DOI: 10.5061/dryad.q573n5tng
title: First insights into population structure and genetic diversity versus host specificity in trypanorhynch tapeworms using multiplexed shotgun genotyping

description: Theory predicts relaxed host specificity and high host vagility should
 contribute to reduced genetic structure in parasites while strict host
 specificity and low host vagility should increase genetic structure.
 Though these predictions are intuitive, they have never been explicitly
 tested in a population genomic framework. Trypanorhynch tapeworms, which
 parasitize sharks and rays (elasmobranchs) as definitive hosts, are the
 only order of elasmobranch tapeworms that exhibit considerable variability
 in their definitive host specificity. This allows for unique combinations
 of host use and geographic range, making trypanorhynchs ideal candidates
 for studying how these traits influence population-level structure and
 genetic diversity. Multiplexed shotgun genotyping (MSG) datasets were
 generated to characterize component population structure and
 infrapopulation diversity for a representative of each trypanorhynch
 suborder: the ray-hosted Rhinoptericola megacantha (Trypanobatoida) and
 the shark-hosted Callitetrarhynchus gracilis (Trypanoselachoida). Adults
 of R. megacantha are more host-specific and less broadly distributed than
 adults of C. gracilis, allowing correlation between these factors and
 genetic structure. Replicate tapeworm specimens were sequenced from the
 same host individual, from multiple conspecific hosts within and across
 geographic regions, and from multiple definitive host species. For R.
 megacantha, population structure coincided with geography rather than host
 species. For C. gracilis, limited population structure was found,
 suggesting a potential link between degree of host specificity and
 structure. Conspecific trypanorhynchs from the same host individual were
 found to be as, or more, genetically divergent from one another as from
 conspecifics from different host individuals. For both species, high
 levels of homozygosity and positive FIS values were documented.
description: Genomic DNA was extracted from specimens of two species of
 elasmobranch tapeworms preserved in 95% ethanol: <em>Rhinoptericola
 megacantha</em> (n=39 worms) and <em>Callitetrarhynchus
 gracilis</em> (n=47 worms) collected from various species of shark
 or ray hosts from various geographic localities. Microscissors were used
 to remove a piece of the strobila and/or scolex of each worm for DNA
 extraction. (To ensure accurate genotyping, DNA was intentionally not
 extracted from gravid proglottids [i.e., proglottids containing eggs]).
 Methods for DNA extraction follow Herzog and Jensen (2022). Extracted
 genomic DNA for all specimens was used to generate two multiplexed shotgun
 genotyping (MSG) libraries using the restriction enzyme MseI and the
 protocol of Andolfatto et al. (2011) with the following modifications: (1)
 Unique in-line barcodes were ligated to digested DNA prior to pooling to
 allow for bioinformatic identification of each specimen after sequencing;
 and (2) following bead purification, pooled libraries were run on a Blue
 Pippin 2% agarose gel cassette (Sage Science, Beverly, MA, USA) to elute
 DNA fragments within a 300–400 bp range. Each of the two multiplexed
 libraries was sequenced on a single flow cell of an Illumina NextSeq 550
 High Output Next Generation Sequencer (Illumina, San Diego, CA, USA) for
 75 bp single end reads. All specimens were included in the first library.
 The second library consisted of a subset of specimens for which
 insufficient read counts were generated following the first round of
 library preparation and sequencing. Library preparation and sequencing was
 completed at the University of Kansas Genome Sequencing Core. For both
 rounds of sequencing, specimens were demultiplexed and low-quality reads
 and adaptor contamination were removed using the process_radtags module of
 Stacks v. 2.53 (Catchen et al. 2013; Rochette et al. 2019) with the ‑r,
 ‑c, and ‑q flags specified. Further filtering was performed using
 Trimmomatic v. 0.39 (Bolger et al. 2014) to remove remaining low-quality
 reads and adaptor contamination, and to enforce a consistent read length
 of 70 bp.
description: Datasets are formatted as zipped fastq files (.fastq.gz), so any
 of the many programs that can utilize fastq files as input will be capable
 processing these data.
description: # First insights into population structure and genetic diversity versus
 host specificity in trypanorhynch tapeworms using multiplexed shotgun
 genotyping *** Two datasets are provided, each as a gzipped tarball. The
 first dataset (trimmed_fastqs_Cgracilis.tar.gz) is for the focal species
 Callitetrarhynchus gracilis (md5 -r key:
 082769af225375407dd36c48e1b72094). The second dataset
 (trimmed_fastqs_Rmegacantha.tar.gz) is for the focal species
 Rhinoptericola megacantha (md5 -r key: d4978a59c296a5dea190c22499b34cfb).
 ## Description of the data and file structure Each dataset contains a
 single concatenated fastq file of demultiplexed, adaptor-trimmed, and raw
 read quality-controlled (via STACKS and Trimmomatic) Illumina reads
 generated for each individual tapeworm sequenced. Files that include
 "combo" in the file name contain read data from both the initial
 sequencing run and a second round of re-sequencing. Files are named by
 specimen code. Additional details for each specimen can be found in
 Supplementary Table S2.