Abstract We quantified macroinvertebrate production and organic matter standing stocks in riffle/run and pool habitats for 2 y in 2 reaches of Big Creek, a 3rd-order stream in southern Illinois, USA. Habitat-weighted secondary production was 24.9 and 26.2 g ash-free dry mass (AFDM) m−2 y−1 in the upper and lower reaches, respectively, in year 1 of the study and 17.6 and 15.1 AFDM m−2 y−1 in year 2. Annual production to biomass (P/B) ratios of the macroinvertebrate assemblages ranged from 7 to 10. Collector-gatherers, which were dominated by nontanypodine Chironomidae and Oligochaeta, accounted for >60% of total habitat-weighted production in both reaches, and consumption estimates based on production efficiencies indicated they consumed high proportions of available organic matter resources ≤250 µm. Macroinvertebrate production in Big Creek was strongly correlated with organic matter standing stocks, and our subsequent analyses of production and organic matter resources across several low-order North American streams suggested standing stocks of small wood, a relatively refractory component of organic matter, are an important component of the relationship between macroinvertebrate production and organic matter. However, the apparent influence of small wood on production may be related to associated physical characteristics of these streams, such as pH and canopy cover. Secondary production estimates in our data set were a function of both adjusted total organic matter exclusive of wood and wood standing stocks. Although production–organic matter relationships may be obscured by other factors at the local level, our results indicate that patterns of macroinvertebrate production across large geographic scales may be driven largely by the availability of detrital resources.
{"title":"Secondary production in a southern Illinois headwater stream: relationships between organic matter standing stocks and macroinvertebrate productivity","authors":"D. A. Walther, M. Whiles","doi":"10.1899/10-006.1","DOIUrl":"https://doi.org/10.1899/10-006.1","url":null,"abstract":"Abstract We quantified macroinvertebrate production and organic matter standing stocks in riffle/run and pool habitats for 2 y in 2 reaches of Big Creek, a 3rd-order stream in southern Illinois, USA. Habitat-weighted secondary production was 24.9 and 26.2 g ash-free dry mass (AFDM) m−2 y−1 in the upper and lower reaches, respectively, in year 1 of the study and 17.6 and 15.1 AFDM m−2 y−1 in year 2. Annual production to biomass (P/B) ratios of the macroinvertebrate assemblages ranged from 7 to 10. Collector-gatherers, which were dominated by nontanypodine Chironomidae and Oligochaeta, accounted for >60% of total habitat-weighted production in both reaches, and consumption estimates based on production efficiencies indicated they consumed high proportions of available organic matter resources ≤250 µm. Macroinvertebrate production in Big Creek was strongly correlated with organic matter standing stocks, and our subsequent analyses of production and organic matter resources across several low-order North American streams suggested standing stocks of small wood, a relatively refractory component of organic matter, are an important component of the relationship between macroinvertebrate production and organic matter. However, the apparent influence of small wood on production may be related to associated physical characteristics of these streams, such as pH and canopy cover. Secondary production estimates in our data set were a function of both adjusted total organic matter exclusive of wood and wood standing stocks. Although production–organic matter relationships may be obscured by other factors at the local level, our results indicate that patterns of macroinvertebrate production across large geographic scales may be driven largely by the availability of detrital resources.","PeriodicalId":49987,"journal":{"name":"Journal of the North American Benthological Society","volume":"21 1","pages":"357 - 373"},"PeriodicalIF":0.0,"publicationDate":"2011-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86446335","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract Low-flow disturbances are predicted to increase in frequency and intensity because of climate change and extensive human water withdrawal, but the effect of decreased flow on aquatic insect communities is not well understood. I explored the resistance of aquatic insects to reduced flow by creating an experimental low-flow disturbance that diverted ∼40 to 80% of the water in 3 replicate streams for 2 summers. I sampled the aquatic insect community in control and treatment reaches before and during the 3-mo water diversions. I used a trait-based approach to analyze the data because traits have the potential to increase mechanistic understanding and predictive capabilities. The analysis focused on 6 traits: desiccation resistance, maximum crawling rate, armoring, size at maturity, rheophily, and habit. Community trait composition underwent strong seasonal shifts, but few consistent responses to reduced flow were observed. The 2 trait states that did appear to confer increased resistance were high crawling rate and armoring. These trait states can provide protection from predators. Thus, biotic interactions might be important during low-flow disturbance.
{"title":"Resistance of aquatic insects to a low-flow disturbance: exploring a trait-based approach","authors":"Annika W. Walters","doi":"10.1899/10-041.1","DOIUrl":"https://doi.org/10.1899/10-041.1","url":null,"abstract":"Abstract Low-flow disturbances are predicted to increase in frequency and intensity because of climate change and extensive human water withdrawal, but the effect of decreased flow on aquatic insect communities is not well understood. I explored the resistance of aquatic insects to reduced flow by creating an experimental low-flow disturbance that diverted ∼40 to 80% of the water in 3 replicate streams for 2 summers. I sampled the aquatic insect community in control and treatment reaches before and during the 3-mo water diversions. I used a trait-based approach to analyze the data because traits have the potential to increase mechanistic understanding and predictive capabilities. The analysis focused on 6 traits: desiccation resistance, maximum crawling rate, armoring, size at maturity, rheophily, and habit. Community trait composition underwent strong seasonal shifts, but few consistent responses to reduced flow were observed. The 2 trait states that did appear to confer increased resistance were high crawling rate and armoring. These trait states can provide protection from predators. Thus, biotic interactions might be important during low-flow disturbance.","PeriodicalId":49987,"journal":{"name":"Journal of the North American Benthological Society","volume":"262 1","pages":"346 - 356"},"PeriodicalIF":0.0,"publicationDate":"2011-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75771494","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract Nutrients and grazers both can regulate benthic algal structure and function in streams, but the relative strength of each factor depends on stream biotic and abiotic conditions. The abundance of stream organisms and nutrient availability can change rapidly after a flood. Thus, nutrient and grazer influences on algal development and how these drivers interact may vary temporally during recovery. We measured benthic structural and functional development for 35 d after a simulated flood in large outdoor mesocosms under a gradient of 6 nutrient loadings crossed with 6 densities of grazing fish (Southern redbelly dace, Phoxinus erythrogaster). Nutrients influenced algal development more than dace did and were better correlated with algal function (area-specific primary productivity and nutrient uptake) than with structure (biomass). Dace influenced all structural variables and biomass-specific gross primary productivity, but their influence was relatively weak and was observed only early in recovery. Dace influence weakened and nutrient influence strengthened during recovery. Understanding context-dependent relationships in postdisturbance community dynamics is essential for predicting ecosystem responses to future changes in nutrient inputs and biodiversity, particularly in systems, such as headwater streams, with frequent disturbance.
{"title":"Dynamic influences of nutrients and grazing fish on periphyton during recovery from flood","authors":"J. Murdock, W. Dodds, K. Gido, M. Whiles","doi":"10.1899/10-039.1","DOIUrl":"https://doi.org/10.1899/10-039.1","url":null,"abstract":"Abstract Nutrients and grazers both can regulate benthic algal structure and function in streams, but the relative strength of each factor depends on stream biotic and abiotic conditions. The abundance of stream organisms and nutrient availability can change rapidly after a flood. Thus, nutrient and grazer influences on algal development and how these drivers interact may vary temporally during recovery. We measured benthic structural and functional development for 35 d after a simulated flood in large outdoor mesocosms under a gradient of 6 nutrient loadings crossed with 6 densities of grazing fish (Southern redbelly dace, Phoxinus erythrogaster). Nutrients influenced algal development more than dace did and were better correlated with algal function (area-specific primary productivity and nutrient uptake) than with structure (biomass). Dace influenced all structural variables and biomass-specific gross primary productivity, but their influence was relatively weak and was observed only early in recovery. Dace influence weakened and nutrient influence strengthened during recovery. Understanding context-dependent relationships in postdisturbance community dynamics is essential for predicting ecosystem responses to future changes in nutrient inputs and biodiversity, particularly in systems, such as headwater streams, with frequent disturbance.","PeriodicalId":49987,"journal":{"name":"Journal of the North American Benthological Society","volume":"17 1","pages":"331 - 345"},"PeriodicalIF":0.0,"publicationDate":"2011-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83136423","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract As part of its ongoing work in biomonitoring, Environment Canada's Canadian Aquatic Biomonitoring Network (CABIN) program has assembled an expert-verified reference collection of 3864 specimens of 604 species of Canadian freshwater macroinvertebrates. Such collections are a key resource for developing a deoxyribonucleic acid (DNA) barcode library to facilitate molecular identification of biomonitoring samples. We examined the problems encountered in using such legacy material to obtain reference barcodes. We focused on the influence of specimen age and preservation history. To supplement work on the reference collection, we determined the time-dependent effects of formalin preservation on DNA-barcode integrity in 4 common arthropod taxa by controlled exposure of fresh material obtained from laboratory cultures. Specimens in the reference collection were preserved with short-term fixation in formalin followed by prolonged preservation in 70% ethanol. Only 19 caddisfly larval specimens out of the total of 650 analyzed returned full-length sequences. In contrast, formalin preservation of freshly collected material for up to 20 d yielded good sequencing success and high-quality sequences. Freshly collected material clearly provides the best basis for the future development of DNA-barcode libraries, and formalin preservation should be avoided where possible to ensure that DNA integrity is maximized.
{"title":"Building freshwater macroinvertebrate DNA-barcode libraries from reference collection material: formalin preservation vs specimen age","authors":"D. Baird, T. Pascoe, Xin Zhou, Mehrdad Hajibabaei","doi":"10.1899/10-013.1","DOIUrl":"https://doi.org/10.1899/10-013.1","url":null,"abstract":"Abstract As part of its ongoing work in biomonitoring, Environment Canada's Canadian Aquatic Biomonitoring Network (CABIN) program has assembled an expert-verified reference collection of 3864 specimens of 604 species of Canadian freshwater macroinvertebrates. Such collections are a key resource for developing a deoxyribonucleic acid (DNA) barcode library to facilitate molecular identification of biomonitoring samples. We examined the problems encountered in using such legacy material to obtain reference barcodes. We focused on the influence of specimen age and preservation history. To supplement work on the reference collection, we determined the time-dependent effects of formalin preservation on DNA-barcode integrity in 4 common arthropod taxa by controlled exposure of fresh material obtained from laboratory cultures. Specimens in the reference collection were preserved with short-term fixation in formalin followed by prolonged preservation in 70% ethanol. Only 19 caddisfly larval specimens out of the total of 650 analyzed returned full-length sequences. In contrast, formalin preservation of freshly collected material for up to 20 d yielded good sequencing success and high-quality sequences. Freshly collected material clearly provides the best basis for the future development of DNA-barcode libraries, and formalin preservation should be avoided where possible to ensure that DNA integrity is maximized.","PeriodicalId":49987,"journal":{"name":"Journal of the North American Benthological Society","volume":"14 1","pages":"125 - 130"},"PeriodicalIF":0.0,"publicationDate":"2011-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83475447","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Park, Xin Zhou, Jason L Robinson, C. J. Geraci, Charles, R. Parker, O. Flint, D. Etnier, D. Ruiter, R. DeWalt, Luke M. Jacobus, P. Hebert
Abstract Deoxyribonucleic acid (DNA) barcoding is an effective tool for species identification and life-stage association in a wide range of animal taxa. We developed a strategy for rapid construction of a regional DNA-barcode reference library and used the caddisflies (Trichoptera) of the Great Smoky Mountains National Park (GSMNP) as a model. Nearly 1000 cytochrome c oxidase subunit I (COI) sequences, representing 209 caddisfly species previously recorded from GSMNP, were obtained from the global Trichoptera Barcode of Life campaign. Most of these sequences were collected from outside the GSMNP area. Another 645 COI sequences, representing 80 species, were obtained from specimens collected in a 3-d bioblitz (short-term, intense sampling program) in GSMNP. The joint collections provided barcode coverage for 212 species, 91% of the GSMNP fauna. Inclusion of samples from other localities greatly expedited construction of the regional DNA-barcode reference library. This strategy increased intraspecific divergence and decreased average distances to nearest neighboring species, but the DNA-barcode library was able to differentiate 93% of the GSMNP Trichoptera species examined. Global barcoding projects will aid construction of regional DNA-barcode libraries, but local surveys make crucial contributions to progress by contributing rare or endemic species and full-length barcodes generated from high-quality DNA. DNA taxonomy is not a goal of our present work, but the investigation of COI divergence patterns in caddisflies is providing new insights into broader biodiversity patterns in this group and has directed attention to various issues, ranging from the need to re-evaluate species taxonomy with integrated morphological and molecular evidence to the necessity of an appropriate interpretation of barcode analyses and its implications in understanding species diversity (in contrast to a simple claim for barcoding failure).
脱氧核糖核酸(DNA)条形码是一种有效的物种鉴定和生命阶段关联的工具，适用于广泛的动物分类群。以美国大烟山国家公园(Great Smoky Mountains National Park, GSMNP)的毛翅目热蝇(caddis蝇)为样本，研究了区域dna条形码参考文库的快速构建策略。从全球毛翅目生命条形码运动中获得了近1000个细胞色素c氧化酶亚基I (COI)序列，代表了以前从GSMNP中记录的209种毛翅目昆虫。这些序列大多来自GSMNP区域以外。另外645个COI序列，代表80个物种，来自GSMNP的3-d生物闪电式(短期，密集采样计划)收集的标本。该联合馆藏提供了212个物种的条形码覆盖，占GSMNP动物群的91%。其他地区样本的加入大大加快了区域dna条形码参考文库的建设。这种策略增加了种内分化，减少了与最近邻近物种的平均距离，但dna条形码库能够区分93%的GSMNP毛翅目物种。全球条形码项目将有助于区域DNA条形码库的建设，但本地调查通过提供稀有或特有物种以及由高质量DNA生成的全长条形码，对进展做出了重要贡献。DNA分类学不是我们目前工作的目标，但对球蝇COI分化模式的研究为该群体更广泛的生物多样性模式提供了新的见解，并引起了人们对各种问题的关注。从综合形态学和分子证据重新评估物种分类学的需要，到条形码分析的适当解释及其在理解物种多样性方面的意义的必要性(与条形码失败的简单主张相反)。
{"title":"Accelerated construction of a regional DNA-barcode reference library: caddisflies (Trichoptera) in the Great Smoky Mountains National Park","authors":"Park, Xin Zhou, Jason L Robinson, C. J. Geraci, Charles, R. Parker, O. Flint, D. Etnier, D. Ruiter, R. DeWalt, Luke M. Jacobus, P. Hebert","doi":"10.1899/10-010.1","DOIUrl":"https://doi.org/10.1899/10-010.1","url":null,"abstract":"Abstract Deoxyribonucleic acid (DNA) barcoding is an effective tool for species identification and life-stage association in a wide range of animal taxa. We developed a strategy for rapid construction of a regional DNA-barcode reference library and used the caddisflies (Trichoptera) of the Great Smoky Mountains National Park (GSMNP) as a model. Nearly 1000 cytochrome c oxidase subunit I (COI) sequences, representing 209 caddisfly species previously recorded from GSMNP, were obtained from the global Trichoptera Barcode of Life campaign. Most of these sequences were collected from outside the GSMNP area. Another 645 COI sequences, representing 80 species, were obtained from specimens collected in a 3-d bioblitz (short-term, intense sampling program) in GSMNP. The joint collections provided barcode coverage for 212 species, 91% of the GSMNP fauna. Inclusion of samples from other localities greatly expedited construction of the regional DNA-barcode reference library. This strategy increased intraspecific divergence and decreased average distances to nearest neighboring species, but the DNA-barcode library was able to differentiate 93% of the GSMNP Trichoptera species examined. Global barcoding projects will aid construction of regional DNA-barcode libraries, but local surveys make crucial contributions to progress by contributing rare or endemic species and full-length barcodes generated from high-quality DNA. DNA taxonomy is not a goal of our present work, but the investigation of COI divergence patterns in caddisflies is providing new insights into broader biodiversity patterns in this group and has directed attention to various issues, ranging from the need to re-evaluate species taxonomy with integrated morphological and molecular evidence to the necessity of an appropriate interpretation of barcode analyses and its implications in understanding species diversity (in contrast to a simple claim for barcoding failure).","PeriodicalId":49987,"journal":{"name":"Journal of the North American Benthological Society","volume":"54 1","pages":"131 - 162"},"PeriodicalIF":0.0,"publicationDate":"2011-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91154468","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract The application of deoxyribonucleic acid (DNA) barcoding in benthic ecology is proceeding rapidly, and a special session held at the 2009 North American Benthological Society Annual Meeting in Grand Rapids, Michigan, USA, brought together benthic scientists working in areas varying from taxonomy to biomonitoring to present the state of the science. The papers arising from this meeting are grouped in this special series of papers. Here, we present a brief introduction to this emerging area of benthic science, highlight the contributions of previous researchers, and provide an overview of these latest contributions to this highly active field. Paper topics include the development of DNA libraries for identification of material from field studies, application of DNA-based taxonomy in the discovery of new faunas, and the use of DNA-based identification in field biomonitoring studies, present and future. In addition, a critique is presented of the use of DNA barcoding in benthology and the potential pitfalls facing researchers who seek to use this method in their future research.
{"title":"Applying DNA barcoding in benthology: the state of the science","authors":"D. Baird, B. W. Sweeney","doi":"10.1899/10-154.1","DOIUrl":"https://doi.org/10.1899/10-154.1","url":null,"abstract":"Abstract The application of deoxyribonucleic acid (DNA) barcoding in benthic ecology is proceeding rapidly, and a special session held at the 2009 North American Benthological Society Annual Meeting in Grand Rapids, Michigan, USA, brought together benthic scientists working in areas varying from taxonomy to biomonitoring to present the state of the science. The papers arising from this meeting are grouped in this special series of papers. Here, we present a brief introduction to this emerging area of benthic science, highlight the contributions of previous researchers, and provide an overview of these latest contributions to this highly active field. Paper topics include the development of DNA libraries for identification of material from field studies, application of DNA-based taxonomy in the discovery of new faunas, and the use of DNA-based identification in field biomonitoring studies, present and future. In addition, a critique is presented of the use of DNA barcoding in benthology and the potential pitfalls facing researchers who seek to use this method in their future research.","PeriodicalId":49987,"journal":{"name":"Journal of the North American Benthological Society","volume":"73 1","pages":"122 - 124"},"PeriodicalIF":0.0,"publicationDate":"2011-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89814283","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
S. Boyer, Alexander A. Howe, Nathan Juergens, M. Hove
Abstract We developed a multilocus deoxyribonucleic acid (DNA)-barcoding approach to identify newly transformed juvenile mussels collected from naturally infested fishes in a federally protected waterway that is home to a diverse mussel community, the St Croix River (Minnesota/Wisconsin, USA). We used new and publicly available data downloaded from GenBank to build reference databases for identified adult mussels. We assessed the efficacy of the mitochondrial loci cytochrome oxidase c subunit I (COI) and nicotinamide adenine dinucleotide dehydrogenase subunit 1 (ND1) for DNA barcoding. We concluded that the barcoding gap between average intra- and interspecific genetic distances is wider for ND1 than for COI, but both loci perform well for species identification in character-based phylogenetic analyses. Almost every species formed a monospecific clade with high bootstrap and posterior-probability support. We obtained newly transformed juvenile mussels by collecting individuals of 3 different fish species that were infested with unionid larvae. We held the fish in aquaria until the mussels emerged naturally. We then extracted DNA and sequenced our loci of interest. When sequences from the juveniles were included in phylogenetic analyses, they grouped with single species (or, in one case, a pair of closely related species) with high bootstrap and posterior-probability support. Identifying juveniles using morphology alone is difficult and, in some cases, impossible. Therefore, our approach will be useful to researchers interested in the relationship between unionid mussels and their fish hosts.
{"title":"A DNA-barcoding approach to identifying juvenile freshwater mussels (Bivalvia:Unionidae) recovered from naturally infested fishes","authors":"S. Boyer, Alexander A. Howe, Nathan Juergens, M. Hove","doi":"10.1899/10-004.1","DOIUrl":"https://doi.org/10.1899/10-004.1","url":null,"abstract":"Abstract We developed a multilocus deoxyribonucleic acid (DNA)-barcoding approach to identify newly transformed juvenile mussels collected from naturally infested fishes in a federally protected waterway that is home to a diverse mussel community, the St Croix River (Minnesota/Wisconsin, USA). We used new and publicly available data downloaded from GenBank to build reference databases for identified adult mussels. We assessed the efficacy of the mitochondrial loci cytochrome oxidase c subunit I (COI) and nicotinamide adenine dinucleotide dehydrogenase subunit 1 (ND1) for DNA barcoding. We concluded that the barcoding gap between average intra- and interspecific genetic distances is wider for ND1 than for COI, but both loci perform well for species identification in character-based phylogenetic analyses. Almost every species formed a monospecific clade with high bootstrap and posterior-probability support. We obtained newly transformed juvenile mussels by collecting individuals of 3 different fish species that were infested with unionid larvae. We held the fish in aquaria until the mussels emerged naturally. We then extracted DNA and sequenced our loci of interest. When sequences from the juveniles were included in phylogenetic analyses, they grouped with single species (or, in one case, a pair of closely related species) with high bootstrap and posterior-probability support. Identifying juveniles using morphology alone is difficult and, in some cases, impossible. Therefore, our approach will be useful to researchers interested in the relationship between unionid mussels and their fish hosts.","PeriodicalId":49987,"journal":{"name":"Journal of the North American Benthological Society","volume":"28 1","pages":"182 - 194"},"PeriodicalIF":0.0,"publicationDate":"2011-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76908525","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
B. W. Sweeney, J. Battle, J. Jackson, Tanya Dapkey
Abstract Four approaches to or levels of identifying macroinvertebrates (amateur/family, expert entomologist/genus, expert entomologist/genus–species, and DNA barcoding/species) were used to assess community structure and water quality in White Clay Creek, Pennsylvania, USA. Macroinvertebrates were collected in March 2008 from 2 riffle sites 3.9 km apart on the same stream. The downstream site was known to be degraded by land and water use. About 98% of the 1617 specimens used for analysis, including small, immature, and damaged specimens, were successfully barcoded (sequenced) for the mitochondrial cytochrome c oxidase subunit I gene. A criterion of 2 to 4% genetic divergence provided good separation of presumptive species. Barcodes increased the taxonomic inventory across the 2 sites by 475% (124 taxa) relative to the amateur level, and 125% (83 taxa) and 70% (62 taxa) relative to the expert genus and species levels, respectively. Barcoding revealed species not currently described in larval taxonomic keys, including multiple (2–11) coexisting congeneric species. That 150 species were revealed by barcoding samples collected on the same date and in the same habitat was unprecedented, as was the fact that 60 cm2 of stream bottom supported an average of 248 to 347 individuals representing 55 to 68 species. Most barcode species were rare, with 42% represented by ≤2 individuals. Across all species, 43 of 89 barcode species were unique to upstream site 11 and 60 of 107 were unique to downstream site 12. In terms of water-quality assessment, most of the 17 metrics studied changed significantly (α = 0.05) when taxonomy changed from family to genus–species (79% and 93% for sites 11 and 12, respectively), and many also changed when taxonomy changed from genus to species (59 and 65% for sites 11 and 12, respectively). The proportion of metrics able to detect a difference (α = 0.05) between sites 11 and 12 increased with improved taxonomic resolution (36, 47, 65, and 76% for family, genus, genus–species, and barcode, respectively). The results revealed a pollution-tolerance gap because barcoding pushed larval taxonomy beyond the available pollution-tolerance data. Regardless, the combined morphological and molecular approach provides a finer resolution for evaluating environmental change associated with both natural and anthropogenic processes. The ability to distinguish larvae at the species level through barcoding finally puts biodiversity assessments for aquatic communities in terms comparable to those used for terrestrial ecosystems where estimates of biodiversity for plants and animals are never quantified at the level of genus or family. We conclude that DNA barcodes of stream macroinvertebrates will improve descriptions of community structure and water quality for both ecological and bioassessment purposes.
{"title":"Can DNA barcodes of stream macroinvertebrates improve descriptions of community structure and water quality?","authors":"B. W. Sweeney, J. Battle, J. Jackson, Tanya Dapkey","doi":"10.1899/10-016.1","DOIUrl":"https://doi.org/10.1899/10-016.1","url":null,"abstract":"Abstract Four approaches to or levels of identifying macroinvertebrates (amateur/family, expert entomologist/genus, expert entomologist/genus–species, and DNA barcoding/species) were used to assess community structure and water quality in White Clay Creek, Pennsylvania, USA. Macroinvertebrates were collected in March 2008 from 2 riffle sites 3.9 km apart on the same stream. The downstream site was known to be degraded by land and water use. About 98% of the 1617 specimens used for analysis, including small, immature, and damaged specimens, were successfully barcoded (sequenced) for the mitochondrial cytochrome c oxidase subunit I gene. A criterion of 2 to 4% genetic divergence provided good separation of presumptive species. Barcodes increased the taxonomic inventory across the 2 sites by 475% (124 taxa) relative to the amateur level, and 125% (83 taxa) and 70% (62 taxa) relative to the expert genus and species levels, respectively. Barcoding revealed species not currently described in larval taxonomic keys, including multiple (2–11) coexisting congeneric species. That 150 species were revealed by barcoding samples collected on the same date and in the same habitat was unprecedented, as was the fact that 60 cm2 of stream bottom supported an average of 248 to 347 individuals representing 55 to 68 species. Most barcode species were rare, with 42% represented by ≤2 individuals. Across all species, 43 of 89 barcode species were unique to upstream site 11 and 60 of 107 were unique to downstream site 12. In terms of water-quality assessment, most of the 17 metrics studied changed significantly (α = 0.05) when taxonomy changed from family to genus–species (79% and 93% for sites 11 and 12, respectively), and many also changed when taxonomy changed from genus to species (59 and 65% for sites 11 and 12, respectively). The proportion of metrics able to detect a difference (α = 0.05) between sites 11 and 12 increased with improved taxonomic resolution (36, 47, 65, and 76% for family, genus, genus–species, and barcode, respectively). The results revealed a pollution-tolerance gap because barcoding pushed larval taxonomy beyond the available pollution-tolerance data. Regardless, the combined morphological and molecular approach provides a finer resolution for evaluating environmental change associated with both natural and anthropogenic processes. The ability to distinguish larvae at the species level through barcoding finally puts biodiversity assessments for aquatic communities in terms comparable to those used for terrestrial ecosystems where estimates of biodiversity for plants and animals are never quantified at the level of genus or family. We conclude that DNA barcodes of stream macroinvertebrates will improve descriptions of community structure and water quality for both ecological and bioassessment purposes.","PeriodicalId":49987,"journal":{"name":"Journal of the North American Benthological Society","volume":"73 1","pages":"195 - 216"},"PeriodicalIF":0.0,"publicationDate":"2011-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84265119","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract A taxonomic perspective of deoxyribonucleic acid (DNA) barcoding is presented here with respect to its use within the freshwater science community. The goals and methods of DNA barcoding and the criticisms leveled at the procedure by the taxonomic community are explained. The major goal of DNA-barcoding efforts is to aid identification of specimens by matching sequences to a sequence library. This goal is achievable, but barcoding efforts must be coupled with a much wider sampling regime and should be done with the full cooperation and collaboration of the taxonomic community. Through collaborative efforts, taxonomists and barcode advocates can build capacity for taxonomy and sequence the vast number of specimens needed to build a truly comprehensive barcode library for use by benthic scientists. Other barcoding goals, such as species diagnosis and biodiversity surveys, are more problematic, but solutions are possible.
{"title":"DNA barcoding: a taxonomic point of view","authors":"R. DeWalt","doi":"10.1899/10-021.1","DOIUrl":"https://doi.org/10.1899/10-021.1","url":null,"abstract":"Abstract A taxonomic perspective of deoxyribonucleic acid (DNA) barcoding is presented here with respect to its use within the freshwater science community. The goals and methods of DNA barcoding and the criticisms leveled at the procedure by the taxonomic community are explained. The major goal of DNA-barcoding efforts is to aid identification of specimens by matching sequences to a sequence library. This goal is achievable, but barcoding efforts must be coupled with a much wider sampling regime and should be done with the full cooperation and collaboration of the taxonomic community. Through collaborative efforts, taxonomists and barcode advocates can build capacity for taxonomy and sequence the vast number of specimens needed to build a truly comprehensive barcode library for use by benthic scientists. Other barcoding goals, such as species diagnosis and biodiversity surveys, are more problematic, but solutions are possible.","PeriodicalId":49987,"journal":{"name":"Journal of the North American Benthological Society","volume":"131 1","pages":"174 - 181"},"PeriodicalIF":0.0,"publicationDate":"2011-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79197402","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract Monitoring water quality with aquatic insects as sentinels requires taxonomic knowledge of adult and immature life stages that is not available in many parts of the world. We used deoxyribonucleic acid (DNA) barcoding to expedite identification of larval caddisflies from 20 sites in the headwaters of the Tigris River in northern Iraq by comparing their mitochondrial cytochrome c oxidase subunit I (COI) sequences to a global reference library (the Trichoptera Barcode of Life). We obtained full-length DNA barcodes for 16 COI haplogroups from 11 genera in 9 Trichoptera families. The most haplogroups and genera were recorded from Sulaimani Province. Two distinct COI haplogroups were found for the genus Psychomyia, and 5 haplogroups were found for Hydropsyche. The Hydropsyche COI haplogroups do not form a monophyletic clade with reference to the world fauna, but 4 out of 5 haplogroups are related to other Palearctic species. Three larval Rhyacophila specimens in a single COI haplogroup are closely related to specimens of Rhyacophila nubila Zetterstedt and Rhyacophila dorsalis (Curtis) from Europe, but adults from Iraq are needed to confirm their species identity.
以水生昆虫为哨兵监测水质需要成虫和未成虫生命阶段的分类学知识，这在世界上许多地方是不具备的。我们使用脱氧核糖核酸(DNA)条形码技术，通过将线粒体细胞色素c氧化酶亚基I (COI)序列与全球参考文库(Trichoptera Barcode of Life)进行比较，加快了伊拉克北部底格里斯河上游20个地点的幼虫鉴定。我们获得了9个毛翅目科11属16个COI单倍群的全长DNA条形码。单倍群和属以苏莱曼尼省最多。在Psychomyia属中发现了2个不同的COI单倍群，Hydropsyche属中发现了5个单倍群。与世界动物群相比，水灵COI单倍群不形成单系进化分支，但5个单倍群中有4个与其他古北区物种相关。同一COI单倍群中的3个幼Rhyacophila标本与欧洲的Rhyacophila nubila Zetterstedt和Rhyacophila dorsalis (Curtis)有密切的亲缘关系，但需要伊拉克的成虫来确认其物种身份。
{"title":"DNA barcoding facilitates description of unknown faunas: a case study on Trichoptera in the headwaters of the Tigris River, Iraq","authors":"C. J. Geraci, M. Al-Saffar, Xin Zhou","doi":"10.1899/10-011.1","DOIUrl":"https://doi.org/10.1899/10-011.1","url":null,"abstract":"Abstract Monitoring water quality with aquatic insects as sentinels requires taxonomic knowledge of adult and immature life stages that is not available in many parts of the world. We used deoxyribonucleic acid (DNA) barcoding to expedite identification of larval caddisflies from 20 sites in the headwaters of the Tigris River in northern Iraq by comparing their mitochondrial cytochrome c oxidase subunit I (COI) sequences to a global reference library (the Trichoptera Barcode of Life). We obtained full-length DNA barcodes for 16 COI haplogroups from 11 genera in 9 Trichoptera families. The most haplogroups and genera were recorded from Sulaimani Province. Two distinct COI haplogroups were found for the genus Psychomyia, and 5 haplogroups were found for Hydropsyche. The Hydropsyche COI haplogroups do not form a monophyletic clade with reference to the world fauna, but 4 out of 5 haplogroups are related to other Palearctic species. Three larval Rhyacophila specimens in a single COI haplogroup are closely related to specimens of Rhyacophila nubila Zetterstedt and Rhyacophila dorsalis (Curtis) from Europe, but adults from Iraq are needed to confirm their species identity.","PeriodicalId":49987,"journal":{"name":"Journal of the North American Benthological Society","volume":"16 1","pages":"163 - 173"},"PeriodicalIF":0.0,"publicationDate":"2011-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84788585","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：