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

M. Pratlong,D. Aurelle,G. Mitta,N. Bensoussan,P. Pontarotti,A. Haguenauer,J. Garrabou,K. Brener,E. Toulza

doi:10.24072/pcjournal.12

Abstract

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.

Highlights

The study of the mechanisms of adaptation by species to their local environment is of great interest in evolutionary biology
The whole dataset has been previously used for the study of sex determinism in C. rubrum (Pratlong et al, 2017); we develop here the study of genetic structure and local adaptation
Local adaptation to depth in the red coral We focused on candidate loci meeting the following criteria: i) detection with ARLEQUIN and pcadapt, ii) significant differentiation between depth, iii) function relevant to the adaptation to thermal regime

Summary

Introduction

The study of the mechanisms of adaptation by species to their local environment is of great interest in evolutionary biology. Particular situations favoring local adaptation or acclimatization are documented, it is often difficult to disentangle the effects of these two mechanisms and establish their relative contributions to adaptability (Palumbi et al, 2014). Understanding these mechanisms has a fundamental interest in the current context of climate change for improving predictive models and proposing management strategies (Mumby et al, 2011; Gagnaire & Gaggiotti, 2016)

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