State of the spread of the exotic parasitoid wasp Leptopilina japonica tracking the route of its invasive host fly Drosophila suzukii in France
Data files
Nov 13, 2025 version files 11.49 MB
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Figure_S1_Tree-RAxML.jpg
11.41 MB
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README.md
7.57 KB
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Table_S1.csv
25.56 KB
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Table_S2.csv
16.23 KB
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Table_S3.csv
1.28 KB
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Table_S4.csv
32.39 KB
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Table_S5.csv
906 B
Nov 20, 2025 version files 11.65 MB
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COI_ITS2_metadata.csv
81.82 KB
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COI_Leptopilina_japonica.txt
46.24 KB
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Figure_S1_Tree-RAxML.jpg
11.41 MB
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ITS2_Leptopilina_japonica.txt
30.65 KB
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README.md
9.53 KB
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Table_S1.csv
25.56 KB
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Table_S2.csv
16.23 KB
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Table_S3.csv
1.28 KB
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Table_S4.csv
32.39 KB
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Table_S5.csv
906 B
Abstract
The spotted-wing drosophila, Drosophila suzukii, is one of the most damaging invasive fruit pests in the world. It infests a wide range of wild and crop host plants, impacting natural habitats and causing significant economic losses. Leptopilina japonica, a predominant larval parasitoid of D. suzukii in the native areas of the fly, is now spontaneously expanding into non-native areas of its fly host. This study documents the presence and genetic structure of L. japonica collected from various wild and cultivated fruits across 11 sites in France in 2023. Leptopilina japonica emerged from 15% of fruit samples and was strongly positively associated with D. suzukii, showing parasitism rates up to 38.5%, notably in Lonicera fruits. Despite this, D. suzukii remained dominant, indicating a limited current biocontrol effect, while native parasitoids were nearly absent from samples. Molecular analyses using COI markers revealed 10 distinct haplotypes of the L. japonica subspecies in France that clustered into three groups, suggesting multiple introductions and/or migration routes into France from Asia, North America, and neighboring European countries. The lack of nuclear diversity measured from ITS2 markers suggests that the colonization is recent and that the populations experienced a bottleneck process. Nevertheless, a more extensive sampling combined with the use of additional genetic markers would be needed to better understand the origin and spread of L. japonica and its consequence on the equilibrium of Drosophila communities.
Dataset DOI: 10.5061/dryad.brv15dvp2
Description of the data and file structure
This dataset contains supplementary materials associated with the publication above.
The data include phylogenetic, molecular, and ecological information related to Leptopilina japonica populations collected in Europe and other regions. Each file provides information necessary to reproduce the analyses and figures presented in the paper.
Files and variables
File: Figure_S1_Tree-RAxML.jpg
Description: Phylogenetic tree inferred using RAxML. Bootstrap support values above 70 show at nodes. In red are marked the COI sequences of Leptopilina japonica obtained in this study.
Format: Image file .jpg
File: Table_S4.csv
Description: Distribution of COI haplotypes of Leptopilina japonica. Summary table of COI haplotype distribution across samples.
Variables
- Haplotype_id: the haplotype number assigned to each COI sequence. The code consists of the prefix Hap_ followed by the haplotype number
- Ref_BM_code/accession_number_NCBI_BOLD: Reference code of the specimen or sequence, corresponding to either the specimen barcode (Ref_BM_code) or a public accession number in NCBI or BOLD
- Status: indicates whether the haplotype was identified as "valid haplotype" or "putative pseudogene (negative frequency mutations)"
- Continent: continent of origin for the sample
- Country: country where the sample was collected
- France_area: the region (North-East, South-East and South-Weast) in France where the specimen was collected where specimens are from outside France, this is marked with a "-"
- Source: Source of the data "this study" or "available data" (for GenBank or BOLD)
Format: .csv
File: Table_S5.csv
Description: Geographical distributions and frequency of haplotypes of L. japonica in different countries.
Variables
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Continent: continent of origin for the sample
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Country: country where the sample was collected
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France_area: the region (North-East, South-East and South-Weast) in France where the specimen was collected where specimens are from outside France, this is marked with a "-"
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Haplotype_id: the haplotype number assigned to each COI sequence. The code consists of the prefix Hap_ followed by the haplotype number. For each haplotype, the frequency numbers are added where the haplotype is not represented; the cell is marked with a "_"
Format: .csv
File: Table_S1.csv
Description: Collection information for insect specimens in France. FIR: Fruit infestation rates.
Variables
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sample_name: unique reference number assigned to each fruit sample collected
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collection_date: date when the sample was collected (DD-MM-YYYY)
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site_name: name of the sampling site
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locality: geographic locality in France
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host_plant: plant species from which the fruits were collected
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weight_of_collected_fruit: total weight of collected fruit from each sample (g)
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Number_of_Drosophila_suzukii: number of D. suzukii individuals emerged from the sample
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FIR_D._suzukii: fruit infestation rate by D. suzukii (100 × number of D. suzukii individuals from fruits collected from a given plant individual / total mass of fruit collected from the same plant individual) (%)
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Number_of_other_Drosophila_species: number of Drosophila individuals other than D. suzukii
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FIR_other_Drosophila_species: Fruit infestation rate by other Drosophila species (100 × number of other Drosophila individuals from fruits collected from a given plant individual / total mass of fruit collected from the same plant individual) (%)
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Number_of_Leptopilina_japonica: number of Leptopilina japonica parasitoids emerged from the sample
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FIR_L._japonica: fruit infestation rate by L. japonica (100 × number of L. japonica individuals from fruits collected from a given plant individual / total mass of fruit collected from the same plant individual) (%)
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Number_of_Asobara_rufescens: number of Asobara rufescens parasitoids emerged from the sample
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FIR_A._rufescens: fruit infestation rate by A. rufescens (100 × number of A. rufescens individuals from fruits collected from a given plant individual / total mass of fruit collected from the same plant individual) (%)
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Number_of_Pachycrepoideus_vindemiae: number of Pachycrepoideus vindemiae parasitoids emerged from the sample
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FIR_P._vindemmiae: fruit infestation rate by P. vindemmiae (100 × number of P. vindemmiae individuals from fruits collected from a given plant individual / total mass of fruit collected from the same plant individual) (%)
Format: .csv
File: Table_S2.csv
Description: Collection information for the Leptopilina japonica specimens for which DNA sequences were obtained in this study and were included in the haplotype network analyses. For each COI or ITS2 marker, GenBank accession numbers were included.
Variables
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Ref_BM_code: unique specimen reference ID
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country: country where the specimen was collected
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locality: sampling locality
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France_site_codes: site code used for sampling locations in France
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host_plant: host plant species from which the sample was obtained. When the information is missing, the case is marked with a "_", or the specimen was collected alive and this was noted
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collection_date: date when the specimen was collected (DD-MM-YYYY)
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Haplotype_COI: Haplotype number assigned based on COI sequence analysis
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COI_accession_number: GenBank accession number corresponding to the COI sequence
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Haplotype_ITS2: Haplotype number assigned based on ITS2 sequence analysis
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ITS2_accession_number: GenBank accession number corresponding to the ITS2 sequence
Format: .csv
File: Table_S3.csv
Description: The values of infestation and parasitism variables in different plant species and locations. FIR: Fruit infestation rates. PR: parasitism rate.
Variables
- Site_code: name of the sampling site
- host_plant: plant species from which the fruits were collected
- FIR_D.suzukii: fruit infestation rate by D. suzukii (100 × number of D. suzukii individuals from fruits collected from a given plant individual / total mass of fruit collected from the same plant individual) (%)
- FIR_other_drosophilids: Fruit infestation rate by other Drosophila species (100 × number of other Drosophila individuals from fruits collected from a given plant individual / total mass of fruit collected from the same plant individual) (%)
- FIR_L._japonica: fruit infestation rate by L. japonica (100 × number of L. japonica individuals from fruits collected from a given plant individual / total mass of fruit collected from the same plant individual) (%)
- FIR_other_parasitoids: Fruit infestation rate by other parasitoids species than L. japonica (100 × number of other parasitoids individuals from fruits collected from a given plant individual / total mass of fruit collected from the same plant individual) (%)
- PR_L._japonica: Parasitism rate by L. japonica (100 × number of L. japonica / [numbers of D. suzukii + other Drosophila + L. japonica + other parasitoids]) (%)
PR_other_parasitoids: Parasitism rate by other parasitoids* *(100 × number of other parasitoids / [numbers of D. suzukii + other Drosophila + L. japonica + other parasitoids]) (%)
Format: .csv
File: COI_ITS2_metadata.csv
Description: This dataset contains molecular sequence information generated for the species Leptopilina japonica. The table includes details on sample origin, molecular markers used, sequence identifiers, GenBank accession numbers, and the final processed (trimmed) sequences obtained after primer removal.
Variables
- Species: The species analyzed, in this dataset, Leptopilina japonica
- Sequence_ID: unique specimen reference ID
- country: The country where the specimen was collected
- city: The locality (city, region, or specific area) where the specimen was collected
- Date: The date the specimen was collected, formatted as dd/mm/yyyy
- molecular_marker: The molecular marker used for sequencing. In this dataset, markers are either COI or ITS2
- GenBank_accesion_number: The accession number assigned to the sequence in GenBank
- Sequence_trimmed: The final DNA sequence obtained after removing both 5’ and 3’ primers, used in downstream genetic analyses
File: COI_Leptopilina_japonica.txt
Description: The .txt file contains the trimmed COI DNA sequences of Leptopilina japonica in a simplified FASTA format. The header begins with the > symbol and contains three comma-separated fields: >Species, molecular_marker, Sequence_ID
Variables
- Leptopilina japonica, the species analyzed in this dataset
- COI: the molecular marker used
- the internal Sequence_ID corresponding to the dataset table
File: ITS2_Leptopilina_japonica.txt
Description: The .txt file contains the trimmed ITS2 DNA sequences of Leptopilina japonica in a simplified FASTA format. The header begins with the > symbol and contains three comma-separated fields: >Species, molecular_marker, Sequence_ID
Variables
- Leptopilina japonica, the species analyzed in this dataset
- ITS2: the molecular marker used
- the internal Sequence_ID corresponding to the dataset table
Changes after Nov 13, 2025:
Following the last review, we added three documents containing nucleotide sequences obtained in this study and supporting the hypotheses of this study.
These are
COI_ITS2_metadata.csv, which contains the collection data for the DNA sequences
COI_Leptopilina_japonica.txt, which represents the alignment of sequences for the COI mitochondrial gene
ITS2_Leptopilina_japonica.txt, which represents the sequences for the ITS2 nuclear gene.
