*Article* **A Comparative Study of Genetic Responses to Short- and Long-Term Habitat Fragmentation in a Distylous Herb** *Hedyotis chyrsotricha* **(Rubiaceae)**

**Na Yuan 1,†, Shujing Wei 2,†, Hans Peter Comes 3, Sisheng Luo 2, Ruisen Lu 4,\* and Yingxiong Qiu 5,\***


**Abstract:** The genetic effects of habitat fragmentation are complex and are influenced by both species traits and landscape features. For plants with strong seed or pollen dispersal capabilities, the question of whether the genetic erosion of an isolated population becomes stronger or is counterbalanced by sufficient gene flow across landscapes as the timescales of fragmentation increase has been less studied. In this study, we compared the population structure and genetic diversity of a distylous herb, *Hedyotis chyrsotricha* (Rubiaceae), in two contrasting island systems of southeast China. Based on RAD-Seq data, our results showed that populations from the artificially created Thousand-Island Lake (TIL) harbored significantly higher levels of genetic diversity than those from the Holocenedated Zhoushan Archipelago (ZA) (*π* = 0.247 vs. 0.208, *H*<sup>O</sup> = 0.307 vs. 0.256, *H*<sup>E</sup> = 0.228 vs. 0.190), while genetic differences between island and mainland populations were significant in neither the TIL region nor the ZA region. A certain level of population substructure was found in TIL populations, and the level of gene flow among TIL populations was also lower than in ZA populations (m = 0.019 vs. 0.027). Overall, our comparative study revealed that genetic erosion has not become much stronger for the island populations of either the TIL or ZA regions. Our results emphasized that the matrix of water in the island system may facilitate the seed (fruit) dispersal of *H. chrysotricha*, thus maintaining population connectivity and providing ongoing resilience to the effects of habitat fragmentation over thousands of years.

**Keywords:** habitat fragmentation; RAD-Seq; *Hedyotis chrysotricha*; genetic diversity; population structure; gene flow
