scholarly journals Tackling inconsistencies among freshwater invertebrate trait databases: harmonising across continents and aggregating taxonomic resolution

2021 ◽  
Author(s):  
Stefan Kunz ◽  
Ben J. Kefford ◽  
Astrid Schmidt‐Kloiber ◽  
Christoph D. Matthaei ◽  
Philippe Usseglio‐Polatera ◽  
...  
Keyword(s):  
Taxonomic Resolution ◽  
Freshwater Invertebrate

scholarly journals Metabarcoding unsorted kick-samples facilitates macroinvertebrate-based biomonitoring with increased taxonomic resolution, while outperforming environmental DNA

2019 ◽  
Author(s):  
Lyndall Pereira-da-Conceicoa ◽  
Vasco Elbrecht ◽  
Andie Hall ◽  
Andrew Briscoe ◽  
Helen Barber-James ◽  
...  
Keyword(s):  
South Africa ◽  
Water Quality ◽  
Quality Assessment ◽  
Environmental Dna ◽  
Water Quality Assessment ◽  
Taxonomic Resolution ◽  
Freshwater Macroinvertebrates ◽  
Invertebrate Diversity ◽  
Freshwater Invertebrate ◽  
Three Rivers

AbstractMany studies have highlighted the potential of DNA-based methods for the biomonitoring of freshwater macroinvertebrates, however only a few studies have investigated homogenisation of bulk samples that include debris to reduce sample-processing time. In order to explore the use of DNA-based methods in water quality assessment in South Africa, this study compares morphological and molecular-based identification of freshwater macroinvertebrates at the mixed higher taxon and mOTU level while investigating abundance and comparing mOTU recovery with historical species records. From seven sites across three rivers in South Africa, we collected a biomonitoring sample, an intensive-search comprehensive sample and an eDNA sample per site. The biomonitoring sample was picked and scored according to standard protocols and the leftover debris and comprehensive samples were homogenised including all debris. DNA-based methods recovered higher diversity than morphology, but did not always recover the same taxa, even at the family level. Regardless of the differences in taxon scores, most DNA-based methods except some eDNA samples, returned the same water quality assessment category as the standard morphology-based assessment. Homogenised comprehensive samples recovered more freshwater invertebrate diversity than all other methods. The eDNA samples recovered 2 to 10 times more mOTUs than any other method, however 90% of reads were non-target and as a result eDNA recovered the lowest target diversity. However, eDNA did find some target taxa that the other methods failed to detect. This study shows that unsorted samples recover the same water quality scores as a morphology-based assessment and much higher diversity scores than both picked and eDNA samples. As a result, there is potential to integrate DNA-based approaches into existing metrics quickly while providing much more information for the development of more refined metrics at the species or mOTU level with distributional data which can be used for conservation and biodiversity management.

scholarly journals Testing the potential of a ribosomal 16S marker for DNA metabarcoding of insects

2016 ◽  
Author(s):  
Vasco Elbrecht ◽  
Pierre Taberlet ◽  
Tony Dejean ◽  
Alice Valentini ◽  
Philippe Usseglio-polatera ◽  
...  
Keyword(s):  
Species Level ◽  
Coi Gene ◽  
Taxonomic Resolution ◽  
Reference Database ◽  
Knowing That ◽  
Freshwater Invertebrate ◽  
Dna Metabarcoding ◽  
Local Reference ◽  
Comprehensive Survey ◽  
Reference Databases

Cytochrome c oxidase I (COI) is a powerful marker for DNA barcoding of animals, with good taxonomic resolution and a large reference database. However, when used for DNA metabarcoding, estimation of taxa abundances and species detection are limited due to primer bias caused by highly variable primer binding sites across the COI gene. Therefore, we explored the ability of the 16S ribosomal DNA gene as an alternative metabarcoding marker for species level assessments. Ten bulk samples, each containing equal amounts of tissue from 52 freshwater invertebrate taxa, were sequenced with the Illumina NextSeq 500 system. In comparison to COI, the 16S marker amplified more insect species and amplified more equally, probably due to decreased primer bias. Rough estimation of biomass might thus be less biased with 16S than with COI. According to these results, the marker choice depends on the scientific question. If the goal is to obtain a taxonomic identification at the species level, then COI is more appropriate due to established reference databases and known taxonomic resolution of this marker, knowing that a greater proportion of species will be missed using COI Folmer primers. If the goal is to obtain a more comprehensive survey in a context where it is possible to build a local reference database, the 16S marker could be more appropriate.

scholarly journals Testing the potential of a ribosomal 16S marker for DNA metabarcoding of insects

2016 ◽  
Author(s):  
Vasco Elbrecht ◽  
Pierre Taberlet ◽  
Tony Dejean ◽  
Alice Valentini ◽  
Philippe Usseglio-polatera ◽  
...  
Keyword(s):  
Species Level ◽  
Coi Gene ◽  
Taxonomic Resolution ◽  
Reference Database ◽  
Knowing That ◽  
Freshwater Invertebrate ◽  
Dna Metabarcoding ◽  
Local Reference ◽  
Comprehensive Survey ◽  
Reference Databases

Cytochrome c oxidase I (COI) is a powerful marker for DNA barcoding of animals, with good taxonomic resolution and a large reference database. However, when used for DNA metabarcoding, estimation of taxa abundances and species detection are limited due to primer bias caused by highly variable primer binding sites across the COI gene. Therefore, we explored the ability of the 16S ribosomal DNA gene as an alternative metabarcoding marker for species level assessments. Ten bulk samples, each containing equal amounts of tissue from 52 freshwater invertebrate taxa, were sequenced with the Illumina NextSeq 500 system. In comparison to COI, the 16S marker amplified more insect species and amplified more equally, probably due to decreased primer bias. Rough estimation of biomass might thus be less biased with 16S than with COI. According to these results, the marker choice depends on the scientific question. If the goal is to obtain a taxonomic identification at the species level, then COI is more appropriate due to established reference databases and known taxonomic resolution of this marker, knowing that a greater proportion of species will be missed using COI Folmer primers. If the goal is to obtain a more comprehensive survey in a context where it is possible to build a local reference database, the 16S marker could be more appropriate.

scholarly journals Community structure of aquatic insects (Ephemeroptera, Plecoptera, and Trichoptera) in Cerrado streams of Paraguay, Paraná, and São Francisco river basins

2013 ◽  
Vol 13 (1) ◽  
pp. 97-107 ◽  
Author(s):  
Renato de Mei Romero ◽  
Mônica Ceneviva-Bastos ◽  
Gustavo Henrique Baviera ◽  
Lilian Casatti
Keyword(s):  
Community Structure ◽  
Aquatic Insects ◽  
Regional Differences ◽  
River Basins ◽  
Taxonomic Composition ◽  
Taxonomic Resolution ◽  
Sao Francisco River ◽  
Original Distribution ◽  
São Francisco River

We evaluated qualitatively and quantitatively the community structure of aquatic insects (Ephemeroptera, Plecoptera, and Trichoptera) in 19 streams in areas of Cerrado in the Paraguay, Paraná, and São Francisco river basins. The number of genera and taxonomic composition were compared at spatial (at the hydrographic basins level) and conservation levels (more preserved and less preserved areas). The influence of spatial and environmental factors in richness and abundance was also evaluated. The geographical distribution of Grumicha, Coryphorus, and Austrotinodes was expanded. The highest Trichoptera richness was found in the São Francisco river basin (F = 5,602, p = 0,004) and a higher number of Ephemeroptera genera occurred in the relatively less preserved sites (F = 6,835, p = 0,009). The pattern of genera distribution was different among basins (R = 0,0336, p = 0,001), but it was similar among relatively less and more preserved areas (R = -0,039, p = 0,737). These findings can be explained by the low impact level in these streams and also by the taxonomic resolution used in this study. Latitude and instream diversity were the most important factors to explain the variation in genera richness and abundance (p = 0.004 and p = 0.026, respectively). Hence, the regional differences can be attributed to spatial influences, quantity or quality of habitats and the original distribution of taxa within each basin.

scholarly journals Comparing the performance of different stream classification systems using aquatic macroinvertebrates

2013 ◽  
Vol 25 (4) ◽  
pp. 406-417 ◽  
Author(s):  
Márlon de Castro Vasconcelos ◽  
Adriano Sanches Melo ◽  
Albano Schwarzbold
Keyword(s):  
Randomization Test ◽  
Classification Systems ◽  
Data Type ◽  
Taxonomic Resolution ◽  
Stream Classification ◽  
Environment Variables ◽  
Family Level ◽  
Community Data ◽  
Performance Results ◽  
Classification Strength

AIM: We evaluated five stream classification systems observing: 1) differences in richness, abundance and macroinvertebrates communities among stream classes within classification systems; and 2) whether classification systems present better performance using macroinvertebrates. Additionally, we evaluated the effects of taxonomic resolution and data type (abundance and presence) on results. METHODS: Five stream classification systems were used, two based on hydroregions, one based on ecoregions by FEOW, a fourth one based on stream orders and the last one based on clusters of environment variables sampled in 37 streams at Rio Grande do Sul state, Brazil. We used a randomization test to evaluate differences of richness and abundance, a db-MANOVA to evaluate the differences of species assemblages and Classification Strength (CS) to evaluate the classifications performance. RESULTS: There were differences of richness and abundance among stream classes within each stream classification. The same result was found for community data, except for stream order classifications in family level. We observed that stream classes obtained for each stream classification differed in terms of environment variables (db-MANOVA). The classification based on environment variables showed higher CS values than other classification systems. The taxonomic resolution was important to the observed results. Data on genera level presented CS values 12% higher than family level for cluster classification, and the data type was dependent on the classification system and taxonomic resolution employed. CONCLUSION: Our results indicate that classifications based on cluster of environment variables was better than other stream classification systems, and similar results using genera level can be obtained for management programs using family resolution in a geographical context similar to this study.

scholarly journals Taxonomic Resolution of the Nematophagous Fungal Isolate ARF18 via Genome Sequencing

2017 ◽  
Vol 5 (34) ◽  
Author(s):  
Sandeep Sharma ◽  
Alex Z. Zaccaron ◽  
John B. Ridenour ◽  
Amy Bradshaw ◽  
Terry L. Kirkpatrick ◽  
...  
Keyword(s):  
Soybean Cyst Nematode ◽  
Heterodera Glycines ◽  
Novel Species ◽  
Biological Control Agent ◽  
Draft Genome ◽  
Control Agent ◽  
Nematophagous Fungus ◽  
Cyst Nematode ◽  
Fungal Isolate ◽  
Taxonomic Resolution

ABSTRACT The taxonomically uncharacterized nematophagous fungus ARF18, which parasitizes cysts, juveniles, and adults of the soybean cyst nematode (Heterodera glycines), was proposed as a nematode biological control agent in 1991. A 46.3-Mb draft genome sequence of this fungus is presented, and a tentative taxonomic identification as a novel species of Brachyphoris is proposed.

scholarly journals The use of DNA barcodes in food web construction—terrestrial and aquatic ecologists unite!

Genome ◽  
2016 ◽  
Vol 59 (9) ◽  
pp. 603-628 ◽  
Author(s):  
Tomas Roslin ◽  
Sanna Majaneva
Keyword(s):  
Food Web ◽  
Food Webs ◽  
Taxonomic Resolution ◽  
Dna Barcodes ◽  
Food Web Structure ◽  
Web Studies ◽  
Web Structure ◽  
Asking Questions ◽  
Web Construction ◽  
Interaction Webs

By depicting who eats whom, food webs offer descriptions of how groupings in nature (typically species or populations) are linked to each other. For asking questions on how food webs are built and work, we need descriptions of food webs at different levels of resolution. DNA techniques provide opportunities for highly resolved webs. In this paper, we offer an exposé of how DNA-based techniques, and DNA barcodes in particular, have recently been used to construct food web structure in both terrestrial and aquatic systems. We highlight how such techniques can be applied to simultaneously improve the taxonomic resolution of the nodes of the web (i.e., the species), and the links between them (i.e., who eats whom). We end by proposing how DNA barcodes and DNA information may allow new approaches to the construction of larger interaction webs, and overcome some hurdles to achieving adequate sample size. Most importantly, we propose that the joint adoption and development of these techniques may serve to unite approaches to food web studies in aquatic and terrestrial systems—revealing the extent to which food webs in these environments are structured similarly to or differently from each other, and how they are linked by dispersal.

Contrasting patterns of genetic structure and disequilibrium in populations of a stone-cased caddisfly (Tasimiidae) from northern and southern Australia

2008 ◽  
Vol 59 (3) ◽  
pp. 235 ◽  
Author(s):  
Alicia Slater Schultheis ◽  
Richard Marchant ◽  
Jane Margaret Hughes
Keyword(s):  
Genetic Structure ◽  
Genetic Differentiation ◽  
Adult Emergence ◽  
Conclusive Evidence ◽  
Emergence Patterns ◽  
Freshwater Invertebrate ◽  
Gene Coi ◽  
Hardy Weinberg Equilibrium ◽  
New Recruits ◽  
Genetic Patchiness

In marine and freshwater invertebrate populations, microscale genetic differentiation or ‘genetic patchiness’ is thought to result from variation in the abundance and genetic composition of new recruits at a particular location. In the present study, the role of the adult emergence patterns in genetic patchiness was examined using mtDNA and two microsatellite loci to compare patterns of genetic differentiation in asynchronously (subtropical) and synchronously emerging (temperate) populations of the stone-cased caddisfly Tasimia palpata. A 550 base pair region of the mitochondrial cytochrome c oxidase subunit I gene (COI) was sequenced in at least 14 individuals from each population. Genetic structure was detected only at the reach scale in the subtropical populations and no genetic differentiation was detected in temperate populations. There were more deviations from Hardy–Weinberg equilibrium (HWE) in subtropical populations than in temperate populations where 44% and 12.5%, respectively, of tests for deviations from HWE were significant. Although distinct patterns of genetic structure and deviations from HWE were observed in the subtropical and temperate populations of T. palpata, no conclusive evidence was found to suggest that the differences are caused by differences in emergence patterns. We hypothesise that genetic patchiness must be caused by post-recruitment processes, most likely the preservation of oviposition ‘hotspots’ in subtropical streams.

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