DOI: 10.5061/dryad.76hdr7t5p
title: Data from: Parasite spillover rather than niche expansion explains infection of host brain by diplostomid eye flukes

description: Parasites often occupy specific sites within their host, which has
 important implications for host performance and parasite transmission.
 Nonetheless, parasitic infections can occur beyond their typical location
 within a host, significantly altering host-parasite interactions. Yet, the
 causes behind the atypical tissue tropism are poorly understood. Here, we
 focus on a ubiquitous group of diplostomid parasites that form diverse
 communities in fish eyes. We used targeted DNA metabarcoding (COX1, 250
 bp) to evaluate potential mechanisms underlying atypical tissue tropism
 from predominantly eye to brain infection in two widespread fish species
 (Eurasian perch and common roach). We found that the most common
 eye-infecting species (Tylodelphys clavata, Diplostomum baeri) are present
 in the brains of perch but not in roach. The bipartite network comprising
 five species and 24 mitochondrial haplotypes revealed no brain-specific
 haplotypes, indicating an apparent lack of genetic divergence between
 brain and eye-infecting parasites. Instead, the prevalence, intensity, and
 diversity of eye infections were positively correlated with brain
 infections. Thus, our results suggest that the most parsimonious mechanism
 underlying brain infection is density-dependent spillover rather than
 parasite divergence-driven niche expansion. We anticipate that
 “off-target” infections are likely to be severely underestimated in nature
 with severe ecological, evolutionary, and medical implications.
description: The data set was obtained by the metabarcoding characterisation
 of the diplostomids communties in the eyes and brain of Eurasian perch
 collected at seven lakes in souther Estonia. This files includes the
 bioinformatic pipeline to process the raw seqeunces (2 x 300 bp read
 length, Illumina Inc., San Diego, California, USA) and the R code for the
 down stream analysis.
description: # Parasite spillover rather than niche expansion explains infection of
 host brain by diplostomid eye flukes
 [https://doi.org/10.5061/dryad.76hdr7t5p](https://doi.org/10.5061/dryad.76hdr7t5p) ## Description of data and file structure This dataset includes the bioinformatic pipeline, R code (Diaz_Suarez_et_al_2024), and data files to run the statistical analysis and plotting of the MS entitled "Parasite spillover rather than niche expansion explains infection of host brain by diplosomid eye flukes". Raw sequences are available in GenBank on accession number PRJNA1078141. All used packages are indicated at the beginning of the R code file (library()). The datasets included are the following: **ASV_new_stric.csv** -&gt; Strict mapping of ASv using the --search_exact function in VSEARCH **TAX_brain_new.csv** -&gt; taxonomic identification of ASV using SINTAX classifier **Metadata_strict.csv** -&gt; Metadata including the lake, infected tissue (eye, brain), infection type (eye, brain, eye-brain) **GLMM_normalised.csv** -&gt; Matrix used to perform the prevalence tables, prevalence plots, GLM (generalized linear models) and LM (liner models). The variables included in the table are; brain_infection (yes=1, no=0), eye_infection (yes=1, no=0), lake, site within lake (site 1 or site 2), host weight (gr), host Forck length FL (mm), Condition factor (KC), total reads assigned to the eye, total reads assigned to the brain, Number of Tylodelphys clavata haplotypes in the eye (nhapTyl_eye), number of Diplostomum baeri haplotypes in the eye (hapBae_eye, number of Diplostomum rauschi n haplotypes in the eye (hapBae_eye), number of Diplostomum spathaceum n haplotypes in the eye (hapSpa_eye), number of Diplostomum pseudospathaceum haplotypes in the eye (hapPse_eye), Total number of haplotypes in the eye (num_haplo_eye), number of Tylodelphys clavata haplotypes in the brain (hapTyl_brain), number of Diplostomum baeri haplotypes in the brain (hapBae_brain), Total number of haplotypes in the brain (num_haplo_brain) **Bipartine_general_2.csv** -&gt; binary presence/absence matrix was constructed for all identified haplotypes. The matrix indicates the number of host individuals infected by each parasite haplotypes belonging to the 5 parasite species. ASV identification is provided in Supplementary material table 3. **Haplonet_clavata.fasta** -&gt; Sequences of seven Tylodelphys clavata haplotypes **Haplonet_baeri.fasta** -&gt; Sequences of seven haplotypes of Diplostomum baeri **freq_baeri.csv** -&gt; Haplotype frequencies of Diplostomum baeri at each lake.  **freq_clavata.csv** -&gt;  Haplotypes frequencies of Tylodelphys clavata at each lake ### Files and variables #### File: bipartine\_general\_2.csv **Description:** binary presence/absence matrix was constructed for all identified haplotypes. The matrix indicates the number of host individuals infected by each parasite haplotypes belonging to the 5 parasite species. The ASV identification is available in Supplementary material table 3. ##### Variables * Brain: number of fish individuals infected by the given haplotype * Eye: number of fish individulas infected by the haplotype #### File: freq\_baeri.csv **Description:**  ##### Variables * Lake: * Hino: * Kasaritsa_Verijarv: * Kisojarv: * Koorkula Valgjarv: * Oisu: * Piigandi: * Saadjarv: #### File: freq\_clavata.csv **Description:**  ##### Variables * lake: * Hino: * Kasaritsa_Verijarv: * Kisojarv: * Koorkula_Valgjarv: * Oisu: * Piigandi: * Saadjarv: #### File: GLMM\_normalised.csv **Description:** Matrix used to perform the prevalence tables, prevalence plots, GLM (generalized linear models), and LM (liner models). The variables included in the table are; brain_infection (yes=1, no=0), eye_infection (yes=1, no=0), lake, site within lake (site 1 or site 2), host weight (gr), host Forck length FL (mm), Condition factor (KC), total reads assigned to the eye, total reads assigned to the brain, Number of Tylodelphys clavata haplotypes in the eye (nhapTyl_eye), number of Diplostomum baeri haplotypes in the eye (hapBae_eye, number of Diplostomum rauschi n haplotypes in the eye (hapBae_eye), number of Diplostomum spathaceum n haplotypes in the eye (hapSpa_eye), number of Diplostomum pseudospathaceum haplotypes in the eye (hapPse_eye), Total number of haplotypes in the eye (num_haplo_eye), number of Tylodelphys clavata haplotypes in the brain (hapTyl_brain), number of Diplostomum baeri haplotypes in the brain (hapBae_brain), Total number of haplotypes in the brain (num_haplo_brain) ##### Variables * sample: fish individual * brain_inf: brain infection (1=yes, 0=no) * eye_inf: eye infection (1=yes, 0=no) * lake: location where the fish was collected * site: site within lake where the fish was collected * weigth(g): fish weight in grams * Fl_mm: total fork length in millimeters * Kc_factor: fish body condition calculated as 100 x W/FL3, where W represents weight in grams and FL represents fork length incentimeters.s * total_reads_eye: total number of bioinformatic reads detected in the eyes of the fish individual * total_reads_brain:total number of bioinformatic reads detected in the brain of the fish individual * hapTyl_eye: total number of different haplotypes (cox1) of *Tylodelphys clavata* in the eyes; * hapBae_eye: total number of different haplotypes (cox1) of *Diplostomum baeri* in the eyes; * hapRau_eye: total number of different haplotypes (cox1) of *Diplostomum rauschi* in eyes * hapSpa_eye: total number of different haplotypes (cox1) of Diplostomum spathaceum in the eyes * hapPse_eye: total number of different haplotypes (cox1) of Diplostomum pseudospathaceum in the eyes * num_haplo_eye: total number of different haplotypes (cox1) of all infected eyes * hapOth_eye:total number of different haplotypes (cox1) of the less frequent species (*Diplostomum rauschi, Diplostomum spathaceum, Diplostomum pseudospathaceum)* * hapTyl_brain: total number of different haplotypes (cox1) of *Tylodelphys clavata* in the brain; * hapBae_brain: total number of different haplotypes (cox1) of *Diplostomum baeri* in the brain * num_haplo_brain: number of different haplotypes (cox1) of all infected brain species; ## Code/software The following pipeline was used to process paired-end sequencing with 2 x 300 bp read length (Illumina Inc., San Diego, California, USA) included in the MS entitled "Parasite spillover rather than niche expansion explains infection of host brain by diplosomid eye flukes". Raw sequences are available at the National Center for Biotechnology Information (NCBI) under accession no. PRJNA1078141 \## The pipeline is based on the material and teaching of "Bioinformatic Methods for Biodiversity Metabarcoding" ([https://learnmetabarcoding.github.io/](https://learnmetabarcoding.github.io/))