Population differentiation and phylogeographic pattern of a relict species, Conandron ramondioides (Gesneriaceae), revealed from sequence polymorphism and haplotypes of the CYCLOIDEA gene

Abstract

Historical events are expected to affect population genetic differentiation and DNA molecular evolution, but the impact of these effects remains a matter of debate. Here, for Conandron ramondioides (Gesneriaceae), we analyzed the genetic structure and phylogeographical pattern of 248 individuals from 13 populations, distributed in mainland China and Taiwan Island, based on the nucleotide sequence and haplotype of the coding sequence of CYCLOIDEA1 (GCYC1). Among the populations, we found a high level of haplotype diversity (h = 0.831) and a relatively low level of nucleotide diversity (D ij = 0.004). Both the haplotype network and the neighbor-joining tree constructed from GCYC1 haplotypes suggest two major geographical groupings, one on the mainland and the other on Taiwan. Consistently, AMOVA analysis revealed high genetic differentiation between these groupings, with 84.65% variation partitioning the two regions, and the two groupings shared no haplotype. On the mainland, population genetic differentiation was correlated with more recent events, presumably Pleistocene glaciations and human activities since the Neolithic. In addition, C. ramondioides GCYC1 rapidly accumulated neutral mutations, consistent with this gene being silenced or down-regulated in actinomorphic lineages of the Lamiales, such as Conandron.

Phylogeographic studies of plants in China: Advances in the past and directions in the future

“…Similarly in northern and northeast China, phylogeographic studies suggest regional expansions and multiple glacial refugia for a limited number of species with glacial refugia being sparsely located in the mountains from the north to the south (e.g., Chen et al, 2008a; Du et al, 2009; Tian et al, 2009; Bai et al, 2010; Guo et al, 2010; Ren et al, 2011; Zeng et al, 2011; An et al, 2012). However, in middle, southern and southeast China, regional expansions were found rarely and only local expansions occurred in the studied species (e.g., Su et al, 2005; Wang & Ge, 2006; Gao et al, 2007; Yan et al, 2007; Qiu et al, 2009a, 2009b; Wang et al, 2009a; Zhou et al, 2010; Chen et al, 2012; Li et al, 2012c; Peng et al, 2012; Xiao et al, 2012; Xie et al, 2012). Despite the quantity of phylogeographic studies not being homogeneous among different regions and different plant groups in China, multiple glacial refugia seem to be a general rule for most species studied (see Qiu et al, 2011).…”

Expression shifts of floral symmetry genes correlate to flower actinomorphy in East Asia endemic Conandron ramondioides (Gesneriaceae)

“…Conandron ramondioides is another relic and paleoendemic genus in East Asia which is also apparently evolved as an actinomorphic reversal from zygomorphic ancestor (Kokubugata and Peng 2004 ; Wang et al 2010 ; Xiao et al 2012 ). Like R. myconi , its corolla tube is lost and five petals are equally large with five stamens fully developed.…”

Genome‐wide RAD sequencing data suggest predominant role of vicariance in Sino‐Japanese disjunction of the monotypic genus Conandron (Gesneriaceae)

“…The isolated nature of C. ramondioides habitats (moist rocks) is enhanced by recent human disturbance, including the tourism activities and hydropower development observed in many populations (Wang, 2004; Xiao, 2005; Wang et al, 2010). All these factors combined compromise successful pollination and seed germination, thereby accelerating the rate of genetic erosion within populations via increased inbreeding and genetic drift (Young et al, 1996; Hsin & Wang, 2018), as well as promoting genetic differentiation among populations and regions (Xiao et al, 2012). ADMIXTURE analysis, PCA, and the phylogenetic tree all indicate that there are three distinct genetic lineages within C. ramondioides , which correspond to the three main regions where the species is present, that is, mainland China, Taiwan Island, and Japan (Figs.…”

“…1, 2B). Hsin (2019), using single‐copy nuclear markers, also identified these three genetic clusters, whereas Xiao et al (2012) also found two genetic clusters for China (i.e., mainland China and Taiwan Island) with the CYCLOIDEA1 (GCYC1) coding sequence. The clear genetic clustering pattern, which has a strong geographic basis, together with a significant positive correlation between genetic distance and geographic distance at the population level ( r = 0.499, P = 0.01; Fig.…”

“…30 Ma (Roalson & Roberts, 2016), making it phylogenetically distinct from other taxa in the Old World Gesneriaceae (Wang, 2004; Weber, 2004; Wang et al, 2010; Roalson & Roberts, 2016). Although several studies have explored the population differentiation of its Chinese populations with DNA markers (Xiao, 2005; Xiao et al, 2012), a detailed study sampling the whole range (including mainland China, Taiwan Island, and Japan) using updated molecular methods is still needed to explore the processes underlying its phylogenetically isolated condition within the Gesneriaceae and the evolutionary history of plant disjunctions in this species‐rich region.…”