Estimating the genetic diversity of Pacific salmon and trout using multigene eDNA metabarcoding

Weitemier, Kevin; Penaluna, Brooke E.; Hauck, Laura; Longway, Lucas J.; Garcia, Tiffany S.; Cronn, Richard

doi:10.1111/mec.15811

Cited by 38 publications

(36 citation statements)

References 123 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Cumulatively, these studies have demonstrated the value of DNA evidence for the management of NNS. Furthermore, observations from both laboratory [47,48] and field studies [49][50][51][52][53][54] have shown that eDNA can provide population genetics inference, but very little work has used this approach to study NNS [55].…”

Section: Introductionmentioning

confidence: 99%

Managing human-mediated range shifts: understanding spatial, temporal and genetic variation in marine non-native species

Holman

Parker-Nance

Bruyn

et al. 2022

Phil. Trans. R. Soc. B

View full text Add to dashboard Cite

The use of molecular tools to manage natural resources is increasingly common. However, DNA-based methods are seldom used to understand the spatial and temporal dynamics of species' range shifts. This is important when managing range shifting species such as non-native species (NNS), which can have negative impacts on biotic communities. Here, we investigated the ascidian NNS Ciona robusta , Clavelina lepadiformis , Microcosmus squamiger and Styela plicata using a combined methodological approach. We first conducted non-molecular biodiversity surveys for these NNS along the South African coastline, and compared the results with historical surveys. We detected no consistent change in range size across species, with some displaying range stability and others showing range shifts. We then sequenced a section of cytochrome c oxidase subunit I (COI) from tissue samples and found genetic differences along the coastline but no change over recent times. Finally, we found that environmental DNA metabarcoding data showed broad congruence with both the biodiversity survey and the COI datasets, but failed to capture the complete incidence of all NNS. Overall, we demonstrated how a combined methodological approach can effectively detect spatial and temporal variation in genetic composition and range size, which is key for managing both thriving NNS and threatened species. This article is part of the theme issue ‘Species’ ranges in the face of changing environments (part I)’.

show abstract

Section: Introductionmentioning

confidence: 99%

Managing human-mediated range shifts: understanding spatial, temporal and genetic variation in marine non-native species

Holman

Parker-Nance

Bruyn

et al. 2022

Phil. Trans. R. Soc. B

View full text Add to dashboard Cite

show abstract

“…Reporting of full COI gene such as through assemblies of draft mitogenomes in the Bemisia whitefly species complex (e.g., Kunz, Tay, Court, et al, 2019;Tay, Elfekih, Polaszek, et al, 2017;Thao & Baumann, 2004;Vyskočilová et al, 2018;Wang et al, 2016) can consolidate the different databases for B. tabaci cryptic species. Linking of other non-standard gene regions (e.g., mitochondrial DNA 12S rRNA and ND2 gene regions) to the standard 5' COI gene region will also further resolve our understanding of species diversity from diverse ecosystems (e.g., Miya, Gotoh, & Sado, 2020;Stefanni et al, 2018;Weitemier et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

A high-throughput amplicon sequencing approach for population-wide species diversity and composition survey

Tay

Court²,

Jacomb³

et al. 2020

Preprint

View full text Add to dashboard Cite

Management of agricultural pests requires an understanding of pest species diversity, their interactions with beneficial insects and spatial-temporal patterns of pest abundance. Invasive and agriculturally important insect pests can build up very high populations, especially in cropping landscapes. Traditionally, sampling effort for species identification involves small sample sizes and is labour intensive. Here, we describe a high throughput sequencing (HTS) PCR amplicon method and associated analytical workflow for a rapid, intensive, high-volume survey of pest species compositions. We demonstrate our method using the Bemisia pest cryptic species complex as examples. The whiteflies Bemisia including the ′tabaci′ species are agriculturally important capable of vectoring diverse plant viruses that cause diseases and crop losses. We use our HTS amplicon platform to simultaneously process high volumes of whitefly individuals, with efficiency to detect rare (i.e., 1%) test-species and beneficial hymenopteran parasitoid species. Field-testing our HTS amplicon method across the Tanzania, Uganda and Malawi cassava cultivation landscapes, we identified the sub-Saharan Africa 1 Bemisia putative species as the dominant pest species, with other cryptic Bemisia species being detected at various abundances. We also provide evidence that Bemisia species compositions can be affected by sampling techniques that target either nymphs or adults. Our method is particularly suitable to molecular diagnostic surveys of cryptic insect species with high population densities. Our approach can be adopted to understand species biodiversity across landscapes, with broad implications for improving trans-boundary biosecurity preparedness, thus contributing to molecular ecological knowledge and the development of control strategies for high-density, cryptic, pest-species complexes.

show abstract

“…Despite the mitochondrial genes being physically linked to each other, mitochondrial haplotypes from eDNA could determine minimum number of individuals and provide information about the origin of the populations (e.g. in the case of the stocks of anadromous fishes found in the ocean (Weitemier et al, 2021)). Additionally, whole mitochondrial genome databases, from verified, vouchered specimens, will also be critical for seafood monitoring, as molecular methods are routinely used to identify species in domestic and international trade (Bourret et al, 2020;Ogden, 2008).…”

Section: Introductionmentioning

confidence: 99%

Affordable de novo generation of fish mitogenomes using amplification-free enrichment of mitochondrial DNA and deep sequencing of long fragments

Ramón-Laca

Gallego

Nichols

2022

Preprint

View full text Add to dashboard Cite

Biomonitoring surveys from environmental DNA make use of metabarcoding tools to describe the community composition. These studies match their sequencing results against public genomic databases to identify the species. However, mitochondrial genomic reference data are yet incomplete, only a few genes may be available, or the suitability of existing sequence data is suboptimal for species level resolution. Here we present a dedicated and cost-effective workflow with no DNA amplification for generating complete fish mitogenomes for the purpose of strengthening fish mitochondrial databases. Two different long-fragment sequencing approaches using Oxford Nanopore sequencing coupled with mitochondrial DNA enrichment were used. One where the enrichment is achieved by preferential isolation of mitochondria followed by DNA extraction and nuclear DNA depletion (‘mitoenrichment’). A second enrichment approach takes advantage of the CRISPR-Cas9 targeted scission on previously dephosphorylated DNA (‘targeted mitosequencing’). The sequencing results varied between tissue, species, and integrity of the DNA. The mitoenrichment method yielded 0.17-12.33 % of sequences on target and a mean coverage ranging from 74.9-805-fold. The targeted mitosequencing experiment from native genomic DNA yielded 1.83-55 % of sequences on target and a 38-2123-fold mean coverage. This helped complete the mitogenome of species with homopolymeric regions, tandem repeats and gene rearrangements. We demonstrate that deep sequencing of long fragments of native fish DNA is possible, can be achieved with low computational resources in a cost-effective manner, exceeding the widespread genome skimming approach, and allowing the discovery of mitogenomes of non-model or understudied fish taxa to a broad range of laboratories worldwide.

show abstract

Estimating the genetic diversity of Pacific salmon and trout using multigene eDNA metabarcoding

Abstract: This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

Cited by 38 publications

References 123 publications

Managing human-mediated range shifts: understanding spatial, temporal and genetic variation in marine non-native species

Managing human-mediated range shifts: understanding spatial, temporal and genetic variation in marine non-native species

A high-throughput amplicon sequencing approach for population-wide species diversity and composition survey

Affordable de novo generation of fish mitogenomes using amplification-free enrichment of mitochondrial DNA and deep sequencing of long fragments

Contact Info

Product

Resources

About