12 results found
Creedy TJ, Andújar C, Meramveliotakis E, et al., 2021, Coming of age for COI metabarcoding of whole organism community DNA: towards bioinformatic harmonisation., Molecular Ecology Resources, ISSN: 1471-8278
Metabarcoding of DNA extracted from community samples of whole organisms (whole organism community DNA, wocDNA) is increasingly being applied to terrestrial, marine and freshwater metazoan communities to provide rapid, accurate and high resolution data for novel molecular ecology research. The growth of this field has been accompanied by considerable development that builds on microbial metabarcoding methods to develop appropriate and efficient sampling and laboratory protocols for whole organism metazoan communities. However, considerably less attention has focused on ensuring bioinformatic methods are adapted and applied comprehensively in wocDNA metabarcoding. In this study we examined over 600 papers and identified 111 studies that performed COI metabarcoding of wocDNA. We then systematically reviewed the bioinformatic methods employed by these papers to identify the state-of-the-art. Our results show that the increasing use of wocDNA COI metabarcoding for metazoan diversity is characterised by a clear absence of bioinformatic harmonisation, and the temporal trends show little change in this situation. The reviewed literature showed (i) high heterogeneity across pipelines, tasks and tools used, (ii) limited or no adaptation of bioinformatic procedures to the nature of the COI fragment, and (iii) a worrying underreporting of tasks, software and parameters. Based upon these findings we propose a set of recommendations that we think the metabarcoding community should consider to ensure that bioinformatic methods are appropriate, comprehensive and comparable. We believe that adhering to these recommendations will improve the long-term integrative potential of wocDNA COI metabarcoding for biodiversity science.
Arribas P, Andujar C, Bidartondo MI, et al., 2021, Connecting high-throughput biodiversity inventories: Opportunities for a site-based genomic framework for global integration and synthesis, Molecular Ecology, Vol: 30, Pages: 1120-1135, ISSN: 0962-1083
High‐throughput sequencing (HTS) is increasingly being used for the characterization and monitoring of biodiversity. If applied in a structured way, across broad geographical scales, it offers the potential for a much deeper understanding of global biodiversity through the integration of massive quantities of molecular inventory data generated independently at local, regional and global scales. The universality, reliability and efficiency of HTS data can potentially facilitate the seamless linking of data among species assemblages from different sites, at different hierarchical levels of diversity, for any taxonomic group and regardless of prior taxonomic knowledge. However, collective international efforts are required to optimally exploit the potential of site‐based HTS data for global integration and synthesis, efforts that at present are limited to the microbial domain. To contribute to the development of an analogous strategy for the nonmicrobial terrestrial domain, an international symposium entitled “Next Generation Biodiversity Monitoring” was held in November 2019 in Nicosia (Cyprus). The symposium brought together evolutionary geneticists, ecologists and biodiversity scientists involved in diverse regional and global initiatives using HTS as a core tool for biodiversity assessment. In this review, we summarize the consensus that emerged from the 3‐day symposium. We converged on the opinion that an effective terrestrial Genomic Observatories network for global biodiversity integration and synthesis should be spatially led and strategically united under the umbrella of the metabarcoding approach. Subsequently, we outline an HTS‐based strategy to collectively build an integrative framework for site‐based biodiversity data generation.
Andujar C, Creedy TJ, Arribas P, et al., 2021, Validated removal of nuclear pseudogenes and sequencing artefacts from mitochondrial metabarcode data, MOLECULAR ECOLOGY RESOURCES, Vol: 21, Pages: 1772-1787, ISSN: 1755-098X
Creedy TJ, Norman H, Tang CQ, et al., 2020, A validated workflow for rapid taxonomic assignment and monitoring of a national fauna of bees (Apiformes) using high throughput DNA barcoding, MOLECULAR ECOLOGY RESOURCES, Vol: 20, Pages: 40-53, ISSN: 1755-098X
Creedy TJ, Ng WS, Vogler A, 2019, Towards accurate species-level metabarcoding of arthropod communities from the tropical forest canopy, Ecology and Evolution, Vol: 6, Pages: 3105-3116, ISSN: 2045-7758
Metabarcoding of arthropod communities can be used for assessing species diversity in tropical forests but the methodology requires validation for accurate and repeatable species occurrences in complex mixtures. This study investigates how the composition of ecological samples affects the accuracy of species recovery. Starting with field-collected bulk samples from the tropical canopy, the recovery of specimens was tested for subsets of different body sizes and major taxa, by assembling these subsets into increasingly complex composite pools. After metabarcoding, we track whether richness, diversity and most importantly composition of any size class or taxonomic subset is affected by the presence of other subsets in the mixture.Operational Taxonomic Units (OTUs) greatly exceeded the number of morphospecies in most taxa, even under very stringent sequencing read filtering. There was no significant effect on the recovered OTU richness of small and medium-sized arthropods when metabarcoded alongside larger arthropods, despite substantial biomass differences in the mixture. The recovery of taxonomic subsets was not generally influenced by the presence of other taxa, although with some exceptions likely due to primer mismatches. Considerable compositional variation within size and taxon-based subcommunities were evident resulting in high beta diversity among samples from within a single tree canopy, but this beta diversity was not affected by experimental manipulation.We conclude that OTU recovery in complex arthropod communities, with sufficient sequencing depth and within reasonable size ranges, is not skewed by variable biomass of the constituent species. This could remove the need for time-intensive manual sorting prior to metabarcoding. However, there remains a chance of taxonomic bias, which may be primer-dependent. There will never be a panacea primer; instead, metabarcoding studies should carefully consider whether the aim is broad-scale turnover, in which case t
McCravy KW, Van Dyke J, Creedy TJ, et al., 2017, Comparison of orchid bee (Hymenoptera: Apidae) species composition collected with four chemical attractants, FLORIDA ENTOMOLOGIST, Vol: 100, Pages: 528-531, ISSN: 0015-4040
Nakamura A, Kitching RL, Cao M, et al., 2017, Forests and Their Canopies: Achievements and Horizons in Canopy Science, Trends in Ecology and Evolution, Vol: 32, Pages: 438-451, ISSN: 1872-8383
Forest canopies are dynamic interfaces between organisms and atmosphere, providing buffered microclimates and complex microhabitats. Canopies form vertically stratified ecosystems interconnected with other strata. Some forest biodiversity patterns and food webs have been documented and measurements of ecophysiology and biogeochemical cycling have allowed analyses of large-scale transfer of CO2, water, and trace gases between forests and the atmosphere. However, many knowledge gaps remain. With global research networks and databases, and new technologies and infrastructure, we envisage rapid advances in our understanding of the mechanisms that drive the spatial and temporal dynamics of forests and their canopies. Such understanding is vital for the successful management and conservation of global forests and the ecosystem services they provide to the world.
McCravy KW, Van Dyke J, Creedy TJ, et al., 2016, Orchid bees (Hymenoptera: Apidae: Euglossini) of Cusuco National Park, State of Cortes, Honduras, FLORIDA ENTOMOLOGIST, Vol: 99, Pages: 765-768, ISSN: 0015-4040
Jocque M, Vanhove MPM, Creedy TJ, et al., 2013, Jewel scarabs (Chrysina sp.) in Honduras: Key species for cloud forest conservation monitoring?, JOURNAL OF INSECT SCIENCE, Vol: 13, ISSN: 1536-2442
Vanhove MPM, Jocque M, Mann DJ, et al., 2012, Small sample, substantial contribution: additions to the Honduran hawkmoth (Lepidoptera: Sphingidae) fauna based on collections from a mountainous protected area (Cusuco National Park), JOURNAL OF INSECT CONSERVATION, Vol: 16, Pages: 629-633, ISSN: 1366-638X
<jats:title>ABSTRACT</jats:title><jats:p>Improved taxonomic methods are needed to quantify declining populations of insect pollinators. This study devises a high-throughput DNA barcoding protocol for a regional fauna (United Kingdom) of bees (Apiformes), consisting of reference library construction, a proof-of-concept monitoring scheme, and the deep barcoding of individuals to assess potential artefacts and organismal associations. A reference database of Cytochrome Oxidase subunit 1 (<jats:italic>cox1</jats:italic>) sequences including 92.4% of 278 bee species known from the UK showed high congruence with morphological taxon concepts, but molecular species delimitations resulted in numerous split and (fewer) lumped entities within the Linnaean species. Double tagging permitted deep illumina sequencing of 762 separate individuals of bees from a UK-wide survey. Extracting the target barcode from the amplicon mix required a new protocol employing read abundance and phylogenetic position, which revealed 180 molecular entities of Apiformes identifiable to species. An additional 72 entities were ascribed to mitochondrial pseudogenes based on patterns of read abundance and phylogenetic relatedness to the reference set. Clustering of reads revealed a range of secondary Operational Taxonomic Units (OTUs) in almost all samples, resulting from traces of insect species caught in the same traps, organisms associated with the insects including a known mite parasite of bees, and the common detection of human DNA, besides evidence for low-level cross-contamination in pan traps and laboratory steps. Custom scripts were generated to conduct critical steps of the bioinformatics protocol. The resources built here will greatly aid DNA-based monitoring to inform management and conservation policies for the protection of pollinators.</jats:p>
Andújar C, Creedy TJ, Arribas P, et al., Validated removal of nuclear pseudogenes and sequencing artefacts from mitochondrial metabarcode data
<jats:title>Abstract</jats:title><jats:p>Metabarcoding of Metazoa using mitochondrial genes may be confounded by both the accumulation of PCR and sequencing artefacts and the co-amplification of nuclear mitochondrial pseudogenes (NUMTs). The application of read abundance thresholds and denoising methods is efficient in reducing noise accompanying authentic mitochondrial amplicon sequence variants (ASVs). However, these procedures do not fully account for the complex nature of concomitant sequences and the highly variable DNA contribution of individuals in a metabarcoding sample. We propose, as a complement to denoising, the metabarcoding Multidimensional Abundance Threshold Evaluation (<jats:italic>metaMATE</jats:italic>) framework, a novel approach that allows comprehensive examination of multiple dimensions of abundance filtering and the evaluation of the prevalence of unwanted concomitant sequences in denoised metabarcoding datasets. <jats:italic>metaMATE</jats:italic> requires a denoised set of ASVs as input, and designates a subset of ASVs as being either authentic (mtDNA haplotypes) or non-authentic ASVs (NUMTs and erroneous sequences) by comparison to external reference data and by analysing nucleotide substitution patterns. <jats:italic>metaMATE</jats:italic> (i) facilitates the application of read abundance filtering strategies, which are structured with regard to sequence library and phylogeny and applied for a range of increasing abundance threshold values, and (ii) evaluates their performance by quantifying the prevalence of non-authentic ASVs and the collateral effects on the removal of authentic ASVs. The output from <jats:italic>metaMATE</jats:italic> facilitates decision-making about required filtering stringency and can be used to improve the reliability of intraspecific genetic information derived from metabarcode data. The framework is implemented in the <jats:italic>metaMATE&
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