Latitude, not geography, globally structures Oscheius tipulae into three deeply divergent lineages

Free-living nematodes are among the most abundant animals on Earth and play critical ecological roles in soil ecosystems. However, the global population structure and evolutionary history of most species remain poorly understood. Here, we analyzed genome-wide variation in Oscheius tipulae using whole-genome sequence data from 31 isolates, including 28 publicly available genomes and three newly collected strains from Korea. Population structure analyses, phylogenomic inference, and ancestry estimation consistently identified three deeply divergent lineages. These analyses did not detect admixture among lineages and collectively supported a predominantly tree-like evolutionary history. Notably, the lineages were structured by latitude rather than geographic proximity. Isolates from similar latitudinal zones clustered together regardless of continental origin, forming three major groups: northern mid-latitude (NML), low-latitude (LL), and southern mid-latitude (SML). This pattern indicates that the lineages have maintained largely independent evolutionary trajectories over extended timescales despite the potential for long-distance dispersal. Furthermore, environmentally associated variants showed significant differentiation among lineages, indicating that environmental selection may contribute to the maintenance of this latitudinally structured diversity. Our results reveal unexpectedly deep global divergence within O. tipulae, and highlight the importance of ecological divergence and long-term lineage retention in shaping the global diversity of this group.