DOI: 10.5061/dryad.18931zd76
title: Positive and negative frequency dependent parasitism in naturally co-occurring lineages of diploid sexual and polyploid asexual Lumbriculus variegatus

description: 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.
description: # Positive and negative frequency dependent parasitism in naturally
 co-occurring lineages of diploid sexual and polyploid asexual Lumbriculus
 variegatus
 [https://doi.org/10.5061/dryad.18931zd76](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/](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](https://www.phenopype.org), with the specific example of L. variegatus here: [https://www.phenopype.org/gallery/projects/worm-length/](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