Il DNA Barcoding come strumento preliminare e speditivo per approfondimenti sistematici, valutazione della biodiversità e biomonitoraggio
Author(s)
Cardoni, Simone
Date Issued
June 17, 2016
Type
Doctoral Thesis
Abstract
Accurate identification of aquatic organisms is a fundamental prerogative to research applied to water biodiversity and biomonitoring. In this work, an overview of the potential applications and the relative effectiveness of the DNA barcoding approach on two distinct case studies is presented: 1) the identification of the species of Ephemeroptera, a key taxonomic group for biomonitoring of water bodies worldwide; 2) the genetic variability of two fish species, Engraulis encrasicolus and Sardina pilchardus, components of some commercial products such as “bianchetto”. The final objective is to set up a regional database that progresses to national and continental scales as a statistically sound basis for cost efficient and repeated measurements of biodiversity, with sufficient resolution to be useful to monitor marine and fresh-water ecology. The barcoding method was applied to 39 Ephemeroptera species and 44 individuals of the two marine species. Sample discrimination and species identification were investigated by evaluating haplotype identity and similarity, intra-/interspecific genetic distances, optimal identification of barcoding gap thresholds, estimates of species monophyly and comparative species matches on available reference libraries. The resolving power of the obtained data was discussed in the light of statistical tools such as Spider R-package, Ptp (Poisson Tree Processes) and dendrograms generated by specific bioinformatics tools. For both Ephemeroptera and the two fish datasets, high levels of species identification were achieved with all the used methodologies. In particular, DNA barcoding showed to be a powerful tool to improve the taxonomic research of Mediterranean Ephemeroptera, further indicating the occurrence of potential cryptic species and highlighting the need for more in-depth studies aimed at updating the current knowledge for this taxonomic group.
Finally, a DNA metabarcoding approach on environmental samples (eDNA) for the two case studies was tested to verify its efficiency for biomonitoring and market quality control through the Next Generation Sequencing approach. The obtained results demonstrated the ability of the technique to detect a large proportion of the taxa present in a natural community, although the presence of some distortions was highlighted. This methodology, althoguh highly promising, will therefore require further experiments and modifications to the experimental designs for a routine application. This new information system (eDNA), properly set and integrated with a local reference database with descriptors of ecological habitats, could improve management efforts on the conservation of aquatic ecosystems, providing the accuracy required to implement the evaluation programs of water quality.
Additional information
Dottorato di ricerca in Ecologia e gestione delle risorse biologiche
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