Integrating DNA data and traditional taxonomy to streamline biodiversity assessment: an example from edaphic beetles in the Klamath ecoregion, California, USA

Abstract

Conservation and land management decisions may be misguided by inaccurate or misinterpreted knowledge of biodiversity. Non-systematists often lack taxonomic expertise necessary for an accurate assessment of biodiversity. Additionally, there are far too few taxonomists to contribute significantly to the task of identifying species for specimens collected in biodiversity studies. While species level identification is desirable for making informed management decisions concerning biodiversity, little progress has been made to reduce this taxonomic deficiency. Involvement of non-systematists in the identification process could hasten species identification. Incorporation of DNA sequence data has been recognized as one way to enhance biodiversity assessment and species identification. DNA data are now technologically and economically feasible for most scientists to apply in biodiversity studies. However, its use is not widespread and means of its application has not been extensively addressed. This paper illustrates how such data can be used to hasten biodiversity assessment of species using a little-known group of edaphic beetles. Partial mitochondrial cytochrome oxidase I was sequenced for 171 individuals of feather-wing beetles (Coleoptera: Ptiliidae) from the Klamath ecoregion, which is part of a biodiversity hotspot, the California Floristic Province. A phylogram of these data was reconstructed via parsimony and the strict consensus of 28,000 equally parsimonious trees was well resolved except for peripheral nodes. Forty-two voucher specimens were selected for further identification from clades that were associated with many synonymous and non-synonymous nucleotide changes. A ptiliid taxonomic expert identified nine species that corresponded to monophyletic groups. These results allowed for a more accurate assessment of ptiliid species diversity in the Klamath ecoregion. In addition, we found that the number of amino acid changes or percentage nucleotide difference did not associate with species limits. This study demonstrates that the complementary use of taxonomic expertise and molecular data can improve both the speed and the accuracy of species-level biodiversity assessment. We believe this represents a means for non-systematists to collaborate directly with taxonomists in species identification and represents an improvement over methods that rely solely on parataxonomy or sequence data.

Using DNA to assess errors in tropical tree identifications: How often are ecologists wrong and when does it matter?

“…Furthermore, our study uncovered 18 named species not previously known from the study region (Madre de Dios, Peru) and discovered 10 species potentially new to science. We agree with Janzen et al (2005) and Caesar et al (2006) that the combination of traditional morphology-based biodiversity inventories with large-scale DNA sequence data generation offers the most fruitful approach to documenting biodiversity in a timely manner in threatened, tropical environments. Tropical ecologists, who often make extensive collections in remote, rarely visited locations, are well poised to take up this approach and contribute substantially and importantly to knowledge of species' distributions and the discovery of new species.…”

“…Alternatively, genetic data in the form of DNA sequences can be used to assess identification errors (Knowlton et al 1992, Caesar et al 2006, Bickford et al 2007, Stuart and Fritz 2008. For example, the genealogical species concept (Baum and Shaw 1995) argues that evolutionarily coherent units can be identified when gene genealogies reveal monophyletic groups of individuals.…”

Assessing Macroinvertebrate Biodiversity in Freshwater Ecosystems: Advances and Challenges in DNA-based Approaches

“…In a real sense, these two endeavors are complementary, with DNA data informing both gaps and problematic areas in taxonomy, and should be applied in a synergistic and iterative fashion (Carew et al 2005;Caesar et al 2006). In practice, benthic invertebrate diversity estimates generally rely on the classification of juvenile individuals or of partial/damaged specimens in a sample that are notoriously difficult to assign to species-level taxonomy due to a lack of informative characters.…”

Inga pitmanii(Fabaceae), a New Species from Madre de Dios, Peru

“…Given that taxonomic expertise and funding are on the decline, we advocate considering such alternative approaches to describing species. A combination of ecological or other biodiversity surveys with large-scale DNA sequencing, as presented here (Dexter et al, 2010), offers the possibility of greatly increasing the rate of documentation of novel species (Janzen et al, 2005;Caesar et al, 2006). This could be particularly critical in tropical ecosystems, which face grave threats and where most undiscovered diversity lies (e.g., Hebert et al, 2004;Janzen et al, 2005).…”