Genomic signatures of the plateless phenotype in the threespine stickleback

Abstract

Understanding the genetic basis of traits involved in adaptive divergence and speciation is one of the most fundamental objectives in evolutionary biology. Toward that end, we look for signatures of extreme plate loss in the genome of freshwater threespine sticklebacks (Gasterosteus aculeatus). Plateless stickleback have been found in only a few lakes and streams across the world; they represent the far extreme of a phenotypic continuum (plate number) that has been studied for years, although plateless individuals have not yet been the subject of much investigation. We use a dense single nucleotide polymorphism dataset made using RADseq to study fish from three freshwater populations containing plateless and low plated individuals, as well as fish from full plated marine populations. Analyses were performed using FastStructure, sliding windows F ST, Bayescan and latent factor mixed models to search for genomic differences between the low plated and plateless phenotypes both within and among the three lakes. At least 18 genomic regions which may contribute to within‐morph plate number variation were detected in our low plated stickleback populations. We see no evidence of a selective sweep between low and plateless fish; rather reduction of plate number within the low plated morph seems to be polygenic.

Linking genotype to phenotype in a changing ocean: inferring the genomic architecture of a blue mussel stress response with genome‐wide association

“…The inferred architecture of this trait – a handful of influential loci with moderate effect sizes – is similar to other genome‐wide association inferences on the architecture of adaptive traits. In stickleback fishes, 10–18 loci were identified as significantly influencing the armoured plate phenotype (Mazzarella et al ., ). In the case of the serotiny traits in lodgepole pine, 11 loci were associated with this important reproductive phenotype with effect sizes nearly identical to those estimated here (Parchman et al ., ).…”

A paradoxical bias in knowledge about Norwegian freshwater fishes: research efforts during 1980-2020

“…These studies concerned the large-scale (Klepaker 1995, 1996, Voje et al 2013) and small-scale distribution (Le Rouzic et al 2011Rouzic et al , Østbye et al 2016Rouzic et al , Østbye et al 2018 of the plate morphs among and within ecosystems, and how it differs depending on various selective processes (Myhre and Klepaker 2009, Bjaerke et al 2010, Mazzarella et al 2015. These studies also included the use of modern genetic/genomic methods (Taugbøl et al 2014, Mazzarella et al 2016. Also, the other main anti-predator defence system -the dorsal and pelvic spines -have been studied (Klepaker et al 2012.…”

Parallel evolution despite low genetic diversity in three-spined sticklebacks

“…Three-spined sticklebacks originated in the northern Pacific [28][29][30], from where they colonized the Atlantic Ocean and then the Baltic Sea, the Mediterranean Sea and the Black Sea [30]. Within all these different biogeographic regions, marine stickleback populations successfully invaded different brackish and freshwater habitats, evolving similar morphological traits as adaptations to life in low salinity environments [26,[31][32][33]. These adaptations involve several traits, such as body armour and lateral-plate reduction in freshwater populations [34], male courtship behaviour [35], body shape, physiological adaptations to different salinities and trophic specialization [31].…”