Dryad
Published January 6, 2021 | Version v1
Dataset Open

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

Creators

  • 1. National University of Singapore
  • 2. Indonesian Institute of Sciences
  • 3. Swedish Museum of Natural History
  • 4. Chinese Academy of Sciences
  • 5. University of California, Berkeley
  • 6. Wildlife Reserves Singapore*
  • 7. University of Western Australia
  • 8. University of Southampton
  • 9. Museum Victoria
  • 10. Syiah Kuala University
  • 11. Jiangsu Normal University

Description

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 Zosteropsphylogeny, 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. 

Notes

Raw FASTQ files of target enriched samples are available on NCBI under BioProject no. PRJNA682287.

Data uploaded: (1) supplementary material, (2) assembled loci, (3) gene trees, (4) abba baba output, and (5) PHRAPL output, (6) ND2 sequences. Please refer to README for more details. 

Funding provided by: Ministry of Education - Singapore
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001459
Award Number: R-154-000-A59-112

Funding provided by: Wildlife Reserves Singapore Conservation Fund
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100009082
Award Number: R-154-000-A99-592

Funding provided by: Croeni Foundation*
Crossref Funder Registry ID:
Award Number: R-154-000-A05-592

Funding provided by: SEABIG Grant*
Crossref Funder Registry ID:
Award Number: R-154-000-648-646

Funding provided by: SEABIG Grant*
Crossref Funder Registry ID:
Award Number: R-154-000-648-733

Funding provided by: University of Southampton
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100000739
Award Number: 511206105

Funding provided by: National Science Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001
Award Number: DEB-1441652

Funding provided by: National Science Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001
Award Number: DEB-1457845

Funding provided by: Croeni Foundation
Crossref Funder Registry ID:
Award Number: R-154-000-A05-592

Funding provided by: SEABIG Grant
Crossref Funder Registry ID:
Award Number: R-154-000-648-646

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