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Genomic analysis of a reef-building coral, Acropora digitifera, reveals complex population structure and a migration network in the Nansei Islands, Japan
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  • Kojin Tsuchiya,
  • Yuna Zayasu,
  • Yuichi Nakajima,
  • Nana Arakaki,
  • Go Suzuki,
  • Nori Satoh,
  • Chuya Shinzato
Kojin Tsuchiya
The University of Tokyo Atmosphere and Ocean Research Institute

Corresponding Author:kojin.t@gmail.com

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Yuna Zayasu
Okinawa Institute of Science and Technology Graduate University
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Yuichi Nakajima
Okinawa Institute of Science and Technology Graduate University
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Nana Arakaki
Okinawa Institute of Science and Technology Graduate University
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Go Suzuki
Japan Fisheries Research and Education Agency Marine Fisheries Research and Development Center
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Nori Satoh
Okinawa Institute of Science and Technology Graduate University
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Chuya Shinzato
The University of Tokyo Atmosphere and Ocean Research Institute
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Abstract

Understanding the structure and connectivity of coral populations is fundamental for developing marine conservation policies, especially in patchy environments such as archipelagos. The Nansei Islands, extending more than 1,000 km in southwestern Japan, are characterized by high levels of biodiversity and endemism, supported by coral reefs, although precise, detailed genetic attributes of corals are still largely unknown. In this study, we conducted population genomic analyses based on genome-wide, single-nucleotide polymorphisms (SNPs) of Acropora digitifera, a common species in the Nansei Islands, for which a complete genome is available. With ~24x sequencing coverage of entire genomes of 303 colonies collected at 21 locations, we identified more than four million genome-wide SNPs. While population structure analyses suggested weak genetic differentiation among sampled locations, the most southwestern location (the west end of the Yaeyama Islands) was genetically similar to the northernmost location (the Tanegashima Islands), separated by >1,000 km. Although examination of a migration network found a general tendency of northward migration along the Kuroshio Current, a substantial amount of southward migration was also detected, indicating important contributions of minor ocean currents to coral larval dispersal. Moreover, heterogeneity in the transition of effective population sizes among locations suggests different histories for individual subpopulations. The unexpected complexity of both past and present population dynamics in the Nansei Islands implies that heterogeneity of ocean currents and local environments, past and present, have influenced the population structure of this species, highlighting the importance of local scale assessments for effective coral restoration and management.
18 Nov 2021Submitted to Molecular Ecology
19 Nov 2021Submission Checks Completed
19 Nov 2021Assigned to Editor
12 Dec 2021Reviewer(s) Assigned
05 Jan 2022Review(s) Completed, Editorial Evaluation Pending
02 Feb 2022Editorial Decision: Revise Minor
02 Mar 2022Review(s) Completed, Editorial Evaluation Pending
02 Mar 20221st Revision Received
03 Mar 2022Reviewer(s) Assigned
09 May 2022Editorial Decision: Revise Minor
04 Jun 2022Review(s) Completed, Editorial Evaluation Pending
04 Jun 20222nd Revision Received
07 Jun 2022Reviewer(s) Assigned
08 Aug 2022Editorial Decision: Accept
Oct 2022Published in Molecular Ecology volume 31 issue 20 on pages 5270-5284. 10.1111/mec.16665