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DNA barcoding and the associated PhylAphidB@se website for the identification of European aphids (Insecta: Hemiptera: Aphididae).

Coeur d'Acier A, Cruaud A, Artige E, Genson G, Clamens AL, Pierre E, Hudaverdian S, Simon JC, Jousselin E, Rasplus JY - PLoS ONE (2014)

Bottom Line: The taxa involved were always morphologically similar or closely related and belonged to species groups known to present taxonomic difficulties.Barcode identification is straightforward and reliable for 80% of species, including some difficult to distinguish on the basis of morphological characters alone.Unsurprisingly, barcodes often failed to distinguish between species from groups for which classical taxonomy has also reached its limits, leading to endless revisions and discussions about species and subspecies definitions.

View Article: PubMed Central - PubMed

Affiliation: INRA, UMR 1062 CBGP (Centre de Biologie pour la Gestion des Populations), Montferrier-sur-Lez, France.

ABSTRACT

Unlabelled: Aphids constitute a diverse group of plant-feeding insects and are among the most important crop pests in temperate regions. Their morphological identification is time-consuming and requires specific knowledge, training and skills that may take years to acquire. We assessed the advantages and limits of DNA barcoding with the standard COI barcode fragment for the identification of European aphids. We constructed a large reference dataset of barcodes from 1020 specimens belonging to 274 species and 87 genera sampled throughout Europe and set up a database-driven website allowing species identification from query sequences.

Results: In this unbiased sampling of the taxonomic diversity of European aphids, intraspecific divergence ranged from 0.0% to 3.9%, with a mean value of 0.29%, whereas mean congeneric divergence was 6.4%, ranging from 0.0% to 15%. Neighbor-joining analysis generated a tree in which most species clustered in distinct genetic units. Most of the species with undifferentiated or overlapping barcodes belonged to the genus Aphis or, to a lesser extent, the genera Brachycaudus, Dysaphis and Macrosiphum. The taxa involved were always morphologically similar or closely related and belonged to species groups known to present taxonomic difficulties.

Conclusions: These data confirm that COI barcoding is a useful identification tool for aphids. Barcode identification is straightforward and reliable for 80% of species, including some difficult to distinguish on the basis of morphological characters alone. Unsurprisingly, barcodes often failed to distinguish between species from groups for which classical taxonomy has also reached its limits, leading to endless revisions and discussions about species and subspecies definitions. In such cases, the development of an effective procedure for the accurate identification of aphid specimens continues to pose a difficult challenge.

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Related in: MedlinePlus

Focus on some problematic clades for barcode assignment.See Figure S4 for the complete NJ tree. Identification numbers of each clade are reported on the tree silhouette. Bootstrap support values >50 are provided. Note that the scale of genetic K2P divergence differs between subtrees.
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pone-0097620-g006: Focus on some problematic clades for barcode assignment.See Figure S4 for the complete NJ tree. Identification numbers of each clade are reported on the tree silhouette. Bootstrap support values >50 are provided. Note that the scale of genetic K2P divergence differs between subtrees.

Mentions: A misleading barcode-based assignment to a particular species could occurs when the maximum sequence divergence among individuals belonging to one species (max-WSD) equals or exceeds the minimum sequence divergence with another species (min-BSD) (Hajibabaei et al., 2006). In our dataset, this situation was encountered for 41 species (dots below the diagonal on Figure 5, species shown in bold in Table S3). Two of these species, Brachycaudus helichrysi and Myzocallis coryli (green dots in Figure 5) were previously identified as species with exceptionally high levels of intraspecific divergence. In the NJ tree (Figure 6.4), specimens of B. helichrysi were segregated into two well supported clades (BP = 100) (containing 16 and 26 specimens, respectively). B. helichrysi was rendered paraphyletic by one specimen of B. spiraeae (Figure 6.4) branching with a high BP value (88) as a sister group to one of the clades. The high degree of intraspecific divergence observed for Myzocallis coryli (Figure 6.1) was due to a single specimen, which diverged strongly from the other representatives of the species. Species paraphyly was due to a single specimen of Myzocallis carpini branching within one clade of M. coryli with a low BP value (BP<50).


DNA barcoding and the associated PhylAphidB@se website for the identification of European aphids (Insecta: Hemiptera: Aphididae).

Coeur d'Acier A, Cruaud A, Artige E, Genson G, Clamens AL, Pierre E, Hudaverdian S, Simon JC, Jousselin E, Rasplus JY - PLoS ONE (2014)

Focus on some problematic clades for barcode assignment.See Figure S4 for the complete NJ tree. Identification numbers of each clade are reported on the tree silhouette. Bootstrap support values >50 are provided. Note that the scale of genetic K2P divergence differs between subtrees.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4045754&req=5

pone-0097620-g006: Focus on some problematic clades for barcode assignment.See Figure S4 for the complete NJ tree. Identification numbers of each clade are reported on the tree silhouette. Bootstrap support values >50 are provided. Note that the scale of genetic K2P divergence differs between subtrees.
Mentions: A misleading barcode-based assignment to a particular species could occurs when the maximum sequence divergence among individuals belonging to one species (max-WSD) equals or exceeds the minimum sequence divergence with another species (min-BSD) (Hajibabaei et al., 2006). In our dataset, this situation was encountered for 41 species (dots below the diagonal on Figure 5, species shown in bold in Table S3). Two of these species, Brachycaudus helichrysi and Myzocallis coryli (green dots in Figure 5) were previously identified as species with exceptionally high levels of intraspecific divergence. In the NJ tree (Figure 6.4), specimens of B. helichrysi were segregated into two well supported clades (BP = 100) (containing 16 and 26 specimens, respectively). B. helichrysi was rendered paraphyletic by one specimen of B. spiraeae (Figure 6.4) branching with a high BP value (88) as a sister group to one of the clades. The high degree of intraspecific divergence observed for Myzocallis coryli (Figure 6.1) was due to a single specimen, which diverged strongly from the other representatives of the species. Species paraphyly was due to a single specimen of Myzocallis carpini branching within one clade of M. coryli with a low BP value (BP<50).

Bottom Line: The taxa involved were always morphologically similar or closely related and belonged to species groups known to present taxonomic difficulties.Barcode identification is straightforward and reliable for 80% of species, including some difficult to distinguish on the basis of morphological characters alone.Unsurprisingly, barcodes often failed to distinguish between species from groups for which classical taxonomy has also reached its limits, leading to endless revisions and discussions about species and subspecies definitions.

View Article: PubMed Central - PubMed

Affiliation: INRA, UMR 1062 CBGP (Centre de Biologie pour la Gestion des Populations), Montferrier-sur-Lez, France.

ABSTRACT

Unlabelled: Aphids constitute a diverse group of plant-feeding insects and are among the most important crop pests in temperate regions. Their morphological identification is time-consuming and requires specific knowledge, training and skills that may take years to acquire. We assessed the advantages and limits of DNA barcoding with the standard COI barcode fragment for the identification of European aphids. We constructed a large reference dataset of barcodes from 1020 specimens belonging to 274 species and 87 genera sampled throughout Europe and set up a database-driven website allowing species identification from query sequences.

Results: In this unbiased sampling of the taxonomic diversity of European aphids, intraspecific divergence ranged from 0.0% to 3.9%, with a mean value of 0.29%, whereas mean congeneric divergence was 6.4%, ranging from 0.0% to 15%. Neighbor-joining analysis generated a tree in which most species clustered in distinct genetic units. Most of the species with undifferentiated or overlapping barcodes belonged to the genus Aphis or, to a lesser extent, the genera Brachycaudus, Dysaphis and Macrosiphum. The taxa involved were always morphologically similar or closely related and belonged to species groups known to present taxonomic difficulties.

Conclusions: These data confirm that COI barcoding is a useful identification tool for aphids. Barcode identification is straightforward and reliable for 80% of species, including some difficult to distinguish on the basis of morphological characters alone. Unsurprisingly, barcodes often failed to distinguish between species from groups for which classical taxonomy has also reached its limits, leading to endless revisions and discussions about species and subspecies definitions. In such cases, the development of an effective procedure for the accurate identification of aphid specimens continues to pose a difficult challenge.

Show MeSH
Related in: MedlinePlus