Abstract
BACKGROUND: The nematode superfamily Strongyloidea represents a prevalent group of gastrointestinal parasites in ruminants and livestock, posing substantial veterinary and economic burdens worldwide. Here we present the first mitochondrial genomic investigation for reconstructing Strongyloidea phylogeny and investigating niche-specific selection dynamics across gastrointestinal habitats (abomasum, small intestine, and large intestine). This study presents a preliminary exploration of the evolutionary adaptations of these agriculturally relevant parasites through comprehensive mitogenomic analysis. RESULTS: Phylogenomic reconstruction revealed strong anatomical clustering with high nodal support. Comparative synteny analyses revealed conserved mitogenome architectures across Strongyloidea species, characterized by pronounced AT-richness. Codon usage patterns showed high consistency in Strongyloide (94% A/U-ending preferred codons), with ENC-plot and neutrality analyses confirming natural selection as the dominant driver. Pervasive purifying selection was observed, but abomasal species showed higher ω values than intestinal counterparts, particularly in ND4. In addition, positive selection was detected exclusively in CYTB within the small intestinal lineage. RELAX analysis identified differential selection signals among the three branches, with significant relaxation observed in ND5 and ND6 genes in the abomasal species. Amino acid polymorphism analyses revealed higher sequence variation in ND genes compared to the highly conserved COX genes. CONCLUSIONS: Our findings demonstrated niche-associated evolutionary trajectories between abomasal and intestinal Strongyloidea branches, reflected in both phylogenetic patterns and molecular evolution rates. The mitogenomic framework established here provided a foundation for future studies integrating expanded datasets, genomic data, and microenvironmental parameters to elucidate precise niche adaptation mechanisms in these economically important parasites.