Genomic changes associated with reproductive and migratory ecotypes in sockeye salmon (Oncorhynchus nerka)

Abstract

25Mechanisms underlying adaptive evolution can best be explored using paired populations 26 displaying similar phenotypic divergence, illuminating the genomic changes associated with 27 specific life history traits. Here we used paired migratory [anadromous vs. resident (kokanee) candidates for divergent selection within at least one ecotype comparison. Eighty-six of these 34 outliers were present in multiple comparisons, with thirty-three detected across multiple 35 catchments. Of particular note, one locus was detected as the most significant outlier between 36 shore and stream-spawning ecotypes in multiple comparisons and across catchments (Columbia, 37 Fraser and Snake). We also detected several islands of divergence, some shared among . CC-BY-NC-ND 4.0 International license It is made available under a (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.

Reinventing the wheel? Reassessing the roles of gene flow, sorting and convergence in repeated evolution

“…Striking examples of such repeated sorting processes include lateral plate ( Eda gene) and pelvic girdle ( pitx1 gene) reduction events across geographically discrete freshwater populations of stickleback (Colosimo et al, 2005; Conte et al, 2012; Jones et al, 2012; Schluter & Conte, 2009; Shapiro et al, 2004). Similar repeated sorting events have also been reported across divergent populations of maize (Guo et al, 2018), wing‐reduced insects (Van Belleghem et al, 2018) and for widespread salmonid reproductive ecotypes (Veale & Russello, 2017). These findings highlight that repeated selection on standing variation can lead to widespread repeated evolution of similarly derived phenotypes (Bassham et al, 2018; Colosimo et al, 2005; Terekhanova et al, 2014).…”

“…A number of recent studies, for example, have highlighted repeated sorting events apparently involving relative ancient polymorphisms (Urban et al, 2021; Van Belleghem et al, 2018) that have been retained in situ across multiple populations. By contrast, several analyses have suggested that such variation can also be secondarily transported, with adaptive alleles introduced to multiple new populations via dispersal (Colosimo et al, 2005; Lescak et al, 2015; Schluter & Conte, 2009; Veale & Russello, 2017). As a third alternative, introgression among taxa presents another mechanism potentially facilitating widespread, repeated selection on variants that are identical by descent (Giska et al, 2019; Lewis et al, 2019; Meier et al, 2017; Svardal et al, 2019; Todesco et al, 2020).…”

“…Recent genomic studies suggest repeated sorting can drive rapid evolutionary shifts over remarkably short time frames (Reid et al, 2016), although in some fascinating cases the actual sources of genetic variation may be ancient (Nelson & Cresko, 2018; van der Valk et al, 2021; Van Belleghem et al, 2018; Veale & Russello, 2017). In addition, emerging evidence suggests that repeated sorting can occur across phylogenetically distinct lineages (Brawand et al, 2014; Brown et al, 2019; Campagna et al, 2019).…”

“…Examples of systems illustrating both convergence and sorting: (g) cichlids (Urban et al, 2021), (h) Zelandoperla stoneflies (McCulloch et al, 2021), (i) Gasterosteus sticklebacks (Fang et al, 2020), (j) shortfin molly (Brown et al, 2019). Examples of repeated sorting: (k) Timema stick insects (Lindtke et al, 2017), (l) maize (Guo et al, 2018), (m) salt marsh beetles (Van Belleghem et al, 2018), (n) cichlids (Brawand et al, 2014), (o) Gasterosteus sticklebacks (Magalhaes et al, 2021), (p) sockeye salmon (Veale & Russello, 2017), (q) mountain hares (Giska et al, 2019), (r) steamer ducks (Campagna et al, 2019). Where single taxa are represented twice, the examples involve different traits and/or contrasting spatial and phylogenetic scales…”

“…By contrast, repeated evolutionary shifts involving more closely related (e.g., congeneric or conspecific) lineages have typically been categorized as “parallel” because they involve similar parental lineages on comparable evolutionary trajectories (Conte et al, 2012). Key examples of such repetitive adaptation include reduction in antipredator armour in independently landlocked stickleback lineages (Colosimo et al, 2005; Terekhanova et al, 2014); parallel mimetic phenotypes in Heliconius butterflies (Brower, 1996); replicated migratory ecotypes of freshwater fishes (Veale & Russello, 2017); insect ecotype pairs adapted to distinct host plants (Nosil et al, 2018; Soria‐Carrasco et al, 2014); similar shifts in flower colour in congeneric plant lineages (Smith & Rausher, 2011); multiple flight reduction events among congeneric bird lineages (Campagna et al, 2019); repeated intraspecific flight loss within insects (Suzuki et al, 2019; Van Belleghem et al, 2018); and repeated pigmentation and eye loss events in multiple cave fish and cave invertebrate populations (Dowling et al, 2002; Herman et al, 2018; Re et al, 2018).…”