Studying Ecosystems With DNA Metabarcoding: Lessons From Biomonitoring of Aquatic Macroinvertebrates

Буш, А. А.; Compson, Zacchaeus G.; Monk, Wendy; Porter, Teresita M.; Steeves, Royce; Emilson, Erik J. S.; Gagné, Nellie; Hajibabaei, Mehrdad; Roy, Mélanie; Baird, Donald J.

doi:10.3389/fevo.2019.00434

Cited by 99 publications

(106 citation statements)

References 96 publications

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“…Our results directly hint at taxonomic identification based on mitochondrial barcoding, which could reveal helpful in cases where morphological examination of fragmentary or undiagnostic shell remains preclude classification. Mollusk aDNA analyses are compatible with shotgun-or mitochondrial metabarcoding-based (Bush et al, 2019) reconstructions of past communities from bulk samples (e.g., Murray et al, 2013;Grealy et al, 2015;Seersholm et al, 2018) or sediment cores (e.g., Giguet-Covex et al, 2014;Pedersen et al, 2016), which could be of relevance to the study of shell middens. Temporal changes in ecosystems detected through such approaches could reveal interesting insights into the timing and impact of environmental changes, biological invasions and extinctions.…”

Section: Potential Of Ancient Mollusk Dna For Ecological Studiesmentioning

confidence: 79%

Unveiling the Ecological Applications of Ancient DNA From Mollusk Shells

et al. 2020

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The shells of marine mollusks represent promising metagenomic archives of the past, adding to bones, teeth, hairs, and environmental samples most commonly examined in ancient DNA research. Seminal work has established that DNA recovery from marine mollusk shells depends on their microstructure, preservation and disease state, and that authentic ancient DNA could be retrieved from specimens as old as 7,000 years. Here, we significantly push the temporal limit for shell DNA recovery to ≥100,000 years with the successful genetic characterization of one Portlandia arctica and one Mytilus mussel sample collected within a dated permafrost layer from the Taimyr Peninsula, Russia. We expand the analysis of ancient DNA in carbonate shells to a larger number of genera (Arctica, Cernuella, Crassostrea, Dreissena, Haliotis, Lymnaea, Margaritifera, Pecten, Ruditapes, Venerupis) from marine, freshwater and terrestrial environments. We demonstrate that DNA from ancient shells can provide sufficient resolution for taxonomic, phylogenetic and/or population assignment. Our results confirm mollusk shells as long-term DNA reservoirs, opening new avenues for the investigation of environmental changes, commercial species management, biological invasion, and extinction. This is especially timely in light of modern threats to biodiversity and ecosystems.

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Section: Potential Of Ancient Mollusk Dna For Ecological Studiesmentioning

confidence: 79%

Unveiling the Ecological Applications of Ancient DNA From Mollusk Shells

et al. 2020

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“…Amongst primer pairs, differences in binding to DNA templates lead to amplification biases, affecting both read abundances and detections of species, so that any single primer set will lead to detections of a subset of species (Elbrecht andLeese 2017, Hajibabaei et al 2019). The mlCOIlintF/HCO2198 primer pair which we used amplifies well across a broad range of arthropod taxa (Leray et al 2013, Brandon-Mong et al 2015, but, in future efforts, we would consider selecting the mlCOIlintF/jgHCO2198 primer pair, which has a more degenerate reverse primer and amplifies well across a broader range of arthropod taxa than the mlCOIlintF/HCO2198 pair (Elbrecht and Leese 2017).…”

Section: Methodological Commentsmentioning

confidence: 99%

“…Sequencing was performed on an Illumina MiSeq platform and reads were processed using RTL Genomics' standard methods with the mlCOIlintF/HCO2198 primer set of Leray et al 2013, yielding a 313 bp region of the COI gene. We selected this primer set because it has been shown to amplify well across a broad set of arthropod groups (Brandon-Mong et al 2015).…”

Section: Sweep Net Samples Of Terrestrial Arthropodsmentioning

confidence: 99%

Towards conserving natural diversity: A biotic inventory by observations, specimens, DNA barcoding and high-throughput sequencing methods

Bowser¹,

Brassfield²,

Dziergowski³

et al. 2020

BDJ

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The Kenai National Wildlife Refuge has been given a broad conservation mandate to conserve natural diversity. A prerequisite for fulfilling this purpose is to be able to identify the species and communities that make up that biodiversity. We tested a set of varied methods for inventory and monitoring of plants, birds and terrestrial invertebrates on a grid of 40 sites in a 938 ha study area in the Slikok Creek watershed, Kenai Peninsula, Alaska. We sampled plants and lichens through observation and specimen-based methods. We surveyed birds using bird call surveys on variable circular plots. We sampled terrestrial arthropods by sweep net sampling, processing samples with High Throughput Sequencing methods. We surveyed for earthworms, using the hot mustard extraction method and identified worm specimens by morphology and DNA barcoding. We examined community membership using clustering methods and Nonmetric Multidimensional Scaling. We documented a total of 4,764 occurrences of 984 species and molecular operational taxonomic units: 87 vascular plants, 51 mosses, 12 liverworts, 111 lichens, 43 vertebrates, 663 arthropods, 9 molluscs and 8 annelid worms. Amongst these records, 102 of the arthropod species appeared to be new records for Alaska. We found three non-native species: Deroceras agreste (Linnaeus, 1758) (Stylommatophora: Agriolimacidae), Dendrobaena octaedra (Savigny, 1826) (Crassiclitellata: Lumbricidae) and Heterarthrus nemoratus (Fallén, 1808) (Hymenoptera: Tenthredinidae). Both D. octaedra and H. nemoratus were found at sites distant from obvious human disturbance. The 40 sites were grouped into five community groups: upland mixed forest, black spruce forest, open deciduous forest, shrub-sedge bog and willow. We demonstrated that, at least for a subset of species that could be detected using these methods, we were able to document current species distributions and assemblages in a way that could be efficiently repeated for the purposes of biomonitoring. While our methods could be improved and additional methods and groups could be added, our combination of techniques yielded a substantial portion of the data necessary for fulfilling Kenai National Wildlife Refuge's broad conservation purposes.

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“…Broader scale applications of metabarcoding can be used to detect seasonal and temporal patterns important for ecosystem restoration and analysis [8][9][10]. We should note that observed differences can result from both large taxonomic differences and from more slight changes that occur between co-occurring related species in an environment [11,12].…”

Section: Introductionmentioning

confidence: 99%

Uncovering Effects from the Structure of Metabarcode Sequences for Metagenetic and Microbiome Analysis

Molik

Pfrender

Emrich

2020

MPs

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The advent of next-generation sequencing has allowed for higher-throughput determination of which species live within a specific location. Here we establish that three analysis methods for estimating diversity within samples—namely, Operational Taxonomic Units; the newer Amplicon Sequence Variants; and a method commonly found in sequence analysis, minhash—are affected by various properties of these sequence data. Using simulations we show that the presence of Single Nucleotide Polymorphisms and the depth of coverage from each species affect the correlations between these approaches. Through this analysis, we provide insights which would affect the decisions on the application of each method. Specifically, the presence of sequence read errors and variability in sequence read coverage deferentially affects these processing methods.

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Studying Ecosystems With DNA Metabarcoding: Lessons From Biomonitoring of Aquatic Macroinvertebrates

Cited by 99 publications

References 96 publications

Unveiling the Ecological Applications of Ancient DNA From Mollusk Shells

Unveiling the Ecological Applications of Ancient DNA From Mollusk Shells

Towards conserving natural diversity: A biotic inventory by observations, specimens, DNA barcoding and high-throughput sequencing methods

Uncovering Effects from the Structure of Metabarcode Sequences for Metagenetic and Microbiome Analysis

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