Multi-scale evolutionary forces shape the phylogeography of an Old World disjunct plant genus Girardinia (Urticaceae)

Understanding how multi-scale evolutionary forces shape plant phylogeographic patterns remains a central challenge in biogeography, particularly for taxa exhibiting intercontinental disjunctions. Girardinia (Urticaceae), with a disjunct distribution across Asia and Africa, provides an ideal system to address this question. We integrated plastid genome and nrDNA sequences from 310 individuals representing 142 populations to reconstruct its spatiotemporal evolutionary history using phylogeographic analyses and ecological niche modeling (ENM). Our results reveal that Girardinia comprises six well differentiated lineages. Clade 1 corresponds to G . bullosa , whereas the remaining five clades (Clades 2–6), which belong to the G . diversifolia complex, cannot be reconciled with the current infraspecific classification, indicating that the existing taxonomy of the genus requires revision. The genus originated in the Hengduan Mountains and Yunnan–Guizhou Plateau (~11.8 Ma) and diversified in geographically disjunct centers during the Late Miocene (~5.3 Ma). This process was likely driven by dispersal and local extinction, coincided with the orogenic uplift of the Tibetan Plateau and subsequent climatic shifts in the Pliocene. Multiple climatic refugia and postglacial expansion were identified in the East African Highlands and East Asia. Signals of Holocene population contraction further suggest recent anthropogenic impacts. Collectively, our findings demonstrate that the observed Old World intercontinental disjunctions are best explained by transoceanic long-distance dispersal, while mountain uplift, climatic oscillations, local extinction and expansion, and human activities have jointly shaped the phylogeographic structure of Girardinia. These results provide broader insights into plant responses to past environmental change.