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
2021 ◽  
Author(s):  
Jack Rojahn ◽  
Luke Pearce ◽  
Dianne M. Gleeson ◽  
Richard P. Duncan ◽  
Dean M. Gilligan ◽  
...  

2019 ◽  
Vol 53 (16) ◽  
pp. 9947-9956 ◽  
Author(s):  
Toshiaki Jo ◽  
Mio Arimoto ◽  
Hiroaki Murakami ◽  
Reiji Masuda ◽  
Toshifumi Minamoto

2021 ◽  
Author(s):  
Naoto Shinohara ◽  
Yuki Hongo ◽  
Momoko Ichinokawa ◽  
Shota Nishijima ◽  
Shuhei Sawayama ◽  
...  

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.


Author(s):  
Lennart Schreiber ◽  
Gustavo Castellanos-Galindo ◽  
Mark Torchin ◽  
Karina Chavarria ◽  
Silke Laakmann ◽  
...  

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.


2021 ◽  
Vol 4 ◽  
Author(s):  
Giulia Riccioni ◽  
Isabelle Domaizon ◽  
Andrea Gandolfi ◽  
Massimo Pindo ◽  
Marine Vautier ◽  
...  

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.


Author(s):  
Ophélie Lebrasseur ◽  
◽  
Aurélie Manin ◽  

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.


2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Didier Pont ◽  
Mathieu Rocle ◽  
Alice Valentini ◽  
Raphaël Civade ◽  
Pauline Jean ◽  
...  

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