scholarly journals Characterizing the spatial signal of environmental DNA in river systems using a community ecology approach

2020 ◽  
Author(s):  
Isabel Cantera ◽  
Jean-Baptiste Decotte ◽  
Tony Dejean ◽  
Jérôme Murienne ◽  
Régis Vigouroux ◽  
...  
Keyword(s):  
General Pattern ◽  
Fish Fauna ◽  
Species Distributions ◽  
Environmental Dna ◽  
Spatial Distance ◽  
Community Similarity ◽  
River Systems ◽  
Detection Distance ◽  
Local Species ◽  
Species Similarity

AbstractEnvironmental DNA (eDNA) is gaining a growing popularity among scientists but its applicability to biodiversity research and management remain limited in river systems by the lack of knowledge about the spatial extent of the downstream transport of eDNA. Up to now, attempts to measure eDNA detection distance compared known species distributions to eDNA results, limiting therefore studies to a few intensively studied rivers. Here we developed a framework to measure the detection distance of eDNA in rivers based on the comparison of faunas across an increasing range of spatial extents, making it independent from knowledge on species distributions. We hypothesized that under short detection distance the similarity between fish faunas should peak between nearby sites, whereas under long detection distance each site should cumulate species from a large upstream area. Applying this framework to the fish fauna of two large and species rich Neotropical river basins (Maroni and Oyapock), we show that fish eDNA detection distance did not exceed a few kilometers. eDNA hence provided inventories of local species communities. Those results were validated by retrieving the distance decay of species similarity, a general pattern in ecology based on the decline of local species community similarity with spatial distance between them. We finally compared species distribution derived from eDNA to the known distribution of the species based on capture data, and this comparison also confirmed a global match between methods, testifying for a short distance of detection of the fauna by eDNA.

scholarly journals Growth responses to soil water potential indirectly shape local species distributions of tropical forest seedlings

2018 ◽  
Author(s):  
Stefan J. Kupers ◽  
Bettina M. J. Engelbrecht ◽  
Andrés Hernández ◽  
S. Joseph Wright ◽  
Christian Wirth ◽  
...  
Keyword(s):  
Tropical Forest ◽  
Water Potential ◽  
Soil Water ◽  
Soil Water Potential ◽  
Species Distributions ◽  
Growth Responses ◽  
Local Species

scholarly journals Characterizing the spatial signal of environmental DNA in river systems using a community ecology approach

2021 ◽  
Author(s):  
Isabel Cantera ◽  
Jean‐Baptiste Decotte ◽  
Tony Dejean ◽  
Jérôme Murienne ◽  
Régis Vigouroux ◽  
...  
Keyword(s):  
Community Ecology ◽  
Environmental Dna ◽  
River Systems

The predicted effects of climate change on local species distributions around Beijing, China

2019 ◽  
Vol 31 (5) ◽  
pp. 1539-1550 ◽  
Author(s):  
Lichun Mo ◽  
Jiakai Liu ◽  
Hui Zhang ◽  
Yi Xie
Keyword(s):  
Climate Change ◽  
Species Distributions ◽  
Local Species ◽  
Beijing China

scholarly journals Characterization of artisanal fisheries in Nepal and potential implications for the conservation and management of Ganges River Dolphin (Platanista gangetica gangetica)

2015 ◽  
Author(s):  
Shambhu Paudel ◽  
Juan C Levesque ◽  
Camilo Saavedra ◽  
Cristina Pita ◽  
Prabhat Pal
Keyword(s):  
Anthropogenic Activities ◽  
Fishing Effort ◽  
Main Channel ◽  
Artisanal Fisheries ◽  
Ganges River ◽  
River Systems ◽  
River Dolphin ◽  
Main River ◽  
Local Species ◽  
The Ganges

The Ganges River dolphin (Platanista gangetica gangetica) (GRD) is classified as one of the most endangered of all cetaceans in the world and the second scarcest freshwater cetacean. The population is estimated to be less than 2,000 individuals. In Nepal’s Narayani, Sapta Koshi, and Karnali river systems, survival of GRD continues to be threatened by various anthropogenic activities, such as dam construction and interactions with artisanal fisheries. A basic description of the geographic scope, economics, and types of gear used in these fisheries would help managers understand the fishery-dolphin interaction conflict and assist with developing potential solutions to reduce interactions between GRD and local fisheries in Nepal. The main purpose of the study was to collect fishery and socio-economic information by conducting interviews with local fishermen in the Narayani, Sapta Koshi, and Karnali river systems. Based on interviews (n = 163), 79 percent of Nepalese fishermen indicated fishing for local species (e.g., mullet [Rhinomugil corsula] or siloroid catfish [Bagarius bagarius]) was their primary form of income. Fishermen reported fishing effort was greater in summer than winter; greatest in the afternoon (1430 hrs ± 0.27) and during low water level conditions; and gear was set 4.8 ± 0.2 days/week. Fishermen reported using eight different types of monofilament nets (gillnets and cast nets). Sixty percent used gillnets less than 10 m long, and less than one third preferred gillnets between 10 and 100 m long; a few used gillnets longer than 100 m. Fishermen usually set their gear close to their village, and about 50 percent preferred to fish in tributaries followed by the main channel behind sandbars and islands, and the main channel near a bank. Fishermen reported seeing more GRD in the main river stem in winter. In summer, fishermen spotted more GRD in tributaries. Most fishermen told us they believed education, awareness, and changing occupations were important for GRD conservation, but they indicated that occupational options were currently limited in Nepal. Nepalese fishermen acknowledged that fisheries posed a risk to GRD, but they believed water pollution, and dam/irrigation development were the greatest threats.

scholarly journals Using eDNA to biomonitor the fish community in a tropical oligotrophic lake

2018 ◽  
Author(s):  
Martha Valdez-Moreno ◽  
Natalia V. Ivanova ◽  
Manuel Elías-Gutiérrez ◽  
Stephanie L. Pedersen ◽  
Kyrylo Bessonov ◽  
...  
Keyword(s):  
Aquatic Ecosystems ◽  
Fish Community ◽  
Fish Fauna ◽  
Environmental Dna ◽  
Reference Sequence ◽  
Coi Gene ◽  
Ion Torrent ◽  
Sequence Database ◽  
Ion Torrent Pgm ◽  
Invasive Fishes

AbstractEnvironmental DNA (eDNA) is an effective approach for detecting vertebrates and plants, especially in aquatic ecosystems, but prior studies have largely examined eDNA in cool temperate settings. By contrast, this study employs eDNA to survey the fish fauna in tropical Lake Bacalar (Mexico) with the additional goal of assessing the possible presence of invasive fishes, such as Amazon sailfin catfish. Sediment and water samples were collected from eight stations in Lake Bacalar on three occasions over a 4-month interval. Each sample was stored in the presence or absence of lysis buffer to compare eDNA recovery. Short fragments (184-187 bp) of the cytochrome c oxidase I (COI) gene were amplified using fusion primers and then sequenced on Ion Torrent PGM and S5 before their source species were determined using a custom reference sequence database constructed on BOLD. In total, eDNA sequences were recovered from 75 species of vertebrates including 47 fishes, 15 birds, 7 mammals, 5 reptiles, and 1 amphibian. Although all species are known from this region, 6 fish species represent new records for the study area, while 2 require verification. Sequences for five species (2 birds, 2 mammals, 1 reptile) were only detected from sediments, while sequences from 52 species were only recovered from water. Because DNA from the Amazon sailfin catfish was not detected, we used a mock eDNA experiment to confirm our methods were appropriate for its detection. We developed protocols that enabled the recovery of eDNA from tropical oligotrophic aquatic ecosystems, and confirmed their effectiveness in detecting diverse species of vertebrates including an invasive species of Amazon catfish.

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 Integrated field, laboratory, and theoretical study of PKD spread in a Swiss prealpine river

2017 ◽  
Vol 114 (45) ◽  
pp. 11992-11997 ◽  
Author(s):  
Luca Carraro ◽  
Enrico Bertuzzo ◽  
Lorenzo Mari ◽  
Inês Fontes ◽  
Hanna Hartikainen ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Lethal Effect ◽  
High Water ◽  
Disease Prevalence ◽  
Environmental Drivers ◽  
Waterborne Diseases ◽  
Infection Dynamics ◽  
Local Species ◽  
Tetracapsuloides Bryosalmonae ◽  
Seasonal Population

Proliferative kidney disease (PKD) is a major threat to wild and farmed salmonid populations because of its lethal effect at high water temperatures. Its causative agent, the myxozoanTetracapsuloides bryosalmonae, has a complex lifecycle exploiting freshwater bryozoans as primary hosts and salmonids as secondary hosts. We carried out an integrated study of PKD in a prealpine Swiss river (the Wigger). During a 3-year period, data on fish abundance, disease prevalence, concentration of primary hosts’ DNA in environmental samples [environmental DNA (eDNA)], hydrological variables, and water temperatures gathered at various locations within the catchment were integrated into a newly developed metacommunity model, which includes ecological and epidemiological dynamics of fish and bryozoans, connectivity effects, and hydrothermal drivers. Infection dynamics were captured well by the epidemiological model, especially with regard to the spatial prevalence patterns. PKD prevalence in the sampled sites for both young-of-the-year (YOY) and adult brown trout attained 100% at the end of summer, while seasonal population decay was higher in YOY than in adults. We introduce a method based on decay distance of eDNA signal predicting local species’ density, accounting for variation in environmental drivers (such as morphology and geology). The model provides a whole-network overview of the disease prevalence. In this study, we show how spatial and environmental characteristics of river networks can be used to study epidemiology and disease dynamics of waterborne diseases.

scholarly journals Fast processing of environmental DNA metabarcoding sequence data using convolutional neural networks

2021 ◽  
Author(s):  
Benjamin Flück ◽  
Laëtitia Mathon ◽  
Stéphanie Manel ◽  
Alice Valentini ◽  
Tony Dejean ◽  
...  
Keyword(s):  
Neural Networks ◽  
Convolutional Neural Networks ◽  
Environmental Changes ◽  
Sequence Data ◽  
Mitochondrial Gene ◽  
Fish Fauna ◽  
Environmental Dna ◽  
Small Region ◽  
Anthropogenic Pressures ◽  
Speed And Accuracy

The intensification of anthropogenic pressures have increased consequences on biodiversity and ultimately on the functioning of ecosystems. To monitor and better understand biodiversity responses to environmental changes using standardized and reproducible methods, novel high-throughput DNA sequencing is becoming a major tool. Indeed, organisms shed DNA traces in their environment and this "environmental DNA" (eDNA) can be collected and sequenced using eDNA metabarcoding. The processing of large volumes of eDNA metabarcoding data remains challenging, especially its transformation to relevant taxonomic lists that can be interpreted by experts. Speed and accuracy are two major bottlenecks in this critical step. Here, we investigate whether convolutional neural networks (CNN) can optimize the processing of short eDNA sequences. We tested whether the speed and accuracy of a CNN are comparable to that of the frequently used OBITools bioinformatic pipeline. We applied the methodology on a massive eDNA dataset collected in Tropical South America (French Guiana), where freshwater fishes were targeted using a small region (60pb) of the 12S ribosomal RNA mitochondrial gene. We found that the taxonomic assignments from the CNN were comparable to those of OBITools, with high correlation levels and a similar match to the regional fish fauna. The CNN allowed the processing of raw fastq files at a rate of approximately 1 million sequences per minute which was ~150 times faster than with OBITools. Once trained, the application of CNN to new eDNA metabarcoding data can be automated, which promises fast and easy deployment on the cloud for future eDNA analyses.

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