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DNA Barcoding to Improve the Taxonomy of the Afrotropical Hoverflies (Insecta: Diptera: Syrphidae).

Jordaens K, Goergen G, Virgilio M, Backeljau T, Vokaer A, De Meyer M - PLoS ONE (2015)

Bottom Line: Nine species pairs showed a low (< 0.03) mean interspecific K2P distance that resulted in several incorrect identifications.Optimal K2P thresholds to differentiate intra- from interspecific K2P divergence were highly different among the three subfamilies (Eristalinae: 0.037, Syrphinae: 0.06, Microdontinae: 0.007-0.02), and among the different general suggesting that optimal thresholds are better defined at the genus level.In addition to providing an alternative identification tool, our study indicates that DNA barcoding improves the taxonomy of Afrotropical hoverflies by selecting (groups of) taxa that deserve further taxonomic study, and by attributing the unknown sex to species for which only one of the sexes is known.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology-Invertebrate Section and Joint Experimental Molecular Unit (JEMU), Royal Museum for Central Africa, Leuvensesteenweg 13, B-3080 Tervuren, Belgium.

ABSTRACT
The identification of Afrotropical hoverflies is very difficult because of limited recent taxonomic revisions and the lack of comprehensive identification keys. In order to assist in their identification, and to improve the taxonomy of this group, we constructed a reference dataset of 513 COI barcodes of 90 of the more common nominal species from Ghana, Togo, Benin and Nigeria (W Africa) and added ten publically available COI barcodes from nine nominal Afrotropical species to this (total: 523 COI barcodes; 98 nominal species; 26 genera). The identification accuracy of this dataset was evaluated with three methods (K2P distance-based, Neighbor-Joining (NJ) / Maximum Likelihood (ML) analysis, and using SpeciesIdentifier). Results of the three methods were highly congruent and showed a high identification success. Nine species pairs showed a low (< 0.03) mean interspecific K2P distance that resulted in several incorrect identifications. A high (> 0.03) maximum intraspecific K2P distance was observed in eight species and barcodes of these species not always formed single clusters in the NJ / ML analayses which may indicate the occurrence of cryptic species. Optimal K2P thresholds to differentiate intra- from interspecific K2P divergence were highly different among the three subfamilies (Eristalinae: 0.037, Syrphinae: 0.06, Microdontinae: 0.007-0.02), and among the different general suggesting that optimal thresholds are better defined at the genus level. In addition to providing an alternative identification tool, our study indicates that DNA barcoding improves the taxonomy of Afrotropical hoverflies by selecting (groups of) taxa that deserve further taxonomic study, and by attributing the unknown sex to species for which only one of the sexes is known.

No MeSH data available.


Frequency histograms of specimen numbers (A), number of haplotypes per species (B) and changes in the number of haplotypes with respect to the number of specimens sampled per species (C).In the latter, for each dot that represents more than one species, the number of species is given. ‘Species’ refers to the number of nominal species. (1): species represented by only one specimen are excluded.
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pone.0140264.g003: Frequency histograms of specimen numbers (A), number of haplotypes per species (B) and changes in the number of haplotypes with respect to the number of specimens sampled per species (C).In the latter, for each dot that represents more than one species, the number of species is given. ‘Species’ refers to the number of nominal species. (1): species represented by only one specimen are excluded.

Mentions: We obtained a mean of 5.32 barcode sequences per species (4.13 if we only consider the unique haplotypes (i.e. individuals with similar barcodes are counted once), with 67.3% of the species represented by at least two barcodes (Fig 3A, S3 Table). If we excluded species represented by a single specimen (N = 32), the number of haplotypes per species (N = 66) ranged from 1 to 19 (Fig 3B, S3 Table), with a mean of 5.65 haplotypes per species. This mean number increased with the number of specimens sampled (Fig 3C). Haplotype numbers increased rapidly with the number of individuals sampled per species (Spearman Rank Rs = 0.971, t = 32.56, N = 66, P < 0.0001), but correlations with mean and maximum intraspecific K2P distances were less strong (Rs = 0.144, t = 1.17, N = 66, P = 0.12 and Rs = 0.51, t = 4.70, N = 66, P < 0.0001, respectively). Thus, greater intraspecific sampling yields more haplotypes, but has no major effect on intraspecific K2P distances.


DNA Barcoding to Improve the Taxonomy of the Afrotropical Hoverflies (Insecta: Diptera: Syrphidae).

Jordaens K, Goergen G, Virgilio M, Backeljau T, Vokaer A, De Meyer M - PLoS ONE (2015)

Frequency histograms of specimen numbers (A), number of haplotypes per species (B) and changes in the number of haplotypes with respect to the number of specimens sampled per species (C).In the latter, for each dot that represents more than one species, the number of species is given. ‘Species’ refers to the number of nominal species. (1): species represented by only one specimen are excluded.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4608823&req=5

pone.0140264.g003: Frequency histograms of specimen numbers (A), number of haplotypes per species (B) and changes in the number of haplotypes with respect to the number of specimens sampled per species (C).In the latter, for each dot that represents more than one species, the number of species is given. ‘Species’ refers to the number of nominal species. (1): species represented by only one specimen are excluded.
Mentions: We obtained a mean of 5.32 barcode sequences per species (4.13 if we only consider the unique haplotypes (i.e. individuals with similar barcodes are counted once), with 67.3% of the species represented by at least two barcodes (Fig 3A, S3 Table). If we excluded species represented by a single specimen (N = 32), the number of haplotypes per species (N = 66) ranged from 1 to 19 (Fig 3B, S3 Table), with a mean of 5.65 haplotypes per species. This mean number increased with the number of specimens sampled (Fig 3C). Haplotype numbers increased rapidly with the number of individuals sampled per species (Spearman Rank Rs = 0.971, t = 32.56, N = 66, P < 0.0001), but correlations with mean and maximum intraspecific K2P distances were less strong (Rs = 0.144, t = 1.17, N = 66, P = 0.12 and Rs = 0.51, t = 4.70, N = 66, P < 0.0001, respectively). Thus, greater intraspecific sampling yields more haplotypes, but has no major effect on intraspecific K2P distances.

Bottom Line: Nine species pairs showed a low (< 0.03) mean interspecific K2P distance that resulted in several incorrect identifications.Optimal K2P thresholds to differentiate intra- from interspecific K2P divergence were highly different among the three subfamilies (Eristalinae: 0.037, Syrphinae: 0.06, Microdontinae: 0.007-0.02), and among the different general suggesting that optimal thresholds are better defined at the genus level.In addition to providing an alternative identification tool, our study indicates that DNA barcoding improves the taxonomy of Afrotropical hoverflies by selecting (groups of) taxa that deserve further taxonomic study, and by attributing the unknown sex to species for which only one of the sexes is known.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology-Invertebrate Section and Joint Experimental Molecular Unit (JEMU), Royal Museum for Central Africa, Leuvensesteenweg 13, B-3080 Tervuren, Belgium.

ABSTRACT
The identification of Afrotropical hoverflies is very difficult because of limited recent taxonomic revisions and the lack of comprehensive identification keys. In order to assist in their identification, and to improve the taxonomy of this group, we constructed a reference dataset of 513 COI barcodes of 90 of the more common nominal species from Ghana, Togo, Benin and Nigeria (W Africa) and added ten publically available COI barcodes from nine nominal Afrotropical species to this (total: 523 COI barcodes; 98 nominal species; 26 genera). The identification accuracy of this dataset was evaluated with three methods (K2P distance-based, Neighbor-Joining (NJ) / Maximum Likelihood (ML) analysis, and using SpeciesIdentifier). Results of the three methods were highly congruent and showed a high identification success. Nine species pairs showed a low (< 0.03) mean interspecific K2P distance that resulted in several incorrect identifications. A high (> 0.03) maximum intraspecific K2P distance was observed in eight species and barcodes of these species not always formed single clusters in the NJ / ML analayses which may indicate the occurrence of cryptic species. Optimal K2P thresholds to differentiate intra- from interspecific K2P divergence were highly different among the three subfamilies (Eristalinae: 0.037, Syrphinae: 0.06, Microdontinae: 0.007-0.02), and among the different general suggesting that optimal thresholds are better defined at the genus level. In addition to providing an alternative identification tool, our study indicates that DNA barcoding improves the taxonomy of Afrotropical hoverflies by selecting (groups of) taxa that deserve further taxonomic study, and by attributing the unknown sex to species for which only one of the sexes is known.

No MeSH data available.