Investigating genomic and phenotypic parallelism between piscivorous and planktivorous lake trout (Salvelinus namaycush) ecotypes by means ofRADseq and morphometrics analyses

Abstract

Repeated adaptive ecological diversification has commonly been reported in fish and has often been associated with trophic niche diversity. The main goal of this study was to investigate the extent of parallelism in the genomic and phenotypic divergence between piscivorous and planktivorous lake trout ecotypes from Laurentian Shield lakes, Canada. This was achieved by documenting the extent of morphological differentiation using geometric morphometrics and linear measurements as well as the pattern of genomic divergence by means of RADseq genotyping (3925 filtered SNPs) in 12 lakes. Our results indicate that the two ecotypes evolved distinct body shape and several linear measurements in parallel. Neutral genetic differentiation was pronounced between all isolated populations (Mean FST = 0.433), indicating no or very limited migration and pronounced genetic drift. Significant genetic differentiation also suggested partial reproductive isolation between ecotypes in the two lakes where they are found in sympatry. Combining different outlier detection methods, we identified 48 SNPs putatively under divergent selection between ecotypes, among which 10 could be annotated and related to functions such as developmental processes and ionic regulation. Finally, our results indicate that parallel morphological divergence is accompanied by both parallel and nonparallel genomic divergence, which is associated with the use of different trophic niches between ecotypes. The results are also discussed in the context of management and conservation of this highly exploited species throughout northern North America.

Lost in parameter space: a road map for stacks

“…For the TRT dataset, M5 was the most suitable value for identifying polymorphism, and this is considerably higher than M2 as most commonly used in salmonid RAD‐seq studies (Lemay & Russello ; Bernatchez et al . ) and in other teleost species (Catchen et al . ; Martin & Feinstein ; Fowler & Buonaccorsi ).…”

Signatures of local adaptation along environmental gradients in a range‐expanding damselfly (Ischnura elegans)

“…The minimal overlap and difference in numbers of SNPs identified between F ST outlier approaches identified may indicate different sensitivities of each approach to the effects of genetic drift and structure. Notably, studies comparing outflank and bayescan have found little overlap between the approaches (e.g., Bernatchez, Laporte, Perrier, Sirois, & Bernatchez, ; Chen, Farrell, Matala, & Narum, ; Micheletti, Matala, Matala, & Narum, ). The significant SNP associations using EAA were unique to each environmental variable in 41%–79% of cases (Table ).…”

Reliance on lakes by salmon, trout and charr (Oncorhynchus,SalmoandSalvelinus): An evaluation of spawning habitats, rearing strategies and trophic polymorphisms

“…One of the most diversely polymorphic species is the lake trout, which exhibits two to four morphs in at least five lakes, differentiated by their trophic specialization, habitat occupancy and mechanism of buoyancy regulation. Lake trout morphs most commonly emerge in large lakes where they become piscivorous or invertivorous and occupy shallow or deep habitats (Muir, Hansen, Bronte, & Krueger, ), indicating multiple parallel evolutionary events (Bernatchez, Laporte, Perrier, Sirois, & Bernatchez, ). A shallow‐water piscivorous form, referred to as the “lean” morph, is slim‐bodied with low lipid content, strongly contrasting with the “fat” morph or “siscowet,” a deep‐water piscivore that is deep‐bodied, high in lipids and consumes different fish species (Hansen et al., ; Ray, Hrabik, & Ebener, ; Zimmerman, Krueger, & Eshenroder, ).…”