Data and code from: Molecular characterization and cophylogenetic relationships between Crassicauda spp. (Nematoda: Spirurida) and cetaceans of the Northwest Atlantic
Data files
Sep 07, 2026 version files 6.33 MB
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18S_alignment.nex
27.87 KB
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host_cox1_alignment.nex
32.73 KB
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host_cox1_tree.newick
804 B
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host_posterior_trees.newick
1.54 MB
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hp_cox1_r_script.R
6.03 KB
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hp_link_table_mcgowen.csv
781 B
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hp_link_table.csv
1.51 KB
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ITS2_alignment.nex
66.36 KB
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jane_best_fit_parasite_tree.tre
1.67 KB
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jane_median_fit_parasite_tree.tre
1.66 KB
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jane_tree_visualization_r_script.R
1.69 KB
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jane_worst_fit_parasite_tree.tre
1.67 KB
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McGowen_Bayes_tree.nex
46.10 KB
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para_cox1_alignment.nex
96.16 KB
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para_cox1_tree.newick
2.02 KB
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para_posterior_trees.newick
4.46 MB
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posterior_mcgowen_r_script.R
12.82 KB
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posterior_trees_r_script.R
14.02 KB
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README.md
12.54 KB
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total_parasite_host_metadata.csv
8.58 KB
Abstract
Evaluating the cophylogenetic relationships between hosts and parasites provides a valuable framework for investigating the evolutionary processes that shape biodiversity, including patterns of host specificity and parasite diversification. This study investigated the evolutionary relationships between cetaceans and their nematode parasites of the genus Crassicauda. This genus was selected because it includes highly virulent species that may regulate host populations. Still, its diversity and evolutionary history remain poorly understood due to limitations in sampling these giant nematodes. To address this gap, we generated sequence data from 13 Crassicauda specimens collected from five cetacean host species in the Northwest Atlantic using mitochondrial (cox1) and nuclear (18S and ITS-2) genes, and combined these with homologous sequences from GenBank to characterize diversity within the genus and to delimit our putative species hypotheses. We assessed host-parasite cophylogenetic relationships by using complementary distance-based (PACo and ParaFit) and event-based (Jane) approaches. Phylogenetic analyses resolved 11 parasite species infecting 15 cetacean species, revealing potential cryptic and underreported diversity. Cophylogenetic analyses recovered significant cophylogenetic signal between host and parasite phylogenies, providing strong evidence that host-parasite associations are more structured than by chance. This signal was robust across multiple analytical parameters; distance-based analyses consistently recovered significant cophylogenetic signal in both consensus and posterior tree analyses. Although event-based reconciliation costs were significantly lower than expected under null models, inferred host-switching events exceeded cospeciation events, indicating incongruence between parasite and host phylogenies. Concordant results across independent methods, together with the known biology and ecology of both the hosts and parasites, support a long-term evolutionary association between Crassicauda and cetaceans shaped by a combination of cospeciation, host-switching, failure-to-diverge, and other evolutionary processes.
Dataset DOI: 10.5061/dryad.95x69p91q
Description of the data and file structure
This dataset contains the specimen metadata, molecular sequence alignments, phylogenetic trees, host-parasite association tables, and R scripts required to replicate analyses in the associated manuscript investigating cophylogenetic relationships between Crassicauda spp. and their cetacean hosts. Crassicauda parasite specimens were collected opportunistically during necropsies of stranded cetaceans recovered along the Northwest Atlantic coast. DNA was extracted, and regions of the mitochondrial cox1 and nuclear 18S and ITS-2 genes were amplified and sequenced. Novel sequences generated in this study were combined with homologous sequences available in GenBank, and phylogenetic relationships were reconstructed using maximum likelihood and Bayesian inference methods. Phylogenetic results were used to evaluate evolutionary relationships within the genus. In conjunction, an ASAP species delimitation analysis was performed using the cox1 alignment to delimit putative species hypotheses. Host-parasite evolutionary relationships were assessed using complementary distance-based (Parafit and PACo) and event-based (Jane) cophylogenetic methods. Distance-based methods were used to evaluate cophylogenetic signal and individual host-parasite link contributions across 100 posterior parasite phylogenies, and event-based methods evaluated phylogenetic congruence and inferred reconciliation event scenarios. Cophylogenetic methods were repeated across multiple phylogenetic inputs, null randomization procedures, and alternative cost schemes. Concordance across alternative phylogenetic inputs, analytical parameters, and complementary cophylogenetic methods was used to evaluate the robustness of inferred evolutionary relationships.
Files and variables
1) Host and Parasite Specimen Metadata
File: total_parasite_host_metadata.csv
Description: Metadata for parasite specimens and their associated hosts included in this study, such as specimen identifiers, collection information, parasite species hypotheses (PSHs), infection site, geographic region, and GenBank accession numbers.
Variables
- Host Species: Scientific name of the associated cetacean host species.
- Parasite Species: Putative species identification of the parasite specimen.
- PSH: Species hypotheses assigned from ASAP species delimitation and phylogenetic analysis.
- ITS-2: GenBank accession number for the ITS-2 sequence.
- 18S: GenBank accession number for the 18S sequence.
- cox1: GenBank accession number for the cox1 sequence.
- Infection Site: Anatomical location where the parasite was collected.
- Geographic Region: General location within the NW Atlantic where the host was collected.
- Reference: The original source of the specimen or sequence from GenBank or this study.
2) Sequence Alignments
File: 18S_alignment.nex
Description: Aligned parasite 18S sequences used for genus-level confirmation.
File: ITS2_alignment.nex
Description: Aligned parasite ITS-2 sequences used for phylogenetic analysis.
File: para_cox1_alignment.nex
Description: Aligned and trimmed parasite cox1 sequences used for phylogenetic analyses.
File: host_cox1_alignment.nex
Description: Aligned host cox1 sequences obtained from GenBank and used to generate the alternative host phylogeny.
3) Phylogenetic Trees
File: para_cox1_tree.newick
Description: The maximum likelihood parasite phylogeny generated from the cox1 alignment. This tree was used as an alternative phylogenetic input for PACo and ParaFit analyses.
File: para_posterior_trees.newick
Description: The parasite posterior probability trees generated from Bayesian phylogenetic analysis. These trees were used as the primary phylogenetic input for the PACo and ParaFit analyses.
File: host_cox1_tree.newick
Description: The maximum-likelihood host cox1 phylogeny used as an alternative phylogenetic input for distance-based cophylogenetic analyses.
File: host_posterior_trees.newick
Description: The posterior sample of host trees generated from Bayesian phylogenetic analysis of the cox1 gene marker. These trees were used as an alternative phylogenetic input to test the sensitivity of the PACo and ParaFit analyses.
File: McGowen_Bayes_tree.nex
Description: The published cetacean backbone phylogeny from McGowen et al. (2020). This phylogeny was used as the primary phylogenetic input for PACo and ParaFit analyses.
4) Host-parasite association data
File: hp_link_table.csv
Description: The host-parasite (referred to as "H-P") association table used to generate binary interaction matrices used in cophylogenetic analyses. Interaction matrices generated from this association table were used in PACo and ParaFit analyses.
Variables
- Host: Scientific name of the host species.
- Parasite: Parasite sequence identifier associated with each host species.
File: hp_link_table_mcgowen.csv
Description: Host-parasite association table used with the McGowen et al. (2020) host phylogeny to generate interaction matrices used in the primary cophylogenetic analysis.
Variables
- Host: Host species identifier that corresponds to the McGowen et al. (2020) host tree (i.e., host-tip labels).
- Parasite: Parasite sequence identifier associated with each host species.
5) Alternative Jane inputs
File: jane_best_fit_parasite_tree.tre
Description: The posterior parasite tree corresponding to the lowest PACo global-fit statistic. This tree was used as an alternative parasite tree topology in Jane analyses.
File: jane_median_fit_parasite_tree.tre
Description: The posterior parasite tree corresponding to the median PACo global-fit statistic. This tree was used as an alternative parasite tree topology in Jane analyses.
File: jane_worst_fit_parasite_tree.tre
Description: The posterior parasite tree corresponding to the highest PACo global-fit statistic. This tree was used as an alternative parasite tree topology in Jane analyses.
6) R script files
File: posterior_mcgowen_r_script.R
Description: The primary cophylogenetic analysis using posterior parasite phylogenies and the published McGowen et al. (2020) host phylogeny.
File: posterior_trees_r_script.R
Description: The alternative cophylogenetic analysis 1 using randomly selected posterior host and parasite phylogenies.
File: hp_cox1_r_script.R
Description: The alternative cophylogenetic analysis 2 using host and parasite cox1 phylogenies.
File: jane_tree_visualization_r_script.R
Description: The script used for preparation (i.e., rerooting and ladderization) and visualization of alternative parasite tree topologies used for manual reconstruction in Jane using the TreeBuilder tool.
Code/software
1) Sequence alignment and phylogenetic analysis
Sequence alignments and phylogenetic analyses were generated in Geneious Prime (version 2026.1.2; Biomatters Ltd.) using the MAFFT (Katoh et al., 2002), RAxML (Stamatakis et al., 2005), and MrBayes (Huelsenbeck & Ronquist, 2001) Geneious plug-ins. Sequence alignments and phylogenetic trees are in standard NEXUS (.nex) and Newick (.newick) file formats.
Species delimitation was performed using Assemble Species by Automatic Partitioning (ASAP) (Puillandre et al., 2021). The ASAP program is available at https://github.com/iTaxoTools/ABGDpy.
2) Cophylogenetic analyses
Distance-based
Distance-based cophylogenetic analyses were performed in R (version 4.4.2) using the packages ape, paco, vegan, permute, purrr, ggplot2, and lattice. The ape package (Paradis & Schliep, 2019) was used to prepare, manipulate, and visualize phylogenetic trees, as well as calculate cophenetic distance matrices. The PACo package (Balbuena et al., 2013; Hutchinson et al., 2017) and the ParaFit function (Legendre et al., 2002), implemented in the ape package, were used to evaluate global cophylogenetic signal and assess individual host–parasite associations.
Event-based
Event-based cophylogenetic analyses were conducted in Jane (version 4) (Conow et al., 2010). Jane is available at: https://www.cs.hmc.edu/~hadas/jane/.
3) R scripts
The four R script files (see Section 6, Files and Variables) included in this repository correspond to the primary and alternative analyses described in the associated manuscript, and utilize the phylogenetic trees and host-parasite association files included in this repository.
- Packages:
- ape
- paco
- vegan
- permute
- purrr
- dplyr
- ggplot2
- lattice
References (in this ReadMe):
Katoh, K., Misawa, K., Kuma, K., & Miyata, T. (2002). MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research, 30(14), 3059–3066. https://doi.org/10.1093/nar/gkf436
Stamatakis, A., Ludwig, T., & Meier, H. (2005). RAxML-III: A fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics, 21(4), 456–463. https://doi.org/10.1093/bioinformatics/bti191
Huelsenbeck, J. P., & Ronquist, F. (2001). MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics, 17(8), 754–755. https://doi.org/10.1093/bioinformatics/17.8.754
Puillandre, N., Brouillet, S., & Achaz, G. (2021). ASAP: Assemble species by automatic partitioning. Molecular Ecology Resources, 21(2), 609–620. https://doi.org/10.1111/1755-0998.13281
Paradis, E., & Schliep, K. (2019). ape 5.0: An environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics, 35(3), 526–528. https://doi.org/10.1093/bioinformatics/bty633
Balbuena, J. A., Míguez-Lozano, R., & Blasco-Costa, I. (2013). PACo: A Novel Procrustes Application to Cophylogenetic Analysis. PLOS ONE, 8(4), e61048. https://doi.org/10.1371/journal.pone.0061048
Hutchinson, M. C., Cagua, E. F., Balbuena, J. A., Stouffer, D. B., & Poisot, T. (2017). paco: Implementing Procrustean Approach to Cophylogeny in R. Methods in Ecology and Evolution, 8(8), 932–940. https://doi.org/10.1111/2041-210X.12736
Legendre, P., Desdevises, Y., & Bazin, E. (2002). A Statistical Test for Host–Parasite Coevolution. Systematic Biology, 51(2), 217–234. https://doi.org/10.1080/10635150252899734
Conow, C., Fielder, D., Ovadia, Y., & Libeskind-Hadas, R. (2010). Jane: A new tool for the cophylogeny reconstruction problem. Algorithms for Molecular Biology, 5(1), 16. https://doi.org/10.1186/1748-7188-5-16
McGowen, M. R., Tsagkogeorga, G., Álvarez-Carretero, S., dos Reis, M., Struebig, M., Deaville, R., Jepson, P. D., Jarman, S., Polanowski, A., Morin, P. A., & Rossiter, S. J. (2020). Phylogenomic Resolution of the Cetacean Tree of Life Using Target Sequence Capture. Systematic Biology, 69(3), 479–501. https://doi.org/10.1093/sysbio/syz068
McGowen, Michael; Tsagkogeorga, Georgia; Álvarez-Carretero, Sandra et al. (2019). Data from: Phylogenomic resolution of the cetacean tree of life using target sequence capture [Dataset]. Dryad. https://doi.org/10.5061/dryad.jq40b0f
Access information
Other publicly accessible locations of the data:
- Sequence data will be available in GenBank under the accession numbers provided in total_parasite_host_metadata.csv.
Data was derived from the following sources:
- The published cetacean host phylogeny (McGowen_Bayes_tree.nex) is included in this repository and is available from the Dryad repository accompanying McGowen et al. (2020): https://doi.org/10.5061/dryad.jq40b0f.