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

National University of Singapore, Singapore
Indonesian Institute of Sciences (LIPI), Indonesia
Swedish Museum of Natural History, Sweden
Institute of Zoology (CAS), China
University of California, Berkeley, United States
Wildlife Reserves Singapore, Singapore
University of Western Australia, Australia
University of Southampton, United Kingdom
Museums Victoria, Australia
Universitas Syiah Kuala, Indonesia
Jiangsu Normal University, China

Dec 22, 2020

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Abstract
Data availability
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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

1. Gwee CY
2. Garg KM
3. Chattopadhyay B
4. Sadanandan KR
5. Prawiradilaga DM
6. Irestedt M
7. Lei F
8. Bloch LM
9. Lee JGH
10. Irham M
11. Haryoko T
12. Soh MCK
13. Peh KSH
14. Rowe KMC
15. Ferasyi TR
16. Wu S
17. Wogan GOU
18. Bowie RCK
19. Rheindt FE
(2020) Phylogenomics of a 'Great Speciator' Reveals Indonesian Archipelago as the Center of Lineage Diversity
Dryad Digital Repository, doi:10.5061/dryad.8931zcrmt.

https://doi.org/10.5061/dryad.8931zcrmt

The following previously published data sets were used

1. Cornetti L
2. Valente LM
3. Dunning LT
4. Quan X
5. Black RA
6. Hébert O
7. Savolainen V
(2015) Zosterops lateralis melanops
NCBI Genome Assembly, 248127.

https://www.ncbi.nlm.nih.gov/genome/40104?genome_assembly_id=248127
1. Leroy T
2. Anselmetti Y
3. Tilak MK
4. Bérard S
5. Csukonyi L
6. Gabrielli M
7. Scornavacca C
8. Milá B
9. Thébaud C
10. Nabholz B
(2019) A bird's white-eye view on neosex chromosome evolution
NCBI AccessionSingapore Ministry of Education: PRJNA530916.

https://www.ncbi.nlm.nih.gov/bioproject?LinkName=genome_bioproject&from_uid=17235

Article and author information

Author details

Chyi Yin Gwee

Biological Sciences, National University of Singapore, Singapore, Singapore

Competing interests
The authors declare that no competing interests exist.
Kritika M Garg

Biological Sciences, National University of Singapore, Singapore, Singapore

Competing interests
The authors declare that no competing interests exist.
Balaji Chattopadhyay

Biological Sciences, National University of Singapore, Singapore, Singapore

Competing interests
The authors declare that no competing interests exist.
Keren R Sadanandan

Biological Sciences, National University of Singapore, Singapore, Singapore

Competing interests
The authors declare that no competing interests exist.
Dewi M Prawiradilaga

Division of Zoology, Indonesian Institute of Sciences (LIPI), Jakarta, Indonesia

Competing interests
The authors declare that no competing interests exist.
Martin Irestedt

Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden

Competing interests
The authors declare that no competing interests exist.
Fumin Lei

Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology (CAS), Beijing, China

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The authors declare that no competing interests exist.
Luke M Bloch

Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, United States

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The authors declare that no competing interests exist.
Jessica GH Lee

Conservation, Wildlife Reserves Singapore, Singapore, Singapore

Competing interests
The authors declare that no competing interests exist.
Mohammad Irham

Division of Zoology, Indonesian Institute of Sciences (LIPI), Jakarta, Indonesia

Competing interests
The authors declare that no competing interests exist.
Tri Haryoko

Division of Zoology, Indonesian Institute of Sciences (LIPI), Jakarta, Indonesia

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The authors declare that no competing interests exist.
Malcolm CK Soh

School of Biological Sciences, University of Western Australia, Perth, Australia

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The authors declare that no competing interests exist.
Kelvin S-H Peh

School of Biological Sciences, University of Southampton, Southampton, United Kingdom

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The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-2921-1341
Karen MC Rowe

Sciences Department, Museums Victoria, Victoria, Australia

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The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-6131-6418
Teuku Reza Ferasyi

Faculty of Veterinary Medicine, Universitas Syiah Kuala, Banda Aceh, Indonesia

Competing interests
The authors declare that no competing interests exist.
Shaoyuan Wu

School of Life Sciences, Jiangsu Normal University, Jiangsu, China

Competing interests
The authors declare that no competing interests exist.
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.
Rauri CK Bowie

Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, United States

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The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-8328-6021
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.

"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.

Copyright

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.