Phylogenetic Data for: Complete mitochondrial sequences from fish-infecting coccidia (Goussia species) reveal highly divergent genome organizations
Description
Phylogenetic analyses related to the article entitled "Complete mitochondrial sequences from fish-infecting coccidia (Goussia species) reveal highly divergent genome organizations" by Slawnych et al. (2025). Three analyses are presented, each with the supporting data, method of tree reconstruction and the resulting tree. Phylogenetic trees were based on: 1) Concatenated nuclear 18S rDNA (18S rDNA) and mitochondrial cytochrome c oxidase subunit 1 (mtCOI) sequences; 2) nuclear 18S rDNA sequences only; and, 3) mtCOI sequences only. Citation for Primary Article: Natasha M. Slawnych, Larsen C. Iorgovits, Alex N. Leveille , Perryn S. Kruth, Sara M. Terier, Winter Kraemer, and John R. Barta. 2025. COMPLETE MITOCHONDRIAL SEQUENCES FROM FISH-INFECTING COCCIDIA (GOUSSIA SPECIES) REVEAL HIGHLY DIVERGENT GENOME ORGANIZATIONS. Journal of Parasitology 111(5) DOI: 10.1645/25-40
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Brief Overview of Phylogenetic Analyses: A combined, partitioned DNA dataset composed of near-complete nu 18S rDNA and mt COI sequences (where available) was assembled using Geneious Prime (2025.0.2) with sequences representing 56 species of coccidia from 4 families (primarily ectotherm-infecting species). Mt COI sequences were available from only 21 of the 56 species. This dataset was used to reconstruct a phylogenetic tree to place G. degiustii and G. leucisci among other related coccidia using the newly generated nu and mt sequences. Analyses and substitution model selection were accomplished essentially as described by Kruth et al. (2020). Briefly, near-complete nu 18S rDNA sequences were aligned (Clustal 1.2.3) and then refined by eye; similarly, mt COI sequences were aligned using the codon-based alignment (Geneious translation alignment – default settings). The alignment consisting of nu 18S rDNA sequences was analyzed using the Hierarchical likelihood ratio tests (hLRT) and the Akaike Information Criterion (AIC) in MrModeltest version 2.3 (Nylander, 2004). The best-fit model identified through both the hLRT and the AIC was the General Time-Reversible (GTR) substitution model. This model was applied to the alignment, accounting for invariant characters and incorporating gamma-distributed rate variation across sites and a proportion of invariable sites (i.e., GTR+I+G, nst=6). The alignment consisting of mt COI sequences was assigned a codon substitution model (translation table 4; i.e., Mold Protozoan Mitochondrial [metmt]) and gamma-distributed rate variation. All phylogenetic reconstructions were conducted using the selected nucleotide substitution models within MrBayes version 3.2.6 (Huelsenbeck and Ronquist, 2001). For the combined 18S rDNA/mtCOI dataset, the individual nu 18S rDNA and mtCOI alignments were combined and designated as partitions within the combined dataset. All Bayesian analyses were conducted through 1,000,000 generations, including a burn-in of 100,000 generations (10%) with 1 tree retained every 1,000 generations (subsample frequency = 1000). Select members of the family Sarcocystidae were used as the taxonomic outgroup. References: Huelsenbeck, J. P., and F. Ronquist. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754–755. Kruth, P. S., C. Michel, J. Amery-Gale, and J. R. Barta. 2020. Full mitochondrial genome and nuclear 18S rDNA sequences refine the taxonomic placement of Choleoeimeria taggarti n. comb. from the prostate of Antechinus flavipes (Yellow-Footed Antechinus). Journal of Parasitology 106: 71–81. Nylander, J. A. A. 2004. MrModeltest v2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University. https://github.com/nylander/MrModeltest2.
Institutions
- University of Guelph