Limits...
The hemiptera (insecta) of Canada: constructing a reference library of DNA barcodes.

Gwiazdowski RA, Foottit RG, Maw HE, Hebert PD - PLoS ONE (2015)

Bottom Line: Our analyses based on both approaches includes 94 species not listed in the most recent Canadian checklist, representing a potential 3% increase in the fauna.We discuss the development of our workflow in the context of prior DNA barcode library construction projects, emphasizing the importance of delineating a set of reference specimens to aid investigations in cases of nomenclatural and DNA barcode discordance.The identification for each specimen in the reference set can be annotated on the Barcode of Life Data System (BOLD), allowing experts to highlight questionable identifications; annotations can be added by any registered user of BOLD, and instructions for this are provided.

View Article: PubMed Central - PubMed

Affiliation: Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.

ABSTRACT
DNA barcode reference libraries linked to voucher specimens create new opportunities for high-throughput identification and taxonomic re-evaluations. This study provides a DNA barcode library for about 45% of the recognized species of Canadian Hemiptera, and the publically available R workflow used for its generation. The current library is based on the analysis of 20,851 specimens including 1849 species belonging to 628 genera and 64 families. These individuals were assigned to 1867 Barcode Index Numbers (BINs), sequence clusters that often coincide with species recognized through prior taxonomy. Museum collections were a key source for identified specimens, but we also employed high-throughput collection methods that generated large numbers of unidentified specimens. Many of these specimens represented novel BINs that were subsequently identified by taxonomists, adding barcode coverage for additional species. Our analyses based on both approaches includes 94 species not listed in the most recent Canadian checklist, representing a potential 3% increase in the fauna. We discuss the development of our workflow in the context of prior DNA barcode library construction projects, emphasizing the importance of delineating a set of reference specimens to aid investigations in cases of nomenclatural and DNA barcode discordance. The identification for each specimen in the reference set can be annotated on the Barcode of Life Data System (BOLD), allowing experts to highlight questionable identifications; annotations can be added by any registered user of BOLD, and instructions for this are provided.

Show MeSH
Species-level summary by family, of library coverage given the Checklist.Families are grouped by suborder, and then by the proportion of species with barcode records. The numbers in the Checklist/library column indicate the number of species for each family in the Checklist, and the number with barcode coverage.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4414572&req=5

pone.0125635.g003: Species-level summary by family, of library coverage given the Checklist.Families are grouped by suborder, and then by the proportion of species with barcode records. The numbers in the Checklist/library column indicate the number of species for each family in the Checklist, and the number with barcode coverage.

Mentions: We present a DNA barcode library for the Hemiptera of Canada containing 20,851 specimens classified in 64 families, 628 genera, and 1849 species, assigned to 1867 BINs that can be accessed at the DOI dx.doi.org/10.5883/DS-HECALIB; instructions for specimen-level access are provided as S1 Instructions. A summary table of the taxonomic contents at the ordinal level for the data-release and library are presented in Table 1. A summary of species-based library coverage at the family level is presented in Fig 3. The species-level diversity for library specimens is presented as an annotated version of the Maw et al. checklist in S6 Table. Annotation for each species in S6 Table includes nomenclature status on the Catalogue of Life [34], specimen numbers, divergence metrics, barcode-sharing, and BIN discordance both within the library, and on BOLD. We find 1,312 library species correspond to concordant BINS—within—the library (368 of these species are represented by singleton BINs); 510 Library species appear to share BINs (are discordant within the library), and 27 have not yet been placed in a BIN (as of this writing); species-specific results are presented in S6 Table. Of the 1,312 library species in concordant or singleton BINs, 919 can be successfully identified based on their concordance on BOLD (741 species are in concordant BINs on BOLD, and 178 are singleton BINs; S6 Table). Lastly, we find 27 library species with > 2% mean intra-specific pairwise divergence, which may represent cryptic species complexes, listed in S7 Table.


The hemiptera (insecta) of Canada: constructing a reference library of DNA barcodes.

Gwiazdowski RA, Foottit RG, Maw HE, Hebert PD - PLoS ONE (2015)

Species-level summary by family, of library coverage given the Checklist.Families are grouped by suborder, and then by the proportion of species with barcode records. The numbers in the Checklist/library column indicate the number of species for each family in the Checklist, and the number with barcode coverage.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4414572&req=5

pone.0125635.g003: Species-level summary by family, of library coverage given the Checklist.Families are grouped by suborder, and then by the proportion of species with barcode records. The numbers in the Checklist/library column indicate the number of species for each family in the Checklist, and the number with barcode coverage.
Mentions: We present a DNA barcode library for the Hemiptera of Canada containing 20,851 specimens classified in 64 families, 628 genera, and 1849 species, assigned to 1867 BINs that can be accessed at the DOI dx.doi.org/10.5883/DS-HECALIB; instructions for specimen-level access are provided as S1 Instructions. A summary table of the taxonomic contents at the ordinal level for the data-release and library are presented in Table 1. A summary of species-based library coverage at the family level is presented in Fig 3. The species-level diversity for library specimens is presented as an annotated version of the Maw et al. checklist in S6 Table. Annotation for each species in S6 Table includes nomenclature status on the Catalogue of Life [34], specimen numbers, divergence metrics, barcode-sharing, and BIN discordance both within the library, and on BOLD. We find 1,312 library species correspond to concordant BINS—within—the library (368 of these species are represented by singleton BINs); 510 Library species appear to share BINs (are discordant within the library), and 27 have not yet been placed in a BIN (as of this writing); species-specific results are presented in S6 Table. Of the 1,312 library species in concordant or singleton BINs, 919 can be successfully identified based on their concordance on BOLD (741 species are in concordant BINs on BOLD, and 178 are singleton BINs; S6 Table). Lastly, we find 27 library species with > 2% mean intra-specific pairwise divergence, which may represent cryptic species complexes, listed in S7 Table.

Bottom Line: Our analyses based on both approaches includes 94 species not listed in the most recent Canadian checklist, representing a potential 3% increase in the fauna.We discuss the development of our workflow in the context of prior DNA barcode library construction projects, emphasizing the importance of delineating a set of reference specimens to aid investigations in cases of nomenclatural and DNA barcode discordance.The identification for each specimen in the reference set can be annotated on the Barcode of Life Data System (BOLD), allowing experts to highlight questionable identifications; annotations can be added by any registered user of BOLD, and instructions for this are provided.

View Article: PubMed Central - PubMed

Affiliation: Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.

ABSTRACT
DNA barcode reference libraries linked to voucher specimens create new opportunities for high-throughput identification and taxonomic re-evaluations. This study provides a DNA barcode library for about 45% of the recognized species of Canadian Hemiptera, and the publically available R workflow used for its generation. The current library is based on the analysis of 20,851 specimens including 1849 species belonging to 628 genera and 64 families. These individuals were assigned to 1867 Barcode Index Numbers (BINs), sequence clusters that often coincide with species recognized through prior taxonomy. Museum collections were a key source for identified specimens, but we also employed high-throughput collection methods that generated large numbers of unidentified specimens. Many of these specimens represented novel BINs that were subsequently identified by taxonomists, adding barcode coverage for additional species. Our analyses based on both approaches includes 94 species not listed in the most recent Canadian checklist, representing a potential 3% increase in the fauna. We discuss the development of our workflow in the context of prior DNA barcode library construction projects, emphasizing the importance of delineating a set of reference specimens to aid investigations in cases of nomenclatural and DNA barcode discordance. The identification for each specimen in the reference set can be annotated on the Barcode of Life Data System (BOLD), allowing experts to highlight questionable identifications; annotations can be added by any registered user of BOLD, and instructions for this are provided.

Show MeSH