Historical Genetic Divergence and Gene Flow Patterns Between Island (Taiwan) and Mainland (China) Populations of Fagus hayatae

Abstract

Fagus hayatae is a deciduous tree lineage that survived as a Quaternary glacial relict, today showing a disjunctive distribution between island Taiwan and mainland China. Using nuclear microsatellite (nSSR) and chloroplast DNA (cpDNA) markers, this study analyzed genetic diversity and phylogeographic history across nine native populations (249 samples in total). Results show that Taiwanese island populations possess higher genetic diversity, but also an extremely high and significant inbreeding coefficient (FIS = 0.96), indicating strong genetic drift and constraints on natural regeneration. A clock-calibrated phylogenetic reconstruction revealed that the Tungshan (TS) lineage in Taiwan was the earliest-diverging branch (ca. 44.61 Ma), while other Taiwanese lineages diverged from the mainland around 8.36 Ma, coinciding with the timing of Taiwan's tectonic uplift. Historical gene flow between the two regions has been extremely limited. Given its unique evolutionary history and conservation risk, this study recommends designating Taiwanese populations, especially the TS lineage, as an independent Evolutionarily Significant Unit (ESU), and calls for urgent in-situ protection measures.

Keywords: Fagus hayatae, genetic diversity, phylogeography, Evolutionarily Significant Unit, inbreeding depression

Methodology and Implementation Steps

This study employed systematic cross-regional sampling and multi-marker molecular techniques, following four main steps:

1. Sample collection and geographic coverage: Leaf tissue was collected from 249 Fagus hayatae samples across steep, native habitats in Taiwan (Tungshan/TS, Peichatienshan/PCTS, and Ayushan/AW, 3 populations) and mainland China (Zhejiang, Hubei, and Sichuan, 6 populations) (Figure 1).
   
2. Dual molecular marker experiments: Ten highly polymorphic nuclear microsatellite (nSSR) loci were screened and used for PCR amplification and genotyping of 184 high-quality DNA samples; the chloroplast atpB-rbcL intergenic region was sequenced for all 249 samples.
3. Bioinformatics and population genetic analysis: GenAlEx and DnaSP software were used to calculate allelic richness and nucleotide diversity. Bayesian clustering was performed in STRUCTURE, and SAMOVA was used to evaluate the effect of geographic isolation (Figure 2).
   
4. Spatiotemporal evolutionary reconstruction: BEAST software was used to estimate lineage divergence times and generate a clock-calibrated phylogenetic tree (Figure 3), while RASP was used to reconstruct ancestral geographic ranges and distinguish vicariance from dispersal events
   

Innovation and Cross-Disciplinary Collaboration

This study pioneered the combined use of maternally inherited cpDNA and biparentally inherited nSSR markers, using a clock-calibrated phylogenetic tree to precisely trace the complete spatiotemporal evolutionary trajectory of this relict species from the Miocene to the present. Overcoming geographic and sampling constraints, this study united Taiwan's National Sun Yat-sen University and Taiwan Forestry Research Institute with Guangxi Normal University (China) and Mahidol University (Thailand), establishing the most complete genetic database to date, offering a model for cross-border conservation collaboration on East Asian relict plants.

Expected Results and Contributions

This study confirmed that Taiwanese island populations have a distinct evolutionary history, establishing them as an Evolutionarily Significant Unit (ESU), particularly the highly divergent, ancient Tungshan (TS) lineage, providing a scientific basis for precise, zone-specific government conservation policy. This study is the first to reveal the extremely high inbreeding in Taiwanese populations (FIS = 0.96), pointing toward practical directions for future assisted pollination and habitat restoration. These findings were published in the leading international journal Frontiers in Plant Science, making a substantive academic contribution to the conservation of subtropical relict forests under global climate change.