Asymmetric introgression and thermal advantage jointly drive climate-mediated lineage turnover in a mixed-ploidy reed.

Species distribution forecasts often ignore intraspecific genetic variation, potentially missing climate-driven lineage shifts within native ranges. We integrated population genomics (495 individuals), common-garden experiments across four sites, and species distribution modeling (837 records) for three genetic lineages of Phragmites australis in China. The octoploid FEAU lineage (haplotype P) showed superior heat tolerance, with Tcrit 1.3 °C higher and T50 0.8 °C higher than the cold-adapted tetraploid CN lineage (haplotypes O/M), and produced greater total biomass in three of four gardens. Genomic analyses revealed bidirectional but asymmetric introgression; admixed individuals exhibited a significant bias toward FEAU ancestry (61.1%), consistent with preferential backcrossing to the octoploid parent. Under the high-emission scenario SSP5-8.5 by 2070, highly suitable habitat for FEAU expanded by 18.6%, whereas CN showed a smaller relative increase, and the subtropical SW lineage remained stable. These results demonstrate that climate change interacts with intraspecific variation through thermal tolerance, biomass advantages, and asymmetric gene flow to drive potential lineage replacement within the native range, a process already suggested by field observations of FEAU expansion in a plateau lake. Our findings argue for integrating evolutionary history and genetic identity into ecological forecasting to better anticipate ecosystem responses under ongoing warming.