Evaluation of biodiversity metrics through environmental DNA metabarcoding compared with visual and capture surveys in river fish community

2019 ◽  
Author(s):  
Hideyuki Doi ◽  
Ryutei Inui ◽  
Shunsuke Matsuoka ◽  
Yoshihisa Akamatsu ◽  
Masuji Goto ◽  
...  
Keyword(s):  
Community Dynamics ◽  
Species Turnover ◽  
Environmental Dna ◽  
List Type ◽  
Visual Capture ◽  
Gamma Diversity ◽  
Community Patterns ◽  
Community Assemblages ◽  
Study Sites ◽  
River Fish

AbstractInformation on alpha (local), beta (between habitats), and gamma (regional) diversity is fundamental to understanding biodiversity as well as the function and stability of community dynamics. The methods like environmental DNA (eDNA) metabarcoding are currently considered useful to investigate biodiversity.We compared the performance of eDNA metabarcoding with visual and capture surveys in estimating alpha/gamma diversity and the variation of the community assemblages of river fish communities, particularly considering community nestedness and turnover.In five rivers across west Japan, with comparing to visual/capture surveys, eDNA metabarcoding detected more species in the study sites, consequently the overall number of species in the region (i.e., gamma diversity) was higher. In particular, the species found by visual/capture surveys were encompassed by those by eDNA metabarcoding.With analyzing the community assemblages between the rivers, we showed the different results between the both methods. While, in the same river, the nestedness and species turnover changing from upstream to downstream did not significantly differ between the both methods. Our results suggest that eDNA metabarcoding may be suitable method, especially for understanding regional community patterns, for fish monitoring in rivers.

scholarly journals Gamma-diversity partitioning of gobiid fishes (Teleostei: Gobiidae) ensemble along of Eastern Tropical Pacific: Biological inventory, latitudinal variation and species turnover

PLoS ONE ◽  
2018 ◽  
Vol 13 (8) ◽  
pp. e0202863 ◽  
Author(s):  
Omar Valencia-Méndez ◽  
Fabián Alejandro Rodríguez-Zaragoza ◽  
Luis Eduardo Calderon-Aguilera ◽  
Omar Domínguez-Domínguez ◽  
Andrés López-Pérez
Keyword(s):  
Species Turnover ◽  
Tropical Pacific ◽  
Latitudinal Variation ◽  
Eastern Tropical Pacific ◽  
Gamma Diversity ◽  
Diversity Partitioning ◽  
Biological Inventory

scholarly journals Taxonomic and Functional Response of Millipedes (Diplopoda) to Urban Soil Disturbance in a Metropolitan Area

Insects ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 25 ◽  
Author(s):  
Zsolt Tóth ◽  
Elisabeth Hornung
Keyword(s):  
Metropolitan Area ◽  
Species Turnover ◽  
Chemical Properties ◽  
Soil Disturbance ◽  
Danube River ◽  
Functional Responses ◽  
Β Diversity ◽  
Functional Richness ◽  
Study Sites ◽  
And Function

Urbanization, as a major cause of local species extinction and biotic homogenization, drastically alters soil life. Millipedes are a key group of soil macrodetritivores and significantly influence soil quality, mainly through their essential role in nutrient cycling. Therefore, studying their taxonomic and functional responses to urban disturbance is crucial, as they contribute to the provision of several soil-related ecosystem services in cities. Differently degraded rural, urban forests and other woody patches (e.g., parks, gardens, and cemeteries) were sampled on Buda and Pest sides of the Budapest metropolitan area divided by the Danube River. We measured the most relevant physical and chemical properties of topsoil to characterize habitats. We applied an urbanization index based on vegetation cover and built-up area of the study sites to quantify urban intensity. The composition of the assemblages was determined by the division of the city along the Danube. Urbanization was associated with a reduction in species and functional richness of millipedes on both sides of Budapest. β diversity and species turnover increased with urban intensity. Urban disturbance was the main driver in assembly of taxonomic and functional community composition. A new species (Cylindroiulus caeruleocinctus (Wood, 1864)) to the fauna of Budapest was found. Detritivore invertebrates depend on leaf litter and other dead organic matter types, therefore microsites providing these resources greatly improve their survival. Due to increasing urban disturbance, it is recommended to provide appropriate detritus and shelter sites as part of the management of green spaces in order to maintain species richness, abundance, and function of species.

Effects of a recent wildfire and clearcuts on ground-dwelling boreal forest spider assemblages

2005 ◽  
Vol 35 (11) ◽  
pp. 2575-2588 ◽  
Author(s):  
Maxim Larrivée ◽  
Lenore Fahrig ◽  
Pierre Drapeau
Keyword(s):  
Boreal Forest ◽  
Black Spruce ◽  
Species Turnover ◽  
Pitfall Traps ◽  
Gamma Diversity ◽  
Clear Cut ◽  
Forestry Practices ◽  
Disturbed Forest ◽  
Catch Rates ◽  
Web Building

Ground-dwelling spider (Araneae) assemblages were compared between recent clearcuts and burned black spruce (Picea mariana (Mill.) BSP) forests. Spiders were sampled using pitfall traps placed in 6 recently burned sites, 6 recently clear-cut sites, and 6 undisturbed sites in eastern Quebec, Canada. A total of 2935 individuals from 95 spider species were identified. Catch rates for hunting spiders were significantly higher in the clear-cut stands than in the burned stands, but between-stand species turnover of hunting spiders was twice as high in the burned stands as in the clear-cut stands. Web-building spiders had similar catch rates in the three stand types, but had the highest species turnover and gamma diversity in the undisturbed sites. Correspondence analysis showed that the composition of the spider assemblages varied among the three types of stands. Spider assemblages found in clearcuts were associated with environmental variables reflecting dry, open, disturbed forest floor, while assemblages found in burned stands were correlated with high percentages of shrub cover and dried moss–lichen substrate and deeper litter. We conclude that ground-living spider assemblages in boreal forest respond very differently to clearcuts and fires and we suggest modifications to present forestry practices to create disturbances that are more similar to wildfires.

Are brown trout replacing or displacing bull trout populations in a changing climate?

2016 ◽  
Vol 73 (9) ◽  
pp. 1395-1404 ◽  
Author(s):  
Robert Al-Chokhachy ◽  
David Schmetterling ◽  
Chris Clancy ◽  
Pat Saffel ◽  
Ryan Kovach ◽  
...  
Keyword(s):  
Brown Trout ◽  
Salmo Trutta ◽  
Species Turnover ◽  
Western Montana ◽  
Conservation Strategies ◽  
Bull Trout ◽  
Growth State ◽  
Population Growth Rates ◽  
Brown Trout Salmo Trutta ◽  
Study Sites

Understanding how climate change may facilitate species turnover is an important step in identifying potential conservation strategies. We used data from 33 sites in western Montana to quantify climate associations with native bull trout (Salvelinus confluentus) and non-native brown trout (Salmo trutta) abundance and population growth rates (λ). We estimated λ using exponential growth state-space models and delineated study sites based on bull trout use for either spawning and rearing (SR) or foraging, migrating, and overwintering (FMO) habitat. Bull trout abundance was negatively associated with mean August stream temperatures within SR habitat (r = −0.75). Brown trout abundance was generally highest at temperatures between 12 and 14 °C. We found bull trout λ were generally stable at sites with mean August temperature below 10 °C but significantly decreasing, rare, or extirpated at 58% of the sites with temperatures exceeding 10 °C. Brown trout λ were highest in SR and sites with temperatures exceeding 12 °C. Declining bull trout λ at sites where brown trout were absent suggest brown trout are likely replacing bull trout in a warming climate.

scholarly journals Sleeping-tree fidelity of the spider monkey shapes community-level seed-rain patterns in continuous and fragmented rain forests

2015 ◽  
Vol 31 (4) ◽  
pp. 305-313 ◽  
Author(s):  
Arturo González-Zamora ◽  
Víctor Arroyo-Rodríguez ◽  
Federico Escobar ◽  
Ken Oyama ◽  
Filippo Aureli ◽  
...  
Keyword(s):  
Forest Type ◽  
Species Turnover ◽  
Seed Rain ◽  
Spider Monkey ◽  
Community Level ◽  
Food Density ◽  
Frequency Of Use ◽  
Repeated Use ◽  
Fragmented Forests ◽  
Study Sites

Abstract:Repeated use of sleeping trees (STs) by frugivores promotes the deposition and aggregation of copious amounts of seed, thus having key implications for seed dispersal and forest regeneration. Seed-rain patterns produced by this behaviour likely depend on the frequency of use of these sites, yet this hypothesis has been poorly tested. We evaluated community-level seed-rain patterns produced by the spider monkey (Ateles geoffroyi) over 13 mo in latrines located beneath 60 STs in the Lacandona rain forest, Mexico. Because this primate is increasingly ‘forced’ to inhabit fragmented landscapes, we tested whether sleeping-tree fidelity (STF) differed among sites and between continuous and fragmented forests. We also tested whether seed-rain patterns were associated with STF within each site and forest type. STF was highly variable among STs (average = 7 mo, range = 1–12 mo), but did not differ among study sites or forest types. STF was positively associated with seed abundance, species diversity and species turnover. Nevertheless, STF tended to be negatively related to seed community evenness. These results are likely due to the most frequently used STs being in areas with greater food density. Our results demonstrate that site fidelity shapes community-level seed-rain patterns and thus has key ecological implications.

scholarly journals Frequency-dependent Maternal Effects across Species and Environments

2017 ◽  
Author(s):  
Rachel M. Germain ◽  
Tess N. Grainger ◽  
Natalie T. Jones ◽  
Benjamin Gilbert
Keyword(s):  
Maternal Effects ◽  
Life Histories ◽  
Community Dynamics ◽  
Seed Mass ◽  
List Type ◽  
Frequency Dependent ◽  
Competitive Environments ◽  
Maternal Provisioning ◽  
Population And Community Dynamics ◽  
Maternal Responses

SummaryMaternal provisioning of offspring in response to environmental conditions (“maternal environmental effects”) has been argued as ‘the missing link’ in plant life histories. Although empirical evidence suggests that maternal responses to abiotic conditions are common, there is little understanding of the prevalence of maternal provisioning in competitive environments.We tested how competition in two soil moisture environments affects maternal provisioning of offspring seed mass. Specifically, we varied conspecific frequency from 90% (intraspecific competition) to 10% (interspecific competition) for 15 pairs of annual plant species that occur in California.We found that conspecific frequency affected maternal provisioning (seed mass) in 48% of species, and that these responses included both increased (20%) and decreased (24%) seed mass. In contrast, 68% of species responded to competition through changes in per capita fecundity (seed number), which generally decreased as conspecific frequency increased. The direction and magnitude of frequency-dependent seed mass depended on the identity of the competitor, even among species in which fecundity was not affected by competitor identity.Synthesis. Our research demonstrates how species responses to different competitive environments manifest through maternal provisioning, and that these responses alter previous estimates of environmental maternal effects and reproductive output; future study is needed to understand their combined effects on population and community dynamics.

scholarly journals eDNA Captures Microhabitat Partitioning in a Kelp Forest Ecosystem

2021 ◽  
Author(s):  
Keira Monuki ◽  
Paul Barber ◽  
Zachary Gold
Keyword(s):  
Southern California ◽  
Surf Zone ◽  
Habitat Preferences ◽  
Kelp Forest ◽  
Environmental Dna ◽  
Marine Biodiversity ◽  
Rocky Reef ◽  
Temporal And Spatial Variability ◽  
Community Assemblages ◽  
Zone Sampling

Environmental DNA (eDNA) metabarcoding is an increasingly important tool for surveying biodiversity in marine ecosystems. However, the scale of temporal and spatial variability in eDNA signatures, and how this variation may impact eDNA-based marine biodiversity assessments, remains uncertain. To address this question, we systematically examined variation in vertebrate eDNA signatures across depth (0 m to 10 m) and horizontal space (nearshore and surf zone) over three successive days in a Southern California kelp forest. Across a broad range of marine vertebrates (teleosts, elasmobranchs, birds, and mammals), results showed significant variation in species richness and community assemblages across 4-5 m depth, reflecting microhabitat depth preferences of common Southern California nearshore rocky reef taxa. We also found significant differences in community assemblages between nearshore and surf zone sampling stations at the same depth, and across three sampling days. Patterns of microhabitat partitioning in eDNA signatures across space and time were largely consistent with known habitat preferences and species behavior. Results highlight the sensitivity of eDNA in capturing fine-scale vertical, horizontal, and temporal variation in marine vertebrate communities, demonstrating the ability of eDNA to capture a highly localized snapshot of marine biodiversity in dynamic coastal environments.

Sign in / Sign up

Export Citation Format

Share Document