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Determining plant-leaf miner-parasitoid interactions: a DNA barcoding approach.

Derocles SA, Evans DM, Nichols PC, Evans SA, Lunt DH - PLoS ONE (2015)

Bottom Line: We found that the 130 bp fragment is variable enough to identify all the species included in this study.Both COI fragments reveal that some leaf miner species could be composed of cryptic species.The network built using the molecular approach was more accurate in describing tri-partite interactions compared with traditional approaches based on morphological criteria.

View Article: PubMed Central - PubMed

Affiliation: School of Biological, Biomedical and Environmental Sciences, University of Hull, Hull, United Kingdom.

ABSTRACT
A major challenge in network ecology is to describe the full-range of species interactions in a community to create highly-resolved food-webs. We developed a molecular approach based on DNA full barcoding and mini-barcoding to describe difficult to observe plant-leaf miner-parasitoid interactions, consisting of animals commonly regarded as agricultural pests and their natural enemies. We tested the ability of universal primers to amplify the remaining DNA inside leaf miner mines after the emergence of the insect. We compared the results of a) morphological identification of adult specimens; b) identification based on the shape of the mines; c) the COI Mini-barcode (130 bp) and d) the COI full barcode (658 bp) fragments to accurately identify the leaf-miner species. We used the molecular approach to build and analyse a tri-partite ecological network of plant-leaf miner-parasitoid interactions. We were able to detect the DNA of leaf-mining insects within their feeding mines on a range of host plants using mini-barcoding primers: 6% for the leaves collected empty and 33% success after we observed the emergence of the leaf miner. We suggest that the low amplification success of leaf mines collected empty was mainly due to the time since the adult emerged and discuss methodological improvements. Nevertheless our approach provided new species-interaction data for the ecological network. We found that the 130 bp fragment is variable enough to identify all the species included in this study. Both COI fragments reveal that some leaf miner species could be composed of cryptic species. The network built using the molecular approach was more accurate in describing tri-partite interactions compared with traditional approaches based on morphological criteria.

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Related in: MedlinePlus

Maximum likelihood tree based on cytochrome c oxidase I (COI) Minibarcode sequences.Bootstrap values are indicated above branches. Scale bar indicates the number of substitutions per site.
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pone.0117872.g002: Maximum likelihood tree based on cytochrome c oxidase I (COI) Minibarcode sequences.Bootstrap values are indicated above branches. Scale bar indicates the number of substitutions per site.

Mentions: A total of 147 insect specimens emerged or dissected from the 407 infested leaves collected: 89 dipteran leaf miners (68 adults and 21 immatures), 10 larvae of lepidopteran leaf miners and 48 adult hymenoptera parasitoids. The COI full barcode was successfully amplified from all adult and immature samples. The COI mini-barcode amplified with ZBJ-ArtF1c and ZBJ-ArtR2c primers was successfully amplified from all adult and immature Diptera and Lepidoptera species. The COI mini-barcode amplified with Uni-MinibarR1 and Uni-MinibarF1 primers was successfully amplified from all adult and immature Diptera and Lepidoptera species, but Scaptomyza flava (Fallén) and Phytomyza spondylii (Robineau-Desvoidy). The 658-bp sequences for COI full barcode (for all adult and immature specimens; Fig. 1) and the 130-bp sequences for COI mini-barocde (for all adults and immatures Diptera and Lepidoptera; Fig. 2) were used to assess nucleotide sequence divergence between and within morphological species and to perform the ML analysis. 260 infested leaves were empty: the leaf mining insects had already emerged when the leaves had been collected (Table 1).


Determining plant-leaf miner-parasitoid interactions: a DNA barcoding approach.

Derocles SA, Evans DM, Nichols PC, Evans SA, Lunt DH - PLoS ONE (2015)

Maximum likelihood tree based on cytochrome c oxidase I (COI) Minibarcode sequences.Bootstrap values are indicated above branches. Scale bar indicates the number of substitutions per site.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4339730&req=5

pone.0117872.g002: Maximum likelihood tree based on cytochrome c oxidase I (COI) Minibarcode sequences.Bootstrap values are indicated above branches. Scale bar indicates the number of substitutions per site.
Mentions: A total of 147 insect specimens emerged or dissected from the 407 infested leaves collected: 89 dipteran leaf miners (68 adults and 21 immatures), 10 larvae of lepidopteran leaf miners and 48 adult hymenoptera parasitoids. The COI full barcode was successfully amplified from all adult and immature samples. The COI mini-barcode amplified with ZBJ-ArtF1c and ZBJ-ArtR2c primers was successfully amplified from all adult and immature Diptera and Lepidoptera species. The COI mini-barcode amplified with Uni-MinibarR1 and Uni-MinibarF1 primers was successfully amplified from all adult and immature Diptera and Lepidoptera species, but Scaptomyza flava (Fallén) and Phytomyza spondylii (Robineau-Desvoidy). The 658-bp sequences for COI full barcode (for all adult and immature specimens; Fig. 1) and the 130-bp sequences for COI mini-barocde (for all adults and immatures Diptera and Lepidoptera; Fig. 2) were used to assess nucleotide sequence divergence between and within morphological species and to perform the ML analysis. 260 infested leaves were empty: the leaf mining insects had already emerged when the leaves had been collected (Table 1).

Bottom Line: We found that the 130 bp fragment is variable enough to identify all the species included in this study.Both COI fragments reveal that some leaf miner species could be composed of cryptic species.The network built using the molecular approach was more accurate in describing tri-partite interactions compared with traditional approaches based on morphological criteria.

View Article: PubMed Central - PubMed

Affiliation: School of Biological, Biomedical and Environmental Sciences, University of Hull, Hull, United Kingdom.

ABSTRACT
A major challenge in network ecology is to describe the full-range of species interactions in a community to create highly-resolved food-webs. We developed a molecular approach based on DNA full barcoding and mini-barcoding to describe difficult to observe plant-leaf miner-parasitoid interactions, consisting of animals commonly regarded as agricultural pests and their natural enemies. We tested the ability of universal primers to amplify the remaining DNA inside leaf miner mines after the emergence of the insect. We compared the results of a) morphological identification of adult specimens; b) identification based on the shape of the mines; c) the COI Mini-barcode (130 bp) and d) the COI full barcode (658 bp) fragments to accurately identify the leaf-miner species. We used the molecular approach to build and analyse a tri-partite ecological network of plant-leaf miner-parasitoid interactions. We were able to detect the DNA of leaf-mining insects within their feeding mines on a range of host plants using mini-barcoding primers: 6% for the leaves collected empty and 33% success after we observed the emergence of the leaf miner. We suggest that the low amplification success of leaf mines collected empty was mainly due to the time since the adult emerged and discuss methodological improvements. Nevertheless our approach provided new species-interaction data for the ecological network. We found that the 130 bp fragment is variable enough to identify all the species included in this study. Both COI fragments reveal that some leaf miner species could be composed of cryptic species. The network built using the molecular approach was more accurate in describing tri-partite interactions compared with traditional approaches based on morphological criteria.

Show MeSH
Related in: MedlinePlus