Aquatic Organisms Research with DNA Barcodes

Elías‐Gutiérrez, Manuel; Hubert, Nicolas; Collins, Rupert A.; Andrade-Sossa, Camilo

doi:10.3390/d13070306

Cited by 12 publications

(8 citation statements)

References 163 publications

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“…Although some libraries are being developed, they host material, in this case, fish, from limited biodiversity regions (Collins et al, 2021). In comparison to the Neotropics, for example, in the middle Amazon Basin, near Leticia (Colombia), in just 40 km 2 , Galvis et al (2006) registered 344 fish species.…”

Section: Methodsmentioning

confidence: 99%

“…In the case of fish, they are the aquatic group with more DNA barcoding studies (Elías-Gutiérrez et al, 2021). Yao et al (2022) analyzed all publications involving fish and eDNA.…”

Section: Current Trendsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…Nevertheless, the studies incorporating DNA barcodes have increased steadily since their inception to nearly 1400 in the year 2020 (Elías-Gutiérrez et al, 2021), despite the predictions of some people about their end (Taylor and Harris, 2012). Accordingly, Elías-Gutiérrez et al (2021) proposed that the advancement today has not been the same with aquatic organisms, and it has been less in freshwaters, with no more than 90 publications in the same year. Most probably, these limited results are due to problems amplifying the proposed standardized gene as DNA barcodes, the first half of cytochrome c oxidase I (COI or COX1), mainly in invertebrates (Elías-Gutiérrez et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

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Relevance of DNA barcodes for biomonitoring of freshwater animals

Elías‐Gutiérrez

Valdéz-Moreno²

2023

Front. Environ. Sci.

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The COI gene, colloquially named the DNA barcode, is a universal marker for species identification in the animal kingdom. Nevertheless, due to the taxonomic impediment, there are various proposals for molecular operational taxonomic units (MOTUs) because high-throughput sequencers can generate millions of sequences in one run. In the case of freshwater systems, it is possible to analyze whole communities through their DNA using only water or sediment as a sample. Using DNA barcodes with these technologies is known as metabarcoding. More than 90% of studies based on eDNA work with MOTUs without previous knowledge of the biodiversity in the habitat. Despite this problem, it has been proposed as the future for biomonitoring. All these studies are biased toward the Global North and focused on freshwater macrofaunae. Few studies include other regions of the world or other communities, such as zooplankton and phytoplankton. The future of biomonitoring should be based on a standardized gene, for example, COI, the most studied gene in animals, or another secondary consensual gene. Here, we analyzed some proposals with 28S or 12S. The studies on eDNA can focus on analyses of the whole community or a particular species. The latter can be an endangered or exotic species. Any eDNA study focused on a community study should have a well-documented DNA baseline linked to vouchered specimens. Otherwise, it will be tough to discriminate between false positives and negatives. Biomonitoring routines based on eDNA can detect a change in a community due to any perturbation of the aquatic ecosystem. Also, it can track changes along the history of an epicontinental environment through the analyses of sediments. However, their implementation will be complex in most megadiverse Neotropical countries due to the lack of these baselines. It has been demonstrated that a rapid functional construction of a DNA baseline is possible, although the curation of the species can take more time. However, there is a lack of governmental interest in this kind of research and subsequent biomonitoring.

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Section: Methodsmentioning

confidence: 99%

“…In the case of fish, they are the aquatic group with more DNA barcoding studies (Elías-Gutiérrez et al, 2021). Yao et al (2022) analyzed all publications involving fish and eDNA.…”

Section: Current Trendsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Relevance of DNA barcodes for biomonitoring of freshwater animals

Elías‐Gutiérrez

Valdéz-Moreno²

2023

Front. Environ. Sci.

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“…The marker MtDNA cytochrome c oxidase 1 (COI) has been commonly used for aquatic species identification—barcoding [ 149 , 150 , 151 ]. However, mtDNA introgression from one species to another has been reported in populations in which hybridization occurs [ 152 , 153 , 154 , 155 ].…”

Section: Introductionmentioning

confidence: 99%

Microsatellites as Molecular Markers with Applications in Exploitation and Conservation of Aquatic Animal Populations

Wenne

2023

Genes

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A large number of species and taxa has been studied for genetic polymorphism. Microsatellites have been known as hypervariable neutral molecular markers with the highest resolution power in comparison with any other markers. However, the discovery of a new type of molecular marker—single nucleotide polymorphism (SNP) has put the existing applications of microsatellites to the test. To ensure good resolution power in studies of populations and individuals, a number of microsatellite loci from 14 to 20 was often used, which corresponds to about 200 independent alleles. Recently, these numbers have tended to be increased by the application of genomic sequencing of expressed sequence tags (ESTs), and the choice of the most informative loci for genotyping depends on the aims of research. Examples of successful applications of microsatellite molecular markers in aquaculture, fisheries, and conservation genetics in comparison with SNPs have been summarized in this review. Microsatellites can be considered superior markers in such topics as kinship and parentage analysis in cultured and natural populations, the assessment of gynogenesis, androgenesis and ploidization. Microsatellites can be coupled with SNPs for mapping QTL. Microsatellites will continue to be used in research on genetic diversity in cultured stocks, and also in natural populations as an economically advantageous genotyping technique.

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