Host-associated mitochondrial structure and broad geographic connectivity in Drepanocephalus associated with migratory cormorants

Digenetic trematodes are important parasites of aquaculture systems, where transmission may be amplified by interactions among aquatic birds, fishes, and snail intermediate hosts. Species boundaries and transmission dynamics within the widespread echinostomatid genus Drepanocephalus remain poorly understood despite reports of pathogenicity in North American aquaculture facilities. Here, we characterize Drepanocephalus recovered from Double-crested Cormorants ( Nannopterum auritus ) in New York State and evaluate their evolutionary relationships using multilocus phylogenetic analyses and next-generation sequencing. Fifteen cormorants were examined, of which seven (47%) were infected with Drepanocephalus . Long-read and short-read sequencing recovered the complete rRNA operon and a near-complete mitochondrial genome, providing the first mitochondrial genomic resources for the genus. Phylogenetic analyses of mitochondrial ( cox 1, nad 1) and nuclear (28S, ITS1–5.8S–ITS2) markers recovered shallow but persistent mitochondrial structure within the D. spathans/auritus complex. Mitochondrial loci and GMYC analyses consistently recovered two major intraspecific lineages, whereas nuclear markers recovered substantially weaker divergence and limited phylogenetic resolution, suggesting incomplete lineage sorting, ongoing gene flow, or both. Haplotype analyses further indicated that mitochondrial structure was more strongly associated with host use than with geographic locality, with lineages largely partitioned between Double-crested and Neotropic cormorant ( N. brasilianus ) transmission systems. Together, these results support broad parasite connectivity across the Americas while revealing previously undescribed host-associated mitochondrial structure. Our findings provide foundational genomic resources for future studies and highlight the role of host ecology in shaping parasite diversification and transmission across continental scales.