DNA barcoding for ecologists.

By A. Valentini, F. Pompanon, P. Taberlet. Trends in Ecology & Evolution, 2009

1,050 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/f957b19c33c0bfee48be9b109997176418e39b3e

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Citations in the corpus

Use of DNA metabarcoding for stomach content analysis in the invasive lionfish Pterois volitans in Puerto Rico (2016, background): “…DNA quality, differential breakdown of that DNA during digestion, and differences in digestion stages (Deagle & Tollit 2007, Troedsson et al. 2009, Valentini et al. 2009b), as well as the objective of identifying several different organisms within the same sample (i.e. the gut) (Valentini et al.…”
A comprehensive and comparative evaluation of primers for metabarcoding eDNA from fish (2020, background): “…universal primers are applied to amplify DNA from a group of organisms that are taxonomically close, and therefore have conserved primer binding sequences, while amplified barcodes should possess variable sites between different species, allowing for taxonomic assignments (Valentini et al., 2009).”
So Many Variables: Joint Modeling in Community Ecology. (2015, background): “If organisms are identified using modern tools such as DNA barcoding and metabarcoding [6,7], their number can be especially large, often in the thousands.”
Applications of next-generation sequencing to the study of biological invasions (2015, background): “…DNA barcoding (Shokralla et al., 2012; Shokralla et al., 2014) by decreasing the cost of sequencing, but more importantly has removed the expensive and time-consuming need to clone amplified eDNA into bacteria before sequencing hundreds of thousands of clones (Valentini et al., 2009).”
Distribution patterns of soil microbial eukaryotes suggests widespread algivory by phagotrophic protists as an alternative pathway for nutrient cycling (2017, background): “…biases by using a fragment whose length is almost constant in all eukaryotes (as opposed to, for instance, the V4 region; de Vargas et al., 2015) and (2) because the fragment is shorter, the probability of generating artefactual diversity (i.e. chimeras) is lower (Valentini et al., 2009).”
Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data (2015, background): “…DNA (eDNA) metabarcoding, that is the simultaneous identification of multiple taxa from the DNA extracted from an environmental sample (e.g. soil, water and faeces samples), is an emerging approach for the study of the present and past biodiversity (Valentini et al. 2009b; Taberlet et al. 2012a).”
Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo (2016, background): “However, they are practical for biodiversity and βdiversity estimates (Valentini et al., 2009).”
Lake sediment multi-taxon DNA from North Greenland records early post-glacial appearance of vascular plants and accurately tracks environmental changes (2015, background): “, 2012), has enabled the parallel retrieval of large amounts of informative data (e.g. Binladen et al., 2007; Valentini et al., 2009; Willerslev et al., 2014).”
ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis (2011, background): “This technique is now considered to be a powerful tool, both for taxonomical (1) and ecological (2) studies.”
Who is eating what: diet assessment using next generation sequencing (2012, methodology): “To minimize representation of contaminants, Valentini et al. (2009a) recommended no more than 35 cycles during PCRs.”
More than just indicators: A review of tropical butterfly ecology and conservation (2010, background): “While the prospect of using standardized DNA sequencing to assist in characterizing tropical butterfly communities is appealing and promising, there are limitations to the approach, including that the identification system relies upon only a single locus (Valentini et al., 2009).”