Positive and negative frequency dependent parasitism in naturally co-occurring lineages of diploid sexual and polyploid asexual Lumbriculus variegatus
Data files
Mar 26, 2025 version files 1.45 GB
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C11_Assembly.fasta
4.15 KB
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C11_C12_D11_18S.fasta
2.14 KB
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C12_Assembly.fasta
4.27 KB
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D11_Assembly.fasta
3.95 KB
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Data_JEB_Tardent2025.xlsx
63.68 KB
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DetectWorms_Reference.yaml
1.47 KB
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phenopype_LV.py
1.78 KB
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R_Analysis_LV.R
15.51 KB
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README.md
5.33 KB
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sequence_names_info_nematodes.xlsx
9.53 KB
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Worm_Images.zip
1.45 GB
Apr 21, 2025 version files 1.45 GB
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C11_Assembly.fasta
4.15 KB
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C11_C12_D11_18S.fasta
2.14 KB
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C12_Assembly.fasta
4.27 KB
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D11_Assembly.fasta
3.95 KB
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Data_JEB_Tardent2025.csv
53.66 KB
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DetectWorms_Reference.yaml
1.47 KB
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phenopype_LV.py
1.78 KB
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R_Analysis_LV.R
15.48 KB
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README.md
5.63 KB
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sequence_names_info_nematodes.csv
362 B
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Worm_Images.zip
1.45 GB
Abstract
Polyploidisation is an important evolutionary force. It drives sympatric speciation through reproductive isolation of different cytotypes, and often leads to loss of sexual reproduction in polyploid lineages. Polyploidisation and asexuality can change how other species engage in ecological interactions with the polyploid lineage and may change coevolutionary dynamics. Here, we quantified the phenotypic divergence in the freshwater oligochaete worm Lumbriculus variegatus, the California blackworm, among its co-occurring sexual diploid (Lineage II) and asexual polyploid (Lineage I) lineages. We further investigated variation in parasite communities and infection prevalence among sympatric and allopatric diploid/polyploid populations. Ten out of 18 populations showed co-existence of both lineages, with 7 populations harbouring only the polyploid lineage. Both worm lineages hosted endoparasitic nematodes, an ectoparasitic rotifer, and one potentially symbiotic gut ciliate. The parasite community similarity and overlapping size range of diploid and polyploid worms points to the ecological similarity of the worm lineages, despite the substantial ploidy and reproductive strategy differentiation. Although parasite prevalence varied independently of worm lineage, prevalence was associated with frequency of local cytotypes. Specifically, the rotifer prevalence was highest on the rare local cytotype, and nematode prevalence was highest on the common local cytotype. These results suggest the presence of both positive and negative frequency dependent parasitism, which may contribute to the co-existence in the L. variegatus species complex.
https://doi.org/10.5061/dryad.18931zd76
Description of the data and file structure
This study examined the distribution of facultative sexual diploid and asexual polyploid aquatic oligochaetes, Lumbriculus variegatus in Switzerland.
A total of 40 samples (with three exceptions, locations HCH =39, location FLO = 39, location KBS = 19) were examined from each of the total 18 locations. The worms were measured using the pipeline phenopype (https://www.phenopype.org/) on 1 - 19 pictures per worm (see folder “pictures_LV”).
Additionally, this study examined the presence and frequency of infections with endoparasitic nematodes, ectoparasitic rotifers and potentially symbiotic ciliates. A few of the nematode samples were sequenced by Sanger sequencing, see sequence_names_info_nematodes.xlsx and the fasta file. The sequences will also be uploaded to NCBI Genbank.
Data collection was done by Nadine Tardent and Tamara Schlegel. Writing Code was done by Nadine Tardent for the analyses in R. The code to measure worm size and area was taken from the examples of phenopype (M.Lürig) with minor modifications made by N. Tardent. The modified code used for phenopype can be found as “phenopype_LV”. The R script used to analyze the data is called “R_Analysis_LV”. The data in the Excel file describes sampling locations, abbreviations for sampling locations used in the publication, whether they were examined for parasites (Set=Parasite) or not (Set = Worms). Parasites were grouped into Nematodes, Rotifers, Ciliates and Other. The file also contains the measurements obtained from phenopype for length (mean_length_pp) area (mean_area_pp), a few worms do not have a size measurement. The column “Coexistence” which specifies whether a location harboured both diploids and polyploids or not.
Files and variables
File: Data_JEB_Tardent2025.csv
Description: Master File used for the Analysis in R. It contains all the info on the worms, parasites and size measurements.
Variables
- ID: Individual ID of the worms.
- Location: Sampling location, full name
- Abbreviation: Abbreviation of the sampling location used in the publication
- Ploidy: Whether the worm is an asexual polyploid or a facultative sexual diploid
- Set: Worms (not examined for parasites) vs. Parasites (examined for parasites)
- Nematodes, Rotifers: How many of each were found on (rotifer) or inside (nematode) of a worm
- Ciliates: How many gut ciliates were found within a worm, categorized into NONE, FEW, MEDIUM, MANY. Few are usually around 10, many are around 50+, medium is in between.
- mean_area_pp: Area in mm^2 of each measured worm, measured with phenopype. It is a mean of several measured pictures, usually between 4-10 (entire range of measurements per worm is 1 -19).
- mean_length_pp: Length in mm of each masured worm, measured with phenopype. It is a mean of several measured pictures, usually between 4-10 (entire range of measurements per worm is 1 -19).
File: DetectWorms_Reference.yaml
Description: yaml file used for the phenopype pipeline to analyze the worm pictures. Sometimes the manual option was activated to delete unwanted pixels (see phenopype.org)
File: phenopype_LV.py
Description: Python script used to analyse the worm pictures. See phenopype.org for details.
File: R_Analysis_LV.R
Description: R File used for statistical analysis and graph production using the file Data_JEB_Tardent2025.xlsx
File: C11_C12_D11_18S.fasta
Description: Fasta file of the 3 nematodes sequenced with Sanger sequencing. they were all cut to the same length to allow pairwise comparison are the Consensus sequences of their respective C11, C12 and D11_assembly.fasta files. The data will be uploaded to Genbank as well.
File: sequence_names_info_nematodes.csv
Description: Excel File indicating which name (C11, C12, D11) belongs to which worm harboring the nematode parasite in the C11/C12/D11_Assembly.fasta files.
Variables
- Seq name: sequence name, can be found in the C11/C12/D11_Assembly.fasta files
- Worm_ID: ID of the worm in which the nematodes were found and extracted from
- Ploidy_Worm Host: ploidy of the worm host
- Location: From which location the worm was sampled
File: Worm_Images.zip
Description: All worm images produced in the study, can be used in the phenopype pipeline.
Code/software
Data Analysis: Fitting models, producing graphs:
R version 4.4.1
R Studio version 2023.6.0.421
R packages used:
ggplot2, v. 3.5.1
dplyr v. 1.1.4
readxl v. 1.4.3
tidyr v. 1.3.1,
car v. 3.1-3,
lme4 v. 1.1-35.5,
glmmTMB v. 1.1.10
Phenopype pipeline (measurement of pictures):
Spyder version 4.1.2
Python version 3.7.7
Phenopype version 3.4.2
The phenopype workflow is very well documented on https://www.phenopype.org, with the specific example of L. variegatus here: https://www.phenopype.org/gallery/projects/worm-length/.
Sequence analysis:
Geneious Prime® 2023.2.1
Change log
Mar 26, 2025 version files:
- Replaced Data_JEB_Tardent2025.xlsx with Data_JEB_Tardent2025.csv
- Changed the R script R_Analysis_LV.R to account for this change (read.csv instead of read-excel)
- Replaced sequence_names_info_nematodes.xlsx with sequence_names_info_nematodes.xlsx