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DNA barcode-based delineation of putative species: efficient start for taxonomic workflows.

Kekkonen M, Hebert PD - Mol Ecol Resour (2014)

Bottom Line: This study tested the congruence of OTUs resulting from the application of three analytical methods (ABGD, BIN, GMYC) to sequence data for Australian hypertrophine moths.This approach revealed 124 OTUs of Hypertrophinae, a more than twofold increase from the currently recognized 51 species.Because this analytical protocol is both fast and repeatable, it provides a valuable tool for establishing a basic understanding of species boundaries that can be validated with subsequent studies.

View Article: PubMed Central - PubMed

Affiliation: Zoology Unit, Finnish Museum of Natural History, University of Helsinki, P.O. Box 17, FI-00014, Helsinki, Finland.

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OTU counts resulting from three delineation methods. Figures below the results for ABGD indicate prior intraspecific divergence (P) values. The two OTU counts for GMYC result from single- and multiple-threshold models.
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fig03: OTU counts resulting from three delineation methods. Figures below the results for ABGD indicate prior intraspecific divergence (P) values. The two OTU counts for GMYC result from single- and multiple-threshold models.

Mentions: The count of OTUs varied from 73 to 222 with both the lowest and highest result produced by ABGD (Fig.3). ABGD analysis with JC69 produced two initial partitions with OTU counts of 73 (P = 0.0129) and 83 (P = 0.0215), whereas use of K2P returned only one initial value of 127 OTUs (P = 0.00774) (Table1). Because the use of p-distance produced strongly discordant outcomes with the initial partition including 140 OTUs (P = 0.00464) and 177 (P = 0.00278) OTUs (Table1), it was omitted. BIN (120 OTUs) and GMYC (123 OTUs) with a single-threshold model produced very similar results, and values close to the 127 OTUs obtained with ABGD and the initial partition of K2P. Similar to many earlier studies, the implementation of GMYC with a multiple-threshold model produced a higher OTU count (139) than the single-threshold model, but it failed to improve the fit of the GMYC model to the data (χ2 = 12.73, d.f. = 15, P < 0.62) (Table2). Also, the likelihood-ratio test rejected the model denoting the presence of more than one species in the data (Table2).


DNA barcode-based delineation of putative species: efficient start for taxonomic workflows.

Kekkonen M, Hebert PD - Mol Ecol Resour (2014)

OTU counts resulting from three delineation methods. Figures below the results for ABGD indicate prior intraspecific divergence (P) values. The two OTU counts for GMYC result from single- and multiple-threshold models.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4264940&req=5

fig03: OTU counts resulting from three delineation methods. Figures below the results for ABGD indicate prior intraspecific divergence (P) values. The two OTU counts for GMYC result from single- and multiple-threshold models.
Mentions: The count of OTUs varied from 73 to 222 with both the lowest and highest result produced by ABGD (Fig.3). ABGD analysis with JC69 produced two initial partitions with OTU counts of 73 (P = 0.0129) and 83 (P = 0.0215), whereas use of K2P returned only one initial value of 127 OTUs (P = 0.00774) (Table1). Because the use of p-distance produced strongly discordant outcomes with the initial partition including 140 OTUs (P = 0.00464) and 177 (P = 0.00278) OTUs (Table1), it was omitted. BIN (120 OTUs) and GMYC (123 OTUs) with a single-threshold model produced very similar results, and values close to the 127 OTUs obtained with ABGD and the initial partition of K2P. Similar to many earlier studies, the implementation of GMYC with a multiple-threshold model produced a higher OTU count (139) than the single-threshold model, but it failed to improve the fit of the GMYC model to the data (χ2 = 12.73, d.f. = 15, P < 0.62) (Table2). Also, the likelihood-ratio test rejected the model denoting the presence of more than one species in the data (Table2).

Bottom Line: This study tested the congruence of OTUs resulting from the application of three analytical methods (ABGD, BIN, GMYC) to sequence data for Australian hypertrophine moths.This approach revealed 124 OTUs of Hypertrophinae, a more than twofold increase from the currently recognized 51 species.Because this analytical protocol is both fast and repeatable, it provides a valuable tool for establishing a basic understanding of species boundaries that can be validated with subsequent studies.

View Article: PubMed Central - PubMed

Affiliation: Zoology Unit, Finnish Museum of Natural History, University of Helsinki, P.O. Box 17, FI-00014, Helsinki, Finland.

Show MeSH