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.

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 INTERAKSI TROFIK KOMUNITAS IKAN DI DANAU MATANO, SULAWESI SELATAN PASCA BERKEMBANGNYA IKAN ASING INVASIF

2019 ◽  
Vol 25 (2) ◽  
pp. 117
Author(s):  
Dimas Angga Hedianto ◽  
Agus Arifin Sentosa
Keyword(s):  
Fish Species ◽  
Native Species ◽  
Fish Community ◽  
Feeding Strategy ◽  
Food Resources ◽  
Native Fish ◽  
Natural Food ◽  
Lake Matano ◽  
Alien Fish ◽  
Alien Fish Species

Interaksi trofik pasca masuknya ikan introduksi ataupun ikan asing invasif merupakan dasar untuk mengkaji tekanan ekologis terhadap ikan asli. Penelitian ini bertujuan untuk menganalisis interaksi trofik komunitas ikan pasca berkembangnya jenis-jenis ikan asing invasif di Danau Matano, Sulawesi Selatan. Ikan contoh diperoleh dari hasil tangkapan jaring insang percobaan, jala lempar, dan seser pada Mei, Oktober, dan November 2015 serta Februari, Juli, dan September 2016. Analisis ekologi trofik yang dilakukan meliputi indeks bagian terbesar, tingkat trofik, luas relung dan tumpang tindih relung makanan, serta pola strategi makan. Hasil penelitian menunjukkan komunitas ikan yang tertangkap di Danau Matano terdiri atas 9 famili, 11 genera, dan 17 spesies. Ikan louhan mendominasi komunitas ikan di Danau Matano sebesar 53,62%. Makanan alami yang banyak dimanfaatkan oleh sejumlah ikan dalam komunitas adalah insekta (Diptera), Gastropoda (Tylomelania sp.), dan larva insekta (Chironomidae). Kelompok trofik komunitas ikan di Danau Matano terdiri atas detritivora, herbivora, insektivora, zoobentivora, dan piscivora. Masuknya ikan introduksi memunculkan kelompok trofik baru (detritivora dan herbivora). Ikan introduksi cenderung memiliki luas relung makanan yang lebih bervariasi. Kompetisi terhadap makanan alami kategori moderat banyak terjadi antara ikan asli dengan louhan. Strategi pola makan ikan asli di Danau Matano cenderung bersifat spesialis, sedangkan ikan introduksi memiliki strategi pola makan yang lebih bervariasi dan oportunistik. Ikan louhan sebagai ikan introduksi dominan yang bersifat invasif mampu memanfaatkan seluruh sumber daya makanan alami yang tersedia dan menempati tingkat trofik tertinggi di Danau Matano. Tekanan ekologi terhadap ikan asli oleh ikan asing invasif di Danau Matano terjadi karena adanya kompetisi terhadap makanan alami.Trophic interactions post-develpment of non-native fish or invasive alien fish species are the basis knowledge for assessing and preventing the ecological pressure on native fish. This research aims to analyze the trophic interactions of fish community post-development of invasive alien fish species in Lake Matano, South Sulawesi. Fish samples were obtained from the catch of experimental gill nets, cast nets, and push nets in May, October, and November 2015 along with February, July, and September 2016. Trophic ecological analysis carried out included index of preponderance, trophic level, niche breadth and niche overlap of natural food, and feeding strategy. The fish community caught in Lake Matano consists of 9 families, 11 genera, and 17 species. Flowerhorn cichlid dominates the fish community in Lake Matano by 53.62%. Natural foods that are widely used by a number of fish in the community are Insecta (Diptera), Gastropods (Tylomelania sp.), and larvae of Insecta (Chironomidae). The guild trophic of fish community in Lake Matano consists of detritivores, herbivores, insectivores, zoobentivores, and piscivores. The introduction of non-native species bring up to new guilds (detritivores and herbivores). Non-native fishes tends to have a variety niche breadth. Moderate competition for natural food resources between native fish and flowerhorn cichlid is quite high. Feeding strategy of native species in Lake Matano tend to be specialist, while non-natives species have more variety and opportunistic. Flowerhorn cichlid as dominant invasive alien fish species is able to utilize all natural food resources and occupies the highest trophic level in Lake Matano. Ecological pressure on native fish by invasive alien fish species in Lake Matano occurs due to competition in obtaining natural food resources.

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 Environmental DNA metabarcoding reveals and unpacks a biodiversity conservation paradox in Mediterranean marine reserves

2021 ◽  
Vol 288 (1949) ◽  
Author(s):  
Emilie Boulanger ◽  
Nicolas Loiseau ◽  
Alice Valentini ◽  
Véronique Arnal ◽  
Pierre Boissery ◽  
...  
Keyword(s):  
Species Richness ◽  
Fish Species ◽  
Fish Assemblages ◽  
Marine Reserves ◽  
Marked Change ◽  
Environmental Dna ◽  
Biodiversity Loss ◽  
Conclusive Evidence ◽  
Anthropogenic Pressure ◽  
Local Species Richness

Although we are currently experiencing worldwide biodiversity loss, local species richness does not always decline under anthropogenic pressure. This conservation paradox may also apply in protected areas but has not yet received conclusive evidence in marine ecosystems. Here, we survey fish assemblages in six Mediterranean no-take reserves and their adjacent fishing grounds using environmental DNA (eDNA) while controlling for environmental conditions. We detect less fish species in marine reserves than in nearby fished areas. The paradoxical gradient in species richness is accompanied by a marked change in fish species composition under different managements. This dissimilarity is mainly driven by species that are often overlooked by classical visual surveys but detected with eDNA: cryptobenthic, pelagic, and rare fishes. These results do not negate the importance of reserves in protecting biodiversity but shed new light on how under-represented species groups can positively react to fishing pressure and how conservation efforts can shape regional biodiversity patterns.

scholarly journals Ichthyofauna of the Mata de Itamacaoca, an urban protected area from the upper Munim River basin, Northern Brazilian Cerrado

2020 ◽  
Vol 20 (4) ◽  
Author(s):  
Elioenai da Silva Oliveira ◽  
Erick Cristofore Guimarães ◽  
Pâmella Silva de Brito ◽  
Lucas de Oliveira Vieira ◽  
Rafael Ferreira de Oliveira ◽  
...  
Keyword(s):  
Species Richness ◽  
River Basin ◽  
Fish Species ◽  
Fish Community ◽  
Linear Models ◽  
Anthropogenic Impacts ◽  
Sampling Site ◽  
Abundant Species ◽  
Diversity Indices ◽  
Alien Invasive Species

Abstract: The Munim River basin is one of the main river drainages of the Hydrological unit Maranhão, but there are few published studies which focus on ichthyological surveys and taxonomic work within this basin. The present study aims to provide a fish species inventory of the Mata da Itamacaoca, one of the few urban protected areas from the upper Munim River basin, comparing the ichthyofauna with other lists by conducted at the upper Munim River basin. A total of 42 collection expeditions were conducted, the sampling was conducted at five collecting sites distributed within the boundaries of Mata de Itamacaoca, upper Munim River basin. Diversity indices were calculated and generalised linear models (GLMs) were employed to assess differences in species richness, diversity and evenness depending on season and location in relation to the reservoir dam wall. In order to visualize fish community differences, non-metric multidimensional scaling (nMDS) and a one-way PERMANOVA was used to understand whether factors of site, season and location to the dam wall had an effect on fish community compositions. A total of six orders, 13 families, and 23 fish species were found, and the order with the highest species richness, considering all reaches, was Characiformes followed by Cichliformes. The most abundant species was Nannostomus beckfordi, while Pimelodella parnahybae and Hoplerythrinus unitaeniatus were the rarer species sampled. There were no alien invasive species collected within the study area. Species richness was significantly higher below the dam wall, but there were no other significant differences in diversity indices with regards to season or location. Fish community composition was significantly different above and below the dam wall and was significantly affected by sampling site. Season did not have an effect on fish community. This study corroborates other studies conducted in the Unidade Hidrológica Maranhão sensu Hubbert and Renno (2006), that the ichthyofaunal composition and taxonomy of species within this region face major data deficits, anthropogenic impacts, this study may be a baseline for comparing similar environments throughout the region.

scholarly journals Macroecology of fish community biomass – size structure: effects of invasive species and river regulation

2019 ◽  
Vol 76 (1) ◽  
pp. 109-122 ◽  
Author(s):  
R. Keller Kopf ◽  
Paul Humphries ◽  
Nick R. Bond ◽  
Neil C. Sims ◽  
Robyn J. Watts ◽  
...  
Keyword(s):  
Invasive Species ◽  
Body Mass ◽  
Common Carp ◽  
Fish Community ◽  
Trophic Ecology ◽  
River Flow ◽  
Native Fish ◽  
Fish Biomass ◽  
Scaling Exponent ◽  
Mass Scaling

The biomass of organisms of different sizes is increasingly being used to explore macroscale variation in food-web and community structure. Here we examine how invasive species and river flow regulation affect native fish biomass and fish community log10 biomass – body mass scaling relationships in Australia’s largest river system, the Murray–Darling. The log10 biomass – body mass scaling exponent (scaling B) of invasive fishes (95% CI: −0.14 to −0.18) was less negative than for native fishes (95% CI: −0.20 to −0.25), meaning that invasive species attained a higher biomass in larger size-classes compared to native species. Flow alteration and invasive common carp (Cyprinus carpio) biomass were correlated with severe reductions in native fish biomass ranging from −47% to −68% (95% CI). Our study provides novel evidence suggesting that invasive and native communities have different biomass – body mass scaling patterns, which likely depend on differences in their trophic ecology and body size distributions. Our results suggest that restoration efforts using environmental flows and common carp control has potential to boost native fish biomass to more than double the current level.

Mangroves as Fish Habitat

2015 ◽  
Keyword(s):  
Water Quality ◽  
Particle Size ◽  
Species Richness ◽  
Fish Species ◽  
Fish Community ◽  
Spatial Scales ◽  
Quality Parameters ◽  
Habitat Characteristics ◽  
Fish Community Structure ◽  
Simultaneous Assessment

<em>Abstract</em>.—Three adjacent tidal creek systems (Page, Kemps, and Broad creeks) on Cape Eleuthera, The Bahamas were studied to quantify the variation in fish community structure and habitat characteristics over small (<5 km) spatial scales. Snorkeling transects were used to census the fish community on a summer new moon during slack high tide and involved the simultaneous assessment of each creek and each zone within the creek (i.e., mouth, middle, and upper) replicated over three consecutive days. The simultaneous assessment (involving large teams) was done to enable direct comparison without spatial sampling being confounded by time. Habitat assessments included measurements of water quality parameters, sediment sampling, and vegetation surveys. Despite their close proximity, creeks differed in both fish community structure and habitat characteristics. Broad Creek had the greatest fish species richness (<em>n </em>= 15), followed by Kemps Creek (<em>n </em>= 14) and Page Creek (<em>n </em>= 10). Mangrove habitats had significantly greater fish species diversity in Broad Creek while sea grass habitats resulted in higher species richness in Page Creek, relative to other habitat types. Mangrove and algal plain habitats had the highest fish species diversity in Kemps Creek. Within creeks, fish abundance was dependent on zonation, with the largest number of fish being found in creek mouths compared to upper sections. Water quality parameters (i.e., temperature, dissolved oxygen, and salinity) differed among the creeks, presumably reflecting creek morphology. Out of the 10 different species of vegetation observed, 60% were found in all tidal creeks. Coarse sand was the predominant particle size for all creeks, with variation in the second most abundant particle size between Page Creek and the others. This study reveals the great heterogeneity of tidal creek fish community and habitat characteristics and illustrates that conservation and management strategies along with monitoring programs must recognize the variation that can occur among and within coastal creeks over relatively small spatial scales.

Influence of Tributary Spatial Position on the Structure of Warmwater Fish Communities

1992 ◽  
Vol 49 (4) ◽  
pp. 671-681 ◽  
Author(s):  
Lewis L. Osborne ◽  
Michael J. Wiley
Keyword(s):  
Species Richness ◽  
Community Structure ◽  
Fish Species ◽  
Fish Community ◽  
Fish Communities ◽  
Drainage Area ◽  
Physical Habitat ◽  
Drainage Network ◽  
Fish Community Structure ◽  
Stream Size

We found a significant and positive relationship between fish species richness and four measures of stream size (drainage area, stream order, link magnitude, and downstream link) in three Illinois drainage basins. Downstream link (incorporating both stream size and size of stream at the next downstream confluence) explained the greatest portion of the variance. This suggests that downstream processes significantly influence the structure of fish communities inhabiting warmwater streams. Significantly higher numbers of fish species were collected from tributary streams (< 259 km2 drainage area) located lower in a drainage network and connected to a main channel system than from similarly sized streams located in the headwaters of a drainage network. The difference in species richness among station treatments was not due to a difference in the number of individuals collected among treatments. We were unable to accept or reject the hypothesis that differences in fish species richness were due to differences in physical habitat. The immigration–extinction hypothesis appears to provide a plausible explanation for the observed pattern in fish community structure within a drainage. The location of a stream channel within a network may provide a general template for fish community structure in warmwater drainages by regulating potential species richness.

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