Fine-scale genetic structure of small fish populations in islands: The case of brook charr Salvelinus fontinalis (Mitchill, 1814) in Saint-Pierre and Miquelon (France)

Island ecosystems, particularly vulnerable to environmental challenges, host many endangered native species. Diadromous fish, in particular, are threatened throughout their marine and freshwater habitats. The conservation of these species requires an in-depth understanding of their genetic diversity and structure, to better understand their adaptive potential. We investigated fine-scale population diversity and structure in native brook charr (Salvelinus fontinalis) by genotyping ten microsatellite loci in 244 individuals at three spatial scales in Saint-Pierre and Miquelon, France. We found limited genetic variability across the archipelago, with particularly low genetic diversity in one island, Langlade. A significant difference in allelic richness was also detected among the three islands, indicating a difference in genetic composition across the archipelago, probably induced by historical stocking actions on both Saint-Pierre and Miquelon. Finally, a strong genetic structure was detected across the archipelago among hydrosystems (overall FST = 0.19) and even within several of them. The presence of predominant inter-island gene flow combined with complete genetic isolation from certain hydrosystems, suggests that this contemporary genetic structure is the result of both natural demographic processes during the species post-glacial colonization, and recent restocking actions. The complex genetic structure of such isolated brook charr subpopulations highlights the importance of considering fine-scale genetic structure in conservation management.

Methods
We aimed to capture a total of 30 individuals per hydrosystems selected (ten in the upstream part, ten in the median part, and ten in the estuarine part) by electrofishing or traditional angling techniques (i.e., cork, spinner or whip fishing). Fish captures were performed in each targeted sampled areas so that we cover the entire area as much as possible.

Captures were made according to CCAC (UQAR CPA-89-22-246) and to the prefectural permit (no. 349). Following the capture, fish were anesthetized with eugenol 100% (Lotus Aroma, Sainte-Julie, QC, Canada), and killed by sectioning the spinal cord for further molecular analyses. The adipose fin was cut and preserved in 95% ethanol. Genomic DNA was extracted using the QIAGEN “DNeasy Blood and tissue” kit (Qiagen, Hilden, Germany). Evidence of null alleles or large allele dropouts was detected for two loci (SfoC88 and Sfo177Lav) with MICRO-CHECKER analyses hence those loci were discarded for further analyses but they are presented here all the same..