Millennial-scale lags in plant assembly are associated with topographic connectivity on the eastern Tibetan Plateau

Abstract Limited topographic connectivity to refugia can delay plant community responses to climate warming, but its influence on long-term community assembly remains unclear. Here we reconstruct plant community dynamics on the eastern Tibetan Plateau over the past 12,000 years using sedimentary ancient DNA records from Dangzi Co and four published datasets, with zeta diversity quantifying shared taxa across sites and time-slices. We examine the roles of climate and topographic connectivity in shaping communities. Warming before 8.5 ka (ka = thousand years before present) triggered upslope migration of lowland woody taxa, but variable topographic connectivity among lakes caused asynchronous assembly. Under a stable mid-Holocene climate (8.5–5.5 ka), niche differentiation increased, promoting community similarity. Subsequent cooling (5.5–3.5 ka) facilitated alpine taxa expansion, maintaining high taxa sharing among lakes. Reduced convergence since 3.5 ka likely reflects cooling and land use. Our findings highlight how topographic connectivity shapes millennial-scale community assembly and biodiversity.