Do genomics and sex predict migration in a partially migratory salmonid fish,<i>Oncorhynchus mykiss</i>?

Kelson, Suzanne J.; Miller, Michael R.; Thompson, Tasha Q.; O’Rourke, Sean; Carlson, Stephanie M.

doi:10.1139/cjfas-2018-0394

Cited by 32 publications

(49 citation statements)

References 56 publications

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“…For the first genotype type, we used a single read sampling approach, where, for each individual, a single base from each site passing the above filters was randomly sampled and used for downstream analyses. This approach creates an “identify by state” (IBS) matrix and mediates the effects of coverage difference (number of sequence reads) between individuals and facilitates the use of samples with low coverage, thus allowing a larger number of samples to be included in downstream analyses than is possible with other approaches (see also Kelson, Miller, Thompson, O'Rourke, & Carlson, ). We used a discriminant analysis of principal components (DAPC) (Jombart, Devillard, & Balloux, ), on the IBS matrix with only SNPs on Omy05 ( n = 415 SNPs) to assign individuals to migratory, heterozygous or resident genotype groups (described further in Kelson et al, ).…”

Section: Methodsmentioning

confidence: 99%

“…This approach creates an “identify by state” (IBS) matrix and mediates the effects of coverage difference (number of sequence reads) between individuals and facilitates the use of samples with low coverage, thus allowing a larger number of samples to be included in downstream analyses than is possible with other approaches (see also Kelson, Miller, Thompson, O'Rourke, & Carlson, ). We used a discriminant analysis of principal components (DAPC) (Jombart, Devillard, & Balloux, ), on the IBS matrix with only SNPs on Omy05 ( n = 415 SNPs) to assign individuals to migratory, heterozygous or resident genotype groups (described further in Kelson et al, ). Second, we called genotypes for all SNPs located on the 500 RAPTURE baits (i.e., SNPs that were enriched during sequencing and therefore had relatively high coverage) using a uniform prior and posterior probability cutoff of 0.95 and refer to this approach as “called genotypes” ( n = 473 SNPs).…”

Section: Methodsmentioning

confidence: 99%

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Temporal dynamics of migration‐linked genetic variation are driven by streamflows and riverscape permeability

et al. 2020

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Landscape permeability is often explored spatially, but may also vary temporally. Landscape permeability, including partial barriers, influences migratory animals that move across the landscape. Partial barriers are common in rivers where barrier passage varies with streamflow. We explore the influence of partial barriers on the spatial and temporal distribution of migration‐linked genotypes of Oncorhynchus mykiss, a salmonid fish with co‐occurring resident and migratory forms, in tributaries to the South Fork Eel River, California, USA, Elder and Fox Creeks. We genotyped >4,000 individuals using RAD‐capture and classified individuals as resident, heterozygous or migratory genotypes using life history‐associated loci. Across four years of study (2014–2017), the permeability of partial barriers varied across dry and wet years. In Elder Creek, the largest waterfall was passable for adults migrating up‐river 4–39 days each year. In this stream, the overall spatial pattern, with fewer migratory genotypes above the waterfall, remained true across dry and wet years (67%–76% of migratory alleles were downstream of the waterfall). We also observed a strong relationship between distance upstream and proportion of migratory alleles. In Fox Creek, the primary barrier is at the mouth, and we found that the migratory allele frequency varied with the annual timing of high flow events. In years when rain events occurred during the peak breeding season, migratory allele frequency was high (60%–68%), but otherwise it was low (30% in two years). We highlight that partial barriers and landscape permeability can be temporally dynamic, and this effect can be observed through changing genotype frequencies in migratory animals.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Temporal dynamics of migration‐linked genetic variation are driven by streamflows and riverscape permeability

et al. 2020

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“…Kelson et al . () found that a combination of MAR genotype and genetic sex predicted 45% of the life‐history variation in O. mykiss , but that resident genotypes could give rise to migrants. MAR genes have been associated with important traits including smoltification, growth rate, developmental rate, survival in seawater and out‐migration of juveniles (Doctor et al ., ; Hale et al ., ; Hecht et al ., ; Pearse et al ., ; Phillis et al ., ).…”

Section: Genetic and Environmental Determinants Of Facultative Migrationmentioning

confidence: 99%

Anadromy, potamodromy and residency in brown trout Salmo trutta: the role of genes and the environment

Ferguson

Reed

Cross

et al. 2019

Journal of Fish Biology

153

176

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Brown trout Salmo trutta is endemic to Europe, western Asia and north‐western Africa; it is a prominent member of freshwater and coastal marine fish faunas. The species shows two resident (river‐resident, lake‐resident) and three main facultative migratory life histories (downstream–upstream within a river system, fluvial–adfluvial potamodromous; to and from a lake, lacustrine–adfluvial (inlet) or allacustrine (outlet) potamodromous; to and from the sea, anadromous). River‐residency v. migration is a balance between enhanced feeding and thus growth advantages of migration to a particular habitat v. the costs of potentially greater mortality and energy expenditure. Fluvial–adfluvial migration usually has less feeding improvement, but less mortality risk, than lacustrine–adfluvial or allacustrine and anadromous, but the latter vary among catchments as to which is favoured. Indirect evidence suggests that around 50% of the variability in S. trutta migration v. residency, among individuals within a population, is due to genetic variance. This dichotomous decision can best be explained by the threshold‐trait model of quantitative genetics. Thus, an individual's physiological condition (e.g., energy status) as regulated by environmental factors, genes and non‐genetic parental effects, acts as the cue. The magnitude of this cue relative to a genetically predetermined individual threshold, governs whether it will migrate or sexually mature as a river‐resident. This decision threshold occurs early in life and, if the choice is to migrate, a second threshold probably follows determining the age and timing of migration. Migration destination (mainstem river, lake, or sea) also appears to be genetically programmed. Decisions to migrate and ultimate destination result in a number of subsequent consequential changes such as parr–smolt transformation, sexual maturity and return migration. Strong associations with one or a few genes have been found for most aspects of the migratory syndrome and indirect evidence supports genetic involvement in all parts. Thus, migratory and resident life histories potentially evolve as a result of natural and anthropogenic environmental changes, which alter relative survival and reproduction. Knowledge of genetic determinants of the various components of migration in S. trutta lags substantially behind that of Oncorhynchus mykiss and other salmonines. Identification of genetic markers linked to migration components and especially to the migration–residency decision, is a prerequisite for facilitating detailed empirical studies. In order to predict effectively, through modelling, the effects of environmental changes, quantification of the relative fitness of different migratory traits and of their heritabilities, across a range of environmental conditions, is also urgently required in the face of the increasing pace of such changes.

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“…We extracted DNA from tissue samples (total n = 3149 individuals) and genotyped individuals as described in Kelson et al. (). In short, we conducted restriction site‐associated DNA (RAD) capture (Ali et al.…”

Section: Methodsmentioning

confidence: 99%

“…), which allowed us to group individuals into clusters of migratory, heterozygous, or resident genotypes (Kelson et al. ).…”

Section: Methodsmentioning

confidence: 99%

Partial migration alters population ecology and food chain length: evidence from a salmonid fish

et al. 2020

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Many migratory species, from monarch butterflies to wildebeest, express partial migration, where only a subset of a population migrates. This intraspecific variation is likely to have large ecological consequences. We studied the ecological consequences of partial migration in a salmonid fish, Oncorhynchus mykiss, in coastal streams in California, USA. One ecotype, steelhead trout, migrates to the ocean, whereas the other, rainbow trout, completes its lifecycle in freshwater. Migration has a strong genetic basis in O. mykiss. In one stream, we found differences in the frequency of migration‐linked genotypes below and above a waterfall barrier (migratory allele frequency of 60% below vs. 31% above). Below the waterfall, in the migratory‐dominated region, the density of young fish (<1 yr old) was approximately twice that in the resident‐dominated region above the waterfall (0.46 vs. 0.26 individuals/m2, respectively), presumably reflecting the higher fecundity of migratory females. Additionally, there were half as many older fish (>1 yr old) in pools downstream of the waterfall (0.05 vs. 0.13 individuals/m2). In a second stream, between‐year variation in the dominance of migratory vs. resident fish allowed us to explore differences in fish density and size structure through time, and we found a consistent pattern. In brief, when migratory genotypes dominated, we found higher densities of young fish and lower densities of older fish, resulting in a simpler size structure, compared to when resident genotypes dominated. Moreover, large resident trout had a slightly higher trophic position than young fish (3.92 vs. 3.42 in one creek and 3.77 vs. 3.17 in the other), quantified with stable isotope data. The difference in fish size structure did not generate trophic cascades. Partial migration is widespread among migratory populations, as is phenotypic divergence between resident and migratory forms, suggesting the potential for widespread ecological effects arising from this common form of intraspecific variation.

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Do genomics and sex predict migration in a partially migratory salmonid fish,Oncorhynchus mykiss?

Cited by 32 publications

References 56 publications

Temporal dynamics of migration‐linked genetic variation are driven by streamflows and riverscape permeability

Temporal dynamics of migration‐linked genetic variation are driven by streamflows and riverscape permeability

Anadromy, potamodromy and residency in brown trout Salmo trutta: the role of genes and the environment

Partial migration alters population ecology and food chain length: evidence from a salmonid fish

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