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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 histogram of the percentage of samples for which a 550–657 bp COI barcode fragment was obtained.The left bar represents the ethanol preserved specimens (period 2013–2014), the other bars represent the pinned specimens (period 1993–2012).
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pone.0140264.g002: Frequency histogram of the percentage of samples for which a 550–657 bp COI barcode fragment was obtained.The left bar represents the ethanol preserved specimens (period 2013–2014), the other bars represent the pinned specimens (period 1993–2012).

Mentions: A total of 513 out of the 640 individuals (80.2%) were successfully sequenced for a COI barcode fragment of >550 bp, representing 90 nominal species of 24 genera (Fig 1; S1 Table). For 11 nominal species no barcode was obtained. Likewise, for four genera (viz. Ceratrichomyia, Meromacroides, Milesia, and Paramixogaster) no barcodes could be sequenced successfully. The success rate of obtaining a >550 bp DNA barcode was higher for the recent, ethanol preserved specimens (321/337 or 95.3%), than for the older, pinned specimens (192/303 or 63.4%) of which the success rate dropped sharply for samples of >10 years old (Fig 2). Together with the ten >550 bp COI barcodes (from nine nominal species) from GenBank (S2 Table), the total DNA barcode dataset comprised 523 COI barcodes, from 98 nominal species belonging to 26 genera (S2 Text). More than one barcode was available for 66 of these taxa (S1 Table, S3 Table), while the remaining 32 had no conspecific in the dataset. One specimen of Methadon cf. mythes (voucher 414D05) clustered within a group of three Microdon (subgenus Microdon) specimens and not with two other Methadon cf. mythes individuals (S1 Fig). Since both genera are very divergent in morphology and DNA sequences it is most likely that this specimen was mislabeled and it was therefore discarded in the identification analyses.


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 histogram of the percentage of samples for which a 550–657 bp COI barcode fragment was obtained.The left bar represents the ethanol preserved specimens (period 2013–2014), the other bars represent the pinned specimens (period 1993–2012).
© Copyright Policy
Related In: Results  -  Collection

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

pone.0140264.g002: Frequency histogram of the percentage of samples for which a 550–657 bp COI barcode fragment was obtained.The left bar represents the ethanol preserved specimens (period 2013–2014), the other bars represent the pinned specimens (period 1993–2012).
Mentions: A total of 513 out of the 640 individuals (80.2%) were successfully sequenced for a COI barcode fragment of >550 bp, representing 90 nominal species of 24 genera (Fig 1; S1 Table). For 11 nominal species no barcode was obtained. Likewise, for four genera (viz. Ceratrichomyia, Meromacroides, Milesia, and Paramixogaster) no barcodes could be sequenced successfully. The success rate of obtaining a >550 bp DNA barcode was higher for the recent, ethanol preserved specimens (321/337 or 95.3%), than for the older, pinned specimens (192/303 or 63.4%) of which the success rate dropped sharply for samples of >10 years old (Fig 2). Together with the ten >550 bp COI barcodes (from nine nominal species) from GenBank (S2 Table), the total DNA barcode dataset comprised 523 COI barcodes, from 98 nominal species belonging to 26 genera (S2 Text). More than one barcode was available for 66 of these taxa (S1 Table, S3 Table), while the remaining 32 had no conspecific in the dataset. One specimen of Methadon cf. mythes (voucher 414D05) clustered within a group of three Microdon (subgenus Microdon) specimens and not with two other Methadon cf. mythes individuals (S1 Fig). Since both genera are very divergent in morphology and DNA sequences it is most likely that this specimen was mislabeled and it was therefore discarded in the identification analyses.

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.