Cryptic biodiversity in streams: a comparison of macroinvertebrate communities based on morphological and DNA barcode identifications

Jackson, John K.; Battle, Juliann M.; White, Bryan P.; Pilgrim, Erik M.; Stein, Eric D.; Miller, Peter E.; Sweeney, Bernard W.

doi:10.1086/675225

Cited by 91Freshwater macroinvertebrate diversity and ecologyEnvironmental DNA in Biodiversity StudiesInvertebrate Taxonomy and Ecology

Cryptic biodiversity in streams: a comparison of macroinvertebrate communities based on morphological and DNA barcode identifications

Jackson, John K., Battle, Juliann M., White, Bryan P., Pilgrim, Erik M., Stein, Eric D., Miller, Peter E., Sweeney, Bernard W.·2014·Freshwater Science

DOI 10.1086/675225

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Abstract

Species-level identifications are difficult or impossible for many larval aquatic macroinvertebrates. We described the taxonomic composition of macroinvertebrate communities from 5 coastal streams in 3 neighboring catchments in southern California. We compared taxonomic identifications based on deoxyribonucleic acid (DNA) barcoding (cytochrome c oxidase subunit I [COI]) with morphological identifications of the same specimens. We examined 5870 individuals, and barcodes with sequence lengths >350 base pairs (bp) for 91% of those specimens. We used the naturally occurring gaps in divergence frequencies for each order (usually 2% level of genetic divergence) to delimit putative species for all taxonomic groups except Simulium (3%) and Baetis (1%). We identified 200 species across these 5 streams. We identified 104 more species via barcodes than via morphology (200 vs 96, a 108% increase). Richness increases were greatest for Chironomidae (60 more species), Ephemeroptera (10 species), Acari (10 species), and Trichoptera (6 species). Forty-five percent of the genera/species identified morphologically represented >2 species. Many (86) species identified with barcodes were represented by only 1 or 2 specimens and were found at only 1 stream. Thus, species rarity (either spatially or numerically) appears to be a common characteristic of these streams. Barcoding increased total richness at each site by 12 to 40 taxa over morphology alone, and increased the difference between reference and impact sites in terms of lost taxa. These results suggest that macroinvertebrate biodiversity in streams has been underestimated substantially in the past, as has the biodiversity lost in response to environmental stress. The potential of DNA barcoding will not be fully realized until we can assign traits, such as habitat preference, ecological function, and pollution tolerance, at the species level.

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Several studies show that DNA-based assessments are superior to morphological assessments in freshwater ecosystems.
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Harvey, L. E., Geraci, C. J., Robinson, J. L., Morse, J. C., Kjer, K. M., & Zhou, X. Y. (2012) · Terrestrial Arthropod Reviews · doi:10.1163/187498312x649512 · Cited by 6 · see citing works

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Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol
Elbrecht, V., & Leese, F. (2015) · PLOS ONE · doi:10.1371/journal.pone.0130324 · Cited by 765 · see citing works
Macroinvertebrates as Biotic Indicators of Environmental Quality
Carter, J. L., Resh, V. H., & Hannaford, M. J. (2017) · Elsevier eBooks · doi:10.1016/b978-0-12-813047-6.00016-4 · Cited by 213 · see citing works
Large-Scale Biomonitoring of Remote and Threatened Ecosystems via High-Throughput Sequencing
Gibson, J. F., Shokralla, S., Curry, C. J., Baird, D. J., Monk, W. A., King, I. W., & Hajibabaei, M. (2015) · PLoS ONE · doi:10.1371/journal.pone.0138432 · Cited by 186 · see citing works
$1 DNA barcodes for reconstructing complex phenomes and finding rare species in specimen‐rich samples
Meier, R., Wong, W., Srivathsan, A., & Foo, M. (2015) · Cladistics · doi:10.1111/cla.12115 · Cited by 177 · see citing works
Performance of amplicon and shotgun sequencing for accurate biomass estimation in invertebrate community samples
Bista, I., Carvalho, G. R., Tang, M., Walsh, K. A., Zhou, X. Y., Hajibabaei, M., Shokralla, S., Seymour, M., Bradley, D. T. C., Liu, S., et al. (2018) · Molecular Ecology Resources · doi:10.1111/1755-0998.12888 · Cited by 147 · see citing works
Studying Ecosystems With DNA Metabarcoding: Lessons From Biomonitoring of Aquatic Macroinvertebrates
Bush, A., Compson, Z. G., Monk, W. A., Porter, T. M., Steeves, R., Emilson, E. J. S., Gagné, N., Hajibabaei, M., Roy, M., & Baird, D. J. (2019) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2019.00434 · Cited by 139 · see citing works
Comparison of environmental DNA and bulk‐sample metabarcoding using highly degenerate cytochrome c oxidase I primers
Macher, J., Vivancos, A., Piggott, J. J., Centeno, F. C., Matthaei, C. D., & Leese, F. (2018) · Molecular Ecology Resources · doi:10.1111/1755-0998.12940 · Cited by 136 · see citing works
Continental-scale patterns of hyper-cryptic diversity within the freshwater model taxon Gammarus fossarum (Crustacea, Amphipoda)
Wattier, R. A., Mamos, T., Copilaş‐Ciocianu, D., Jelić, M., Ollivier, A., Chaumot, A., Danger, M., Felten, V., Piscart, C., Žganec, K., et al. (2020) · Scientific Reports · doi:10.1038/s41598-020-73739-0 · Cited by 105 · see citing works
Multiple-stressor effects on stream invertebrates: DNA barcoding reveals contrasting responses of cryptic mayfly species
Macher, J., Salis, R. K., Blakemore, K. S., Tollrian, R., Matthaei, C. D., & Leese, F. (2015) · Ecological Indicators · doi:10.1016/j.ecolind.2015.08.024 · Cited by 102 · see citing works
Identifying North American freshwater invertebrates using DNA barcodes: are existing COI sequence libraries fit for purpose?
Curry, C. J., Gibson, J. F., Shokralla, S., Hajibabaei, M., & Baird, D. J. (2018) · Freshwater Science · doi:10.1086/696613 · Cited by 88 · see citing works
DNA metabarcoding and morphological macroinvertebrate metrics reveal the same changes in boreal watersheds across an environmental gradient
Emilson, C. E., Thompson, D. G., Venier, L., Porter, T. M., Swystun, T., Chartrand, D. T., Capell, S. S., & Hajibabaei, M. (2017) · Scientific Reports · doi:10.1038/s41598-017-13157-x · Cited by 87 · see citing works
Comparison of DNA metabarcoding and morphological identification for stream macroinvertebrate biodiversity assessment and monitoring
Serrana, J. M., Miyake, Y., Gamboa, M., & Watanabe, K. (2019) · Ecological Indicators · doi:10.1016/j.ecolind.2019.02.008 · Cited by 81 · see citing works
Cryptic diversity of caddisflies in the Balkans: the curious case of Ecclisopteryx species (Trichoptera: Limnephilidae)
Previšić, A., Graf, W., Vitecek, S., Kučinić, M., Bálint, M., Keresztes, L., Pauls, S. U., & Waringer, J. A. (2014) · Arthropod Systematics & Phylogeny · doi:10.3897/asp.72.e31792 · Cited by 68 · see citing works
Does DNA barcoding improve performance of traditional stream bioassessment metrics?
Stein, E. D., White, B. P., Mazor, R. D., Jackson, J. K., Battle, J. M., Miller, P. E., Pilgrim, E. M., & Sweeney, B. W. (2014) · Freshwater Science · doi:10.1086/674782 · Cited by 60 · see citing works
Self-citation
Distribution and population genetic variation of cryptic species of the Alpine mayfly Baetis alpinus (Ephemeroptera: Baetidae) in the Central Alps
Leys, M., Keller, I., Räsänen, K., Gattolliat, J., & Robinson, C. T. (2016) · BMC Evolutionary Biology · doi:10.1186/s12862-016-0643-y · Cited by 50 · see citing works
Adding DNA barcoding to stream monitoring protocols – What’s the additional value and congruence between morphological and molecular identification approaches?
Chapuis, S., Herder, F., & Geiger, M. F. (2021) · PLoS ONE · doi:10.1371/journal.pone.0244598 · Cited by 42 · see citing works
Macroinvertebrate community diversity and habitat quality relationships along a large river from targeted eDNA metabarcode assays
Marshall, N. T., & Stepien, C. A. (2020) · Environmental DNA · doi:10.1002/edn3.90 · Cited by 39 · see citing works
A DNA barcode database of Australia’s freshwater macroinvertebrate fauna
Carew, M. E., Nichols, S. J., Batovska, J., Clair, R. S., Murphy, N. P., Blacket, M. J., & Shackleton, M. E. (2017) · Marine and Freshwater Research · doi:10.1071/mf16304 · Cited by 38 · see citing works
Assessing the relevance of DNA metabarcoding compared to morphological identification for lake phytoplankton monitoring
Gelis, M. M. N., Canino, A., Bouchez, A., Domaizon, I., Laplace-Treyture, C., Rimet, F., & Alric, B. (2024) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2023.169774 · Cited by 34 · see citing works
Performance of DNA metabarcoding, standard barcoding and morphological approaches in the identification of insect biodiversity
Salis, R. K., Sunde, J., Gubonin, N., Franzén, M., & Forsman, A. (2024) · Molecular Ecology Resources · doi:10.1111/1755-0998.14018 · Cited by 34 · see citing works
Delineating closely related species with DNA barcodes for routine biological monitoring
Carew, M. E., & Hoffmann, A. A. (2015) · Freshwater Biology · doi:10.1111/fwb.12587 · Cited by 34 · see citing works
Can high-throughput sequencing detect macroinvertebrate diversity for routine monitoring of an urban river?
Carew, M. E., Kellar, C. R., Pettigrove, V. J., & Hoffmann, A. A. (2017) · Ecological Indicators · doi:10.1016/j.ecolind.2017.11.002 · Cited by 34 · see citing works
Gap analysis for DNA-based biomonitoring of aquatic ecosystems in China
Li, F., Zhang, Y., Altermatt, F., Zhang, X., Cai, Y., & Yang, Z. (2022) · Ecological Indicators · doi:10.1016/j.ecolind.2022.108732 · Cited by 33 · see citing works
DNA barcode assessment of Mediterranean mayflies (Ephemeroptera), benchmark data for a regional reference library for rapid biomonitoring of freshwaters
Cardoni, S., Tenchini, R., Ficulle, I., Piredda, R., Simeone, M. C., & Belfiore, C. (2015) · Biochemical Systematics and Ecology · doi:10.1016/j.bse.2015.07.035 · Cited by 33 · see citing works
Environmental DNA of preservative ethanol performed better than water samples in detecting macroinvertebrate diversity using metabarcoding
Wang, Y., Chen, K., Gao, J., Wang, M., Dong, J., Xie, Y., Giesy, J. P., Jin, X., & Wang, B. (2021) · Diversity and Distributions · doi:10.1111/ddi.13284 · Cited by 30 · see citing works
Hidden biodiversity in Neotropical streams: DNA barcoding uncovers high endemicity of freshwater macroinvertebrates at small spatial scales
León, L. F. D., Cornejo, A., Gavilán, R. G., & Aguilar, C. (2020) · PLoS ONE · doi:10.1371/journal.pone.0231683 · Cited by 29 · see citing works
Ethanol eDNA Reveals Unique Community Composition of Aquatic Macroinvertebrates Compared to Bulk Tissue Metabarcoding in a Biomonitoring Sampling Scheme
Persaud, S. F., Cottenie, K., & Gleason, J. E. (2021) · Diversity · doi:10.3390/d13010034 · Cited by 26 · see citing works
The influence of macroinvertebrate abundance on the assessment of freshwater quality in The Netherlands
Beentjes, K. K., Speksnijder, A. G. C. L., Schilthuizen, M., Schaub, B. E. M., & van der Hoorn, B. (2018) · Metabarcoding and Metagenomics · doi:10.3897/mbmg.2.26744 · Cited by 24 · see citing works
Cryptic lineages of a common alpine mayfly show strong life‐history divergence
Leys, M., Keller, I., Robinson, C. T., & Räsänen, K. (2017) · Molecular Ecology · doi:10.1111/mec.14026 · Cited by 22 · see citing works
DNA Barcoding for Species Identification of Insect Skins: A Test on Chironomidae (Diptera) Pupal Exuviae
Kranzfelder, P., Ekrem, T., & Stur, E. (2017) · Journal of Insect Science · doi:10.1093/jisesa/iex075 · Cited by 21 · see citing works
Metabarcoding of native and invasive species in stomach contents of Great Lakes fishes
Mychek‐Londer, J. G., Chaganti, S. R., & Heath, D. D. (2020) · PLoS ONE · doi:10.1371/journal.pone.0236077 · Cited by 21 · see citing works
Towards routine DNA metabarcoding of macroinvertebrates using bulk samples for freshwater bioassessment: Effects of debris and storage conditions on the recovery of target taxa
Nichols, S. J., Kefford, B. J., Campbell, C. D., Bylemans, J., Chandler, E., Bray, J. P., Shackleton, M., Robinson, K. L., Carew, M. E., & Furlan, E. M. (2019) · Freshwater Biology · doi:10.1111/fwb.13443 · Cited by 20 · see citing works
Stream macroinvertebrate reintroductions: A cautionary approach for restored urban streams
Clinton, S. M., Hartman, J., Macneale, K. H., & Roy, A. H. (2022) · Freshwater Science · doi:10.1086/721471 · Cited by 20 · see citing works
Taxonomic resolution based on DNA barcoding affects environmental signal in metacommunity structure
Martin, G. K., Adamowicz, S. J., & Cottenie, K. (2016) · Freshwater Science · doi:10.1086/686260 · Cited by 19 · see citing works
DNA barcoding and faunistic criteria for a revised taxonomy of Italian Ephemeroptera
Tenchini, R., Cardoni, S., Piredda, R., Simeone, M. C., & Belfiore, C. (2018) · The European Zoological Journal · doi:10.1080/24750263.2018.1480732 · Cited by 19 · see citing works
Congruent population genetic structure but differing depths of divergence for three alpine stoneflies with similar ecology and geographic distributions
Hotaling, S., Giersch, J. J., Finn, D. S., Tronstad, L. M., Jordan, S., Serpa, L. E., Call, R. G., Muhlfeld, C. C., & Weisrock, D. W. (2018) · Freshwater Biology · doi:10.1111/fwb.13223 · Cited by 19 · see citing works
DNA barcodes for dragonflies and damselflies (Odonata) of Mindanao, Philippines
Casas, P. A. S., Sing, K., Lee, P.-S., Nuñeza, O. M., Villanueva, R. J. T., & Wilson, J. (2017) · Mitochondrial DNA Part A · doi:10.1080/24701394.2016.1267157 · Cited by 16 · see citing works
DNA metabarcoding unravels unknown diversity and distribution patterns of tropical freshwater invertebrates
Zieritz, A., Lee, P., Eng, W. W. H., Lim, S. Y., Sing, K. W., Chan, W. N., Loo, J.-S., Mahadzir, F. N., Ng, T. H., Yeo, D. C. J., et al. (2022) · Freshwater Biology · doi:10.1111/fwb.13926 · Cited by 15 · see citing works
DNA barcoding to assess diet of larval eastern hellbenders in North Carolina
Unger, S. D., Williams, L. A., Diaz, L., & Jachowski, C. M. B. (2019) · Food Webs · doi:10.1016/j.fooweb.2019.e00134 · Cited by 14 · see citing works
The importance of taxonomic resolution for additive beta diversity as revealed through DNA barcoding
Bringloe, T. T., Cottenie, K., Martin, G. K., & Adamowicz, S. J. (2016) · Genome · doi:10.1139/gen-2016-0080 · Cited by 13 · see citing works
DNA barcoding and first records of two rare Adicella species (Trichoptera: Leptoceridae) in Croatia
Ćukušić, A., Ćuk, R., Previšić, A., Podnar, M., Delić, A., & Kučinić, M. (2017) · Biologia · doi:10.1515/biolog-2017-0087 · Cited by 13 · see citing works
Exploring the potential of metabarcoding to disentangle macroinvertebrate community dynamics in intermittent streams
Laini, A., Beermann, A. J., Bolpagni, R., Burgazzi, G., Elbrecht, V., Zizka, V. M. A., Leese, F., & Viaroli, P. (2020) · Metabarcoding and Metagenomics · doi:10.3897/mbmg.4.51433 · Cited by 13 · see citing works
Non-invasive genetic monitoring for the threatened valley elderberry longhorn beetle
Nagarajan, R. P., Goodbla, A. M., Graves, E. E., Baerwald, M. R., Holyoak, M., & Schreier, A. D. (2020) · PLoS ONE · doi:10.1371/journal.pone.0227333 · Cited by 12 · see citing works
DNA barcoding and metabarcoding of highly diverse aquatic mites (Acarina) can improve their use in routine biological monitoring
Carew, M. E., Yow, W. K., Robinson, K. L., Coleman, R. A., & Hoffmann, A. A. (2022) · Marine and Freshwater Research · doi:10.1071/mf21291 · Cited by 10 · see citing works
Current and Future Challenges of Conserving Freshwater Biodiversity: A Molecular Perspective
Hughes, J. M. (2015) · Pertanika journal of tropical agricultural science · Cited by 9 · see citing works
A novel framework for phytoplankton biomonitoring: Trait assignment of 23S rRNA sequences
Tapolczai, K., Rimet, F., Ćirić, M. D., Ballot, A., Laplace-Treyture, C., & Alric, B. (2025) · Ecological Indicators · doi:10.1016/j.ecolind.2025.113361 · Cited by 9 · see citing works
Genetic diversity of marine oligochaetous clitellates in selected areas of the South Atlantic as revealed by DNA barcoding
Prantoni, A. L., Belmonte-Lopes, R., Lana, P. D. C., & Erséus, C. (2018) · Invertebrate Systematics · doi:10.1071/is17029 · Cited by 9 · see citing works
Chironomidae of the Upper Saint Croix River, Wisconsin
Egan, A. T., & Ferrington, L. C. (2019) · Transactions of the American Entomological Society · doi:10.3157/061.145.0307 · Cited by 8 · see citing works
An Accessible Metagenomic Strategy Allows for Better Characterisation of Invertebrate Bulk Samples
Callens, M., Berre, G. L., den Bulcke, L. V., Lolivier, M., & Derycke, S. (2025) · Molecular Ecology Resources · doi:10.1111/1755-0998.14126 · Cited by 6 · see citing works
Determining diets for fishes (Actinopterygii) from a small interior British Columbia, Canada stream: a comparison of morphological and molecular approaches
O'Dell, A., Flores, A., Schwarzfeld, M. D., Erasmus, D. J., Heath, D. D., Huber, D. P. W., & Shrimpton, J. M. (2020) · The Canadian Entomologist · doi:10.4039/tce.2020.25 · Cited by 6 · see citing works
Feeding ecology of a highly aerial bird during its long breeding season
Fernandes, S., Mata, V. A., & da Silva, L. P. (2022) · Avian Research · doi:10.1016/j.avrs.2022.100073 · Cited by 6 · see citing works
Spatial and phylogenetic structure of Alpine stonefly assemblages across seven habitats using DNA-species
Gamboa, M., Serrana, J. M., Takemon, Y., Monaghan, M. T., & Watanabe, K. (2023) · Oecologia · doi:10.1007/s00442-023-05321-0 · Cited by 5 · see citing works
Dissecting biodiversity: assessing the taxonomic, functional and phylogenetic structure of an insect metacommunity in a river network using morphological and metabarcoding data
Laini, A., Stubbington, R., Beermann, A. J., Burgazzi, G., Datry, T., Viaroli, P., Wilkes, M., Zizka, V. M. A., Saccò, M., & Leese, F. (2023) · The European Zoological Journal · doi:10.1080/24750263.2023.2197924 · Cited by 5 · see citing works
Basic and applied uses of molecular approaches in freshwater ecology
Hughes, J. M., Finn, D. S., Monaghan, M. T., Schultheis, A. S., & Sweeney, B. W. (2014) · Freshwater Science · doi:10.1086/675254 · Cited by 5 · see citing works
Self-citation
DNA barcoding: A practical tool for the taxonomy and species identification of entomofauna
Szyp-Borowska, I., & Sikora, K. (2019) · Forest Research Papers · doi:10.2478/frp-2019-0021 · Cited by 5 · see citing works
Mechanisms of the impact of hydropower development on phytoplankton diversity and community assembly in the lower Jinsha River
XinYi, Z. H. O. U., Zhou, X., Zhang, J., ChuBin, W. E. N. G., & Xu, M. (2024) · Scientia Sinica Technologica · doi:10.1360/sst-2024-0250 · Cited by 4 · see citing works
Environmental Matrices Need Consideration: Insights From Water and Biofilm Environmental DNA for Multi‐Taxonomic Biomonitoring
Gauvin, P., Domaizon, I., Bouchez, A., & Rimet, F. (2025) · Environmental DNA · doi:10.1002/edn3.70079 · Cited by 4 · see citing works
A survey of aquatic macroinvertebrates in a river from the dry corridor of Nicaragua using biological indices and DNA barcoding
Mendoza‐Ramírez, B. H., Páiz-Medina, L., Salvatierra‐Suárez, T., Hernández, N. D. S., & Huete‐Pérez, J. A. (2022) · Ecology and Evolution · doi:10.1002/ece3.9487 · Cited by 4 · see citing works
Temporal patterns of genetic diversity in Baetis tricaudatus (Ephemeroptera:Baetidae) from the Russian River, northern California
Stauffer‐Olsen, N. J., O’Grady, P., & Resh, V. H. (2017) · Freshwater Science · doi:10.1086/691973 · Cited by 4 · see citing works
Evaluating water quality for Amazonian streams along the interoceanic highway in Peru using macroinvertebrates collected by hand and with leaf packs
Sweeney, B. W., Battle, J. M., Funk, D. H., Flowers, W., Gonzales, T., Huamantinco, A. A., Jackson, J. K., & Arnold, M. (2020) · Limnologica · doi:10.1016/j.limno.2020.125759 · Cited by 4 · see citing works
Self-citation
Comparing morphological and DNA-based bioassessment methodologies for macroinvertebrates in Neotropical streams: a case study from Ecuador
Jijón, G., Errigo, I. M., Wicks, J., Goldston, N. N., Davis, L., Davis, D., Standring, S., Chaston, J. M., Frandsen, P. B., & Ríos‐Touma, B. (2025) · Metabarcoding and Metagenomics · doi:10.3897/mbmg.9.138172 · Cited by 3 · see citing works
Combined water and detritus sampling is the most effective strategy to detect environmental DNA of macroinvertebrates in rivers
Shi, K., He, Y., Yu, J., Zhao, Y., Wang, H., & Cui, Y. (2025) · Ecological Indicators · doi:10.1016/j.ecolind.2025.113782 · Cited by 3 · see citing works
DNA barcoding revels first records of three rare coleopteran genera in Northern lakes of Egypt.
Kheirallah, D. A. M. (2020) · Brazilian Journal of Biology · doi:10.1590/1519-6984.234428 · Cited by 3 · see citing works
Towards a Canary Islands barcode database for soil biodiversity: revealing cryptic and unrecorded mite species diversity within insular soils
Santos, I., Suárez, D., MORAZA, M. L., Arribas, P., & Andújar, C. (2024) · Biodiversity Data Journal · doi:10.3897/bdj.12.e113301 · Cited by 3 · see citing works
Diet Analysis of Maumee River Fishes using Cytochrome C Oxidase (COI) DNA Metabarcoding ― Insights into a Critical Time of Year
Shortridge, M. G. (2016) · OhioLink ETD Center (Ohio Library and Information Network) · Cited by 3 · see citing works
Cytochrome Oxidase I Sequences from Northern and Southern California Suggest Cryptic Baetis (Ephemeroptera: Baetidae) Species
Stauffer‐Olsen, N. J., O’Grady, P., & Resh, V. H. (2019) · Western North American Naturalist · doi:10.3398/064.079.0207 · Cited by 3 · see citing works
Watershed survey of streams in western Bhutan with macroinvertebrates, water chemistry, bacteria and DNA barcodes
Battle, J. M., Sweeney, B. W., Currinder, B., Aufdenkampe, A. K., Fisher, B. A., & Islam, N. (2024) · Journal of Threatened Taxa · doi:10.11609/jott.8954.16.11.26089-26103 · Cited by 2 · see citing works
Self-citation
Detecting signatures of competition from observational data: a combined approach using DNA barcoding, diversity partitioning and checkerboards at small spatial scales
Bringloe, T. T., Adamowicz, S. J., Harvey, V. F. I., Jackson, J. K., & Cottenie, K. (2016) · Freshwater Biology · doi:10.1111/fwb.12732 · Cited by 2 · see citing works
Self-citation
The first record of Tinodes antonioi Botosaneanu & Taticchi-Viganò, 1974 (Insecta, Trichoptera) in Croatia with DNA barcoding and ecological data and notice of biodiversity and distribution of the genus Tinodes in Croatia
Kučinić, M., Ćukušić, A., Podnar, M., Landeka, M., Marina Tartaglie 2, 1. 0., Plavec, H., Grožnjanska 18, 1. 0. Z., Plantak, M., Akimbekova, N., Žalac, S., et al. (2016) · Natura Croatica · doi:10.20302/nc.2016.25.9 · Cited by 2 · see citing works
Integrative taxonomy supports two new species of Chimarra Stephens, 1829 from Brazil (Trichoptera: Philopotamidae)
Moreira, P. D., Dumas, L. L., Rozo, M. P., Desidério, G. R., & Takiya, D. M. (2022) · Arthropod Systematics & Phylogeny · doi:10.3897/asp.80.e76559 · Cited by 2 · see citing works
DNA barcodes for Great Salt Lake brine flies establish a baseline for monitoring changes in biodiversity
Haney, S., Bedolla, O., & Clark, J. B. (2022) · Inland Waters · doi:10.1080/20442041.2022.2144084 · Cited by 1 · see citing works
Two New Species of the Genus Caryanda Stål, 1878 (Orthoptera: Acrididae) from Yunnan, China Identified Based on Morphological and Molecular Data
LI, F.-T., Song, H., Zhao, Y., Chen, J.-Y., Yang, J., Li, M., & Mao, B.-Y. (2026) · Insects · doi:10.3390/insects17020164 · Cited by 1 · see citing works
Identification of DNA Corpse in Ordo Diptera Familia Calliphoridae Larvae in CSF1PO, TH01, and TPOX Locus Using Polymerase Chain Reaction (PCR) Methods
Purwanti, T. (2020) · Indian Journal of Forensic Medicine & Toxicology · doi:10.37506/ijfmt.v14i4.12175 · Cited by 1 · see citing works
Removing invasive stream macrofauna shifts nontarget invertebrate mesofauna through facilitation
Whitt, J., Patrick, C. J., Lisi, P. J., McIntyre, P. B., Blum, M. J., & Hogan, J. D. (2025) · Ecosphere · doi:10.1002/ecs2.70489 · Cited by 1 · see citing works
Ecosystem recovery in restored saltmarshes detected through invertebrate communities
Quadri-Adrogué, A., Trevathan‐Tackett, S. M., Bell, K., & Wartman, M. (2026) · Restoration Ecology · doi:10.1111/rec.70401 · Cited by 1 · see citing works
Molecular identification of some species of dragonfly (Odonata: Anisoptera) using COXI gene and DNA barcodes from Basrah Province, Southern Iraq
Ahmed, H. K., & Kareem, D. K. (2024) · Journal of Aquatic Research and Sustainability · doi:10.69517/jars.2024.01.01.0003 · Cited by 1 · see citing works
Influence of water source on alpine stream community structure: linking morphological and metabarcoding approaches
Preston, D. L., Hotaling, S., Errigo, I. M., Frandsen, P. B., Price, T. L., Hamilton, T. L., Anderson, K. E., Yevak, S., & Morse, J. F. (2024) · Aquatic Sciences · doi:10.1007/s00027-024-01134-2 · Cited by 1 · see citing works
Insights into species diversity of the genus Hydropsyche Pictet, 1834 (Hydropsychidae, Trichoptera) from the Lake Kinneret catchment (Israel)
Beermann, A. J., Uekötter, L., Leese, F., Lorenz, A. W., & Hershkovitz, Y. (2017) · Aquatic Insects · doi:10.1080/01650424.2017.1351567 · Cited by 1 · see citing works
A comparison of genetically and morphometrically identified macroinvertebrate community index scores with implications for aquatic life use attainment
Fayram, A. H., Wood, J. S., & Swigle, B. D. (2021) · Environmental Monitoring and Assessment · doi:10.1007/s10661-021-09525-w · Cited by 1 · see citing works
Efficiency of DNA Barcodes for Identification and Documenting Aquatic Insect Diversity in Rice Fields
Pramual, P., Thanee, I., Uttaruk, Y., Thaijarern, J., & Wongpakam, K. (2020) · Tropical Natural History · doi:10.58837/tnh.20.2.169512 · Cited by 1 · see citing works
Diversity of Sericostomatidae (Trichoptera) Caddisflies in the Montseny Mountain RangePreprint
Macher, J., Weiss, M., Beermann, A. J., & Leese, F. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/057844 · Cited by 1 · see citing works
Assessing the Diversity of Antarctic and New Zealand Arthropods through DNA Barcoding
Beet, C. R. (2016) · Research Commons (University of Waikato) · Cited by 1 · see citing works
DNA barcoding vs morphology: Assessing different methods for invertebrate identification and determination of industrial effluent impactsPreprint
Dutheil, L. M., Cottenie, K., Sonnenberg, H., Steinke, D., & Adamowicz, S. J. (2026) · Research Square · doi:10.21203/rs.3.rs-8253547/v1 · Cited by 1 · see citing works
Spatial and phylogenetic structure of Alpine stonefly community assemblages across seven habitats using DNA-speciesPreprint
Gamboa, M., Serrana, J. M., Takemon, Y., Monaghan, M. T., & Watanabe, K. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/765578
Molecular techniques to assess fish diet and describe prey availability
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The efficacy of DNA barcoding in the classification, biodiversity and environmental assessment of benthic macroinvertebratesPreprint
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Authors: Jackson, J. K., Battle, J. M., White, B. P., Pilgrim, E. M., Stein, E. D., Miller, P. E., & Sweeney, B. W.
Affiliations: Stroud Water Research Center (US)
Southern California Coastal Water Research Project (US)
Environmental Protection Agency (US)
University of Guelph (CA)
ORCID: Jackson, John K.
Stein, Eric D.
Sweeney, Bernard W.
Venue: Freshwater Science
Publisher: University of Chicago Press
Published: 2014-03
Volume: 33
Issue: 1
Pages: 312-324
ISSN: 2161-9549 (ISSN-L)
2161-9565
DOI: 10.1086/675225
OpenAlex: W2139394020
Cited by: 91
References: 83
Citations by year: 2026: 6 · 2025: 8 · 2024: 7 · 2023: 2 · 2022: 8 · 2021: 4 · 2020: 11 · 2019: 9 · 2018: 8 · 2017: 10 · 2016: 8 · 2015: 7 · 2014: 3
FWCI: 8.12
Type: journal article
Language: en
Open access: closed
Locations: Freshwater Science (publishedVersion)
BioOne Complete (BioOne) (submittedVersion)
Topics: Physical Sciences › Environmental Science › Ecology › Freshwater macroinvertebrate diversity and ecology
Physical Sciences › Environmental Science › Ecology › Environmental DNA in Biodiversity Studies
Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Invertebrate Taxonomy and Ecology
Keywords: DNA barcoding, macroinvertebrate communities, stream biodiversity, cryptic species, species delimitation, morphological identification, COI, Chironomidae, Ephemeroptera, Trichoptera, mites, species richness, species rarity, coastal streams, environmental stress, biodiversity loss, Southern California

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Cryptic biodiversity in streams: a comparison of macroinvertebrate communities based on morphological and DNA barcode identifications

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