Science Inventory

Do DNA barcoding delimitation methods affect our view of stream biodiversity?

Citation:

White, B., E. PILGRIM, R. Mazor, AND E. Stein. Do DNA barcoding delimitation methods affect our view of stream biodiversity? Presented at Society of Freshwater Science, Louisville, KY, May 20 - 24, 2012.

Impact/Purpose:

The objective of this task is to develop molecular indicators to evaluate the integrity and sustainability of aquatic fish, invertebrate, and plant communities (GPRA goal 4.5.2). Specifically, this subtask aims to evaluate methods for the measurement of: fish and invertebrate community composition, especially for morphologically indistinct (cryptic) species population genetic structure of aquatic indicator species and its relationship to landscape determinants of population structure (to aid in defining natural assessment units and to allow correlation of population substructure with regional stressor coverages) genetic diversity within populations of aquatic indicator species, as an indicator of vulnerability to further exposure and as an indicator of cumulative exposure patterns of temporal change in genetic diversity of aquatic indicator species, as a monitoring tool for establishing long-term population trends.

Description:

How we delimit molecular operational taxonomic units (MOTUs) is an important aspect in the use of DNA barcoding for bioassessment. Four delimitation methods were examined to gain an understanding of their relative strengths at organizing data from 5300 specimens collected during a single study. two additive distance methods, a phylogenetic-based method using bootstrap support (BSS) values formonophyletic clades, and the newly released BOLD Barcode Index Number (BIN) algorithm were evaluated. We found that the automated additive distance method and the Barcode BIN method were the quickest and yielded similar final data sets to manually delimited MOTU, and allowed for the quickest identification of discrepancies between morphological and molecular identifications. The bootstrap-based method yielded the least ambiguous barcode clusters. This suggests that different barcode delimitation methods can be used with minimal effect on MOTU delimitation, but that automated methods are eeded to assess large data sets of 5000+ nucleotide sequences.

URLs/Downloads:

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Record Details:

Record Type: DOCUMENT (PRESENTATION/POSTER)
Product Published Date: 05/20/2012
Record Last Revised: 09/05/2013
OMB Category: Other
Record ID: 241373

Organization:

U.S. ENVIRONMENTAL PROTECTION AGENCY

OFFICE OF RESEARCH AND DEVELOPMENT

NATIONAL EXPOSURE RESEARCH LABORATORY

ECOLOGICAL EXPOSURE RESEARCH DIVISION

MOLECULAR ECOLOGY RESEARCH BRANCH