Trapped in the cradle: Karst formation isolates an ancient lineage of wren-babbler (Gypsophila) leading to cryptic speciation

Cryptic speciation from landscape fragmentation presents a major challenge for biodiversity inventories in the geologically complex karst regions of Southwest China. Despite recent discoveries of hidden diversity in various karst-adapted taxa, the avian diversity of this region remains incompletely documented. Here, we investigate the evolutionary status of the Huanjiang population of the Streaked Wren-babbler (Gypsophila brevicaudata). Our methodology relies on the integration of population genomics, mitogenomics, and preliminary morphological evaluations. Our phylogenomic analyses identify the Huanjiang population as a deeply divergent and reciprocally monophyletic clade. It forms the sister-group to the clade of the stevensi subspecies and the nominate Streaked Wren-babbler (G. brevicaudata) lineages, rather than occupying a basal position within the genus. Mitogenomic evidence unambiguously anchors the initial divergence of this population to the Late Miocene (∼8.16 Ma). Demographic reconstructions indicate the status of the Huanjiang population as a “geological relict” trapped in ancient paleo-karst refugia. This geographic confinement created a historical barrier against the stevensi populations in younger neo-karst regions. Consequently, the Huanjiang population exhibits a complete lack of the Pleistocene introgression common among its southern congeners. This prolonged strict isolation has led to severe genomic erosion. Key indicators of this decline include elevated inbreeding levels and a high mutational load. These patterns show a stark contrast to the post-glacial demographic expansion of the G. b. stevensi populations. The combination of robust genomic boundaries and observable phenotypic variations provides compelling evidence for species-level differentiation. Therefore, we propose the promotion of the previously described subspecies Gypsophila brevicaudata huanjiangensis to full species status as the Huanjiang Wren-babbler (Gypsophila huanjiangensis Zhou, 1999). Ultimately, our findings highlight the critical function of the Southwest China Karst as an evolutionary museum and emphasize the urgency for the conservation of its localized ancient biota.