Taxonomic resolution based on DNA barcoding affects environmental signal in metacommunity structure

Identification of the species origin of pollen has many applications, including assessment of plant–pollinator networks, reconstruction of ancient plant communities, product authentication, allergen monitoring, and forensics. Such applications, however, have previously been limited by microscopy-based identification of pollen, which is slow, has low taxonomic resolution, and has few expert practitioners. One alternative is pollen DNA barcoding, which could overcome these issues. Recent studies demonstrate that both chloroplast and nuclear barcoding markers can be amplified from pollen. These recent validations of pollen metabarcoding indicate that now is the time for researchers in various fields to consider applying these methods to their research programs. In this paper, we review the nascent field of pollen DNA barcoding and discuss potential new applications of this technology, highlighting existing limitations and future research developments that will improve its utility in a wide range of applications.

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Nanopore sequencing of long ribosomal DNA amplicons enables portable and simple biodiversity assessments with high phylogenetic resolution across broad taxonomic scale

10.1101/358572 ◽

2018 ◽

Cited By ~ 6

Author(s):

Henrik Krehenwinkel ◽

Aaron Pomerantz ◽

James B. Henderson ◽

Susan R. Kennedy ◽

Jun Ying Lim ◽

...

Keyword(s):

Dna Barcoding ◽

Ribosomal Dna ◽

Scale Up ◽

Community Diversity ◽

Taxonomic Resolution ◽

Taxonomic Assignment ◽

Accurate Identification ◽

Phylogenetic Structure ◽

Biodiversity Crisis ◽

Phylogenetic Resolution

AbstractBackgroundIn light of the current biodiversity crisis, DNA barcoding is developing into an essential tool to quantify state shifts in global ecosystems. Current barcoding protocols often rely on short amplicon sequences, which yield accurate identification of biological entities in a community, but provide limited phylogenetic resolution across broad taxonomic scales. However, the phylogenetic structure of communities is an essential component of biodiversity. Consequently, a barcoding approach is required that unites robust taxonomic assignment power and high phylogenetic utility. A possible solution is offered by sequencing long ribosomal DNA (rDNA) amplicons on the MinION platform (Oxford Nanopore Technologies).ResultsUsing a dataset of various animal and plant species, with a focus on arthropods, we assemble a pipeline for long rDNA barcode analysis and introduce a new software (MiniBar) to demultiplex dual indexed nanopore reads. We find excellent phylogenetic and taxonomic resolution offered by long rDNA sequences across broad taxonomic scales. We highlight the simplicity of our approach by field barcoding with a miniaturized, mobile laboratory in a remote rainforest. We also test the utility of long rDNA amplicons for analysis of community diversity through metabarcoding and find that they recover highly skewed diversity estimates.ConclusionsSequencing dual indexed, long rDNA amplicons on the MinION platform is a straightforward, cost effective, portable and universal approach for eukaryote DNA barcoding. Long rDNA amplicons scale up DNA barcoding by enabling the accurate recovery of taxonomic and phylogenetic diversity. However, bulk community analyses using long-read approaches may introduce biases and will require further exploration.

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Adding DNA barcoding to stream monitoring protocols – What’s the additional value and congruence between morphological and molecular identification approaches?

PLoS ONE ◽

10.1371/journal.pone.0244598 ◽

2021 ◽

Vol 16 (1) ◽

pp. e0244598

Author(s):

Simone Behrens-Chapuis ◽

Fabian Herder ◽

Matthias F. Geiger

Keyword(s):

Dna Barcoding ◽

Cost Benefit Analysis ◽

Ecological Status ◽

Species Level ◽

Aquatic Macroinvertebrates ◽

Taxonomic Resolution ◽

Morphological Identification ◽

Stream Monitoring ◽

Monitoring Protocols ◽

Additional Value

Although aquatic macroinvertebrates and freshwater fishes are important indicators for freshwater quality assessments, the morphological identification to species-level is often impossible and thus especially in many invertebrate taxa not mandatory during Water Framework Directive monitoring, a pragmatism that potentially leads to information loss. Here, we focus on the freshwater fauna of the River Sieg (Germany) to test congruence and additional value in taxa detection and taxonomic resolution of DNA barcoding vs. morphology-based identification in monitoring routines. Prior generated morphological identifications of juvenile fishes and aquatic macroinvertebrates were directly compared to species assignments using the identification engine of the Barcode of Life Data System. In 18% of the invertebrates morphology allowed only assignments to higher systematic entities, but DNA barcoding lead to species-level assignment. Dissimilarities between the two approaches occurred in 7% of the invertebrates and in 1% of the fishes. The 18 fish species were assigned to 20 molecular barcode index numbers, the 104 aquatic invertebrate taxa to 113 molecular entities. Although the cost-benefit analysis of both methods showed that DNA barcoding is still more expensive (5.30–8.60€ per sample) and time consuming (12.5h), the results emphasize the potential to increase taxonomic resolution and gain a more complete profile of biodiversity, especially in invertebrates. The provided reference DNA barcodes help building the foundation for metabarcoding approaches, which provide faster sample processing and more cost-efficient ecological status determination.

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Discrimination of Cricotopus species (Diptera: Chironomidae) by DNA barcoding

Bulletin of Entomological Research ◽

10.1017/s0007485308005865 ◽

2008 ◽

Vol 98 (6) ◽

pp. 555-563 ◽

Cited By ~ 33

Author(s):

C.S. Sinclair ◽

S.E. Gresens

Keyword(s):

Water Quality ◽

Cytochrome Oxidase ◽

Dna Barcoding ◽

Mitochondrial Gene ◽

Accurate Method ◽

Taxonomic Resolution ◽

Molecular Approaches ◽

Putative Species ◽

Sequence Variations ◽

Wide Range

AbstractChironomids (Diptera) typically comprise the most abundant group of macroinvertebrates collected in water quality surveys. Species in the genus Cricotopus display a wide range of tolerance for manmade pollutants, making them excellent bioindicators. Unfortunately, the usefulness of Cricotopus is overshadowed by the difficulty of accurately identifying larvae using current morphological keys. Molecular approaches are now being used for identification and taxonomic resolution in many animal taxa. In this study, a sequence-based approach for the mitochondrial gene, cytochrome oxidase I (COI), was developed to facilitate identification of Cricotopus species collected from Baltimore area streams. Using unique COI sequence variations, we developed profiles for seven described Cricotopus sp., four described Orthocladius sp., one described Paratrichocladius sp. and one putative species of Cricotopus. In addition to providing an accurate method for identification of Cricotopus, this method will make a useful contribution to the development of keys for Nearctic Cricotopus.

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The importance of taxonomic resolution for additive beta diversity as revealed through DNA barcoding

Genome ◽

10.1139/gen-2016-0080 ◽

2016 ◽

Vol 59 (12) ◽

pp. 1130-1140 ◽

Cited By ~ 6

Author(s):

Trevor T. Bringloe ◽

Karl Cottenie ◽

Gillian K. Martin ◽

Sarah J. Adamowicz

Keyword(s):

Dna Barcoding ◽

Species Turnover ◽

Spatial Scales ◽

Species Level ◽

Taxonomic Resolution ◽

Diversity Partitioning ◽

Spatial Design ◽

Β Diversity ◽

Caddisfly Larvae ◽

Additive Measures

Additive diversity partitioning (α, β, and γ) is commonly used to study the distribution of species-level diversity across spatial scales. Here, we first investigate whether published studies of additive diversity partitioning show signs of difficulty attaining species-level resolution due to inherent limitations with morphological identifications. Second, we present a DNA barcoding approach to delineate specimens of stream caddisfly larvae (order Trichoptera) and consider the importance of taxonomic resolution on classical (additive) measures of beta (β) diversity. Caddisfly larvae were sampled using a hierarchical spatial design in two regions (subarctic Churchill, Manitoba, Canada; temperate Pennsylvania, USA) and then additively partitioned according to Barcode Index Numbers (molecular clusters that serve as a proxy for species), genus, and family levels; diversity components were expressed as proportional species turnover. We screened 114 articles of additive diversity partitioning and found that a third reported difficulties with achieving species-level identifications, with a clear taxonomic tendency towards challenges identifying invertebrate taxa. Regarding our own study, caddisfly BINs appeared to show greater subregional turnover (e.g., proportional additive β) compared to genus or family levels. Diversity component studies failing to achieve species resolution due to morphological identifications may therefore be underestimating diversity turnover at larger spatial scales.

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Examination of two new technologies to assess the diet of woodland caribou: video recorders attached to collars and DNA barcoding

Canadian Journal of Forest Research ◽

10.1139/cjfr-2013-0108 ◽

2013 ◽

Vol 43 (10) ◽

pp. 897-900 ◽

Cited By ~ 21

Author(s):

Steven G. Newmaster ◽

Ian D. Thompson ◽

Royce A.D. Steeves ◽

Arthur R. Rodgers ◽

Aron J. Fazekas ◽

...

Keyword(s):

Dna Barcoding ◽

Rangifer Tarandus ◽

New Technologies ◽

Early Spring ◽

Taxonomic Resolution ◽

Conservation Strategies ◽

Late Winter ◽

Woodland Caribou ◽

Fecal Samples ◽

Novel Technologies

The diet of woodland caribou (Rangifer tarandus caribou Gmelin, 1788) in the boreal zone of North America is poorly understood. In large part this is because they occur at low densities in environments that are difficult to access. The only method available for identifying food requirements of wildlife has been histological examination of fecal samples, a technique that suffers from a number of serious limitations. Our study used fecal samples from 125 woodland caribou and animal-borne videos to address two questions: (1) How do the new technologies, video cameras and DNA barcoding, compare with conventional diet analyses of fecal pellets? and (2) Can these techniques be used to determine the diet of woodland caribou? Our results show that microhistology estimates provide an inaccurate approximation of diet; <15% correlation with either barcoding or video techniques. Taxonomic resolution of the histology estimates was very low. Taxonomic resolution to species found in fecal samples was good using video (42%) but better using DNA barcoding (94%). DNA barcoding and video technologies provided dietary data that were highly correlated (70%) among major groups of plants, with terrestrial lichens dominating the late winter through early spring diet. The high species resolution of DNA barcoding may be supplemented by information on habitat preference and degree of feeding selectivity obtained by video surveillance. These novel technologies may be important tools for identifying critical habitat requirements and associated conservation strategies needed for elusive wildlife species that are endangered.

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The applicability of DNA barcoding for dietary analysis of sika deer

DNA Barcodes ◽

10.1515/dna-2015-0021 ◽

2015 ◽

Vol 3 (1) ◽

Cited By ~ 14

Author(s):

Fumiko Nakahara ◽

Haruko Ando ◽

Hideyuki Ito ◽

Asako Murakami ◽

Naoki Morimoto ◽

...

Keyword(s):

Dna Barcoding ◽

Sika Deer ◽

Food Plants ◽

Forest Understory ◽

Taxonomic Resolution ◽

Fecal Dna ◽

Dietary Analysis ◽

Global Database ◽

Loop Region ◽

The Impact

AbstractIn Japan, overgrazing by sika deer (Cervus nippon) has been suggested to cause a decline in forest understory vegetation. DNA barcoding has become an accepted method for analyzing the diets of animals and may be useful for evaluating the impact of sika deer on vegetation. However, the applicability of DNA barcoding in the dietary analysis of sika deer, particularly whether all of the food plants can be detected with sufficient taxonomic resolution and whether the results can be evaluated quantitatively, has not been investigated. We conducted a feeding trial by feeding five plant species to a captive sika deer and sequenced the chloroplast trnL P6 loop region from the sika deer’s fecal DNA using the Ion PGM sequencer. We detected the sequences of all of the food plants at the species level using the local (selfproduced) database and at the genus or family level with the global database. Although the sequences of some major food plants were detected with high frequency, the proportion of consumed food plants did not match the proportion of sequences obtained from fecal DNA. With further technical advances and the further completeness of the sequence database for vegetation, DNA barcoding will be a useful tool for the dietary study of sika deer.

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DNA Barcoding for Delimitation of Putative Mexican Marine Nematodes Species

Diversity ◽

10.3390/d12030107 ◽

2020 ◽

Vol 12 (3) ◽

pp. 107 ◽

Cited By ~ 3

Author(s):

Arely Martínez-Arce ◽

Alberto De Jesús-Navarrete ◽

Francesca Leasi

Keyword(s):

Dna Barcoding ◽

Low Cost ◽

Nematode Species ◽

Molecular Data ◽

Coi Gene ◽

Taxonomic Resolution ◽

Species List ◽

Nematode Diversity ◽

Coi Sequences ◽

Morphological And Molecular Data

Nematode biodiversity is mostly unknown; while about 20,000 nematode species have been described, estimates for species diversity range from 0.1 to 100 million. The study of nematode diversity, like that of meiofaunal organisms in general, has been mostly based on morphology-based taxonomy, a time-consuming and costly task that requires well-trained specialists. This work represents the first study on the taxonomy of Mexican nematodes that integrates morphological and molecular data. We added eleven new records to the Mexican Caribbean nematode species list: Anticomidae sp.1, Catanema sp.1, Enoploides gryphus, Eurystomina sp.1, Haliplectus bickneri, Metachromadora sp.1, Odontophora bermudensis, Oncholaimus sp.1, Onyx litorale, Proplatycoma fleurdelis, and Pontonema cf. simile. We improved the COI database with 57 new sequences from 20 morphotypes. All COI sequences obtained in this work are new entries for the international genetic databases GenBank and BOLD. Among the studied sites, we report the most extensive species record (12 species) at Cozumel. DNA barcoding and species delineation methods supported the occurrence of 20 evolutionary independent entities and confirmed the high taxonomic resolution of the COI gene. Different approaches provided consistent results: ABGD and mPTP methods disentangled 20 entities, whereas Barcode Index Numbers (BINs) recovered 22 genetic species. Results support DNA barcoding being an efficient, fast, and low-cost method to integrate into morphological observations in order to address taxonomical shortfalls in meiofaunal organisms.

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