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Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA

Port, Jesse A ; O'Donnell, James L ; Romero‐Maraccini, Ofelia C ; Leary, Paul R ; Litvin, Steven Y ; Nickols, Kerry J ; Yamahara, Kevan M ; Kelly, Ryan P

Molecular ecology, 2016-01, Vol.25 (2), p.527-541 [Periódico revisado por pares]

England: Blackwell Scientific Publications

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  • Título:
    Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA
  • Autor: Port, Jesse A ; O'Donnell, James L ; Romero‐Maraccini, Ofelia C ; Leary, Paul R ; Litvin, Steven Y ; Nickols, Kerry J ; Yamahara, Kevan M ; Kelly, Ryan P
  • Assuntos: animal communities ; Animals ; Biodiversity ; California ; DNA ; DNA Barcoding, Taxonomic ; DNA primers ; Ecosystem ; ecosystems ; eDNA ; Environmental Monitoring - methods ; fauna ; fish ; Fishes - classification ; Fishes - genetics ; genes ; genetic markers ; habitats ; Kelp ; mammals ; Mammals - classification ; Mammals - genetics ; marine fish ; metabarcoding ; monitoring ; next generation sequencing ; Original ; ORIGINAL ARTICLES ; polymerase chain reaction ; ribosomal RNA ; RNA, Ribosomal - genetics ; surveys ; Vertebrates - classification ; Vertebrates - genetics
  • É parte de: Molecular ecology, 2016-01, Vol.25 (2), p.527-541
  • Notas: http://dx.doi.org/10.1111/mec.13481
    ark:/67375/WNG-9H3R28TZ-3
    istex:B7378173D533A1675BAA015B33685D4C9CE58482
    ArticleID:MEC13481
    Fig. S1. Number of reads per tag assigned to field samples, positive controls (i.e. mock communities and swordfish tissue) and negative controls (i.e. filtration and extraction blanks) after demultiplexing. Fig. S2. Venn diagram of bony fish taxa and marine mammals as detected by eDNA vs. visual survey for the combined sample sites. Fig. S3. Spatial trends in eDNA and visual count data across the transect and habitats shown on a log(x) scale. Fig. S4. Sequence alignment of the 12S rRNA primer-binding sites for taxa present in Monterey Bay and the mock community.Table S1. (A) Composition of the artificial communities used as positive controls. The two communities contained either equal (community 1) or increasing (community 2) concentrations of tissue DNA. (B) Sequence counts for each taxon present in the three positive controls. Table S2. Taxonomic annotation and read counts for sequences not matching species in our 12S database at specified blast and megan thresholds. Table S3. Visual fish survey counts for each sample site. Table S4. Pairwise-comparisons of taxon abundance between (A) habitat types and (B) sample sites within the same habitat. Table S5. Statistical tests of beta-diversity (A) between sites within the same habitat and (B) between habitats (R2 values).
    David and Lucile Packard Foundation - No. 2014-39952
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    SourceType-Scholarly Journals-1
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  • Descrição: Preserving biodiversity is a global challenge requiring data on species’ distribution and abundance over large geographic and temporal scales. However, traditional methods to survey mobile species’ distribution and abundance in marine environments are often inefficient, environmentally destructive, or resource‐intensive. Metabarcoding of environmental DNA (eDNA) offers a new means to assess biodiversity and on much larger scales, but adoption of this approach for surveying whole animal communities in large, dynamic aquatic systems has been slowed by significant unknowns surrounding error rates of detection and relevant spatial resolution of eDNA surveys. Here, we report the results of a 2.5 km eDNA transect surveying the vertebrate fauna present along a gradation of diverse marine habitats associated with a kelp forest ecosystem. Using PCR primers that target the mitochondrial 12S rRNA gene of marine fishes and mammals, we generated eDNA sequence data and compared it to simultaneous visual dive surveys. We find spatial concordance between individual species’ eDNA and visual survey trends, and that eDNA is able to distinguish vertebrate community assemblages from habitats separated by as little as ~60 m. eDNA reliably detected vertebrates with low false‐negative error rates (1/12 taxa) when compared to the surveys, and revealed cryptic species known to occupy the habitats but overlooked by visual methods. This study also presents an explicit accounting of false negatives and positives in metabarcoding data, which illustrate the influence of gene marker selection, replication, contamination, biases impacting eDNA count data and ecology of target species on eDNA detection rates in an open ecosystem.
  • Editor: England: Blackwell Scientific Publications
  • Idioma: Inglês
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