Demographic histories shape population genomics of the common coral grouper (Plectropomus leopardus)

Samuel D. Payet; M. S. Pratchett; P. Saenz-Agudelo; Michael L. Berumen; Joseph DiBattista; H. B. Harrison

doi:10.1111/eva.13450

Demographic histories shape population genomics of the common coral grouper (Plectropomus leopardus)

Samuel D. Payet, M. S. Pratchett, P. Saenz-Agudelo, Michael L. Berumen, Joseph DiBattista, H. B. Harrison

Research output: Contribution to journal › Article › peer-review

6 Scopus citations

Abstract

Many coral reef fishes display remarkable genetic and phenotypic variation across their geographic ranges. Understanding how historical and contemporary processes have shaped these patterns remains a focal question in evolutionary biology, since they reveal how diversity is generated and how it may respond to future environmental change. Here we compare the population genomics and demographic histories of a commercially and ecologically important coral reef fish, the common coral grouper (Plectropomus leopardus [Lacépède 1802]), across two adjoining regions (the Great Barrier Reef; GBR, and the Coral Sea, Australia) spanning approximately 14 degrees of latitude and 9 degrees of longitude. We analysed 4,548 single nucleotide polymorphism (SNP) markers across 11 sites and show that genetic connectivity between regions is low, despite their relative proximity (~ 100 km) and an absence of any obvious geographic barrier. Inferred demographic histories using 10,479 markers suggest that the Coral Sea population was founded by a small number of GBR individuals and that divergence occurred ~ 190 kya under a model of isolation with asymmetric migration. We detected population expansions in both regions, but estimates of contemporary effective population sizes were approximately 50 % smaller in Coral Sea sites, which also had lower genetic diversity. Our results suggest that P. leopardus in the Coral Sea have experienced a long period of isolation that precedes the recent glacial period (~ 10 – 120 kya) and may be vulnerable to localised disturbances due to their relative reliance on local larval replenishment. While it is difficult to determine the underlying events that led to the divergence of Coral Sea and GBR lineages, we show that even geographically proximate populations of a widely dispersed coral reef fish can have vastly different evolutionary histories.

Original language	English (US)
Journal	Evolutionary Applications
DOIs	https://doi.org/10.1111/eva.13450
State	Published - Jul 17 2022

Bibliographical note

KAUST Repository Item: Exported on 2022-09-14
Acknowledgements: The authors acknowledge this research took place on the land and sea country of Traditional Owners, and recognize their continuing connection to land, water and community in the Great Barrier Reef and Coral Sea. This research was funded by an ARC Discovery Early Career Research Award to H.B. Harrison (DE160101141) and the Director of National P arks, Australia. S.D. P ayet was supported by a James Cook University P ostgraduate Research Scholarship. P . Saenz-Agudelo was supported by Fondo Nacional de Desarrollo Científico y Tecnológico (Grant Fondecyt 1190710). The authors would like to thank P. Sayre for field and logistical support in the Coral Sea. The authors also wish to thank the relevant staff at P arks Australia, with particular mention given to A. Warmbrunn and M. Russell. For research permits the authors thank Parks Australia, the Great Barrier Reef Marine Park Authority, and the Queensland Fisheries Department. For animal ethics approvals the authors thank the James Cook U nive r s ity A nima l Ethic s c ommittee. The findings and views expressed are those of the authors and do not necessarily represent the views of P arks Australia, the Director of National Parks or the Australian Government.

ASJC Scopus subject areas

General Agricultural and Biological Sciences
Genetics
Ecology, Evolution, Behavior and Systematics

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10.1111/eva.13450

https://repository.kaust.edu.sa/bitstream/10754/679807/1/Evolutionary%20Applications%20-%202022%20-%20Payet%20-%20Demographic%20histories%20shape%20population%20genomics%20of%20the%20common%20coral%20grouper%20.pdf

Cite this

@article{b5591737cd274e9384e1d73d47c74b99,

title = "Demographic histories shape population genomics of the common coral grouper (Plectropomus leopardus)",

abstract = "Many coral reef fishes display remarkable genetic and phenotypic variation across their geographic ranges. Understanding how historical and contemporary processes have shaped these patterns remains a focal question in evolutionary biology, since they reveal how diversity is generated and how it may respond to future environmental change. Here we compare the population genomics and demographic histories of a commercially and ecologically important coral reef fish, the common coral grouper (Plectropomus leopardus [Lac{\'e}p{\`e}de 1802]), across two adjoining regions (the Great Barrier Reef; GBR, and the Coral Sea, Australia) spanning approximately 14 degrees of latitude and 9 degrees of longitude. We analysed 4,548 single nucleotide polymorphism (SNP) markers across 11 sites and show that genetic connectivity between regions is low, despite their relative proximity (~ 100 km) and an absence of any obvious geographic barrier. Inferred demographic histories using 10,479 markers suggest that the Coral Sea population was founded by a small number of GBR individuals and that divergence occurred ~ 190 kya under a model of isolation with asymmetric migration. We detected population expansions in both regions, but estimates of contemporary effective population sizes were approximately 50 % smaller in Coral Sea sites, which also had lower genetic diversity. Our results suggest that P. leopardus in the Coral Sea have experienced a long period of isolation that precedes the recent glacial period (~ 10 – 120 kya) and may be vulnerable to localised disturbances due to their relative reliance on local larval replenishment. While it is difficult to determine the underlying events that led to the divergence of Coral Sea and GBR lineages, we show that even geographically proximate populations of a widely dispersed coral reef fish can have vastly different evolutionary histories.",

author = "Payet, {Samuel D.} and Pratchett, {M. S.} and P. Saenz-Agudelo and Berumen, {Michael L.} and Joseph DiBattista and Harrison, {H. B.}",

note = "KAUST Repository Item: Exported on 2022-09-14 Acknowledgements: The authors acknowledge this research took place on the land and sea country of Traditional Owners, and recognize their continuing connection to land, water and community in the Great Barrier Reef and Coral Sea. This research was funded by an ARC Discovery Early Career Research Award to H.B. Harrison (DE160101141) and the Director of National P arks, Australia. S.D. P ayet was supported by a James Cook University P ostgraduate Research Scholarship. P . Saenz-Agudelo was supported by Fondo Nacional de Desarrollo Cient{\'i}fico y Tecnol{\'o}gico (Grant Fondecyt 1190710). The authors would like to thank P. Sayre for field and logistical support in the Coral Sea. The authors also wish to thank the relevant staff at P arks Australia, with particular mention given to A. Warmbrunn and M. Russell. For research permits the authors thank Parks Australia, the Great Barrier Reef Marine Park Authority, and the Queensland Fisheries Department. For animal ethics approvals the authors thank the James Cook U nive r s ity A nima l Ethic s c ommittee. The findings and views expressed are those of the authors and do not necessarily represent the views of P arks Australia, the Director of National Parks or the Australian Government.",

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month = jul,

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doi = "10.1111/eva.13450",

language = "English (US)",

journal = "Evolutionary Applications",

issn = "1752-4571",

publisher = "John Wiley and Sons Inc.",

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T1 - Demographic histories shape population genomics of the common coral grouper (Plectropomus leopardus)

AU - Payet, Samuel D.

AU - Pratchett, M. S.

AU - Saenz-Agudelo, P.

AU - Berumen, Michael L.

AU - DiBattista, Joseph

AU - Harrison, H. B.

N1 - KAUST Repository Item: Exported on 2022-09-14 Acknowledgements: The authors acknowledge this research took place on the land and sea country of Traditional Owners, and recognize their continuing connection to land, water and community in the Great Barrier Reef and Coral Sea. This research was funded by an ARC Discovery Early Career Research Award to H.B. Harrison (DE160101141) and the Director of National P arks, Australia. S.D. P ayet was supported by a James Cook University P ostgraduate Research Scholarship. P . Saenz-Agudelo was supported by Fondo Nacional de Desarrollo Científico y Tecnológico (Grant Fondecyt 1190710). The authors would like to thank P. Sayre for field and logistical support in the Coral Sea. The authors also wish to thank the relevant staff at P arks Australia, with particular mention given to A. Warmbrunn and M. Russell. For research permits the authors thank Parks Australia, the Great Barrier Reef Marine Park Authority, and the Queensland Fisheries Department. For animal ethics approvals the authors thank the James Cook U nive r s ity A nima l Ethic s c ommittee. The findings and views expressed are those of the authors and do not necessarily represent the views of P arks Australia, the Director of National Parks or the Australian Government.

PY - 2022/7/17

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N2 - Many coral reef fishes display remarkable genetic and phenotypic variation across their geographic ranges. Understanding how historical and contemporary processes have shaped these patterns remains a focal question in evolutionary biology, since they reveal how diversity is generated and how it may respond to future environmental change. Here we compare the population genomics and demographic histories of a commercially and ecologically important coral reef fish, the common coral grouper (Plectropomus leopardus [Lacépède 1802]), across two adjoining regions (the Great Barrier Reef; GBR, and the Coral Sea, Australia) spanning approximately 14 degrees of latitude and 9 degrees of longitude. We analysed 4,548 single nucleotide polymorphism (SNP) markers across 11 sites and show that genetic connectivity between regions is low, despite their relative proximity (~ 100 km) and an absence of any obvious geographic barrier. Inferred demographic histories using 10,479 markers suggest that the Coral Sea population was founded by a small number of GBR individuals and that divergence occurred ~ 190 kya under a model of isolation with asymmetric migration. We detected population expansions in both regions, but estimates of contemporary effective population sizes were approximately 50 % smaller in Coral Sea sites, which also had lower genetic diversity. Our results suggest that P. leopardus in the Coral Sea have experienced a long period of isolation that precedes the recent glacial period (~ 10 – 120 kya) and may be vulnerable to localised disturbances due to their relative reliance on local larval replenishment. While it is difficult to determine the underlying events that led to the divergence of Coral Sea and GBR lineages, we show that even geographically proximate populations of a widely dispersed coral reef fish can have vastly different evolutionary histories.

AB - Many coral reef fishes display remarkable genetic and phenotypic variation across their geographic ranges. Understanding how historical and contemporary processes have shaped these patterns remains a focal question in evolutionary biology, since they reveal how diversity is generated and how it may respond to future environmental change. Here we compare the population genomics and demographic histories of a commercially and ecologically important coral reef fish, the common coral grouper (Plectropomus leopardus [Lacépède 1802]), across two adjoining regions (the Great Barrier Reef; GBR, and the Coral Sea, Australia) spanning approximately 14 degrees of latitude and 9 degrees of longitude. We analysed 4,548 single nucleotide polymorphism (SNP) markers across 11 sites and show that genetic connectivity between regions is low, despite their relative proximity (~ 100 km) and an absence of any obvious geographic barrier. Inferred demographic histories using 10,479 markers suggest that the Coral Sea population was founded by a small number of GBR individuals and that divergence occurred ~ 190 kya under a model of isolation with asymmetric migration. We detected population expansions in both regions, but estimates of contemporary effective population sizes were approximately 50 % smaller in Coral Sea sites, which also had lower genetic diversity. Our results suggest that P. leopardus in the Coral Sea have experienced a long period of isolation that precedes the recent glacial period (~ 10 – 120 kya) and may be vulnerable to localised disturbances due to their relative reliance on local larval replenishment. While it is difficult to determine the underlying events that led to the divergence of Coral Sea and GBR lineages, we show that even geographically proximate populations of a widely dispersed coral reef fish can have vastly different evolutionary histories.

UR - http://hdl.handle.net/10754/679807

UR - https://onlinelibrary.wiley.com/doi/10.1111/eva.13450

U2 - 10.1111/eva.13450

DO - 10.1111/eva.13450

M3 - Article

C2 - 36051464

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JO - Evolutionary Applications

JF - Evolutionary Applications

ER -

Demographic histories shape population genomics of the common coral grouper (Plectropomus leopardus)

Abstract

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