Understanding PCR Processes to Draw Meaningful Conclusions from Environmental DNA Studies

Kelly, Ryan P.; Shelton, Andrew O.; Gallego, Ramón

doi:10.1038/s41598-019-48546-x

Cited by 219 publications

(229 citation statements)

References 67 publications

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“…They found that the DNeasy Blood and Tissue Kit was optimal for eDNA extraction in most cases because it is non-toxic, simple, and less costly than other kits. The cost of PowerWater kit is higher than the DNeasy kit, but its PCR inhibitor removal can effectively improve PCR amplification and data quality [15,63]. Stoeckle et al [64] systematically evaluated the influence of different environmental variables and inhibitors and found that the presence of sediment was the main factor responsible for lower eDNA detection in the water samples, regardless of whether flowing or still water was used.…”

Section: Edna Extraction Methodsmentioning

confidence: 99%

Standards for Methods Utilizing Environmental DNA for Detection of Fish Species

Shu

Ludwig

Peng

2020

Genes

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Environmental DNA (eDNA) techniques are gaining attention as cost-effective, non-invasive strategies for acquiring information on fish and other aquatic organisms from water samples. Currently, eDNA approaches are used to detect specific fish species and determine fish community diversity. Various protocols used with eDNA methods for aquatic organism detection have been reported in different eDNA studies, but there are no general recommendations for fish detection. Herein, we reviewed 168 papers to supplement and highlight the key criteria for each step of eDNA technology in fish detection and provide general suggestions for eliminating detection errors. Although there is no unified recommendation for the application of diverse eDNA in detecting fish species, in most cases, 1 or 2 L surface water collection and eDNA capture on 0.7-μm glass fiber filters followed by extraction with a DNeasy Blood and Tissue Kit or PowerWater DNA Isolation Kit are useful for obtaining high-quality eDNA. Subsequently, species-specific quantitative polymerase chain reaction (qPCR) assays based on mitochondrial cytochrome b gene markers or eDNA metabarcoding based on both 12S and 16S rRNA markers via high-throughput sequencing can effectively detect target DNA or estimate species richness. Furthermore, detection errors can be minimized by mitigating contamination, negative control, PCR replication, and using multiple genetic markers. Our aim is to provide a useful strategy for fish eDNA technology that can be applied by researchers, advisors, and managers.

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Section: Edna Extraction Methodsmentioning

confidence: 99%

Standards for Methods Utilizing Environmental DNA for Detection of Fish Species

Shu

Ludwig

Peng

2020

Genes

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“…First, although RRA may not provide a reliable quantitative proxy in all DNA‐metabarcoding applications (De Barba et al, 2014; Deagle et al, 2019), its use for herbivore diet analysis with trn L‐P6 has been supported by strong correlations between (a) the RRA of food‐plant taxa and the proportional biomass of those taxa consumed by sheep in feeding trials (Willerslev et al, 2014) and (b) the RRA of C 4 grasses and estimates of proportional C 4 ‐plant consumption derived from carbon stable‐isotope ratios, including a nearly 1:1 correlation across seven ruminant and non‐ruminant species in our study system (Kartzinel et al, 2015). Moreover, RRA is less sensitive than presence–absence‐based approaches to the inclusion of low‐abundance reads (including potential sequencing errors and contaminants) and does not require the use of arbitrary thresholds for deciding whether rare taxa are present in or absent from a sample (Deagle et al, 2019; Kelly, Olaf Shelton, & Gallego, 2019). Importantly, we do not compare the absolute value of any diversity metric to those reported in other studies, but instead focus exclusively on the relative patterns of diversity obtained based on many samples that were analysed using identical PCR protocols.…”

Section: Methodsmentioning

confidence: 99%

Multiple dimensions of dietary diversity in large mammalian herbivores

Kartzinel

Pringle

2020

Journal of Animal Ecology

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1. Theory predicts that trophic specialization (i.e. low dietary diversity) should make consumer populations sensitive to environmental disturbances. Yet diagnosing specialization is complicated both by the difficulty of precisely quantifying diet composition and by definitional ambiguity: what makes a diet 'diverse'? 2. We sought to characterize the relationship between taxonomic dietary diversity (TDD) and phylogenetic dietary diversity (PDD) in a species-rich community of large mammalian herbivores in a semi-arid East African savanna. We hypothesized that TDD and PDD would be positively correlated within and among species, because taxonomically diverse diets are likely to include plants from many lineages.3. By using DNA metabarcoding to analyse 1,281 faecal samples collected across multiple seasons, we compiled high-resolution diet profiles for 25 sympatric largeherbivore species. For each of these populations, we calculated TDD and PDD with reference to a DNA reference library for local plants.4. Contrary to our hypothesis, measures of TDD and PDD were either uncorrelated or negatively correlated with each other. Thus, these metrics reflect distinct dimensions of dietary specialization both within and among species. In general, grazers and ruminants exhibited greater TDD, but lower PDD, than did browsers and non-ruminants. We found significant seasonal variation in TDD and/or PDD for all but four species (Grevy's zebra, buffalo, elephant, Grant's gazelle); however, the relationship between TDD and PDD was consistent across seasons for all but one of the 12 best-sampled species (plains zebra). 5.Our results show that taxonomic generalists can be phylogenetic specialists, and vice versa. These two dimensions of dietary diversity suggest contrasting implications for efforts to predict how consumers will respond to climate change and other environmental perturbations. For example, populations with low TDD may be sensitive to phylogenetically 'random' losses of food species, whereas populations with low PDD may be comparatively more sensitive to environmental changes that disadvantage entire plant lineages-and populations with low dietary diversity in both taxonomic and phylogenetic dimensions may be most vulnerable of all. K E Y W O R D S community phylogenetics, food web networks, grazer-browser continuum, megafauna, niche partitioning, specialism-generalism trade-off, ungulate foraging ecology Additional supporting information may be found online in the Supporting Information section. How to cite this article: Kartzinel TR, Pringle RM. Multiple dimensions of dietary diversity in large mammalian herbivores.

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“…To confirm the spatial resolution of our eDNA communities, we used non-metric multidimensional scaling (nMDS) ordination of eDNA indices for all ASVs within each technical replicate (Port et al, 2016). To derive this index, we first normalized taxon-specific ASV counts into proportions within a technical replicate, and then transformed the proportion values such that the maximum across all samples is scaled to 1 for each taxon (Kelly, Shelton & Gallego, 2019). Such indexing improves our ability to track trends in abundance of individual taxa in time and space by correcting for both differences in read depth among samples and differences in amplification efficiency among sequences; mathematically, it is equivalent to the Wisconsin double-standardization for community ecology as implemented in the vegan package for R (Oksanen et al, 2013).…”

Section: Community Compositionmentioning

confidence: 99%

A halo of reduced dinoflagellate abundances in and around eelgrass beds

Jacobs-Palmer

Gallego

Ramón-Laca

et al. 2020

PeerJ

Self Cite

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Seagrass beds provide a variety of ecosystem services, both within and outside the bounds of the habitat itself. Here we use environmental DNA (eDNA) amplicons to analyze a broad cross-section of taxa from ecological communities in and immediately surrounding eelgrass (Zostera marina). Sampling seawater along transects extending alongshore outward from eelgrass beds, we demonstrate that eDNA provides meter-scale resolution of communities in the field. We evaluate eDNA abundance indices for 13 major phylogenetic groups of marine and estuarine taxa along these transects, finding highly local changes linked with proximity to Z. marina for a diverse group of dinoflagellates, and for no other group of taxa. Eelgrass habitat is consistently associated with dramatic reductions in dinoflagellate abundance both within the contiguous beds and for at least 15 m outside, relative to nearby sites without eelgrass. These results are consistent with the hypothesis that eelgrass-associated communities have allelopathic effects on dinoflagellates, and that these effects can extend in a halo beyond the bounds of the contiguous beds. Because many dinoflagellates are capable of forming harmful algal blooms (HABs) toxic to humans and other animal species, the apparent salutary effect of eelgrass habitat on neighboring waters has important implications for public health as well as shellfish aquaculture and harvesting.

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Understanding PCR Processes to Draw Meaningful Conclusions from Environmental DNA Studies

Cited by 219 publications

References 67 publications

Standards for Methods Utilizing Environmental DNA for Detection of Fish Species

Standards for Methods Utilizing Environmental DNA for Detection of Fish Species

Multiple dimensions of dietary diversity in large mammalian herbivores

A halo of reduced dinoflagellate abundances in and around eelgrass beds

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