Discordant Phylogeographic Patterns in Ecologically Similar Sympatric Sister Species: Revisiting the Null Hypothesis of Comparative Phylogeography

Aim Elucidating the complex factors underlying the current geographic patterns of biodiversity is a central goal in biogeography and phylogeography. Comparative phylogeographic studies of co‐distributed species have often addressed this issue by attributing observed differences in population structures to differences in interpretable traits between species. However, this approach implicitly relies on the largely untested assumption that species sharing similar ecological, spatial, and phylogenetic contexts should exhibit similar population structures. In this study, we revisited this null assumption of comparative phylogeography by comparing the population structures of two sympatric sister species with high ecological similarity using high‐throughput genomic data. Location Coastal regions of the Japanese archipelago. Taxon Two goby species of the genus Chaenogobius. Methods We obtained restriction‐site associated DNA sequencing data and partial mitochondrial sequences for C. gulosus . These data were combined with published data for C. annularis to investigate the spatial and temporal differences and similarities in population structure and demography between the two species. Results Our analyses revealed a fine‐scale population structure of C. gulosus , comprising four intraspecific lineages and multiple hybrid zones. The origin of the intraspecific lineages of C. gulosus was estimated to be four to five‐fold younger than that of C. annularis , with a different number of intraspecific lineages. Conversely, the geographical distribution of some intraspecific lineages and hybridization zones was similar between species. Main Conclusions These findings demonstrate that the phylogeographic origin can differ even between sympatric sister species with high ecological similarity. Our results highlight the role of factors beyond easily predictable deterministic effects, such as subtle ecological differences or stochasticity in shaping geographical patterns of biodiversity.