Asymmetric introgression and thermal advantage jointly drive climate-mediated lineage turnover in a mixed-ploidy reed
Species distribution forecasts commonly overlook intraspecific genetic variation, missing a potentially important mechanism of ecosystem change: climate-driven range shifts among lineages within a species native range. Here we integrate population genomic analysis of 495 individuals, multi-site common garden experiments, and species distribution modeling based on 837 occurrence records for three major genetic lineages of the foundation grass Phragmites australis in China. The octoploid FEAU lineage (haplotype P) exhibits superior heat tolerance (critical temperature Tcrit and T50) and produces significantly greater total biomass in three of four common gardens compared to the cold-adapted CN lineage (tetraploid, haplotypes O/M), which occupies a climatic niche with lower annual mean temperature (Bio1) and mean temperature of the wettest quarter (Bio8). Genomic analyses further reveal bidirectional but asymmetric introgression, with admixed individuals showing a systematic bias toward FEAU ancestry. Under the high-emission scenario (SSP5-8.5) by 2070, projected highly suitable habitat for the FEAU lineage expands by 18.6%, while the CN lineage shows a smaller relative increase. By contrast, the subtropical SW lineage (haplotypes U/I) exhibits limited and stable suitable habitat. These results demonstrate that climate change interacts with intraspecific variation among polyploidy-associated lineages, manifested through differences in thermal tolerance, biomass production, and asymmetric gene flow, to drive potential lineage replacement within a 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 climate warming.