Data and Code for: Thermal niche divergence mediates climate-driven cryptic invasion and replacement within a native range

This repository contains the primary data and R code supporting the findings of the research article titled "Cryptic native expansion under climate change: intraspecific replacement driven by polyploidy-mediated divergence in thermal tolerance". Our study investigates the mechanisms of intraspecific replacement among major lineages of the common reed (Phragmites australis) in China, specifically the native CN lineage and the introduced FEAU lineage. We integrate population genetics, common garden experiments, physiological assays, and ecological niche modeling to demonstrate that polyploidy-mediated divergence in thermal tolerance is a key driver of this replacement under climate change. The dataset and code are organized to facilitate reproducibility and further analysis. The contents include: Genetic Data: Microsatellite (SSR) Genotyping: Raw read count tables and final genotype data for 495 P. australis individuals from across China, genotyped at 42 polymorphic microsatellite loci. (The raw sequence read data were submitted to the NCBI Sequence Read Archive with the BioProject ID of PRJNA1126092.) Population Genetic Analysis: Input files and scripts for conducting Bayesian population structure analysis with STRUCTURE map and Principal Coordinates Analysis (PCoA) using the polysat package in R. Bioclimatic & Distribution Data: Occurrence Records: A comprehensive dataset of 837 georeferenced records for the CN, FEAU, and SW lineages in China. Niche & SDM Analysis: R scripts for conducting bioclimatic niche comparisons (PCA, niche overlap) and for building and projecting future distribution models using MaxEnt via the Wallace platform. Common Garden Experiment Data: Phenotypic Measurements: Raw data on growth traits (e.g., total biomass, shoot height, shoot density, Specific Leaf Area (SLA)) from two independent common garden experiments (2017 and 2021) conducted across multiple latitudinal sites. Statistical Analysis Scripts: R code for calculating trait means and standard errors, and for performing pairwise t-tests to compare lineage performance within each garden. Heat Tolerance Physiology Data: Chlorophyll Fluorescence (Fv/Fm): Raw measurements of the maximum quantum yield of PSII following a graded heat stress treatment (from 25°C to 60°C). Heat Tolerance Parameters: R scripts (including the custom psiiht function) for fitting logistic decay models to the Fv/Fm data and calculating the critical temperature (Tcrit), T50, and T95 parameters for each genotype. Code for statistical comparison (t-test) between lineages is also provided. Data & Code Availability Statement:All data are provided in tab-delimited (.txt or .csv) formats. Analysis scripts are written in R