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PASSIFOR: A reference library of DNA barcodes for French saproxylic beetles (Insecta, Coleoptera).

Rougerie R, Lopez-Vaamonde C, Barnouin T, Delnatte J, Moulin N, Noblecourt T, Nusillard B, Parmain G, Soldati F, Bouget C - Biodivers Data J (2015)

Bottom Line: Saproxylic beetles - associated with dead wood or with other insects, fungi and microorganisms that decompose it - play a major role in forest nutrient cycling.Species were identified by expert taxonomists, and each record is linked to a voucher specimen to enable future morphological examination.We also highlight and briefly discuss cases of low interspecific divergences, as well as cases of high intraspecific divergences that might represent cases of overlooked or cryptic diversity.

View Article: PubMed Central - PubMed

Affiliation: Muséum national d'Histoire Naturelle, Sorbonne Universités, Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205 - CNRS, MNHN, UPMC, EPHE, Paris, France ; INRA UR633 Zoologie Forestière, Orléans, France.

ABSTRACT
Saproxylic beetles - associated with dead wood or with other insects, fungi and microorganisms that decompose it - play a major role in forest nutrient cycling. They are important ecosystem service providers and are used as key bio-indicators of old-growth forests. In France alone, where the present study took place, there are about 2500 species distributed within 71 families. This high diversity represents a major challenge for specimen sorting and identification. The PASSIFOR project aims at developing a DNA metabarcoding approach to facilitate and enhance the monitoring of saproxylic beetles as indicators in ecological studies. As a first step toward that goal we assembled a library of DNA barcodes using the standard genetic marker for animals, i.e. a portion of the COI mitochondrial gene. In the present contribution, we release a library including 656 records representing 410 species in 40 different families. Species were identified by expert taxonomists, and each record is linked to a voucher specimen to enable future morphological examination. We also highlight and briefly discuss cases of low interspecific divergences, as well as cases of high intraspecific divergences that might represent cases of overlooked or cryptic diversity.

No MeSH data available.


Frequency distribution of within-species (normalized, in pink) and within-genus (green) K2P distances for records of the PASSIFOR library (sequences longer than 400 bp only: 597 records, 388 species). Table of distances is provided as Suppl. material 4 and Suppl. material 5.
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Figure 761577: Frequency distribution of within-species (normalized, in pink) and within-genus (green) K2P distances for records of the PASSIFOR library (sequences longer than 400 bp only: 597 records, 388 species). Table of distances is provided as Suppl. material 4 and Suppl. material 5.

Mentions: All 656 sequences of the library where used to build a Neighbor-Joining (NJ) tree as illustrated in Suppl. material 3. For the analysis of intraspecific and interspecific distances, we reduced the dataset to sequences longer than 400bp (597 records, 388 species). General summary statistics at the species, genus and family levels are given in Table 3; Fig. 2 shows the frequency distributions of genetic distances within species (normalized) and within genus. Fig. 3 represents the distribution of maximum intraspecific distances (singletons excluded) plotted against distances to Nearest Neighbour within the library. Overall, we observe a conspicuous bimodal pattern suggesting the existence of a marked "barcode gap" between intraspecific and interspecific genetic divergence. We note however that in the vast majority of species our sampling remains too limited, both taxonomically (sister species often unsampled) and numerically (intraspecific divergence undocumented for most species) to test the extent of this gap and its consistency.


PASSIFOR: A reference library of DNA barcodes for French saproxylic beetles (Insecta, Coleoptera).

Rougerie R, Lopez-Vaamonde C, Barnouin T, Delnatte J, Moulin N, Noblecourt T, Nusillard B, Parmain G, Soldati F, Bouget C - Biodivers Data J (2015)

Frequency distribution of within-species (normalized, in pink) and within-genus (green) K2P distances for records of the PASSIFOR library (sequences longer than 400 bp only: 597 records, 388 species). Table of distances is provided as Suppl. material 4 and Suppl. material 5.
© Copyright Policy - creative-commons-attribution
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4355675&req=5

Figure 761577: Frequency distribution of within-species (normalized, in pink) and within-genus (green) K2P distances for records of the PASSIFOR library (sequences longer than 400 bp only: 597 records, 388 species). Table of distances is provided as Suppl. material 4 and Suppl. material 5.
Mentions: All 656 sequences of the library where used to build a Neighbor-Joining (NJ) tree as illustrated in Suppl. material 3. For the analysis of intraspecific and interspecific distances, we reduced the dataset to sequences longer than 400bp (597 records, 388 species). General summary statistics at the species, genus and family levels are given in Table 3; Fig. 2 shows the frequency distributions of genetic distances within species (normalized) and within genus. Fig. 3 represents the distribution of maximum intraspecific distances (singletons excluded) plotted against distances to Nearest Neighbour within the library. Overall, we observe a conspicuous bimodal pattern suggesting the existence of a marked "barcode gap" between intraspecific and interspecific genetic divergence. We note however that in the vast majority of species our sampling remains too limited, both taxonomically (sister species often unsampled) and numerically (intraspecific divergence undocumented for most species) to test the extent of this gap and its consistency.

Bottom Line: Saproxylic beetles - associated with dead wood or with other insects, fungi and microorganisms that decompose it - play a major role in forest nutrient cycling.Species were identified by expert taxonomists, and each record is linked to a voucher specimen to enable future morphological examination.We also highlight and briefly discuss cases of low interspecific divergences, as well as cases of high intraspecific divergences that might represent cases of overlooked or cryptic diversity.

View Article: PubMed Central - PubMed

Affiliation: Muséum national d'Histoire Naturelle, Sorbonne Universités, Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205 - CNRS, MNHN, UPMC, EPHE, Paris, France ; INRA UR633 Zoologie Forestière, Orléans, France.

ABSTRACT
Saproxylic beetles - associated with dead wood or with other insects, fungi and microorganisms that decompose it - play a major role in forest nutrient cycling. They are important ecosystem service providers and are used as key bio-indicators of old-growth forests. In France alone, where the present study took place, there are about 2500 species distributed within 71 families. This high diversity represents a major challenge for specimen sorting and identification. The PASSIFOR project aims at developing a DNA metabarcoding approach to facilitate and enhance the monitoring of saproxylic beetles as indicators in ecological studies. As a first step toward that goal we assembled a library of DNA barcodes using the standard genetic marker for animals, i.e. a portion of the COI mitochondrial gene. In the present contribution, we release a library including 656 records representing 410 species in 40 different families. Species were identified by expert taxonomists, and each record is linked to a voucher specimen to enable future morphological examination. We also highlight and briefly discuss cases of low interspecific divergences, as well as cases of high intraspecific divergences that might represent cases of overlooked or cryptic diversity.

No MeSH data available.