Biology subjects

Beacham, T. D.

Publications and source records attributed to Beacham, T. D..

8 recordsLinked to original sources

bioRxiv2023

Population genomics of harbour seal Phoca vitulina from northern British Columbia through California and comparison to the western Atlantic sub-species

The harbour seal Phoca vitulina is a ubiquitous pinniped species found throughout coastal waters of the Northern Hemisphere. Harbour seal impacts on ecosystem dynamics may be significant due to their high abundance and food web position. Two subspecies exist in North America, P. v. richardii in the Pacific Ocean, and P. v. vitulina in the Atlantic. Strong natal philopatry of harbour seals can result in fine-scale genetic structure and isolation-by-distance. Management of harbour seals is expected to benefit from improved resolution of seal population structure and dynamics. Here we use genotyping-by-sequencing to genotype 146 harbour seals from the eastern Pacific Ocean (i.e., British Columbia (BC), Oregon, and California) and the western Atlantic Ocean (i.e., Quebec, Newfoundland, and Labrador). Using 12,742 identified variants, we confirm the recently identified elevated genetic diversity in the eastern Pacific relative to the western Atlantic and greatest differentiation between the subspecies. Further, we demonstrate that this is independent of reference genome bias or other potential technical artefacts. Coast-specific analyses with 8,933 and 3,828 variants in Pacific and Atlantic subspecies, respectively, identify divergence between BC and Oregon-California, and between Quebec and Newfoundland-Labrador. Unexpected PCA outlier clusters were observed in two populations due to cryptic relatedness of individuals; subsequently, closely related samples were removed. Admixture analysis indicates an isolation-by-distance signature where Oregon seals contained some of the BC signature, whereas California did not. Additional sampling is needed in the central and north coast of BC to determine whether a discrete separation of populations exists within the region.

genomics↗

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↗

bioRxiv2021

In-field genetic stock identification of overwintering coho salmon in the Gulf of Alaska: Evaluation of Nanopore sequencing for remote real-time deployment

Genetic stock identification (GSI) by single nucleotide polymorphism (SNP) sequencing has become the gold standard for stock identification in Pacific salmon, which are found in mixed-stocks during the oceanic phase of their lifecycle. Sequencing platforms currently applied require large batch sizes and multi-day processing in specialized facilities to perform genotyping by the thousands. However, recent advances in third-generation single-molecule sequencing platforms, like the Oxford Nanopore minION, provide base calling on portable, pocket-sized sequencers and hold promise for the application of real-time, in-field stock identification on variable batch sizes. Here we report and evaluate utility and comparability of at-sea stock identification of coho salmon Oncorhynchus kisutch based on targeted SNP amplicon sequencing on the minION platform during the International Year of the Salmon Signature Expedition to the Gulf of Alaska in the winter of 2019. Long read sequencers are not optimized for short amplicons, therefore we concatenate amplicons to increase coverage and throughput. Nanopore sequencing at-sea yielded stock assignment for 50 of the 80 assessed individuals. Nanopore-based SNP calls agreed with Ion Torrent based genotypes in 83.25%, but assignment of individuals to stock of origin only agreed in 61.5% of individuals highlighting inherent challenges of Nanopore sequencing, such as resolution of homopolymer tracts and indels. However, poor representation of assayed coho salmon in the queried baseline dataset contributed to poor assignment confidence on both platforms. Future improvements will focus on lowering turnaround time, accuracy, throughput, and cost, as well as augmentation of the existing baselines, specifically in stocks from coastal northern BC and Alaska. If successfully implemented, Nanopore sequencing will provide an alternative method to the large-scale laboratory approach. Genotyping by amplicon sequencing in the hands of diverse stakeholders could inform management decisions over a broad expanse of the coast by allowing the analysis of small batches in remote areas in near real-time.

genetics↗

bioRxiv2020

Population structure of eulachon Thaleichthys pacificus from Northern California to Alaska using single nucleotide polymorphisms from direct amplicon sequencing

Eulachon Thaleichthys pacificus, a culturally and ecologically important anadromous smelt (Family Osmeridae), ranges from Northern California to the southeast Bering Sea. In recent decades, some populations have experienced declines. Here we use a contig-level genome assembly combined with previously published RADseq-derived markers to construct an amplicon panel for eulachon. Using this panel, we develop a filtered genetic baseline of 521 variant loci genotyped in 1,989 individuals from 14 populations ranging from Northern California through Central Alaska. Consistent with prior genetic studies, the strongest separation occurs among three main regions: from Northern California up to and including the Fraser River; north of the Fraser River to southeast Alaska; and within the Gulf of Alaska. Separating the Fraser River from southern US populations, and refining additional substructure within the central coast may be possible in mixed-stock analysis; this will be addressed in future work. The amplicon panel outperformed the previous microsatellite panel, and thus will be used in future mixed-stock analyses of eulachon in order to provide new insights for management and conservation of eulachon.

genetics↗

bioRxiv2019

Demographic history, linked selection, and recombination shape the genomic landscape of a broadly distributed Pacific salmon.

A thorough reconstruction of historical processes is essential for a comprehensive understanding the mechanisms shaping patterns of genetic diversity. Indeed, past and current conditions influencing effective population size have important evolutionary implications for the efficacy of selection, increased accumulation of deleterious mutations, and loss of adaptive potential. Here, we gather extensive genome-wide data that represent the extant diversity of the Coho salmon (Oncorhynchus kisutch) to address two objectives. We demonstrate that a single glacial refugium is the source of most of the present-day genetic diversity, with detectable inputs from a putative secondary micro-refugium. We found statistical support for a scenario whereby ancestral populations located south of the ice sheets expanded in postglacial time, swamping out most of the diversity from other putative micro-refugia. Demographic inferences revealed that genetic diversity was also affected by linked selection in large parts of the genome. Moreover, we demonstrate that the recent demographic history of this species generated regional differences in the load of deleterious mutations among populations, a finding that mirrors recent results from human populations and provides increased support for models of expansion load. We propose that insights from these historical inferences should be better integrated in conservation planning of wild organisms, which currently focuses largely on neutral genetic diversity and local adaptation, with the role of potentially maladaptive variation being generally ignored.

evolutionary biology↗

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↗