Phylogenomics of white-eyes, a 'great speciator', reveals Indonesian archipelago as the center of lineage diversity

  1. Chyi Yin Gwee
  2. Kritika M Garg
  3. Balaji Chattopadhyay
  4. Keren R Sadanandan
  5. Dewi M Prawiradilaga
  6. Martin Irestedt
  7. Fumin Lei
  8. Luke M Bloch
  9. Jessica GH Lee
  10. Mohammad Irham
  11. Tri Haryoko
  12. Malcolm CK Soh
  13. Kelvin S-H Peh
  14. Karen MC Rowe
  15. Teuku Reza Ferasyi
  16. Shaoyuan Wu
  17. Guinevere OU Wogan
  18. Rauri CK Bowie
  19. Frank E Rheindt  Is a corresponding author
  1. National University of Singapore, Singapore
  2. Indonesian Institute of Sciences (LIPI), Indonesia
  3. Swedish Museum of Natural History, Sweden
  4. Institute of Zoology (CAS), China
  5. University of California, Berkeley, United States
  6. Wildlife Reserves Singapore, Singapore
  7. University of Western Australia, Australia
  8. University of Southampton, United Kingdom
  9. Museums Victoria, Australia
  10. Universitas Syiah Kuala, Indonesia
  11. Jiangsu Normal University, China

Abstract

Archipelagoes serve as important 'natural laboratories' which facilitate the study of island radiations and contribute to the understanding of evolutionary processes. The white-eye genus Zosterops is a classical example of a 'great speciator', comprising c. 100 species from across the Old World, most of them insular. We achieved an extensive geographic DNA sampling of Zosterops by using historical specimens and recently collected samples. Using over 700 genome-wide loci in conjunction with coalescent species tree methods and gene flow detection approaches, we untangled the reticulated evolutionary history of Zosterops, which comprises three main clades centered in Indo-Africa, Asia, and Australasia, respectively. Genetic introgression between species permeates the Zosterops phylogeny, regardless of how distantly related species are. Crucially, we identified the Indonesian archipelago, and specifically Borneo, as the major centre of diversity and the only area where all three main clades overlap, attesting to the evolutionary importance of this region.

Data availability

All data generated or analysed during this study are included in Dryad database: https://doi.org/10.5061/dryad.8931zcrmt. Raw FASTQ files of target enriched samples are available on NCBI under BioProject no. PRJNA682287.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Chyi Yin Gwee

    Biological Sciences, National University of Singapore, Singapore, Singapore
    Competing interests
    The authors declare that no competing interests exist.
  2. Kritika M Garg

    Biological Sciences, National University of Singapore, Singapore, Singapore
    Competing interests
    The authors declare that no competing interests exist.
  3. Balaji Chattopadhyay

    Biological Sciences, National University of Singapore, Singapore, Singapore
    Competing interests
    The authors declare that no competing interests exist.
  4. Keren R Sadanandan

    Biological Sciences, National University of Singapore, Singapore, Singapore
    Competing interests
    The authors declare that no competing interests exist.
  5. Dewi M Prawiradilaga

    Division of Zoology, Indonesian Institute of Sciences (LIPI), Jakarta, Indonesia
    Competing interests
    The authors declare that no competing interests exist.
  6. Martin Irestedt

    Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
    Competing interests
    The authors declare that no competing interests exist.
  7. Fumin Lei

    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology (CAS), Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  8. Luke M Bloch

    Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Jessica GH Lee

    Conservation, Wildlife Reserves Singapore, Singapore, Singapore
    Competing interests
    The authors declare that no competing interests exist.
  10. Mohammad Irham

    Division of Zoology, Indonesian Institute of Sciences (LIPI), Jakarta, Indonesia
    Competing interests
    The authors declare that no competing interests exist.
  11. Tri Haryoko

    Division of Zoology, Indonesian Institute of Sciences (LIPI), Jakarta, Indonesia
    Competing interests
    The authors declare that no competing interests exist.
  12. Malcolm CK Soh

    School of Biological Sciences, University of Western Australia, Perth, Australia
    Competing interests
    The authors declare that no competing interests exist.
  13. Kelvin S-H Peh

    School of Biological Sciences, University of Southampton, Southampton, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2921-1341
  14. Karen MC Rowe

    Sciences Department, Museums Victoria, Victoria, Australia
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6131-6418
  15. Teuku Reza Ferasyi

    Faculty of Veterinary Medicine, Universitas Syiah Kuala, Banda Aceh, Indonesia
    Competing interests
    The authors declare that no competing interests exist.
  16. Shaoyuan Wu

    School of Life Sciences, Jiangsu Normal University, Jiangsu, China
    Competing interests
    The authors declare that no competing interests exist.
  17. Guinevere OU Wogan

    Museum of Vertebrate Zoology and Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
  18. Rauri CK Bowie

    Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8328-6021
  19. Frank E Rheindt

    Department of Biological Sciences, National University of Singapore, Singapore, Singapore
    For correspondence
    dbsrfe@nus.edu.sg
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8946-7085

Funding

Singapore Ministry of Education (R-154-000-A59-112)

  • Frank E Rheindt

Wildlife Reserved Singapore Conservation Fund (R-154-000-A99-592)

  • Frank E Rheindt

Croeni Foundation (R-154-000-A05-592)

  • Frank E Rheindt

SEABIG (R-154-000-648-646)

  • Balaji Chattopadhyay

SEABIG (R-154-000-648-733)

  • Balaji Chattopadhyay

University of Southampton research grant (511206105)

  • Kelvin S-H Peh

US National Science Foundation grant (DEB-1441652)

  • Rauri CK Bowie

US National Science Foundation grant (DEB-1457845)

  • Rauri CK Bowie

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Rosalyn Gloag, University of Sidney, Australia

Publication history

  1. Received: September 3, 2020
  2. Accepted: December 21, 2020
  3. Accepted Manuscript published: December 22, 2020 (version 1)
  4. Version of Record published: December 31, 2020 (version 2)
  5. Version of Record updated: January 6, 2021 (version 3)

Copyright

© 2020, Gwee et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Chyi Yin Gwee
  2. Kritika M Garg
  3. Balaji Chattopadhyay
  4. Keren R Sadanandan
  5. Dewi M Prawiradilaga
  6. Martin Irestedt
  7. Fumin Lei
  8. Luke M Bloch
  9. Jessica GH Lee
  10. Mohammad Irham
  11. Tri Haryoko
  12. Malcolm CK Soh
  13. Kelvin S-H Peh
  14. Karen MC Rowe
  15. Teuku Reza Ferasyi
  16. Shaoyuan Wu
  17. Guinevere OU Wogan
  18. Rauri CK Bowie
  19. Frank E Rheindt
(2020)
Phylogenomics of white-eyes, a 'great speciator', reveals Indonesian archipelago as the center of lineage diversity
eLife 9:e62765.
https://doi.org/10.7554/eLife.62765

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