Polyphyly and Deep Evolutionary History of Piscine Coccidia: Mitochondrial Genomics of a New Goussia Species From Pacific Saury ( Cololabis saira )

ABSTRACT

The genus Goussia Labbé 1896 represents a polyphyletic assemblage of piscine coccidia whose systematics remain poorly resolved due to morphological convergence and limited genomic data. Here we describe Goussia sairae n. sp. from the liver of Pacific saury ( Cololabis saira ) in the Northwestern Pacific, characterized through integrated morphological, histopathological, and molecular analyses. Long‐read amplicon sequencing of single‐oocyst isolates enabled the first complete mitochondrial genome assembly for a marine Goussia species, revealing two co‐existing mitogenome genotypes (99.3% identity) within individual oocysts—the first robust evidence consistent with intra‐oocyst mitochondrial heterogeneity in the Eimeriidae. Phylogenetic reconstructions based on nuclear 18S ribosomal RNA and concatenated mitochondrial protein‐coding genes robustly supported the polyphyly of Goussia sensu lato, recovering five major lineages. A time‐calibrated Bayesian phylogeny dated the marine‐freshwater divergence to the Early Jurassic (median 197 million years ago; 95% HPD: 124–275 Mya), congruent with the ancient divergence of their respective teleost host groups. These findings support re‐evaluation of the current generic boundaries of Goussia and suggest that the hyper‐divergent Epicellular lineage may warrant recognition as a distinct family basal to the Eimeriorina.