scholarly journals The value of quantitative environmental DNA analyses for the management of invasive and endangered native fish

2021 ◽  
Author(s):  
Jack Rojahn ◽  
Luke Pearce ◽  
Dianne M. Gleeson ◽  
Richard P. Duncan ◽  
Dean M. Gilligan ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Native Fish ◽  
Dna Analyses

scholarly journals Improving the detection of rare native fish species in environmental DNA metabarcoding surveys

2021 ◽  
Author(s):  
Jack Rojahn ◽  
Dianne M. Gleeson ◽  
Elise Furlan ◽  
Tim Haeusler ◽  
Jonas Bylemans
Keyword(s):  
Fish Species ◽  
Environmental Dna ◽  
Native Fish ◽  
Dna Metabarcoding

scholarly journals Improving the detection of rare native fish species in environmental DNA metabarcoding surveys

2021 ◽  
Vol 4 ◽  
Author(s):  
Jack Rojahn ◽  
Dianne Gleeson ◽  
Elise Furlan ◽  
Tim Haeusler ◽  
Jonas Bylemans
Keyword(s):  
Rare Species ◽  
Native Species ◽  
Environmental Dna ◽  
Detection Sensitivity ◽  
Native Fish ◽  
Sampling Effort ◽  
Maxent Model ◽  
Detection Probabilities ◽  
Blocking Primer ◽  
The Impact

The presence of threatened or endangered species often strongly influences management and conservation decisions. Within the Murray–Darling Basin (MDB), Australia, the presence of threatened native fish affects the management and allocation of water resources. These decisions are currently based on traditional fisheries data and a predictive MaxEnt model. However, it is important to verify the model's predictive power given the implication it may have, but this requires methods with a high detection sensitivity for rare species. Although the use of environmental DNA (eDNA) metabarcoding achieves a higher detection sensitivity compared with traditional methods, earlier surveys in the MDB have shown that the highly abundant and invasive common carp (Cyprinus carpio) can reduce detection probabilities for rare species. Consequently, a polymerase chain reaction (PCR) blocking primer designed to block the amplification of carp eDNA could increase the detection probabilities for rare native species while simultaneously reducing the required sampling effort and survey costs. Although PCR blocking primers are often used in ancient DNA and dietary studies, no aquatic eDNA metabarcoding study to date has evaluated the potential benefits of using PCR blocking primers. A laboratory and field‐based pilot study was used to address this knowledge gap and assess the impact of a blocking primer on the detection probabilities of native species and the minimum sampling effort required. Results showed that the inclusion of the blocking primer increased the detection probabilities for native species by 10–20% and reduced the minimum required sampling effort by 25–50%. These findings provide important insights into possible methods for optimizing eDNA metabarcoding surveys for the detection of rare aquatic species.

scholarly journals Zooarchaeology and Ancient DNA, part 2: new substrates and perspectives

2021 ◽  
Vol 1 (35) ◽  
pp. 196-204
Author(s):  
Ophélie Lebrasseur ◽  
◽  
Aurélie Manin ◽  
Keyword(s):  
Ancient Dna ◽  
Environmental Dna ◽  
Biological Structure ◽  
Dna Preservation ◽  
Dna Analyses ◽  
The Past ◽  
Sequencing Technologies ◽  
Human Animal ◽  
Selection Of ◽  
Time Boundary

The last decade has seen important technological and methodological advances in the field of palaeogenomics, constantly pushing back the time boundary and broadening our understanding of past human-animal interactions. As well as the development of sequencing technologies, a variety of organic material is being (re)evaluated as potential substrates for DNA analyses. The authors here review a selection of these, including collagenous (leather and parchment), keratinous (hair and feather) and calcified (shell and eggshell) material, and environmental DNA including coprolite. The authors focus on the biological structure of these materials in relation to DNA preservation, highlighting their singularity in comparison to bones and teeth, and inform on some of their direct applications. Finally, the authors consider some of the new perspectives these substrates can bring to our understanding of the past, notably surrounding manufacturing practices and health.

Predation on native fish eggs by invasive round goby revealed by species‐specific gut content DNA analyses

2020 ◽  
Vol 30 (8) ◽  
pp. 1566-1577
Author(s):  
Elisabeth Lutz ◽  
Philipp Emanuel Hirsch ◽  
Karen Bussmann ◽  
Joschka Wiegleb ◽  
Hans‐Peter Jermann ◽  
...  
Keyword(s):  
Round Goby ◽  
Native Fish ◽  
Gut Content ◽  
Fish Eggs ◽  
Dna Analyses ◽  
Species Specific

scholarly journals Environmental DNA revealed the fish community of Hokkaido Island, Japan, after invasion by rainbow trout

2020 ◽  
Vol 8 ◽  
Author(s):  
Akio Imamura ◽  
Kana Hayami ◽  
Masayuki Sakata ◽  
Toshifumi Minamoto
Keyword(s):  
Invasive Species ◽  
Species Richness ◽  
Rainbow Trout ◽  
Fish Species ◽  
Seasonal Changes ◽  
Fish Community ◽  
Environmental Dna ◽  
Native Fish ◽  
Native Salmonids ◽  
Hokkaido Island

In freshwater ecosystems, invasive salmonid fishes can have a significant impact on native fish species. Detecting the invasion and its negative effects is critical for the conservation of native fish communities. We examined the species composition and seasonal changes in the freshwater fish community, including salmonids, on the Kamikawa Plain, Hokkaido Island, Japan, using environmental DNA (eDNA) metabarcoding. We detected 23 fish species in 176 samples collected from 16 sites over 12 months (October 2018 – August 2019). Between 11 and 20 species were detected at each site, including five native salmonids (Oncorhynchus masou, Oncorhynchus keta, Parahucho perryi, Salvelinus leucomaenis leucomaenis and Salvelinus malma krascheninnikova). The invasive alien rainbow trout Oncorhynchus mykiss was detected at all 16 sites and it was the most commonly detected salmonid. Although we found no obvious competitive exclusion of native salmonids by rainbow trout in the study area, the invasive species occurred more often and at more sites than any of the natives. We also determined the occurrence and seasonal changes in the fish community, classified as native salmonids, invasive rainbow trout, Cypriniformes and other benthic fishes. There were fewer species overall in winter, but the sites with higher species richness in winter were on the lower reaches of the river. In addition, we detected domestic invaders, such as the topmouth gudgeon, Pseudorasbora parva, although they were less prevalent than rainbow trout. These results show the effectiveness of eDNA metabarcoding, which can be used for surveying species richness at an ecosystem scale. In particular, the detection of the early stages of establishment and spread of invasive species can be achieved by eDNA monitoring.

The diversity of arthropods in homes across the United States as determined by environmental DNA analyses

2016 ◽  
Vol 25 (24) ◽  
pp. 6214-6224 ◽  
Author(s):  
Anne A. Madden ◽  
Albert Barberán ◽  
Matthew A. Bertone ◽  
Holly L. Menninger ◽  
Robert R. Dunn ◽  
...  
Keyword(s):  
United States ◽  
Environmental Dna ◽  
The United States ◽  
Dna Analyses

Discrimination of Leonurus japonicus and Leonurus cardiaca by phytochemical and DNA analyses

Planta Medica ◽  
2014 ◽  
Vol 80 (16) ◽  
Author(s):  
M Monschein ◽  
T Holzer ◽  
V Wolkinger ◽  
H Heuberger ◽  
R Seidenberger ◽  
...  
Keyword(s):  
Dna Analyses ◽  
Leonurus Cardiaca

Flow cytometric DNA analyses of frozen samples from children's solid tumors

Pathology ◽  
1993 ◽  
Vol 25 (4) ◽  
pp. 388-393 ◽  
Author(s):  
Christine M. Smyth ◽  
Megan A. Helmer ◽  
Luciano Dalla Pozza ◽  
Peter B Rowe
Keyword(s):  
Solid Tumors ◽  
Dna Analyses ◽  
Flow Cytometric
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