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DNA barcode data accurately assign higher spider taxa.

Jonathan A Coddington1, Ingi Agnarsson2, Ren-Chung Cheng3

  • 1National Museum of Natural History, Smithsonian Institution , Washington , D.C. , United States.

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|August 23, 2016
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Summary

DNA barcoding offers a fast and affordable method for identifying species, even when databases are incomplete. This study establishes reliable thresholds for using DNA sequence identity to accurately assign spiders to genera and families.

Keywords:
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Area of Science:

  • Molecular biology
  • Taxonomy
  • Bioinformatics

Background:

  • DNA barcoding is a rapidly advancing method for taxonomic identification, offering speed and cost-effectiveness compared to traditional methods.
  • Existing DNA databases and taxonomic references are imperfect, and a comprehensive species-level database is currently impractical due to the vast number of undescribed species.
  • The need exists to accurately assign unidentified species to higher taxonomic ranks like genera and families, which have more complete and stable global inventories.

Purpose of the Study:

  • To assess the accuracy of DNA barcoding for assigning spiders to genus and family levels.
  • To determine reliable sequence identity thresholds for accurate higher taxonomic assignments in spiders.
  • To evaluate the impact of database completeness on the accuracy of DNA-based taxonomic identification.

Main Methods:

  • A test library of CO1 sequences from 816 spider species, 313 genera, and 49 families was curated.
  • BLAST queries were performed for each sequence against the library, and the top ten hits with percent sequence identity (PIdent) were recorded.
  • Heuristic thresholds for accurate genus (>95% PIdent) and family (≥91% PIdent) assignments were established based on minimizing errors.

Main Results:

  • Accurate genus-level assignment was achieved with PIdent values >95%, and family-level assignment with PIdent values ≥91%.
  • Identification accuracy increased with greater representation in the library, with all higher taxon assignments being correct when >5 genera/family and >15 species/genus were included.
  • Database quality significantly impacts accuracy, with taxonomic and sequencing errors in public databases contributing to outliers.

Conclusions:

  • Using percent sequence identity of conventional DNA barcode sequences is a feasible and accurate method for identifying animals to genus and family levels.
  • Establishing accurate and comprehensive reference libraries of families and genera is crucial for reliable, accessible, and rapid higher-level taxonomic identification.
  • This approach could provide accurate taxonomic identifications cheaply and accessibly within a few years, rather than decades.