Biology subjects

Withler, R. E.

Publications and source records attributed to Withler, R. E..

5 recordsLinked to original sources

bioRxiv2024

Revealing the evolutionary history and contemporary population structure of Pacific salmon in the Fraser River through genome resequencing

The Fraser River once supported massive salmon returns, but now years with half of the recorded historical maximum are considered good. There is substantial interest from surrounding communities, governments, and other groups to increase salmon returns for both human use and for functional ecosystems. To help generate resources for this endeavour, we resequenced hundreds of genomes at moderate coverage ([~]16x) of Chinook (Oncorhynchus tshawytscha), coho (O. kisutch), and sockeye salmon (O. nerka) from the Fraser River. The resequenced genomes are an important resource that can give us new insights. In this study, we found evidence that Chinook salmon have 1.5-2x more polymorphic loci than coho or sockeye salmon. Using principal component analysis (PCA) and admixture analysis, we also identified genetic groups similar to those previously identified with only a few microsatellite markers. As the higher density data supports these previous genetic groups, it suggests that the identity of these groups is not overly sensitive to the number of genetic markers or when the groups were sampled. With the increased resolution from resequenced genomes, we were able to further identify factors influencing these genetic groups, including isolation-by-distance, migration barriers, recolonization from different glacial refugia, and environmental factors like precipitation. We were also able to identify 20 potentially adaptive loci among the genetic groups by analyzing runs of homozygosity. All of the resequenced genomes have been submitted to a public database where they can be used as a reference for the contemporary genomics of Fraser River salmon. Article SummaryConcerns over Fraser River salmon declines led us to generate resources to better understand the genetics of these salmon. Our findings were similar to previous studies that examined a very small fraction of the genetic markers examined here. We expanded upon previous studies by identifying possible influences on the genetics of Fraser River salmon. These included environmental factors, historical differences, and a lack of connectivity in the river caused by the Fraser Canyon.

evolutionary biology↗

bioRxiv2022

Isolation-by-distance and population-size history inferences from the coho salmon (Oncorhynchus kisutch) genome

Coho salmon (Oncorhynchus kisutch) are a culturally and economically important species that return from multiyear ocean migrations to spawn in rivers that flow to the Northern Pacific Ocean. Southern stocks of coho salmon have significantly declined over the past quarter century, and unfortunately, conservation efforts have not reversed this trend. To assist in stock management and conservation efforts, we generated two chromosome-level genome assemblies and sequenced 24 RNA-seq libraries to better annotate the coho salmon genome assemblies. We also resequenced the genomes of 83 coho salmon across their North American range to identify nucleotide variants, characterize the broad effects of isolation-by-distance using a genome-wide association analysis approach, and understand the demographic histories of these salmon by modeling population size from genome-wide data. We observed that more than 13% of all SNPs were associated with latitude (before multiple test correction), likely an affect of isolation-by-distance. From demographic history modeling, we estimated that the SNP latitudinal gradient likely developed as recently as 8,000 years ago. In addition, we identified four genes each harboring multiple SNPs associated with latitude; all of these SNPs were also predicted to modify the function of the gene. Three of these genes have roles in cell junction maintenance and may be involved in osmoregulation. This signifies that ocean salinity may have been a factor influencing coho salmon recolonization after the last glaciation period - generating the current pattern of variation in these three genes.

genomics↗

bioRxiv2021

Genome assembly, transcriptome and SNP database for chum salmon (Oncorhynchus keta)

Chum salmon (Oncorhynchus keta) is the species with the widest geographic range of the anadromous Pacific salmonids. Chum salmon is the second largest of the Pacific salmon, behind Chinook salmon, and considered the most plentiful Pacific salmon by overall biomass. This species is of significant commercial and economic importance: on average the commercial chum salmon fishery has the second highest processed value of the Pacific salmon within British Columbia. The aim of this work was to establish genomic baseline resources for this species. Our first step to accomplish this goal was to generate a chum salmon reference genome assembly from a doubled-haploid chum salmon. Gene annotation of this genome was facilitated by an extensive RNA-seq database we were able to create from multiple tissues. Range-wide resequencing of chum salmon genomes allowed us to categorize genome-wide geographic variation, which in turn reinforced the idea that genetic differentiation was best described on a regional, rather than at a stock-specific, level. Within British Columbia, chum salmon regional groupings were described at the conservation unit (CU) level, and there may be substructure within particular CUs. Genome wide associations of phenotypic sex to SNP genetic markers identified two clear peaks, a very strong peak on Linkage Group 15, and another on Linkage Group 3. With these new resources, we were better able to characterize the sex-determining region and gain further insights into sex determination in chum salmon and the general biology of this species.

genomics↗

bioRxiv2021

The pink salmon genome: uncovering the genomic consequences of a strict two-year life-cycle

Pink salmon (Oncorhynchus gorbuscha) adults are the smallest of the five Pacific salmon native to the western Pacific Ocean. Pink salmon are also the most abundant of these species and account for a large proportion of the commercial value of the salmon fishery worldwide. A strict two-year life-history of most pink salmon generates temporally isolated populations that spawn either in even-years or odd-years. To uncover the influence of this genetic isolation, reference genome assemblies were generated for each year-class and whole genome re-sequencing data was collected from salmon of both year-classes. The salmon were sampled from six Canadian rivers and one Japanese river. At multiple centromeres we identified peaks of Fst between year-classes that were millions of base-pairs long. The largest Fst peak was also associated with a million base-pair chromosomal polymorphism found in the odd-year genome near a centromere. These Fst peaks may be the result of centromere drive or a combination or reduced recombination and genetic drift, and they could influence speciation. Other regions of the genome influenced by odd-year and even-year temporal isolation and tentatively under selection were mostly associated with genes related to immune function, organ development/maintenance, and behaviour.

genomics↗

bioRxiv2017

Parallel epigenetic modifications induced by hatchery rearing in a Pacific Salmon

Highlights- First study to highlight parallel epigenetic modifications induced by hatchery rearing as a potential explanatory mechanism for rapid change in fitness\n\nSummaryA puzzling question in conservation biology is how to maintain overall fitness of individuals bred in captive environment upon release into the wild, especially for rehabilitating declining or threatened species [1,2]. For salmonid species, a heritable change in fitness related traits and gene expression has been reported to occur in a single generation of captivity in hatchery environment [3-5]. Such rapid changes are congruent with models of inadvertent domestication selection which may lead to maladaptation in the natural environment [4]. Arguably, the underlying mechanism by which captivity may induce fitness difference between wild and captive congeners is still poorly understood. Short-term selection on complex phenotypic traits is expected to induce subtle changes in allele frequency over multiple loci [7-9]. Yet, most studies investigating the molecular basis for rapid change in fitness related traits occurring in hatchery have concentrated their effort on finding evidence for selection at the genome level by identifying loci with large effect.\n\nNumerous wild stocks of Pacific anadromous salmon and trout (genus Oncorhynchus and Salmo) have experienced fluctuating abundance over the past century, with a series of sharp declines [6-8]. With the objectives of preserving ecosystem integrity, enhancing declining populations and sustaining fisheries, conservation hatcheries have been flourishing. This is particularly true along the North American Pacific coast where billions of salmonids, all species included, are released each year. Despite substantial improvement of production management, the beneficial ecological role of hatcheries in enhancing and restoring wild stocks is still debated, mainly because of the reduced fitness and maladaptation of hatchery-fish when released in the wild [3,5,9]. Although previous studies showed that domestication selection was involved in such fitness impairment, they also observed that different environmental conditions (e.g. reduced fish density) significantly modulated the physiological acclimation to hatchery environment [4].\n\nEnvironmental stimuli are especially relevant during early embryonic development, which also correspond to a sensitive methylation reprogramming window in vertebrates [10,11]. It is therefore plausible that differences in rearing environment during early development may result in epigenetic modifications that could in turn impact on fitness. However, the only epigenetic study to date pertaining to captive rearing in salmonids and performed using methylation-sensitive amplified fragments (MSAP) failed to identify significant changes in methylation profile associated with hatchery rearing [12]\n\nHere, we used a higher resolution approach to compare the genome-wide pattern of methylation in hatchery-reared juvenile (smolt) Coho Salmon with that of their wild counterparts in two geographically distant rivers in British Columbia, Canada. Using a reduced representation bisulfite sequencing (RRBS) approach covering an average per individual of about 70 million cytosines in CpG context, we identified 100 methylated regions (DMRs) that differed in parallel between hatchery and natural origin salmon in both rivers. The total variance of epigenetic variation among individuals explained by river or origin and rearing environment in a RDA model was 16% (adj.R2=0.16), and both variables equally explained about 8% of the variance after controlling for each other. The gene ontology analysis revealed that regions with different methylation levels between hatchery and natural origin salmon showed enrichment for ion homeostasis, synaptic and neuromuscular regulation, immune and stress response, and control of locomotion functions. We further identified 15,044 SNPs that allowed detection of significant differences between either rivers or sexes. However, no effect of rearing environment was observed, confirming that hatchery and natural origin fish of a given river belong to the same panmictic population, as expected based on the hatchery programs applied in these rivers (see Supplementary experimental procedures). Moreover, neither a standard genome-scan approach nor a polygenic statistical framework allowed detection of selective effects within a single generation between hatchery and natural origin salmon. Therefore, this is the first study to demonstrate that parallel epigenetic modifications induced by hatchery rearing during early development may represent a potential explanatory mechanism for rapid change in fitness-related traits previously reported in salmonids.

genomics↗