scholarly journals Evaluation of environmental DNA surveys for identifying occupancy and spatial distribution of Pacific Lamprey ( Entosphenus tridentatus ) and Lampetra spp. in a Washington coast watershed

2019 ◽  
Vol 1 (2) ◽  
pp. 131-143 ◽  
Author(s):  
Carl O. Ostberg ◽  
Dorothy M. Chase ◽  
Marshal S. Hoy ◽  
Jeffrey J. Duda ◽  
Michael C. Hayes ◽  
...  
Keyword(s):  
Spatial Distribution ◽  
Environmental Dna ◽  
Pacific Lamprey ◽  
Entosphenus Tridentatus

scholarly journals Predicting larval metamorphosis of Pacific lamprey Entosphenus tridentatus through measurements of length and mass

2020 ◽  
Vol 97 (3) ◽  
pp. 804-816
Author(s):  
Timothy A. Whitesel ◽  
Michelle McGree ◽  
Gregory S. Silver
Keyword(s):  
Larval Metamorphosis ◽  
Pacific Lamprey ◽  
Entosphenus Tridentatus

scholarly journals Fish community assessment with eDNA metabarcoding: effects of sampling design and bioinformatic filtering

2017 ◽  
Vol 74 (9) ◽  
pp. 1362-1374 ◽  
Author(s):  
Nathan T. Evans ◽  
Yiyuan Li ◽  
Mark A. Renshaw ◽  
Brett P. Olds ◽  
Kristy Deiner ◽  
...  
Keyword(s):  
Spatial Distribution ◽  
Species Richness ◽  
Spatial Resolution ◽  
Spatial Patterns ◽  
Water Body ◽  
Fish Community ◽  
Sampling Design ◽  
Environmental Dna ◽  
Body Type ◽  
Multiple Samples

Species richness is a metric of biodiversity that represents the number of species present in a community. Traditional fisheries assessments that rely on capture of organisms often underestimate true species richness. Environmental DNA (eDNA) metabarcoding is an alternative tool that infers species richness by collecting and sequencing DNA present in the ecosystem. Our objective was to determine how spatial distribution of samples and “bioinformatic stringency” affected eDNA-metabarcoding estimates of species richness compared with capture-based estimates in a 2.2 ha reservoir. When bioinformatic criteria required species to be detected only in a single sample, eDNA metabarcoding detected all species captured with traditional methods plus an additional 11 noncaptured species. However, when we required species to be detected with multiple markers and in multiple samples, eDNA metabarcoding detected only seven of the captured species. Our analysis of the spatial patterns of species detection indicated that eDNA was distributed relatively homogeneously throughout the reservoir, except near the inflowing stream. We suggest that interpretation of eDNA metabarcoding data must consider the potential effects of water body type, spatial resolution, and bioinformatic stringency.

scholarly journals Vertical distribution of prokaryotes communities and predicted metabolic pathways in New Zealand wetlands, and potential for environmental DNA indicators of wetland condition

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0243363
Author(s):  
Jamie R. Wood ◽  
Olivia R. Burge ◽  
Nic Bolstridge ◽  
Karen Bonner ◽  
Beverley Clarkson ◽  
...  
Keyword(s):  
Climate Change ◽  
Spatial Distribution ◽  
New Zealand ◽  
Metabolic Pathways ◽  
Environmental Dna ◽  
Aerobic Respiration ◽  
Biological Processes ◽  
Wetland Condition ◽  
Wetland Drainage ◽  
Assessment And Monitoring

Globally, wetlands are in decline due to anthropogenic modification and climate change. Knowledge about the spatial distribution of biodiversity and biological processes within wetlands provides essential baseline data for predicting and mitigating the effects of present and future environmental change on these critical ecosystems. To explore the potential for environmental DNA (eDNA) to provide such insights, we used 16S rRNA metabarcoding to characterise prokaryote communities and predict the distribution of prokaryote metabolic pathways in peats and sediments up to 4m below the surface across seven New Zealand wetlands. Our results reveal distinct vertical structuring of prokaryote communities and metabolic pathways in these wetlands. We also find evidence for differences in the relative abundance of certain metabolic pathways that may correspond to the degree of anthropogenic modification the wetlands have experienced. These patterns, specifically those for pathways related to aerobic respiration and the carbon cycle, can be explained predominantly by the expected effects of wetland drainage. Our study demonstrates that eDNA has the potential to be an important new tool for the assessment and monitoring of wetland health.

scholarly journals Environmental DNA analysis reveals the spatial distribution, abundance, and biomass of Japanese eels at the river‐basin scale

2019 ◽  
Vol 29 (3) ◽  
pp. 361-373 ◽  
Author(s):  
Hikaru Itakura ◽  
Ryoshiro Wakiya ◽  
Satoshi Yamamoto ◽  
Kenzo Kaifu ◽  
Takuya Sato ◽  
...  
Keyword(s):  
Spatial Distribution ◽  
River Basin ◽  
Dna Analysis ◽  
Environmental Dna ◽  
River Basin Scale ◽  
Basin Scale

Marine biology of the pacific lamprey Entosphenus tridentatus

2019 ◽  
Vol 29 (4) ◽  
pp. 767-788 ◽  
Author(s):  
Benjamin J. Clemens ◽  
Laurie Weitkamp ◽  
Kevin Siwicke ◽  
Joy Wade ◽  
Julianne Harris ◽  
...  
Keyword(s):  
Marine Biology ◽  
Pacific Lamprey ◽  
The Pacific ◽  
Entosphenus Tridentatus

scholarly journals Spatial distribution of environmental DNA in a nearshore marine habitat

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3044 ◽  
Author(s):  
James L. O’Donnell ◽  
Ryan P. Kelly ◽  
Andrew Olaf Shelton ◽  
Jameal F. Samhouri ◽  
Natalie C. Lowell ◽  
...  
Keyword(s):  
Spatial Distribution ◽  
Spatial Scales ◽  
Environmental Dna ◽  
Pcr Primers ◽  
Ecological Monitoring ◽  
Life History Stage ◽  
Illumina Platform ◽  
Marine Habitat ◽  
Biological Communities ◽  
Marine Surface

In the face of increasing threats to biodiversity, the advancement of methods for surveying biological communities is a major priority for ecologists. Recent advances in molecular biological technologies have made it possible to detect and sequence DNA from environmental samples (environmental DNA or eDNA); however, eDNA techniques have not yet seen widespread adoption as a routine method for biological surveillance primarily due to gaps in our understanding of the dynamics of eDNA in space and time. In order to identify the effective spatial scale of this approach in a dynamic marine environment, we collected marine surface water samples from transects ranging from the intertidal zone to four kilometers from shore. Using PCR primers that target a diverse assemblage of metazoans, we amplified a region of mitochondrial 16S rDNA from the samples and sequenced the products on an Illumina platform in order to detect communities and quantify their spatial patterns using a variety of statistical tools. We find evidence for multiple, discrete eDNA communities in this habitat, and show that these communities decrease in similarity as they become further apart. Offshore communities tend to be richer but less even than those inshore, though diversity was not spatially autocorrelated. Taxon-specific relative abundance coincided with our expectations of spatial distribution in taxa lacking a microscopic, pelagic life-history stage, though most of the taxa detected do not meet these criteria. Finally, we use carefully replicated laboratory procedures to show that laboratory treatments were remarkably similar in most cases, while allowing us to detect a faulty replicate, emphasizing the importance of replication to metabarcoding studies. While there is much work to be done before eDNA techniques can be confidently deployed as a standard method for ecological monitoring, this study serves as a first analysis of diversity at the fine spatial scales relevant to marine ecologists and confirms the promise of eDNA in dynamic environments.

Occurrence of larval Pacific lamprey Entosphenus tridentatus from Japan, detected by random amplified polymorphic DNA (RAPD) analysis

2005 ◽  
Vol 52 (3) ◽  
pp. 297-301 ◽  
Author(s):  
Yuji Yamazaki ◽  
Norio Fukutomi ◽  
Norio Oda ◽  
Koichi Shibukawa ◽  
Yasuo Niimura ◽  
...  
Keyword(s):  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Pacific Lamprey ◽  
Entosphenus Tridentatus
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