Detecting genomic variation underlying phenotypic characteristics of reintroduced Coho salmon (Oncorhynchus kisutch)

Horn, Rebekah L.; Kamphaus, Cory M.; Murdoch, Keely; Narum, Shawn R.

doi:10.1007/s10592-020-01307-0

Cited by 11 publications

(13 citation statements)

References 61 publications

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“…Mapping, alignment trimming, and filtering to the charr reference genome were performed with BWA-MEM v 0.7.12, SAMtools v 1.5 using a mapping quality threshold of 10, and SAMblaster v 0.1.24 (Faust & Hall, 2014), while filtering for a quality score threshold of 20 was performed by BBMap v 37.93 (Bushnell, sourceforge.net/projects/bbmap/, accessed 20-11-2019), and summarized with Fastqc v 0.11.7 (Andrews, 2010). SNP filtering was carried out using common parameters for salmonid species, found below (Horn et al, 2020). Duplicate sequences and unpaired reads were filtered using SAMtools, BBMap, and Picard tools with a minimum fastq trimming length of 25 bp.…”

Section: Pool-seq Pipeline and Snp Discoverymentioning

confidence: 99%

Neutral and adaptive drivers of genomic change in introduced brook trout (Salvelinus fontinalis) populations revealed by pooled sequencing

Brookes

Jeon

Derry

et al. 2022

Ecology and Evolution

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Understanding the drivers of successful species invasions is important for conserving native biodiversity and for mitigating the economic impacts of introduced species. However, whole‐genome resolution investigations of the underlying contributions of neutral and adaptive genetic variation in successful introductions are rare. Increased propagule pressure should result in greater neutral genetic variation, while environmental differences should elicit selective pressures on introduced populations, leading to adaptive differentiation. We investigated neutral and adaptive variation among nine introduced brook trout (Salvelinus fontinalis) populations using whole‐genome pooled sequencing. The populations inhabit isolated alpine lakes in western Canada and descend from a common source, with an average of ~19 (range of 7–41) generations since introduction. We found some evidence of bottlenecks without recovery, no strong evidence of purifying selection, and little support that varying propagule pressure or differences in local environments shaped observed neutral genetic variation differences. Putative adaptive loci analysis revealed nonconvergent patterns of adaptive differentiation among lakes with minimal putatively adaptive loci (0.001%–0.15%) that did not correspond with tested environmental variables. Our results suggest that (i) introduction success is not always strongly influenced by genetic load; (ii) observed differentiation among introduced populations can be idiosyncratic, population‐specific, or stochastic; and (iii) conservatively, in some introduced species, colonization barriers may be overcome by support through one aspect of propagule pressure or benign environmental conditions.

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Section: Pool-seq Pipeline and Snp Discoverymentioning

confidence: 99%

Neutral and adaptive drivers of genomic change in introduced brook trout (Salvelinus fontinalis) populations revealed by pooled sequencing

Brookes

Jeon

Derry

et al. 2022

Ecology and Evolution

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“…Genomic DNA was extracted from 286 fish using a Chelex extraction method (Sweet et al, 1996). Libraries were prepared with NEBNext Ultra kits with a modified version of the protocol to reduce reaction volumes (see detailed protocol in Horn et al, 2020). Briefly here, DNA of each sample was first quantified and normalized, before being randomly fragmented using dsDNA fragmentase (NEB, We used the "PPalign" module in the PoolParty pipeline to perform bioinformatics .…”

Section: Whole Genome Resequencing and Snp Detectionmentioning

confidence: 99%

Whole genome resequencing reveals genomic regions associated with thermal adaptation in redband trout

Chen

Narum

2020

Molecular Ecology

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A goal of studying local adaptation is to identify the underlying genetic variation (i.e., genes and nucleotide polymorphisms) in natural populations. However, it is a challenging task since in most natural ecosystems, multiple environmental factors work together in complex ways to alter selection on a combination of traits and influence overall fitness. For example, water temperature has a pervasive effect on development, swimming performance, reproduction, and survival of ectothermic aquatic species (Beacham & Murray, 1989

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“…Our approach to genome resequencing was to target low read depth for individually barcoded samples and then to combine sequence reads from individuals of the same phenotype for further analyses of the four groups: resident male, anadromous male, resident female, and anadromous female. To prepare the libraries for whole-genome resequencing, individuals were barcoded, and a NEBNext Ultra enzymatic fragmentation protocol was followed ( Horn et al, 2020 ). Briefly, we extracted DNA according to a Chelex extraction method ( Sweet et al, 1996 ).…”

Section: Methodsmentioning

confidence: 99%

Whole-Genome Resequencing to Evaluate Life History Variation in Anadromous Migration of Oncorhynchus mykiss

Collins

Romero²,

Zendt³

et al. 2022

Front. Genet.

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Anadromous fish experience physiological modifications necessary to migrate between vastly different freshwater and marine environments, but some species such as Oncorhynchus mykiss demonstrate variation in life history strategies with some individuals remaining exclusively resident in freshwater, whereas others undergo anadromous migration. Because there is limited understanding of genes involved in this life history variation across populations of this species, we evaluated the genomic difference between known anadromous (n = 39) and resident (n = 78) Oncorhynchus mykiss collected from the Klickitat River, WA, USA, with whole-genome resequencing methods. Sequencing of these collections yielded 5.64 million single-nucleotide polymorphisms that were tested for significant differences between resident and anadromous groups along with previously identified candidate gene regions. Although a few regions of the genome were marginally significant, there was one region on chromosome Omy12 that provided the most consistent signal of association with anadromy near two annotated genes in the reference assembly: COP9 signalosome complex subunit 6 (CSN6) and NACHT, LRR, and PYD domain–containing protein 3 (NLRP3). Previously identified candidate genes for anadromy within the inversion region of chromosome Omy05 in coastal steelhead and rainbow trout were not informative for this population as shown in previous studies. Results indicate that the significant region on chromosome Omy12 may represent a minor effect gene for male anadromy and suggests that this life history variation in Oncorhynchus mykiss is more strongly driven by other mechanisms related to environmental rearing such as epigenetic modification, gene expression, and phenotypic plasticity. Further studies into regulatory mechanisms of this trait are needed to understand drivers of anadromy in populations of this protected species.

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Detecting genomic variation underlying phenotypic characteristics of reintroduced Coho salmon (Oncorhynchus kisutch)

Cited by 11 publications

References 61 publications

Neutral and adaptive drivers of genomic change in introduced brook trout (Salvelinus fontinalis) populations revealed by pooled sequencing

Neutral and adaptive drivers of genomic change in introduced brook trout (Salvelinus fontinalis) populations revealed by pooled sequencing

Whole genome resequencing reveals genomic regions associated with thermal adaptation in redband trout

Whole-Genome Resequencing to Evaluate Life History Variation in Anadromous Migration of Oncorhynchus mykiss

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