Pronounced genetic differentiation in Fokienia hodginsii revealed by simple sequence repeat markers

Abstract

Fokienia hodginsii is a Tertiary relict conifer of the monotypic genus Fokienia (Cupressaceae s.l.). Currently, the species is distributed in southern China, northern Vietnam, and northern Laos and listed as a “near threatened” species by the IUCN. In this study, a total of 427 individuals of F. hodginsii were sampled from China and Vietnam to characterize its genetic diversity and population differentiation. Based on the profiles of 12 simple sequence repeat (SSR) markers, we observed a high level of genetic diversity in F. hodginsii at the species level (H e =0.635), albeit slightly lower than that of its sister species Chamaecyparis obtusa. Signals of bottleneck events were detected in the populations GXDMS, GXHJ, V‐PXB, and V‐HB, probably due to Pleistocene glaciations or overexploitation in recent years. Pronounced genetic differentiation (F st = 0.157) was found in this species. The inbreeding index (F is = 0.176 ± 0.024) indicated that F. hodginsii has a mixed mating system. Significant correlation was found between the pairwise genetic differentiation and geographic distance (r = 0.882, p = 0.01), suggesting that genetic differentiation among the populations follows the model of isolation by distance (IBD). STRUCTURE analysis and principal coordinate analysis revealed that these populations were divided into four groups: the western China group located mainly in the Yunnan–Guizhou Plateau, the central China group located mostly in the Luoxiao Mountains and Nanling Mountains, the eastern China group located in the Wuyi Mountains and the Vietnam group containing two populations in Vietnam. The different terrains and elevations of populations may be the most likely factors leading to the differentiation between the western China group and the central China group, while the geographic isolation caused by the lack of appropriate habitats may greatly contribute to the differentiation between the central China group and the eastern China group. Based on the results, some conservation suggestions for this species are provided, such as establishing seed orchards and multiple nature reserves.

Distinct Genetic Structure Reflects Ploidy Level Differentiation in Newly Discovered, Extremely Small Populations of Xanthocyparis vietnamensis from Southwestern China

“…Our population genetic survey revealed moderate genetic differentiation (F ST 0.125) among X. vietnamensis populations in southwestern China. This is similar to the mean values of anemochores (0.13) (Nybom, 2004), lower than those of F.hodginsii (0.157) (Yin et al, 2018), C. macrolepis (0.163) (Liao et al, 2015), A. ziyuanensis (0.209-0.250) (Tang et al, 2008), and G. pensilis (0.452, some populations are plantations) (Wu et al, 2020) in a similar geographic region. Varied topography of mountain regions in the tropic and adjacent areas tended to harbor Tertiary relict species and subdivide some species into isolated and divergent populations, which may have evolved independently during late Tertiary climate changes and Quaternary climate fluctuations (Hewitt, 2000;Tang et al, 2018).…”

First Fossil Fokienia (Cupressaceae) in South China and Its Palaeogeographic and Palaeoecological Implications

“…In addition, combined with the obvious phylogeographic structure and ENM results, it seems the F. hodginsii survived in four refuges during the last glacial episodes, which is consistent with the multiple refugia patterns of relict species in subtropical China (Yin et al, 2020). The F. hodginsii population has a relatively high genetic diversity, which may be related to its long history in a variety of geographical habitats (Yin et al, 2018, Yin et al, 2020. However, the fossils (F. shengxianensis He, Sun & Liu, F. catenulata (Bell) R.W.…”

Neogene and Quaternary climate changes shaped the lineage differentiation and demographic history of Fokienia hodginsii (Cupressaceae s.l.), a Tertiary relict in East Asia

“…To further investigate whether limited historical gene flow occurred between geographical groups (based on samova ), we estimated the mutation‐scaled migration rate ( M ) using model‐based coalescent analysis in Migrate 3.6.8 (Beerli, 2006) based on previously reported SSR data (Yin et al, 2018). In total, 10 short chains (500 000 trees) and five long chains (1 000 000 trees) were used under the continuous Brownian motion model with constant mutation rates for all loci, discarding the first 25% of records as burn‐in.…”

“…Previous studies on F. hodginsii have generally focused on seed breeding, nursery technology, plantation cultivation, essential oil extraction, and the development and utilization of other resources (Zhao, 2005; Huang et al, 2013). Recently, we identified high genetic diversity and pronounced genetic differentiation between populations of F. hodginsii (Yin et al, 2018) based on the simple sequence repeat (SSR) markers developed by Ding et al (2017).…”