My Ph.D. dissertation focused on the molecular evolution of disease-resistance genes in wild rice. Molecular evolutionary analysis methods are useful for identifying functional genes and for investigating how sequence variation contributes to changes in gene function. In the 1980s, Dr. Motoo Kimura proposed the neutral theory, which explains genetic variation through stochastic processes and challenged the long-standing view that variation is primarily shaped by natural selection. The neutral theory later became the basis of statistical null hypotheses used to test whether specific gene sequences are under natural selection, such as Tajima’s D test, representing an important methodological advancement.

Using the wild rice blast-resistance gene Pi-ta, we constructed phylogenetic trees and observed reduced sequence variation, a high ratio of nonsynonymous to synonymous substitutions, and geographically structured variation. These results suggest that Pi-ta in wild rice may have been shaped by repeated selective sweeps and functional constraints rather than simple population expansion. We further propose that recent selective sweeps may have occurred during the early stages of rice domestication, potentially associated with a host shift of the rice blast pathogen—from millet to wild rice or cultivated rice—thereby explaining the observed genetic variation. These findings were published in the journal Genetics.

In 2008, I visited the Smithsonian National Museum of Natural History in the United States with support from the National Museum of Natural Science to examine developments in plant DNA barcoding. At that time, an official plant DNA barcode had not yet been finalized. The Smithsonian adopted a strategy based on evaluating diverse tree species in tropical rainforests, using a 50-hectare Barro Colorado Island (BCI) plot in Panama containing 296 tree species to establish experimental workflows and construct phylogenetic trees based on DNA barcodes, extending their application into ecological research.

In 2010, I used plant materials from selected tree species in the Fushan and Lienhuachih forest plots and conducted preliminary experiments at the Smithsonian National Museum of Natural History under the guidance of Dr. John Kress. I also learned database management and analytical methods for DNA barcoding. Phylogenetic community trees constructed using plant DNA barcodes, combined with large-scale ecological datasets, have been applied in phylogenetic community ecology, a rapidly emerging interdisciplinary field.

In ecology, Dr. Stephen P. Hubbell proposed the neutral theory in 2001, which explains community patterns through stochastic processes, similar in concept to the neutral theory in molecular evolution. It serves as a statistical null hypothesis for ecological analysis. In community ecology, the neutral hypothesis can be tested through randomization of phylogenetic community trees, becoming a key approach in the field. With the development of analytical software, this framework has matured into a rapidly growing interdisciplinary area. The study of phylogenetic community structure is currently my main research focus.