ORCID Profile
0000-0001-5722-058X
Current Organisation
York University
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Publisher: Cold Spring Harbor Laboratory
Date: 02-04-2019
DOI: 10.1101/597302
Abstract: DNA metabarcoding allows the analysis of insect communities faster and more efficiently than ever before. However, metabarcoding can be conducted through several alternative approaches, and the consistency of results across methods has rarely been studied. We compare the results obtained by DNA metabarcoding of the same communities using two different markers – COI and 16S – and three different s ling methods – homogenized Malaise trap s les (homogenate), preservative ethanol from the same s les, and soil s les. Our results indicate that COI and 16S offer partly complementary information on Malaise trap s les, with each marker detecting a significant number of species not detected by the other. Different s ling methods offer highly ergent estimates of community composition. The community recovered from preservative ethanol of Malaise trap s les is quite distinct from that recovered from homogenate. Small and weakly sclerotized insects tend to be overrepresented in ethanol, with some exceptions that could be related to taxon-specific traits. For soil s les, highly degenerate COI primers pick up large amounts of non-target DNA and only 16S provides adequate analyses of insect ersity. However, even with 16S, very little overlap in MOTU content was found between the trap and the soil s les. Our results demonstrate that no metabarcoding approach is all-comprehensive in itself. For instance, DNA extraction from preservative ethanol is not a valid replacement for destructive bulk extraction but a complement. In future metabarcoding studies, both should ideally be used together to achieve comprehensive representation of the target community.
Publisher: Cold Spring Harbor Laboratory
Date: 30-05-2020
DOI: 10.1101/2020.05.27.116905
Abstract: As global bio ersity declines, there’s an increasing need to create an educated and engaged society. Having people from all ages participate in measuring bio ersity where they live helps to create awareness. Recently, the use of environmental DNA (eDNA) for bio ersity surveys has gained momentum. Here, we test whether s ling eDNA and metabarcoding can be used for rapid urban bio ersity surveys for educational purposes. We s led 2×1 L of water from each of 15 locations in the city of Trondheim, Norway, including a variety of freshwater, marine and brackish habitats. DNA was extracted, lified in triplicate for the COI gene and sequenced. The obtained data were analysed on the novel mBRAVE platform, an online open access software and computing resource. The water s les were collected in two days by two people and the lab analysis was completed in five days by one person. Overall, we detected the presence of 501 taxa identified as belonging to 435 species, representing 90 orders and 18 phyla. On average, only 5.4% of the taxa were shared among six replicates per site. Based on the observed ersity, three distinct clusters were detected and related to geographic distribution of sites. There were some taxa shared between the habitats, with a substantial presence of terrestrial biota. Our results match expected patterns of bio ersity in the landscape and show that with minimal s ling effort, hundreds of species can be detected. Thus, using eDNA analysis of water is promising for rapid bio ersity surveys, and it is likely that more detailed results could be obtained by optimising field and lab methods for particular groups of interest. We recommend that rapid eDNA surveys, with openly available services and softwares, can be used to raise awareness in the importance of bio ersity.
Publisher: Wiley
Date: 24-10-2020
DOI: 10.1002/EDN3.152
Publisher: Wiley
Date: 18-09-2019
No related grants have been discovered for Daniel Marquina.