Genetic Differentiation of Chinese Fir Populations From Mainland China and Taiwan as Revealed by Genotyping‐By‐Sequencing Analysis, With Implication for Taxonomic Position of the Species

Climate change and strait isolation during the glacial period had a profound effect on the differentiation of gymnosperms on both sides of the Taiwan Strait. The taxonomic status and population structure of <i>Cunninghamia konishii</i> (Taiwan) and <i>C. lanceolata</i> (mainland China) remain contentious due to conflicting morphological and molecular evidence. Thus, we sampled 92 accessions from seven natural populations, six from mainland China and one from Taiwan, and conducted high-throughput genotyping-by-sequencing (GBS) analysis. The northern marginal population exhibited the lowest genetic diversity (<i>θπ</i> = 4.828 × 10^-3), while the Taiwan population had the highest (<i>θπ</i> = 5.821 × 10^-3), reflecting its role as a glacial refugium, while mainland populations retained lower diversity due to post-glacial bottlenecks. There was little difference in Tajima's D values of selection pressure between mainland China and Taiwan. However, significant gene flow (<i>Nm</i> = 2.839) was observed, combined with low <i>F</i> _<i>ST</i> values (0.072-0.122), which indicate low genetic differentiation among <i>C. lanceolata</i> and <i>C. konishii</i>. Migration analysis indicated a high probability of unidirectional gene flow from mainland China to Taiwan, with the Dongshan Land Bridge facilitating pre-glacial gene flow. We conclude that <i>C. konishii</i> represents an ecotype of <i>C. lanceolata</i> , shaped by environmental plasticity and incomplete isolation. This study enhances our understanding of the gene flow and evolutionary processes shaping the species and offers new insights into their taxonomic classification.