Section: Evolutionary Biology
Topic: Evolution, Genetics/Genomics, Population biology

Separate the wheat from the chaff: genomic scan for local adaptation in the red coral Corallium rubrum

10.24072/pcjournal.12 - Peer Community Journal, Volume 1 (2021), article no. e31.

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Genomic data allow an in-depth and renewed study of local adaptation. The red coral (Corallium rubrum, Cnidaria) is a highly genetically structured species and a promising model for the study of adaptive processes along an environmental gradient. Here, we used RAD-Sequencing in order to study the vertical genetic structure of this species and to search for signals of local adaptation to depth and thermal regime in the red coral. Previous studies have shown different thermotolerance levels according to depth in this species which could correspond to genetic or environmental differences. We designed a sampling scheme with six pairs of shallow vs deep populations distributed in three geographical regions as replicates. Our results showed significant differentiation among locations and among sites separated by around 20 m depth. The tests of association between genetics and environment allowed the identification of candidate loci under selection but with a potentially high rate of false positive. We discuss the methodological obstacles and biases encountered for the detection of selected loci in such a strongly genetically structured species. On this basis, we also discuss the significance of the candidate loci for local adaptation detected in each geographical region and the evolution of red coral populations along environmental gradients.

Published online:
DOI: 10.24072/pcjournal.12
Type: Research article

Pratlong, M. 1, 2; Haguenauer, A. 1, 3; Brener, K. 4; Mitta, G. 4; Toulza, E. 4; Garrabou, J. 5, 6; Bensoussan, N. 7; Pontarotti, P. 2, 8; Aurelle, D. 1, 5, 9

1 Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE, Marseille, France
2 Aix Marseille Univ, CNRS, Centrale Marseille, I2M, Equipe Evolution Biologique et Modélisation, Marseille, France
3 CRIOBE - Perpignan, USR3278 CRIOBE EPHE-CNRS-UPVD, France
4 IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France
5 Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
6 Institute of Marine Sciences (ICM-CSIC), Barcelona, 08003, Spain
7 IPSO FACTO, SCOPArl, Pole Océanologie, Marseille, 13001, France
8 Aix Marseille Univ, IRD, APHM, Microbe, Evolution, Phylogénie, Infection, IHU Méditerranée Infection, Marseille, France
9 Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, 75005 Paris, France
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights
     author = {Pratlong, M. and Haguenauer, A. and Brener, K. and Mitta, G. and Toulza, E. and Garrabou, J. and Bensoussan, N. and Pontarotti, P. and Aurelle, D.},
     title = {Separate the wheat from the chaff: genomic scan for local adaptation in the red coral {\protect\emph{Corallium} rubrum}},
     journal = {Peer Community Journal},
     eid = {e31},
     publisher = {Peer Community In},
     volume = {1},
     year = {2021},
     doi = {10.24072/pcjournal.12},
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AU  - Pratlong, M.
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AU  - Bensoussan, N.
AU  - Pontarotti, P.
AU  - Aurelle, D.
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%A Pratlong, M.
%A Haguenauer, A.
%A Brener, K.
%A Mitta, G.
%A Toulza, E.
%A Garrabou, J.
%A Bensoussan, N.
%A Pontarotti, P.
%A Aurelle, D.
%T Separate the wheat from the chaff: genomic scan for local adaptation in the red coral Corallium rubrum
%J Peer Community Journal
%D 2021
%V 1
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Pratlong, M.; Haguenauer, A.; Brener, K.; Mitta, G.; Toulza, E.; Garrabou, J.; Bensoussan, N.; Pontarotti, P.; Aurelle, D. Separate the wheat from the chaff: genomic scan for local adaptation in the red coral Corallium rubrum. Peer Community Journal, Volume 1 (2021), article  no. e31. doi : 10.24072/pcjournal.12.

PCI peer reviews and recommendation, and links to data, scripts, code and supplementary information: 10.24072/pci.evolbiol.100061

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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