1
|
Woodcock TS, Boyle EE, Roughley RE, Kevan PG, Labbee RN, Smith ABT, Goulet H, Steinke D, Adamowicz SJ. The diversity and biogeography of the Coleoptera of Churchill: insights from DNA barcoding. BMC Ecol 2013; 13:40. [PMID: 24164967 PMCID: PMC3819705 DOI: 10.1186/1472-6785-13-40] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 10/16/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Coleoptera is the most diverse order of insects (>300,000 described species), but its richness diminishes at increasing latitudes (e.g., ca. 7400 species recorded in Canada), particularly of phytophagous and detritivorous species. However, incomplete sampling of northern habitats and a lack of taxonomic study of some families limits our understanding of biodiversity patterns in the Coleoptera. We conducted an intensive biodiversity survey from 2006-2010 at Churchill, Manitoba, Canada in order to quantify beetle species diversity in this model region, and to prepare a barcode library of beetles for sub-arctic biodiversity and ecological research. We employed DNA barcoding to provide estimates of provisional species diversity, including for families currently lacking taxonomic expertise, and to examine the guild structure, habitat distribution, and biogeography of beetles in the Churchill region. RESULTS We obtained DNA barcodes from 3203 specimens representing 302 species or provisional species (the latter quantitatively defined on the basis of Molecular Operational Taxonomic Units, MOTUs) in 31 families of Coleoptera. Of the 184 taxa identified to the level of a Linnaean species name, 170 (92.4%) corresponded to a single MOTU, four (2.2%) represented closely related sibling species pairs within a single MOTU, and ten (5.4%) were divided into two or more MOTUs suggestive of cryptic species. The most diverse families were the Dytiscidae (63 spp.), Staphylinidae (54 spp.), and Carabidae (52 spp.), although the accumulation curve for Staphylinidae suggests that considerable additional diversity remains to be sampled in this family. Most of the species present are predatory, with phytophagous, mycophagous, and saprophagous guilds being represented by fewer species. Most named species of Carabidae and Dytiscidae showed a significant bias toward open habitats (wet or dry). Forest habitats, particularly dry boreal forest, although limited in extent in the region, were undersampled. CONCLUSIONS We present an updated species list for this region as well as a species-level DNA barcode reference library. This resource will facilitate future work, such as biomonitoring and the study of the ecology and distribution of larvae.
Collapse
Affiliation(s)
- Thomas S Woodcock
- School of Environmental Science, University of Guelph, 50 Stone Rd. E., Guelph, ON, Canada
| | - Elizabeth E Boyle
- Biodiversity Institute of Ontario & Department of Integrative Biology, University of Guelph, 50 Stone Rd. E., Guelph, ON, Canada
| | - Robert E Roughley
- Department of Entomology, University of Manitoba, Winnipeg, MB, Canada
| | - Peter G Kevan
- School of Environmental Science, University of Guelph, 50 Stone Rd. E., Guelph, ON, Canada
| | - Renee N Labbee
- Biodiversity Institute of Ontario & Department of Integrative Biology, University of Guelph, 50 Stone Rd. E., Guelph, ON, Canada
| | - Andrew B T Smith
- Canadian Museum of Nature, P.O. Box 3443, Station D, Ottawa, ON, Canada
| | - Henri Goulet
- Canadian National Collection, 960 Carling Ave., Ottawa, ON, Canada
| | - Dirk Steinke
- Biodiversity Institute of Ontario & Department of Integrative Biology, University of Guelph, 50 Stone Rd. E., Guelph, ON, Canada
| | - Sarah J Adamowicz
- Biodiversity Institute of Ontario & Department of Integrative Biology, University of Guelph, 50 Stone Rd. E., Guelph, ON, Canada
| |
Collapse
|
2
|
Laforest BJ, Winegardner AK, Zaheer OA, Jeffery NW, Boyle EE, Adamowicz SJ. Insights into biodiversity sampling strategies for freshwater microinvertebrate faunas through bioblitz campaigns and DNA barcoding. BMC Ecol 2013; 13:13. [PMID: 23557180 PMCID: PMC3651337 DOI: 10.1186/1472-6785-13-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 03/14/2013] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Biodiversity surveys have long depended on traditional methods of taxonomy to inform sampling protocols and to determine when a representative sample of a given species pool of interest has been obtained. Questions remain as to how to design appropriate sampling efforts to accurately estimate total biodiversity. Here we consider the biodiversity of freshwater ostracods (crustacean class Ostracoda) from the region of Churchill, Manitoba, Canada. Through an analysis of observed species richness and complementarity, accumulation curves, and richness estimators, we conduct an a posteriori analysis of five bioblitz-style collection strategies that differed in terms of total duration, number of sites, protocol flexibility to heterogeneous habitats, sorting of specimens for analysis, and primary purpose of collection. We used DNA barcoding to group specimens into molecular operational taxonomic units for comparison. RESULTS Forty-eight provisional species were identified through genetic divergences, up from the 30 species previously known and documented in literature from the Churchill region. We found differential sampling efficiency among the five strategies, with liberal sorting of specimens for molecular analysis, protocol flexibility (and particularly a focus on covering diverse microhabitats), and a taxon-specific focus to collection having strong influences on garnering more accurate species richness estimates. CONCLUSIONS Our findings have implications for the successful design of future biodiversity surveys and citizen-science collection projects, which are becoming increasingly popular and have been shown to produce reliable results for a variety of taxa despite relying on largely untrained collectors. We propose that efficiency of biodiversity surveys can be increased by non-experts deliberately selecting diverse microhabitats; by conducting two rounds of molecular analysis, with the numbers of samples processed during round two informed by the singleton prevalence during round one; and by having sub-teams (even if all non-experts) focus on select taxa. Our study also provides new insights into subarctic diversity of freshwater Ostracoda and contributes to the broader "Barcoding Biotas" campaign at Churchill. Finally, we comment on the associated implications and future research directions for community ecology analyses and biodiversity surveys through DNA barcoding, which we show here to be an efficient technique enabling rapid biodiversity quantification in understudied taxa.
Collapse
Affiliation(s)
- Brandon J Laforest
- Faculty of Environmental Studies, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Amanda K Winegardner
- Department of Biology, McGill University, 1205 Docteur Penfield, Montréal, QC, H2X 2K6, Canada
| | - Omar A Zaheer
- Department of Integrative Biology, University of Guelph, 50 Stone Rd. E, Guelph, ON, N1G 2W1, Canada
- Biodiversity Institute of Ontario, University of Guelph, 50 Stone Rd. E, Guelph, ON, N1G 2W1, Canada
| | - Nicholas W Jeffery
- Department of Integrative Biology, University of Guelph, 50 Stone Rd. E, Guelph, ON, N1G 2W1, Canada
- Biodiversity Institute of Ontario, University of Guelph, 50 Stone Rd. E, Guelph, ON, N1G 2W1, Canada
| | - Elizabeth E Boyle
- Department of Integrative Biology, University of Guelph, 50 Stone Rd. E, Guelph, ON, N1G 2W1, Canada
- Biodiversity Institute of Ontario, University of Guelph, 50 Stone Rd. E, Guelph, ON, N1G 2W1, Canada
| | - Sarah J Adamowicz
- Department of Integrative Biology, University of Guelph, 50 Stone Rd. E, Guelph, ON, N1G 2W1, Canada
- Biodiversity Institute of Ontario, University of Guelph, 50 Stone Rd. E, Guelph, ON, N1G 2W1, Canada
| |
Collapse
|
3
|
Renaud AK, Savage J, Adamowicz SJ. DNA barcoding of Northern Nearctic Muscidae (Diptera) reveals high correspondence between morphological and molecular species limits. BMC Ecol 2012; 12:24. [PMID: 23173946 PMCID: PMC3537539 DOI: 10.1186/1472-6785-12-24] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 10/16/2012] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Various methods have been proposed to assign unknown specimens to known species using their DNA barcodes, while others have focused on using genetic divergence thresholds to estimate "species" diversity for a taxon, without a well-developed taxonomy and/or an extensive reference library of DNA barcodes. The major goals of the present work were to: a) conduct the largest species-level barcoding study of the Muscidae to date and characterize the range of genetic divergence values in the northern Nearctic fauna; b) evaluate the correspondence between morphospecies and barcode groupings defined using both clustering-based and threshold-based approaches; and c) use the reference library produced to address taxonomic issues. RESULTS Our data set included 1114 individuals and their COI sequences (951 from Churchill, Manitoba), representing 160 morphologically-determined species from 25 genera, covering 89% of the known fauna of Churchill and 23% of the Nearctic fauna. Following an iterative process through which all specimens belonging to taxa with anomalous divergence values and/or monophyly issues were re-examined, identity was modified for 9 taxa, including the reinstatement of Phaonia luteva (Walker) stat. nov. as a species distinct from Phaonia errans (Meigen). In the post-reassessment data set, no distinct gap was found between maximum pairwise intraspecific distances (range 0.00-3.01%) and minimum interspecific distances (range: 0.77-11.33%). Nevertheless, using a clustering-based approach, all individuals within 98% of species grouped with their conspecifics with high (>95%) bootstrap support; in contrast, a maximum species discrimination rate of 90% was obtained at the optimal threshold of 1.2%. DNA barcoding enabled the determination of females from 5 ambiguous species pairs and confirmed that 16 morphospecies were genetically distinct from named taxa. There were morphological differences among all distinct genetic clusters; thus, no cases of cryptic species were detected. CONCLUSIONS Our findings reveal the great utility of building a well-populated, species-level reference barcode database against which to compare unknowns. When such a library is unavailable, it is still possible to obtain a fairly accurate (within ~10%) rapid assessment of species richness based upon a barcode divergence threshold alone, but this approach is most accurate when the threshold is tuned to a particular taxon.
Collapse
Affiliation(s)
- Anaïs K Renaud
- Department of Entomology, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
- Department of Biological Sciences, Bishop’s University, Sherbrooke, Québec J1M 1Z7, Canada
| | - Jade Savage
- Department of Biological Sciences, Bishop’s University, Sherbrooke, Québec J1M 1Z7, Canada
| | - Sarah J Adamowicz
- Biodiversity Institute of Ontario & Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| |
Collapse
|