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DNA Barcode Accumulation Curves for Understudied Taxa and Areas

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DNA Barcode Accumulation Curves for Understudied Taxa and Areas Molecular Ecology Resources (2009) 9 (Suppl. 1), 208–216 doi: 10.1111/j.1755-0998.2009.02646.x BARCODINGBlackwell Publishing Ltd ARTHROPODS DNA barcode accumulation curves for understudied taxa and areas M. ALEX SMITH,* JOSE FERNANDEZ-TRIANA,* ROB ROUGHLEY† and PAUL D. N. HEBERT* *Biodiversity Institute of Ontario, Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1, †Department of Entomology, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2 Abstract Frequently, the diversity of umbrella taxa is invoked to predict patterns of other, less well-known, life. However, the utility of this strategy has been questioned. We tested whether a phylogenetic diversity (PD) analysis of CO1 DNA barcodes could act as a proxy for standard methods of determining sampling efficiency within and between sites, namely that an accumulation curve of barcode diversity would be similar to curves generated using morphology or nuclear genetic markers. Using taxa at the forefront of the taxonomic impediment — parasitoid wasps (Ichneumonidae, Braconidae, Cynipidae and Diapriidae), contrasted with a taxon expected to be of low diversity (Formicidae) from an area where total diversity is expected to be low (Churchill, Manitoba), we found that barcode accumu- lation curves based on PD were significantly different in both slope and scale from curves generated using names based on morphological data, while curves generated using nuclear genetic data were only different in scale. We conclude that these differences clearly identify the taxonomic impediment within the strictly morphological alpha-taxonomy of these hyperdiverse insects. The absence of an asymptote within the barcode PD trend of parasitoid wasps reflects the as yet incomplete sampling of the site (and more accurately its total diversity), while the morphological analysis asymptote represents a collision with the taxonomic impediment rather than complete sampling. We conclude that a PD analysis of standardized DNA barcodes can be a transparent and reproducible triage tool for the management and conservation of species and spaces. Keywords: Braconidae, Churchill, CO1, Cynipidae, cytochrome c oxidase 1, Diapriidae, Formicidae, Ichneumonidae, Manitoba, phylogenetic diversity, species abundance curve, triage Received 22 October 2008; revision received 16 January 2009; accepted 27 January 2009 does exist tends to be biased towards larger, more ‘charis- Introduction matic’ fauna (Renner & Häuser 2007). As a consequence, Ongoing habitat destruction, degradation and fragmen- patterns of diversity within these groups are frequently tation have resulted in escalating potentially catastrophic invoked to predict patterns of other, less well-known, losses of biodiversity (Vitousek et al. 1997; Hoffmeister et al. frequently smaller-sized, taxa [umbrella, flagship or 2005). The role of biodiversity estimates in the identification surrogates (Andelman & Fagan 2000)]. Unfortunately, the and protection of areas of overlap and endemism have utility of a strategy of surrogacy is questionable due to the traditionally been provided through the infrastructure of radically different processes that drive patterns of diversity morphological taxonomy (Godfray & Knapp 2004). Howe- of different grain size (dispersal, history, etc.). Surrogacy ver, taxonomists are not evenly distributed throughout may be most attractive to conservationists largely because the entirety of biological diversity, and what expertise that of their recognition of incomplete understanding of a particular habitat or area (Andelman & Fagan 2000). Although smaller, primarily invertebrate taxa are known Correspondence: M. Alex Smith, Fax: 519-824-5703; to turnover at very small spatial scales (Fisher et al. 2000) E-mail: [email protected] and potentially provide a very finely grained information © 2009 Blackwell Publishing Ltd BARCODING ARTHROPODS 209 source for biodiversity assessment (Underwood & Fisher nonsignificantly different patterns of identification (as in 2006) — their use as a management or conservation tool has Smith et al. 2005). This could provide significant accelera- been constricted by the taxonomic impediment (Bolton tion in terms of between-site comparisons (as in Smith et al. 1994; Gotelli 2004). There are simply far too many unnamed 2005; Forest et al. 2007), but also for within-site measures and/or unknown taxa to assure funding or management of sampling efficiency. In the case of the latter, a standard agencies that the biological currency of what is being measure of efficient sampling, a species accumulation compared between areas/times are truly the same units curve (Gottelli & Colwell 2001), could be augmented by the because of the absence of a taxonomic currency. DNA calculation of a DNA barcode accumulation curve (DBAC). barcoding, a process whereby a single, standard locus is Because of the standardization of the approach, inferences used as a species-level-equivalent tag (Hebert et al. 2003), based on such a curve would be transparent to future may provide conservationists and managers with a method researchers and directly comparable across time and space that permits the inclusion of smaller-sized taxa in biological to other sampling regimes and taxa. surveys (Smith et al. 2005), both through the democratiza- We tested whether PD assessments of collections made tion of access to taxonomy through DNA (Janzen 2004) and in sub-Arctic Canada (Churchill, Manitoba) in 2006 for through the new acceleration of alpha-taxonomy through parasitoid wasps and ants: (i) would increase in an asymp- an integrative taxonomy that includes digital information totic fashion with sampling intensity; (ii) that this accumu- such as barcoding (Fisher & Smith 2008). lation would not be significantly different from the However, this does not completely exploit the potentiality taxonomic accumulation identified using such names as of the technology, as the high-throughput capacity of a could be assigned based on morphology; and (iii) further, DNA pipeline remains constrained by the taxonomic that this barcode trend would not be significantly different impediment (increased efficiency in morphospecies recog- from patterns using a single nuclear locus. nition is only truly efficient if there are available human Supporting these hypotheses would suggest that an resources skilled in measuring and characterizing the analysis of DNA barcode PD could be a critical triage tool resultant piles). One important adaptation of the capacity for conservation biologists and managers, providing that a DNA barcoding approach provides to biodiversity transparent and reproducible estimates of within- and surveys is as a standardized measure of diversity [phylo- between-site diversity at a rate that is unapproachable genetic diversity or PD (Faith 1994; Crozier 1997)] within for the most taxonomically labile groups and virtually and between sites (for example, see Forest et al. 2007). impossible for the vast majority of life where the viscosity Using a single gene to estimate a phylogeny is widely of taxonomic information has historically discouraged accepted as unwise (Maddison 1997). However, here it the inclusion of the small and the unknown in surveys of is more precise to say that we are using a single-gene diversity. DNA barcode’s phyletic (or lineage) diversity rather than phylogenetic (or of relating to the evolutionary history Methods and development of a species or taxonomic grouping vs. the historical pattern of relationships between species or Field collection and subsampling other groups resulting from divergence from their common ancestor) to represent the ‘cloud of gene histories that ... are We studied two different Hymenoptera groups: ants part of the species tree’ (Maddison 1997), and we are not (Formicidae) and parasitoid wasps (Braconidae, Ichneu- concluding that the mitochondrial gene tree represents the mnidae, Cynipidae and Diapriidae). Samples were collected totality of the entire species tree. Indeed, while not being as part of the PROBE campaign carried out between a phylogenetic analysis on its own, barcoding as a tool for 2005–2006 (ants) and 2006–2007 (parasitoid wasps). rapid initial biodiversity assessment can lead to subse- Specimens were collected using Malaise traps and pitfall quent systematic and nomenclatorial studies to the extent traps, checked and emptied once per week. The traps that additional data support this move (Smith et al. 2005; were set up at 11 locations in the vicinity of the town of Fisher & Smith 2008). Churchill. We tested whether the phyletic measure of this mito- The specimens were preserved in 100% ethanol and chondrial DNA (mtDNA) tree is a reasonable and useful transported back to the Biodiversity Institute of Ontario, proxy of diversity information when we cannot hope to Guelph (ants) and the Canadian National Collection of know the entire species tree on timescales needed for con- Insects, Arachnids and Nematodes (CNC), Ottawa (parasitoid servation or ecology. Calibrating such a PD approach to wasps), where they were removed from ethanol in no diversity assessment would offer a researcher the full intended order — and thus sampling should approach speed of a DNA-based approach. Furthermore, it allows one random — although it was not designed to be a priori. The to avoid the issue of species/barcode equivalence if the specimens were pinned or placed in gel-capsules, photo- trends produced in proof of principle comparisons provide graphed and a single leg removed
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