, 2024. "Allopolyploid origin and diversification of the Hawaiian endemic mints," Nature Communications, Nature, vol. 15(1), pages 1-17, December.

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