# 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

## TL;DR

This study uses genetic analysis to show that Chinese fir populations in mainland China and Taiwan are closely related, with minimal genetic differences and significant gene flow, suggesting they are the same species.

## Contribution

The study provides new genetic evidence supporting the classification of C. konishii as an ecotype of C. lanceolata.

## Key findings

- The Taiwan population showed the highest genetic diversity, indicating it was a glacial refugium.
- Significant gene flow from mainland China to Taiwan was observed, with low genetic differentiation between the two populations.
- C. konishii is classified as an ecotype of C. lanceolata, shaped by environmental factors and incomplete isolation.

## Abstract

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 Cunninghamia konishii (Taiwan) and
C. lanceolata
(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 (θπ = 4.828 × 10−3), while the Taiwan population had the highest (θπ = 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 (Nm = 2.839) was observed, combined with low F

ST
values (0.072–0.122), which indicate low genetic differentiation among
C. lanceolata
and C. konishii. 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 C. konishii represents an ecotype of
C. lanceolata
, 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.

This study investigates the genetic diversity and taxonomic status of
Cunninghamia lanceolata
and Cunninghamia konishii, exploring their differentiation due to climate change and glacial isolation. Genotyping‐by‐sequencing (GBS) analysis of 92 accessions revealed minimal genetic differentiation and significant gene flow from mainland China to Taiwan, suggesting that C. konishii is an ecotype of
C. lanceolata
, rather than a distinct species.