scholarly journals Novel insights into marine fish biodiversity across a pronounced environmental gradient using replicated environmental DNA analyses

2021 ◽  
Author(s):  
Molly Victoria Czachur ◽  
Mathew Seymour ◽  
Simon Creer ◽  
Sophie Heyden
Keyword(s):  
Marine Fish ◽  
Environmental Gradient ◽  
Environmental Dna ◽  
Dna Analyses ◽  
Fish Biodiversity

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 Particle Size Distribution of Environmental DNA from the Nuclei of Marine Fish

2019 ◽  
Vol 53 (16) ◽  
pp. 9947-9956 ◽  
Author(s):  
Toshiaki Jo ◽  
Mio Arimoto ◽  
Hiroaki Murakami ◽  
Reiji Masuda ◽  
Toshifumi Minamoto
Keyword(s):  
Particle Size ◽  
Particle Size Distribution ◽  
Size Distribution ◽  
Marine Fish ◽  
Environmental Dna

Marine Fish Biodiversity Survey 2005-2013

2015 ◽  
Author(s):  
Tim Tim McClanahan
Keyword(s):  
Marine Fish ◽  
Biodiversity Survey ◽  
Fish Biodiversity

scholarly journals Seasonal variation in the relative importance of assembly processes in marine fish communities as determined by environmental DNA analyses

2021 ◽  
Author(s):  
Naoto Shinohara ◽  
Yuki Hongo ◽  
Momoko Ichinokawa ◽  
Shota Nishijima ◽  
Shuhei Sawayama ◽  
...  
Keyword(s):  
Marine Fish ◽  
Seasonal Changes ◽  
Variation Partitioning ◽  
Environmental Filtering ◽  
Fish Communities ◽  
Environmental Dna ◽  
Compositional Variation ◽  
Short Time Scale ◽  
Relative Importance ◽  
Spatial Processes

Compositional variation among local communities is a result of environmental (e.g., environmental filtering) and spatial (e.g., dispersal limitation) processes. Growing evidence suggests that their relative importance varies temporally, but little is known about the short-time scale dynamics, that is, seasonality. Using marine fish communities in a Japanese bay as a model system, we tested the hypothesis that seasonal changes in the environment induce a shift in the relative importance of environmental and spatial processes. We used one-year monthly monitoring data obtained using environmental DNA and conducted a variation partitioning analysis to decompose the two processes. The relative importance of environmental and spatial processes was comparable averaged over the year but changed seasonally. During summer, when lower dissolved oxygen concentrations may adversely affect organisms, species composition was more explained by space despite larger environmental heterogeneity than in other seasons. This suggests that environmental processes weakened during the season with extremely severe environments, likely due to the random loss of individuals. We conclude that the assembly processes of communities of mobile organisms, such as fishes, can shift even within a year in response to seasonal changes in environmental severity. The results also indicate the applicability of eDNA techniques for community assembly studies.

scholarly journals Enviromental DNA (eDNA) reveals potential for interoceanic fish invasions across the Panama Canal

2021 ◽  
Author(s):  
Lennart Schreiber ◽  
Gustavo Castellanos-Galindo ◽  
Mark Torchin ◽  
Karina Chavarria ◽  
Silke Laakmann ◽  
...  
Keyword(s):  
Marine Fish ◽  
New Records ◽  
Fish Fauna ◽  
Environmental Dna ◽  
Diversity Indices ◽  
Molecular Data ◽  
Panama Canal ◽  
Marine Fish Species ◽  
Cytochrome Oxidase Subunit ◽  
The Pacific

Interoceanic canals can facilitate biological invasions as they connect the world’s oceans and dissolve dispersal barriers between bioregions. As a consequence, multiple opportunities for biotic exchange arise and the resulting establishment of migrant species often causes adverse ecological and economic impacts. The Panama Canal is a key region for biotic exchange as it connects the Pacific and Atlantic Oceans in Central America. In this study, we used two complementary methods (environmental DNA (eDNA) and gillnetting) to survey fish communities in this unique waterway. Using COI (cytochrome oxidase subunit I) metabarcoding, we detected a total of 142 taxa, including evidence for the presence of sixteen Atlantic and eight Pacific marine fish inside different sections of the Canal. Of these, ten are potentially new records of marine taxa detected in the freshwater segment of the Canal. Molecular data did not capture all species caught with gillnets, but generally provided a more complete image of the fish fauna. Diversity indices based on eDNA surveys revealed significant differences across different sections of the Canal reflecting in part the prevailing environmental conditions. The observed increase in the presence of marine fish species in the Canal indicates a growing potential for interoceanic exchange of fishes across the Isthmus. Monitoring using eDNA is a rapid and efficient way to assess potential changes in the fishes of this important waterway.

scholarly journals Alpine freshwater fish biodiversity assessment: an intercalibration test for metabarcoding method set up

2021 ◽  
Vol 4 ◽  
Author(s):  
Giulia Riccioni ◽  
Isabelle Domaizon ◽  
Andrea Gandolfi ◽  
Massimo Pindo ◽  
Marine Vautier ◽  
...  
Keyword(s):  
Freshwater Fish ◽  
Population Decline ◽  
Environmental Dna ◽  
Well Being ◽  
Taxonomic Resolution ◽  
Anthropogenic Pressure ◽  
Biodiversity Assessment ◽  
Good Efficiency ◽  
Essential Information ◽  
Fish Biodiversity

Environmental DNA (eDNA) based methods (Fig. 1) are proving to be a promising tool for freshwater fish biodiversity assessment in Europe within the Water Framework Directive (WFD, 2000/60/EC) especially for large rivers and lakes where current fish monitoring techniques have known shortcomings. Freshwater fish are actively involved in aquatic ecosystems functioning and diversity, contributing to the health, well-being and economy in every geographic realm. Unfortunately, many freshwater fish are experiencing critical population decline with risk of local or global extinction because of intense anthropogenic pressure. Within the EU project Eco-AlpsWater, advanced high throughput sequencing (HTS) techniques are used to improve the traditional WFD monitoring approaches by using environmental DNA (eDNA) collected in Alpine waterbodies. To evaluate the performance of the metabarcoding approach specifically designed to measure freshwater fish biodiversity in Alpine lakes and rivers, an intercalibration test was performed. This exercise forecasted the use of mock samples containing either tissue-extracted DNA of different target species or water collected from aquaculture tanks to mimic real environmental water sampling and processing. Moreover, three water samples collected in Lake Bourget (France) were used to compare the efficiency of taxonomic assignments in natural and mock community samples. Our results highlighted a good efficiency of the molecular laboratory protocols for HTS and a good amplification success of the selected primers, providing essential information concerning the taxonomic resolution of the 12S mitochondrial marker. As further confirmation, different concentration of species DNA in the mock samples were well represented by the relative read abundance. This preliminary test confirmed the applicability of eDNA metabarcoding analyses for the biomonitoring of freshwater fish inhabiting Alpine and perialpine lakes and rivers.

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.

scholarly journals Environmental DNA reveals quantitative patterns of fish biodiversity in large rivers despite its downstream transportation

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Didier Pont ◽  
Mathieu Rocle ◽  
Alice Valentini ◽  
Raphaël Civade ◽  
Pauline Jean ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Large Rivers ◽  
Fish Biodiversity
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