The concatenated nuclear gene and plastome datasets of the Aralia-Panax complex, and the Aralia-Panax complex occurrences

This resulted in 624 loci being removed from the final dataset and subsequent analyses. Therefore, the final dataset included 312 orthologs.For plastid genome assembly, we firstly extracted coding genes and intergenic spacers from the reference genome of Panax bipinnatifidus (GenBank accession NC043952). Consistent with the nuclear Hyb-Seq analytical pipeline, we mapped trimmed clean reads to the plastid loci using BWA, and reads corresponding to each plastid locus were assembled separately with SPAdes.

The plastome matrix had an aligned length of 128,839 bp.The Aralia-Panax complex occurrences were obtained from the Global Biodiversity Information Facility (doi.org/10.15468/dl.n25jar; doi.org/10.15468/dl.wuuwj3). Only specimen records were retained, records with missing or invalid geographic coordinates, obvious georeferencing errors, and duplicated localities were subsequently removed. To reduce spatial sampling bias and spatial autocorrelation, occurrence records were spatially rarefied by retaining a single record within a minimum distance of 10 km.

After spatial rarefaction, a final geo-referenced dataset with 6259 occurrence points was compiled for modelling the distribution of the Aralia-Panax complex.