IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-32637-x.html
   My bibliography  Save this article

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
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-32637-x
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-022-32637-x?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Sangeet Lamichhaney & Jonas Berglund & Markus Sällman Almén & Khurram Maqbool & Manfred Grabherr & Alvaro Martinez-Barrio & Marta Promerová & Carl-Johan Rubin & Chao Wang & Neda Zamani & B. Rosemary G, 2015. "Evolution of Darwin’s finches and their beaks revealed by genome sequencing," Nature, Nature, vol. 518(7539), pages 371-375, February.
    2. Heng Li & Richard Durbin, 2011. "Inference of human population history from individual whole-genome sequences," Nature, Nature, vol. 475(7357), pages 493-496, July.
    3. 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.
    4. 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.
    5. Daniel J. Lawson & Lucy van Dorp & Daniel Falush, 2018. "A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots," Nature Communications, Nature, vol. 9(1), pages 1-11, December.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    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.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Estavoyer, Maxime & François, Olivier, 2022. "Theoretical analysis of principal components in an umbrella model of intraspecific evolution," Theoretical Population Biology, Elsevier, vol. 148(C), pages 11-21.
    2. Ya-Mei Ding & Xiao-Xu Pang & Yu Cao & Wei-Ping Zhang & Susanne S. Renner & Da-Yong Zhang & Wei-Ning Bai, 2023. "Genome structure-based Juglandaceae phylogenies contradict alignment-based phylogenies and substitution rates vary with DNA repair genes," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    3. Romain Fournier & Zoi Tsangalidou & David Reich & Pier Francesco Palamara, 2023. "Haplotype-based inference of recent effective population size in modern and ancient DNA samples," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    4. Guangping Huang & Lingyun Song & Xin Du & Xin Huang & Fuwen Wei, 2023. "Evolutionary genomics of camouflage innovation in the orchid mantis," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    5. Legried, Brandon & Terhorst, Jonathan, 2022. "Rates of convergence in the two-island and isolation-with-migration models," Theoretical Population Biology, Elsevier, vol. 147(C), pages 16-27.
    6. Jörn Bethune & April Kleppe & Søren Besenbacher, 2022. "A method to build extended sequence context models of point mutations and indels," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    7. Carmi, Shai & Wilton, Peter R. & Wakeley, John & Pe’er, Itsik, 2014. "A renewal theory approach to IBD sharing," Theoretical Population Biology, Elsevier, vol. 97(C), pages 35-48.
    8. Tiziana Maria Sirangelo & Richard Andrew Ludlow & Tatiana Chenet & Luisa Pasti & Natasha Damiana Spadafora, 2023. "Multi-Omics and Genome Editing Studies on Plant Cell Walls to Improve Biomass Quality," Agriculture, MDPI, vol. 13(4), pages 1-19, March.
    9. Aoki, Kenichi & Wakano, Joe Yuichiro, 2022. "Hominin forager technology, food sharing, and diet breadth," Theoretical Population Biology, Elsevier, vol. 144(C), pages 37-48.
    10. Yupeng Sang & Zhiqin Long & Xuming Dan & Jiajun Feng & Tingting Shi & Changfu Jia & Xinxin Zhang & Qiang Lai & Guanglei Yang & Hongying Zhang & Xiaoting Xu & Huanhuan Liu & Yuanzhong Jiang & Pär K. In, 2022. "Genomic insights into local adaptation and future climate-induced vulnerability of a keystone forest tree in East Asia," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    11. Kimmel, Marek & Wojdyła, Tomasz, 2016. "Genetic demographic networks: Mathematical model and applications," Theoretical Population Biology, Elsevier, vol. 111(C), pages 75-86.
    12. Jason Flannick & Joshua M Korn & Pierre Fontanillas & George B Grant & Eric Banks & Mark A Depristo & David Altshuler, 2012. "Efficiency and Power as a Function of Sequence Coverage, SNP Array Density, and Imputation," PLOS Computational Biology, Public Library of Science, vol. 8(7), pages 1-13, July.
    13. 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.
    14. José Cerca & Bent Petersen & José Miguel Lazaro-Guevara & Angel Rivera-Colón & Siri Birkeland & Joel Vizueta & Siyu Li & Qionghou Li & João Loureiro & Chatchai Kosawang & Patricia Jaramillo Díaz & Gon, 2022. "The genomic basis of the plant island syndrome in Darwin’s giant daisies," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    15. Haifei Hu & Armin Scheben & David Edwards, 2018. "Advances in Integrating Genomics and Bioinformatics in the Plant Breeding Pipeline," Agriculture, MDPI, vol. 8(6), pages 1-18, May.
    16. Rong Wang & Chao-Nan Liu & Simon T. Segar & Yu-Ting Jiang & Kai-Jian Zhang & Kai Jiang & Gang Wang & Jing Cai & Lu-Fan Chen & Shan Chen & Jing Cheng & Stephen G. Compton & Jun-Yin Deng & Yuan-Yuan Din, 2024. "Dipterocarpoidae genomics reveal their demography and adaptations to Asian rainforests," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    17. Jerome Kelleher & Alison M Etheridge & Gilean McVean, 2016. "Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes," PLOS Computational Biology, Public Library of Science, vol. 12(5), pages 1-22, May.
    18. Deng, Yun & Song, Yun S. & Nielsen, Rasmus, 2021. "The distribution of waiting distances in ancestral recombination graphs," Theoretical Population Biology, Elsevier, vol. 141(C), pages 34-43.
    19. Simone Scalabrin & Gabriele Magris & Mario Liva & Nicola Vitulo & Michele Vidotto & Davide Scaglione & Lorenzo Terra & Manuela Rosanna Ruosi & Luciano Navarini & Gloria Pellegrino & Jorge Carlos Berny, 2024. "A chromosome-scale assembly reveals chromosomal aberrations and exchanges generating genetic diversity in Coffea arabica germplasm," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    20. Ran Tian & Yaolei Zhang & Hui Kang & Fan Zhang & Zhihong Jin & Jiahao Wang & Peijun Zhang & Xuming Zhou & Janet M. Lanyon & Helen L. Sneath & Lucy Woolford & Guangyi Fan & Songhai Li & Inge Seim, 2024. "Sirenian genomes illuminate the evolution of fully aquatic species within the mammalian superorder afrotheria," Nature Communications, Nature, vol. 15(1), pages 1-19, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-32637-x. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.