DNA barcoding vs. morphological identification of larval fish and embryos in Lake Huron: Advantages to a molecular approach

Hulley, Emily N.; Taylor, N D; Zarnke, Andrew M.; Somers, Christopher M.; Manzon, Richard G.; Wilson, Joanna Y.; Boreham, Douglas R.

doi:10.1016/j.jglr.2018.07.013

Cited by 16 publications

(16 citation statements)

References 28 publications

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“…The two species that we could not distinguish on a molecular basis-E. nigrum and E. podostemone-are both members of subgenus Boleostoma; while they are closely related phylogenetically, screening of a longer fragment of the COI gene or of other mitochondrial sequences that distinguish them [25] could provide the basis for development of diagnostic barcoding markers. Similar issues were found regarding inability of COI to resolve members of genus Coregonus, the whitefishes, by Hulley et al [19].…”

Section: Molecular Versus Phenotypic Characterization Of Larval Darterssupporting

confidence: 66%

“…The sites encompassed a longitudinal gradient of known Etheostoma and Percina habitats and represented spatial variation in environmental conditions encountered by larval darters. Each site was sampled an average of 14.6 (13-16) times in 2015 and 17.2 (15)(16)(17)(18)(19) times in 2018, equivalent to one sample every 5.3 (4.9-6) days in 2015, and one sample every 4.2 (3.8-4.9) days in 2018.…”

Section: Field Methodsmentioning

confidence: 99%

“…With the molecular identifications in hand, we assessed whether counts of pre-anal myomeres (PM) were useful for identification of larval darters of the upper Roanoke River, as is the case for many darters [29]. P. rex had the highest median PM count of 24, followed by P. nevisense (22), P. roanoka (19), E. nigrum/podostemone (17), E. vitreum (17), and E. flabellare (15). Critically for our purposes, there was overlap across species ( Figure 1); therefore, PM count alone cannot reliably distinguish all larval darter species of the upper Roanoke River system.…”

Section: Correspondence Of Molecular Identifications With Phenotypic mentioning

confidence: 99%

“…[16][17][18]. Comparison of DNA barcoding and morphological identification of larval fish and embryos from Lake Huron in Canada [19] showed that while each method has pros and cons, barcoding was more cost-effective and efficient for monitoring at a large scale. However, applications of DNA barcoding to the study of freshwater stream fish communities are relatively few.…”

Section: Introductionmentioning

confidence: 99%

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Drift of Larval Darters (Family Percidae) in the Upper Roanoke River Basin, USA, Characterized Using Phenotypic and DNA Barcoding Markers

Buckwalter

Angermeier

Argentina

et al. 2019

Fishes

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Larval fish ecology is poorly characterized because sampling is difficult and tools for phenotypically identifying larvae are poorly developed. While DNA barcoding can help address the latter problem, ‘universal’ primers do not work for all fish species. The Roanoke River in the southeastern United States includes seven darters (Family Percide: Tribe Etheostomatini). We made 393 collections of larval fishes in 2015 and 2018, examined darter larvae for morphometric and pigmentation traits, developed PCR primers amplifying darter DNA, and evaluated three gear types for collecting larval darters. Amplified DNA sequences for 1351 larvae matched archived mitochondrial cytochrome oxidase I sequences for darters occurring in the ecosystem. Larval darters were classified to genus with 100% accuracy using the ratio of pectoral fin length to body length; however, identification to species using morphometrics alone was subject to a misclassification rate of 11.8%, which can be resolved by considering pigmentation patterns. Gear-types varied considerably in their capture efficacy for larval darters; most Percina larvae were collected in drift nets. Larval Percina species appeared in the drift before Etheostoma species in both study years. Application of molecular genetic and phenotypic tools to larval fish identification can advance understanding of larval darter ecology.

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Section: Molecular Versus Phenotypic Characterization Of Larval Darterssupporting

confidence: 66%

Section: Field Methodsmentioning

confidence: 99%

Section: Correspondence Of Molecular Identifications With Phenotypic mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Drift of Larval Darters (Family Percidae) in the Upper Roanoke River Basin, USA, Characterized Using Phenotypic and DNA Barcoding Markers

Buckwalter

Angermeier

Argentina

et al. 2019

Fishes

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“…DNA metabarcoding is proposed as a tool to reduce the time and cost necessary for morphological identification: the cost of DNA metabarcoding using high throughput sequencing techniques (HTS) is comparable to or even lower than traditional morphology-based methods (Hulley et al, 2018;Yu et al, 2012). The use of DNA metabarcoding could also result in substantial reduction in time spent on identification.…”

Section: Discussionmentioning

confidence: 99%

DNA metabarcoding adds valuable information for management of biodiversity in roadside stormwater ponds

Sun

Majaneva

Sokolova

et al. 2019

Ecology and Evolution

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Stormwater ponds are used to compensate for the adverse effects that road runoff might have on the natural environment. Depending on their design and placement, stormwater ponds can act as both refugia and traps for local biodiversity. To evaluate the impact of stormwater ponds on biodiversity, it is critical to use effective and precise methods for identification of life associated with the water body. DNA metabarcoding has recently become a promising tool for identification and assessment of freshwater biodiversity. Using both morphology and DNA metabarcoding, we analyze species richness and biological composition of samples from 12 stormwater ponds and investigate the impact of pond size and pollution levels in the sediments and water column on the macroinvertebrate community structure. DNA metabarcoding captured and identified more than twice the number of taxa compared to morphological identification. The (dis)similarity of macroinvertebrate community composition in different ponds showed that the ponds appear better separated in the results obtained by DNA metabarcoding, but that the explained variation is higher for the results obtained by morphologically identification, since it provides abundance data. The reliance on morphological methods has limited our perception of the aquatic biodiversity in response to anthropogenic stressors, thereby providing inaccurate information for appropriate design and management of stormwater ponds; these drawbacks can be overcome by DNA metabarcoding. Synthesis and applications. The results indicate that DNA metabarcoding is a useful tool in identifying species, especially Diptera, which are difficult to determine. Application of DNA metabarcoding greatly increases the number of species identified at each sampling site, thereby providing a more accurate information regarding the way the ponds function and how they are affected by management. OPEN PRACTICES This article has earned an Open Data Badge for making publicly available the digitally‐shareable data necessary to reproduce the reported results. The data is available at https://www.ebi.ac.uk/ena/data/view/PRJEB30841.

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DNA barcoding of terrestrial invasive plant species in Southwest Michigan

Nath,

VanSlambrouck,

Yao

et al. 2024

Plant Direct

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Because of the detrimental effects of terrestrial invasive plant species (TIPS) on native species, ecosystems, public health, and the economy, many countries have been actively looking for strategies to prevent the introduction and minimize the spread of TIPS. Fast and accurate detection of TIPS is essential to achieving these goals. Conventionally, invasive species monitoring has relied on morphological attributes. Recently, DNA‐based species identification (i.e., DNA barcoding) has become more attractive. To investigate whether DNA barcoding can aid in the detection and management of TIPS, we visited multiple nature areas in Southwest Michigan and collected a small piece of leaf tissue from 91 representative terrestrial plant species, most of which are invasive. We extracted DNA from the leaf samples, amplified four genomic loci (ITS, rbcL, matK, and trnH‐psbA) with PCR, and then purified and sequenced the PCR products. After careful examination of the sequencing data, we were able to identify reliable DNA barcode regions for most species and had an average PCR‐and‐sequencing success rate of 87.9%. We found that the species discrimination rate of a DNA barcode region is inversely related to the ease of PCR amplification and sequencing. Compared with rbcL and matK, ITS and trnH‐psbA have better species discrimination rates (80.6% and 63.2%, respectively). When ITS and trnH‐psbA are simultaneously used, the species discrimination rate increases to 97.1%. The high species/genus/family discrimination rates of DNA barcoding indicate that DNA barcoding can be successfully employed in TIPS identification. Further increases in the number of DNA barcode regions show little or no additional increases in the species discrimination rate, suggesting that dual‐barcode approaches (e.g., ITS + trnH‐psbA) might be the efficient and cost‐effective method in DNA‐based TIPS identification. Close inspection of nucleotide sequences at the four DNA barcode regions among related species demonstrates that DNA barcoding is especially useful in identifying TIPS that are morphologically similar to other species.

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DNA barcoding vs. morphological identification of larval fish and embryos in Lake Huron: Advantages to a molecular approach

Cited by 16 publications

References 28 publications

Drift of Larval Darters (Family Percidae) in the Upper Roanoke River Basin, USA, Characterized Using Phenotypic and DNA Barcoding Markers

Drift of Larval Darters (Family Percidae) in the Upper Roanoke River Basin, USA, Characterized Using Phenotypic and DNA Barcoding Markers

DNA metabarcoding adds valuable information for management of biodiversity in roadside stormwater ponds

DNA barcoding of terrestrial invasive plant species in Southwest Michigan

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