Print
Genetic delimitation of Oreocharis species from Hainan Island
expand article infoShao-Jun Ling, Xin-Ting Qin, Xi-Qiang Song, Li-Na Zhang, Ming-Xun Ren
‡ Hainan University, Haikou, China
Open Access

Abstract

Hainan Island harbours an extraordinary diversity of Gesneriaceae with 14 genera and 23 species, amongst which two species and one variety are recognised in the genus Oreocharis. These three Oreocharis taxa are all Hainan-endemics and show a complex geographical distribution pattern with considerable morphological intermixtures. In this study, we combined DNA (nuclear ITS sequences and cpDNA trnL-trnF and ycf1b) to evaluate genetic delimitation for 12 Oreocharis populations from the island, together with morphological similarity analysis using 16 morphological traits. The results showed Hainan Oreocharis taxa were monophyletic with relative low genetic diversity within populations, highly significant genetic differentiation amongst populations and a significant phylogeographical structure. The 12 populations formed three genetically distinct groups, roughly correspondent to the currently recognised two species and one unknown lineage. The PCA analyses of morphological traits indicate three distinctive groups, differing mainly in petal colour and corolla shapes. The roles of river and mountain isolations in the origin and distribution of these three lineages are discussed.

Keywords

genetic differentiation, genetic diversity, morphological similarity, Oreocharis

Introduction

Hainan Island is the largest tropical island in China, with an area of 33,920 km2. As a biodiversity hotspot in the world (Myers et al. 2000), Hainan Island has a species-rich and remarkable endemic flora (Francisco-Ortega et al. 2010), which is remarkably richer in endemic genus than Taiwan Island (36,193 km2) and contains almost twice the number of Gesneriaceae species than Sri Lanka (65,610 km2), which is twice the size of Hainan Island (Ranasinghe et al. 2019). The richest biodiversity is concentrated in the south-central mountains of the island (Li and Wang 2005; Xing 2012; Yang 2013), such as Mt. Wuzhi (the highest peak with 1867 m) and Mt. Yingge (1812 m). Xing (2012) and Ling et al. (2017) identified 14 genera and 23 species of Gesneriaceae on Hainan Island, amongst which two genera (Metapetrocosmea W.T. Wang and Cathayanthe Chun) and eight species (including one variety) are endemic (Ling et al. 2017; Jiang et al. 2017).

Interestingly, there are three recognised taxa of Oreocharis Bentham on Hainan Island (O. flavida Merrill, O. dasyantha Chun and O. dasyantha Chun var. ferruginosa Pan) and all are endemic to the island (Wei 2010; Xing 2012; Yang 2013; Ling et al. 2017). During three years’ observation, we found these Oreocharis taxa to possess diverse floral syndromes in a single currently recognised species and mixed distribution of different species (Wei 2010; Xing 2012; Yang 2013), together with considerable genetic differentiations amongst populations (Xing et al. 2018). The presence of a variety, i.e. O. dasyantha var. ferruginosa, further complicates the taxonomy classification of Hainan Oreocharis.

Here, we sampled 12 populations of Oreocharis taxa covering its entire distribution range on Hainan Island and examined their molecular phylogenetic relationships with one nuclear DNA fragment and two combined chloroplast DNA sequences separately. We also quantitatively analysed 16 morphological traits with principal component analysis (PCA). We aim to determine (1) whether or not the currently recognised three species or variety can be supported by genetic data (2) what factors (e.g. geographic isolation, pollination isolation, climate or intrinsic traits) are responsible for the evolution and maintenance of these Hainan-endemic Oreocharis?

Materials and methods

Materials collection and DNA extraction

Twelve geographic populations of Oreocharis taxa covering all the suitable habitats of the genus on the island were collected, including populations DW (Dongwu in Bawangling), DE (Donger in Bawangling), FT (Futou in Bawangling), NG (Nangao), HM (Mt. Houmi), JF (Mt. Jianfeng) and CH (Chahe at the foot of Mt. Jianfeng) from O. dasyantha, populations QX (Mt. Qixian), WZA (Wuzhi A in Mt. Wuzhi) and WZB (Wuzhi B in Mt. Wuzhi) from O. flavida and populations YG (Mt. Yingge) and LM (Mt. Limu) from unidentified Oreocharis sp. (Table 1, Fig. 1). Fresh leaves were collected from the south-central mountains in Hainan Island in 2015, 2016 and 2017 and dry stored in silica gel. In total, 238 leaf samples from 12 populations that represented the whole geographical range of Oreocharis taxa on Hainan Island were collected (Fig. 1).

Table 1.

Sampled populations and nucleotypes/haplotypes information calculated from nrDNA and cpDNA of 12 Oreocharis populations. Private nucleotypes/haplotypes (nucleotype/haplotype occurs in only one population) are given in Bold.

Putative populations Sampling site Population Longitude/ Latitude Sampling size Elevation (m) ITS trnL-F and ycf1b
Haplotype (No. of individuals) Hd Pi × 103 Haplotype (No. of individuals) Hd Pi × 103
O. dasyantha Dongwu in Mt. Bawang DW 109°41'52"/ 18°53'55" 17 1163 H1(17) 0 0 H2(17) 0 0
Donger in Mt. Bawang DE 109°10'27"/ 19°05'07" 9 1011 H1(9) 0 0 H2(7), H3(2) 0.389 0.75
Mt. Futou FT 109°41'01"/ 18°53'51" 11 1200 H1(11) 0 0 H2(11) 0 0
Mt. Nangao NG 109°19'06"/ 19°10'48" 19 1350 H1(19) 0 0 H2(18), H18(1) 0.105 0.07
O. dasyantha var. ferruginosa Mt. Houmi HM 109°08'44"/ 18°53'50" 51 1400 H8(51) 0 0 H4(14), H5(1), H6(1), H7(29), H8(1), H9(1), H10(7) 0.622 0.52
Mt. Jianfeng JF 108°52'43"/ 18°43'10" 15 1100 H8(15) 0 0 H11(15) 0 0
Riverside at Chahe CH 108°59'00"/ 18°44'30" 10 300 H9(9), H10(1) 0.2 0.31 H1(10) 0 0
O. flavida Mt. Qixian QX 109°42'16"/ 18°42'41" 17 1100 H7(17) 0 0 H19(17) 0 0
Mt. Wuzhi WZA 109°41'52"/ 18°53'55" 32 1800 H2(32) 0 0 H20(32) 0 0
Mt. Wuzhi WZB 109°41'29"/ 18°54'19" 7 1058 H2(1), H3(2), H4(1), H5(1), H6(2) 0.905 2.51 H20(4), H21(3) 0.571 0.37
Oreocharis sp. Mt. Yingge YG 109°33'06"/ 19°02'21" 16 1249 H11(1), H12(10), H13(3), H14(1), H15(1) 0.6 1.92 H22(11), H23(5) 0.458 0.29
Mt. Limu LM 109°44'44"/ 19°10'10" 34 1350 H12(27), H16(7) 0.337 0.52 H12(26), H13(1),H14(3), H15(2), H16(1), H17(1) 0.414 0.49
Sum 238 2.042 5.26 2.559 2.49
Figure 1. 

Sampling sites and nucleotype and haplotype distribution of nuclear ITS (a) and cpDNA trnL-F and ycf1b (b) of Oreocharis lineages in Hainan Island.

Total genomic DNA for each individual was extracted using CTAB methods (Doyle and Doyle 1987) and served as a template for the polymerase chain reaction. AL2000 DNA marker (Aidlab Biotechnologies Co. Ltd) was used to detect DNA quality and quantity on 0.8% agarose gels stained with 2.5 μl Goldview (Aidlab Biotechnologies Co. Ltd) in DTU-48 spectrophotometer (Hangzhou Miu Instruments Co. Ltd, China).

PCR amplification and sequencing

One nuclear ribosomal DNA (nrDNA) sequence, the ITS region comprising spacer 1, the 5.8S gene and spacer 2 (White et al. 1990) and two chloroplast DNA (cpDNA) intron–spacer region trnL-trnF (Taberlet et al. 1991) and ycf1b (Dong et al. 2015) were used in this study (Table 2). PCR reactions were set up in a volume of 25 μl consisting of 20 μl ddH2O, 2.5 μl 10×Buffer, 0.5 μl dNTPs (10 mM), 0.5 μl each 5 μM primer, 0.5 μl DNA template and 0.5 μl 5 U/μl Taq polymerase (Aidlab Biotechnologies Co. Ltd). PCR was conducted in a 2720 Thermal cycler (Applied Biosystems by Life Technologies, made in Singapore) and Veriti 96-Well Thermal Cycler (Applied Biosystems by Life Technologies, made in Singapore). The PCR programme for nrDNA and trnL-trnF was designed for an initial denaturation at 94 °C 5 min, followed by 35 cycles of 1 min at 94 °C, 1 min at 55 °C, 1 min at 72 °C and with a final extension of 10 min at 72 °C. Amplification of ycf1b used the following protocol: 4 min at 94 °C, 35 cycles of 30 s at 94 °C, 40 s at 58 °C and 1 min at 72 °C, ending with 10 min at 72 °C. All the PCR products were checked by electrophoresis. Then purification and sequencing of PCR products were finally sequenced by an ABI 3730 DNA Analyzer based on the BigDye Terminator Cycle Sequencing Ready Kit (Applied Biosystems, Foster City, CA) in BGI (Beijing Genomics Institution), the chemistry and primers being used above in BGI.

Table 2.

Primers used for DNA amplification of Oreocharis taxa and genetic diversity. S, polymorphic sites, h, number of haplotypes, Hd, haplotypes diversity, π, nucleotide diversity, K, average number of nucleotide difference.

DNA fragment Primers sequences S h Hd π K Fragment size Tajima’s D Fu’s Fs Reference
ITS ITS4: 5’TCCTCCGCTTATTGATATGC 3’ 56 16 0.820 0.02178 14.067 670 bp 1.53380 17.662*** White et al. 1990
ITS5 HP: 5’GGAAGGAGAAGTCGTAACAAGG 3’
trnL-F c: 5’CGAAATCGGTAGC GCTACG 3’ 16 11 0.805 0.00428 3.460 843 bp 0.77872 2.529 Taberlet 1991
f: 5’ATTTGAACTGGTGA CACGAG 3’
ycf1b ycf1bF: 5’ACATATG CCAAAGTGATGGAAAA 3’ 29 12 0.871 0.01243 8.890 725 bp 2.05208 12.821*** Dong et al. 2015
ycf1bR: 5’CCTCGCCGAAAATCTGATTGTTGTGAAT 3’
trnL-F and ycf1b 55 23 0.887 0.00845 13.214 1568 bp 1.33642 8.426*

The systematic position of Oreocharis taxa in Hainan Island

In order to explore the systematic position of Oreocharis taxa in Hainan Island, we followed Möller et al. (2011a, b) and Chen et al. (2014) and used 57 other Oreocharis species with suitable DNA sequences in the study. Finally, a total of 60 species were included in the phylogenetic analysis. We manually aligned all sequences using MEGA v.6.5 (Kumar et al. 2008) and excluded ambiguous positions from the alignments. The two no-coding gene ITS1/2 and trnL-trnF were concatenated to a single matrix by the programme SequenceMatrix v.1.7.8 (Vaidya et al. 2011) after a congruency test by PAUP* 4.0a164 (Swofford 2003). We inferred the optimal model of nucleotide substitution by MRMODELTEST 2.3 (Nylander 2004), based on the AIC (Akaike Information Criteria) (Akaike 1981). In addition, the most suitable model GTR+I+G was used in both ML and BI analysis. Maximum Likelihood (ML) analysis was conducted using MEGA v.6.5 (Kumar et al. 2008) with the optimal substitution models to carry out 1000 bootstrap (BS) replicates. Bayesian Inference (BI) analysis was conducted using MrBayes version 3.1.2 (Huelsenbeck and Ronquist 2001). The Markov Chain Monte Carlo (MCMC) was analysed for 10 million generations and sampling every 10000 generations for two independent Bayesian runs. The first 2500 trees (25% of total trees) were discarded as burn-in and the remaining trees were summarised in a 50% majority-rule consensus tree with the posterior probabilities (PP). The mean and posterior of each branch were visualised by FIGTREE v.1.4.2 (Rambaut 2009). Sequences used are showed in Appendix 2.

Genetic diversity and differentiation

The original chromatograms from both directions of the ITS and cpDNA sequences obtained were evaluated with the software BioEdit (Hall 1999) for base confirmation and contiguous sequences editing, then sequences were manually aligned, where necessary, using MEGA v.6.5 (Kumar et al. 2008) and ambiguous positions were excluded from the alignments. All sequences have been deposited in GenBank (MK587942MK588003). Subsequently, we combined the two no-coding cpDNA regions as a single locus by the programme SequenceMatrix v.1.7.8 (Vaidya et al. 2011). Then, we performed a Partition Homogeneity Test based on the combined cpDNA and an Incongruence Length Difference Test, based on combined ITS and cpDNA using PAUP* v. 4.0a164 (Swofford 2003).

The number of nucleotypes/haplotypes, number of nucleotypes/polymorphic sites (S), nucleotype/haplotype diversity (h), nucleotide diversity (π) and measures of DNA divergence (K) values were analysed by the programme DNASP v. 6.12.01 (Rozas et al. 2017) for each population and Fu’s Fs (Fu 1997) and Tajima’s D (Tajima 1989) values were tested for vital deviations from the null hypothesis of neutral evolution and constant population size, based on the ITS and cpDNA sequences separately. We generated the geographical distribution of nucleotypes/haplotypes according to sampling information (Table 1).

Genetic diversity within populations (Hs; Nei 1973), in total populations (HT), total gene diversity index (NST) and genetic differentiation index within populations (GST) were measured using Haplonst (Pons and Petit 1996) and GST and NST compared by the U test (Pons and Petit 1996) based on the ITS and cpDNA sequences separately.

The Analysis of Molecular Variance (AMOVA) was conducted to estimate genetic variation which was assigned within and amongst populations using GENALEX v. 6.503 (Peakall and Smouse 2012), based on the ITS and cpDNA sequences separately.

Phylogenetic relationships

Phylogenetic relationships of nucleotypes/haplotypes were inferred with BI using MrBayes v. 3.2.6 (Ronquist et al. 2012). According to test above, O. sinohenryi, which had the closest phylogenetic relationships with the Hainan Oreocharis taxa, were used as outgroups with sequences of nrDNA.

Prior to Bayesian analysis, the optimal model of nucleotide substitution was detected for each gene using MRMODELTEST v. 2.3 (Nylander 2004), based on the AIC (Akaike 1981). Two independent Bayesian runs of MCMC were performed for 10 million generations, sampling every 10000 generations. We accessed the Chain convergence in Tracer v. 1.7.1 (Rambaut and Drummond 2007) by checking the effective sample size (ESS) that was larger than 200 for each parameter. To further explore the relationships amongst unique nucleotypes, genealogical relationships were inferred from Median-Joining network (MJ) of NETWORK v. 5.001 (http://www.fluxus-Engineering.com/).

Neighbour-joining (NJ) tree and structure

All sequences of each population were chosen to represent effective geographic populations themselves. The method for the Neighbour-joining (NJ) tree was selected to build the phylogenetic relationship of Oreocharis taxa populations in Hainan Island by MEGA v.6.5, with Kimura two-parameter model (Kimura 1980), based on the ITS and two combined cpDNA sequences separately.

A Bayesian clustering approach conducted in STRUCTURE v. 2.3.4 (Earl and Vonholdt 2012) was used to detect the population genetic structure of the Hainan Oreocharis taxa, based on ITS and combined cpDNA sequences separately. The number of possible clusters (K) was set from 1 to 10 and each K run 10 times. Each run comprised a burn-in period of 1 × 105 interactions with 1 × 105MCMC steps after burning. The most suitable value of K was determined from Structure Harvester (Pritchard et al. 2000; http://taylor0.biology.ucla.edu/structureHarvester/) by using ΔK and the log-likelihood value. Finally, the result from programme STUCTURE for the best K value was drawn in CLUMPAK server (Jakobsson and Rosenberg 2007; http://clumpak.tau.ac.il/index.html).

Isolation by distance (IBD)

To detect whether there was local genetic variation under geographically limited dispersal, isolation by distance (IBD) for each population was tested by a Mantel test in GENALEX between pairwise genetic distance (uncorrected sequence divergence (Dxy) for nuclear DNA and cpDNA) and geographical distance.

Morphological traits

To characterise phenotype diversity and differences amongst populations, we measured and observed 16 morphological characters, including floral and leaf traits of at least 30 individuals for each population. The measured floral traits were, (i) corolla colour (yellow tube with orange lip, yellow, orange), (ii) corolla shape and type (tubular, thin tubular, campanulate), (iii) corolla width (< 1.49 cm, 1.5 cm - 1.99 cm, > 2.0 cm), (iv) corolla mouth width (< 0.5 cm, > 0.5 cm), (v) floral tube length (< 0.99 cm, 1 cm - 1.49 cm, > 1.5 cm), (vi) sepal length (short, long) and (vii) number of petals (five, six).

Five stamen traits were included in the analyses: (i) anther position (included-anthers hidden inside the floral tube, floral throat-anthers lying in the throat of floral tube, exerted-anthers are exposed outside the floral tube), (ii) stamen type (monomorphic, didynamous), (iii) pollen presentation (simultaneous, separately for each pair), (iv) anther shape (oval, horseshoe) and (v) hair on filament (absent, present).

Two stigma characters and two leaf traits were also included in the analyses: (i) location of stigma (included-stigma hidden inside the floral tube, throat-stigma lying in the throat of floral tube, exerted-stigma is exposed outside the floral tube), (ii) number of stigma (one, two), (iii) serration of leaf edge (present, absent) and (iv) leaf epidermal hair in abaxial side (absent, present). Measurements were taken with a rectilinear scale and rounded to the nearest 0.1 mm.

Principal Component Analysis (PCA) was conducted in SPSS v. 19.0 (Liu and Li 2014) to determine the traits with the highest value for classification and the plotting map.

Results

Monophyly of the Hainan Oreocharis taxa

The combined ITS1/2 and trnL-F datasets of Hainan Oreocharis taxa with other 57 Oreocharis species were 568 and 871 bp long, amongst which 233 and 89 were polymorphic sites and 141 and 38 were parsimony informative sites, respectively. The aligned dataset was 1439 bp long with a total number of 305 polymorphic sites measured, of which 160 were parsimony informative sites. There was no significant incongruence, based on the incongruence length difference (ILD) test between the ITS1/2 and trnL-F (p > 0.05).

Both the BI and ML analysis showed Hainan Oreocharis taxa being monophyly with PP (posterior probability) = 0.79 and BS (bootstrap value) = 38% (Appendix 1). In addition, O. sinohenryi, whose regions are restricted in South China (Guangxi and Guangdong Province), is the sister to Hainan Oroecharis taxa in the current tree with relatively high support (Appendix 1).

Genetic diversity and differentiation

The aligned ITS sequence matrix comprised in total of 670 basepairs (bp). A total number of 56 polymorphic sites were present, of which 48 were parsimony-informative, which allowed the identification of 16 different nucleotypes from a size of 238 samples (Table 1, Fig. 1a). Four nucleotypes, H1, H2, H8 and H12, were shared amongst populations, the other 12 nucleotypes were private, i.e. present in only one population (Table 1, Fig. 1a).

The combined alignment of the two cpDNA regions was in total 1615 bp long (858 and 757 bp for trnL-trnF and ycf1b, respectively) with a significant rate of homogeneity (P = 1) in the congruency test, indicating that there was no significant difference in the laboratory between the two cpDNA regions. The alignment contained 55 polymorphic sites and 8 indels (Table 2). A total of 23 chloroplast haplotypes were present amongst the 238 samples (Fig. 1b, Table 1). Of these, only two haplotypes, H2 and H20, were shared amongst several populations, whereas the other 21 haplotypes were private (Table 1, Fig. 1b). The combined dataset, based on ITS and cpDNA as pairwise ILD tests, showed that the two DNA regions were not significantly different from each other (P > 0.05).

Haplotypes diversity (Hd) and nucleotide diversity (Pi) for each population are summarized in Table 1 and there is little difference between nrDNA and cpDNA. Generally, except for population WZB, YG and LM presented high genetic diversity in both nrDNA and cpDNA, nuclear gene ITS in population CH and chloroplast gene trnL-F and ycf1b in population DE, NG and HM showed variable genetic diversity, the rest of the populations having very low nucleotide and haplotype diversity (Table 1).

In total, the average intrapopulation diversity HS was lower than the genetic diversity HT. Both in ITS and cpDNA sequences, total gene diversity index (NST) was not significantly greater than the genetic differentiation index within populations (GST, P > 0.05), revealing that Hainan Oreocharis taxa have no correspondence between haplotype comparability and geographic distribution (Appendix 3).

The AMOVA indicated that almost all variation (99% and 97%) was partitioned amongst populations, which was higher than the variation (1% and 3%) within populations, based on the ITS and cpDNA data, respectively, revealing highly significant genetic differentiation amongst populations (Table 3).

Table 3.

Genetic diversity and Analysis of Molecular Variance (AMOVA) based on the ITS and combined trnL-F and ycf1b sequences in Oreocharis taxa.

DNA fragment HS HT GST NST Source of variation d.f. Sum of squares Variance components Percentage of variation (%) F ST r
ITS 0.170 0.884 0.808 0.982 Amongst populations 11 2353.579 213.962 11.176 99%
Within populations 226 28.698 0.127 0.127 1% 2382.277
cpDNA 0.215 0.913 0.765 0.977 Amongst populations 11 2497.917 227.083 11.848 97%
Within populations 226 88.752 0.393 0.393 3% 2586.668

Phylogenetic relationship

Both phylogenetic trees, based on ITS nucleotypes and cpDNA haplotypes, indicated that nucleotypes/haplotypes can be separated into three main groups with strong bayesian probabilities (> 0.95) (Figs 2, 3). The nucleotype/haplotype network of nuclear DNA and cpDNA was concordant with the phylogenetic relationship, which presented three centrally located nodes, representing possible ancestral haplotypes with a high frequency (Figs 2b, 3b). The rest of the haplotypes were connected to the central haplotypes by one to four steps in a star-like network. In the network of nuclear DNA, nucleotypes H1 and H8 occurred at the highest frequency, indicating they probably are ancestral nucleotypes of O. dasyantha. In the network of cpDNA, haplotypes H12 may be the ancestral haplotypes of O. flavida since it was at the centrally located nodes with highest occupied frequency.

Figure 2. 

Bayesian Inference tree (a) using MrBayes and network (b) showing the genetic relationships amongst the observed ITS nucleotypes of Hainan Oreocharis populations. Numbers on branches indicate the bootstrap values for MP/MB and posterior probability. The relative sizes of the circles in the network are proportional to the nucleotype frequencies and missing nucleotypes are represented by a small black spot.

Neighbour-joining (NJ) tree and Population structure

The results of the NJ tree, based on nrDNA and cpDNA, suggested 12 populations were clearly clustered into three major groups, which well corresponded to the three defined Oreocharis taxa in Hainan Island, i.e. O. dasyantha (includes O. dasyantha var. ferruginosa), O. flavida and Oreocharis sp. Additionally, the analyses also presented a close relationship between O. flavida and Oreocharis sp., then with O. dasyantha.

Figure 3. 

Bayesian Inference tree (a) and network (b) of trnL-F and ycf1b haplotypes of Oreocharis populations in Hainan Island. Posterior probabilities are given above branches. The relative sizes of the circles in the network are proportional to the haplotype frequencies and missing haplotypes are represented by a small black spot.

Although the signal was stronger for cpDNA (Rxy = 0.473, P < 0.001) than for nuclear DNA (Rxy = 0.257, P < 0.001), the relationship between genetic and geographical distance for 12 populations was significant both in nuclear DNA and cpDNA (Appendix 3).

Ordinations of morphological traits

According to the floral syndromes, the Principal Component Analysis of 16 floral characters of Hainan Oreocharis populations can be divided into three clusters (Fig. 5): (1) tubular, zygomorphic flowers with yellow tube but orange limbs, monomorphic stamens, pollen presentation separated (populations DW, DE, FT, NG, HM, CH and JF of O. dasyantha and O. dasyantha var. ferruginosa); (2) campanulate, zygomorphic, orange flower with included stamen and stigma (populations WZA, WZB and QX of O. flavida); (3) thin tubular, zygomorphic yellow flower with included didynamous stamens (populations YG and LM of Oreocharis sp.). The corolla colour and corolla shapes may play a key role in ordinations of morphological traits with high values of 45.41% and 34.04%, followed by location of stigma and length of the corolla tube with the values 9.293% and 5.272%.

Discussion

Monophyly of the Hainan Oreocharis taxa

The phylogenetic tree showed that Hainan Oreocharis taxa are monophyly (Appendix 1), suggesting a single dispersal of Oreocharis into Hainan Island. The sister species to Hainan Oreocharis is O. sinohenryi, which is restricted to South China including Guangxi and Guangdong provinces. Hainan Island is only about 30 km from these provinces, thus such observed pattern can be simply explained by geographic relationships.

Genetic diversity and structure

Most Oreocharis populations hold very low nucleotide and haplotype diversity (Table 1) and overall populations revealed a high level of genetic differentiation (Table 3) and a significant phylogeographical structure. The three groups, i.e. O. flavida, O. dasyantha (including the variety O. dasyantha var. ferruginosa) and an unknown species showed clear geographical isolations associated with three different river ranges. O. dasyantha are found mostly in the watershed of the Changhua River (the secondly largest river on the island), O. flavida distributes in Mt. Wuzhi and Mt. Qixian, the upper reaches of the Wanquan River. The unknown species is restricted in the upper reaches of the largest river on the island, i.e. Nandu River. We concluded that these three groups may have evolved and maintained largely through allopatric differentiations.

Mountains can also probably explain such observed pattern with geographic isolation of these groups. Almost all Oreocharis populations in Hainan Island were restricted in > 1000 m high-elevation mountains with massive humidity, such that the island-like habitat became fragmented caused by a deep and wide valley in the complicated mountains system, which resulted in blocking of gene flow of Oreocharis populations with weak seed dispersal ability even at the fine scale (Xing et al. 2018).

Genetic differentiation and species delimitation

Li et al. (2019) found that geographic isolation by Changhua River is a driving force for the strong population differentiation in the Hainan-endemic Primulina heterotricha Merr. and Metapetrocosmea peltata (Merr. et Chun) W. T. Wang. Our results can also be explained by the isolation of Changhua River (Figs 1, 4), which indicated that Changhua River may play a key role in driving population divergence and speciation of the Hainan Oreocharis taxa (Xing et al. 2018; Li et al. 2019).

Figure 4. 

Neighbour-joining (NJ) tree based on ITS (a) and combined trnL-F and ycf1 (c) with the results of STRUCTURE, based on ITS (b) and combined trnL-F and ycf1 (d).

Secondly, the ‘sky island’ caused by high mountains may also cause such genetic differentiation for montane species (Palma-Silva et al. 2011; Tapper et al. 2014; Robin et al. 2015). Mountain tops in Hainan Island have tropical mountain cloud forests (> 1200 m) in Mt. Wuzhi, Mt. Yingge, Mt. Bawang, Mt. Jianfeng and Mt. Limu (Wang et al. 2016) which fragmented and restricted the island-like habitat of Oreocharis taxa. Alpine plant radiations have accelerated speciation with trait diversification (Sanderson 1998; Colin and Ruth 2006; Hughes and Atchison 2015) and, in general, these radiations are geared to be recent and rapid (Linder 2008). Almost all Oreocharis taxa in Hainan Island lived in high mountains except Population CH, which grew in a low-altitude habitat and held a distinct structure from other high-altitude populations of O. dasyantha, indicating the sky-island effect may drive population divergence and speciation.

According to morphological traits, all the 12 Oreocharis populations were also grouped into three clusters and corolla colour, shape and types are the main characters for distinguishing groups (Fig. 5; Ling et al. 2017). Such differences in floral syndromes further indicate the Oreocharis on Hainan Island should be recognised as three different lineages (species). Besides two species (includes one variety) currently recognised in Hainan Island, populations from Mt. Limu and Mt. Yingge should be treated as a new species or subspecies, which is still in need of further illumination.

Figure 5. 

Principle Component Analysis of 16 morphological traits for the Hainan Oreocharis populations. Different clusters are shown in red circles.

Acknowledgements

This work was funded by Innovative Team Program of Hainan Natural Science Foundation (2018CXTD331), National Natural Science Foundation of China (31670230 and 41871041), the Postgraduate Innovation Project of Biological Science of Tropical Agriculture and Forest Institute, Hainan University. We thank Mt. Bing-Qi Li from Mt. Limu Nature Reserve and staff of Bawangling and Yinggeling National Nature Reserve for providing help in the field.

References

  • Chen WH, Shui YM, Yang JB, Wang H, Nishii K, Wen F, Zhang ZR, Möller M (2014) Taxonomic Status, Phylogenetic Affinities and Genetic Diversity of a Presumed Extinct Genus, Paraisometrum W.T. Wang (Gesneriaceae) from the Karst Regions of Southwest China. PLoS One 9(9): e107967. https://doi.org/10.1371/journal.pone.0107967
  • Colin H, Ruth E (2006) Island radiation on a continental scale: exceptional rates of plant diversification after uplift of the Andes. PNAS 103(27): 10334–10339. https://doi.org/10.1073/pnas.0601928103
  • Dong W, Xu C, Li C, Sun Y, Zuo Y, Shi S, Cheng T, Guo J, Zhou S (2015) ycf1, the most promising plastid DNA barcode of land plants. Scientific Reports 5: 8348. https://doi.org/10.1038/srep08348
  • Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19(1): 11–15.
  • Earl DA, Vonholdt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources 4(2): 359–361. https://doi.org/10.1007/s12686-011-9548-7
  • Francisco-Ortega J, Wang ZS, Wang FG, Xing FW, Liu H, Xv H, Xu WX, Luo YB, Song XQ, Gale S, Boufford DE, Maunder M, An SQ (2010) Seed Plant Endemism on Hainan Island: A Framework for Conservation Actions. Botanical Review 76(3): 346–376. https://doi.org/10.1007/s12229-010-9055-7
  • Fu YX (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147(2): 915.
  • Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids. Symp. Ser. 1999: 95–98.
  • Hughes CE, Atchison GW (2015) The ubiquity of alpine plant radiations: From the Andes to the Hengduan Mountains. The New Phytologist 207(2): 275–282. https://doi.org/10.1111/nph.13230
  • Jakobsson M, Rosenberg NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23(14): 1801–1806. https://doi.org/10.1093/bioinformatics/btm233
  • Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16(2): 11–120. https://doi.org/10.1007/BF01731581
  • Kumar S, Nei M, Dudley J, Tamura K (2008) MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Briefings in Bioinformatics 9(4): 299–306. https://doi.org/10.1093/bib/bbn017
  • Li ZY, Wang YZ (2005) Plants of Gesneriaceae in China. Henan Science and Technology Publishing House, Zhengzhou.
  • Li G, Ling SJ, Chen WF, Ren MX, Tang L (2019) Effects of geographic isolation caused by Changhua River on genetic diversity of Hainan-endemic Metapetrocosmea peltata (Gesneriaceae). Guihaia.
  • Ling SJ, Meng QW, Tang L, Ren MX (2017) Pollination syndromes of Chinese Gesneriaceae: a comparative study between Hainan Island and neighboring regions. Botanical Review 83: 59–74. https://doi.org/10.1007/s12229-017-9181-6
  • Liu M, Li XY (2014) Comprehensive analysis of SPSS v19.0 statistical analysis. Tsinghua University press, Beijing.
  • Möller M, Forrest A, Wei YG, Weber A (2011a) A molecular phylogenetic assessment of the advanced Asiatic and Malesian didymocarpoid Gesneriaceae with focus on non-monophyletic and monotypic genera. Plant Systematics and Evolution 292(3–4): 223–248. https://doi.org/10.1007/s00606-010-0413-z
  • Möller M, Middleton D, Nishii K, Wei YG, Sontag S, Weber A (2011b) A new delineation for Oreocharis incorporating an additional ten genera of Chinese Gesneriaceae. Phytotaxa 23(1): 1–36. https://doi.org/10.11646/phytotaxa.23.1.1
  • Myers N, Mittermeier RA, Mittermeier CG, Fonseca GAB, Kent J (2000) Biodiversity hotspots for conservation priorities. Nature 403(6772): 853–858. https://doi.org/10.1038/35002501
  • Nei M (1973) Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences of the United States of America 70(12): 3321–3323. https://doi.org/10.1073/pnas.70.12.3321
  • Nylander JAA (2004) MrModeltest v2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University.
  • Palma-Silva C, Wendt T, Pinheiro F, Barbara T, Fay MF, Cozzolino S, Lexer C (2011) Sympatric bromeliad species (Pitcairnia spp.) facilitate tests of mechanisms involved in species cohesion and reproductive isolation in Neotropical inselbergs. Molecular Ecology 20(15): 3185–3201. https://doi.org/10.1111/j.1365-294X.2011.05143.x
  • Peakall R, Smouse PE (2012) GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics (Oxford, England) 28(19): 2537–2539. https://doi.org/10.1093/bioinformatics/bts460
  • Pons O, Petit RJ (1996) Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics 144: 1237–1245.
  • Robin VV, Vishnudas CK, Gupta P, Ramakrishnan U (2015) Deep and wide valleys drive nested phylogeographic patterns across a montane bird community. Proceedings of the Royal Society B Biological Sciences 282: 20150861. https://doi.org/10.1098/rspb.2015.0861
  • Ronquist F, Teslenko M, Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP (2012) MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61(3): 539–542. https://doi.org/10.1093/sysbio/sys029
  • Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, Sánchez-Gracia A (2017) DnaSP 6. DNA Sequence Polymorphism Analysis of Large Datasets. Molecular Biology and Evolution 34: 3299–3302. https://doi.org/10.1093/molbev/msx248
  • Swofford DL (2003) PAUP*: Phylogenetic Analysis Using Parsimony (* and other Methods). Version 4. Sunderland: Sinauer Associates.
  • Taberlet P, Gielly L, Pautou G, Bouvet J (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology 17(5): 1105–1109. https://doi.org/10.1007/BF00037152
  • Tajima T (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585–595.
  • Tapper SL, Byrne M, Yates CJ, Keppel G, Hopper SD, Van Niel K, Schut AGT, Mucina L, Wardell-Johnson GW (2014) Isolated with persistence or dynamically connected? Genetic patterns in a common granite outcrop endemic. Diversity & Distributions 20(9): 987–1001. https://doi.org/10.1111/ddi.12185
  • Vaidya G, Lohman DJ, Meier R (2011) SequenceMatrix: Concatenation software for the fast assembly of multi-gene datasets with character set and codon information. Cladistics-the International Journal of the Willi Hennig Society 27(2): 171–180. https://doi.org/10.1111/j.1096-0031.2010.00329.x
  • Wang XX, Long WX, Yang XB, Xiong MH, Kang Y, Huang J, Wang X, Hong XJ, Zhou ZL, Lu YQ, Fang J, Li SX (2016) Patterns of plant diversity within and among three tropical cloud forest communities in Hainan Island. Acta Phytoecologica Sinica 40(05): 469–479. https://doi.org/10.17521/cjpe.2016.0021
  • Wei YG (2010) Gesneriaceae of South China. Guangxi Science and Technology Publishing House, Nanning.
  • Xing FW (2012) Inventory of Plant Species Diversity of Hainan. Huazhong University of Science and Technology Press, Wuhan.
  • Xing EN, Xu ST, Ren MX (2018) Age structure and gene flows of fine-scale populations of Oreocharis dasyantha (Gesneriaceae), an alpine herb endemic to Hainan Island. Journal of Tropical Biology 9(1): 37–46.
  • Yang XB (2013) Flora of Hainan. Science Press, Beijing, 367–369.

Appendix 1

Molecular phylogeny for Hainan Oreocharis taxa and 57 Oreocharis species based on combined ITS1/2 and trnL-trnF, there was no significant incongruence based on the incongruence length different (ILD) test between the ITS1/2 and trnL-trnF. Bayesian posterior probability (PP) and ML bootstrap values (BS) are showed above branches. Hainan Oreocharis taxa were showed in grey.

Appendix 2

List of Hainan Oreocharis taxa and 57 Oreocharis species used in the phylogenetic analysis, including respective Genbank accession and voucher numbers.

Species trnL-trnF ITS1/2 Voucher number
Oreocharis acaulis (Merr.) Mich.Möller & A.Weber HQ633012 HQ632916 M.Möller MMO 09-1605
Oreocharis amabilis Dunn KM232654.1 KJ475433.1 Carles 587
Oreocharis argyreia Chun ex Pan HQ632919.1 HQ633015.1 M.Möller MMO 07-1131
Oreocharis aurea Dunn KM062914.1 KM063154.1 M.Möller MMO 06-980
Oreocharis auricula (S.Moore) C.B.Clarke FJ501482.1 DQ912664.1 M.Möller MMO 03-304
Oreocharis begoniifolia (H.W.Li) Mich.Möller & A.Weber KM062926.1 KM063166.1 M.Möller MMO 08-1221
Oreocharis benthamii C.B.Clarke JF697584.1 JF697572.1 M.Möller MMO 08-1317
Oreocharis brachypodus J.M. Li & Z.M.Li KR476564.1 KR337019.1 Jia-Mei Li 2304
Oreocharis burttii (W.T.Wang) Mich.Möller & A.Weber JF697582.1 JF697570.1 F.Wen 2010-05
Oreocharis chienii (Chun) Mich.Möller & A.Weber KM062908.1 KM063148.1 JXU0008123
Oreocharis cinnamomea Anthony KM062921.1 KM063161.1 PE-02053073
Oreocharis concava (Craib) Mich.Möller & A.Weber KM062930.1 KM063170.1 PE-02053062
Oreocharis convexa (Craib) Mich.Möller & A.Weber FJ501337.1 FJ501506.1 M.Möller MMO 01-176
Oreocharis cordatula (Craib) Pellegrin KM062922.1 KM063162.1 PE-02053432
Oreocharis cotinifolia (W.T.Wang) Mich.Möller & A.Weber HQ632914 HQ633010 Q.M.Chuan 01
Oreocharis craibii Mich.Möller & A.Weber HQ632921 HQ633017 M.Möller MMO 07-1072
Oreocharis dalzielii (W.W.Sm.) Mich.Möller & A.Weber JF697571 JF69783 F.Wen 2010-06
Oreocharis dentata A.L.Weitzman & L.E.Skog KM062916.1 KM063156.1 GH00353683
Oreocharis dimorphosepala (W.H. Chen & Y.M. Shui) Mich.Möller KM062925.1 KM063165.1 Y. M.Shui & al. 85333
Oreocharis dinghushanensis (W.T.Wang) Mich.Möller & A.Weber GU350643 GU350675 Lin Q.B. LQB06-01
Oreocharis duyunensis Z.Y. Li, X.G. Xiang &Z.Y. Guo MG722858.1 MG722856.1 PE-02114626
Oreocharis elliptica Anthony KM063155.1 KM062915.1 CDBI0130369
Oreocharis esquirolii Léveillé HQ633011 HQ632915 D.W.Zhang 723
Oreocharis eximia (Chun ex K.Y.Pan) Mich.Möller & A.Weber KM062919.1 KM063159.1 PE-02052811
Oreocharis farreri (Craib) Mich.Möller & A.Weber JF697585 JF697573 Zhou Ping ZP 2010-020
Oreocharis georgei Anthony KM062917.1 KM063157.1 PE-02053075
Oreocharis hekouensis (Y.M.Shui & W.H.Chen) Mich.Möller & A.Weber KM062934.1 KM063174.1 KUN-1219106
Oreocharis henryana Oliver JF697586.1 JF697574.1 CSH0017984
Oreocharis heterandra D.Fang & D.H.Qin KM232655.1 KJ475432.1 PE-02052999
Oreocharis hirsuta Barnett KM062913.1 KM063153.1 Put 3428
Oreocharis humilis (W.T.Wang) Mich.Möller & A.Weber GU350633 GU350665 Liang R.H.SC-YB
Oreocharis jiangxiensis (W.T.Wang) Mich.Möller & A.Weber HQ633029 HQ632933 M.Möller MMO 09-1451
Oreocharis jinpingensis W. H. Chen & Y. M. KM062923.1 KM063163.1 Y.M. Shui et al. 91309
Oreocharis lancifolia (Franch.) Mich.Möller & A.Weber HQ632924 HQ633020 M.Möller and P.Zhou MMO 09-1624
Oreocharis leiophylla Wang GU350676 GU350644 Zhou X.R. ZXR-05-01
Oreocharis longifolia (Craib) Mich.Möller & A.Weber HQ632934 HQ633030 M.Möller MMO 08-1239
Oreocharis lungshengensis (W.T.Wang) Mich.Möller & A.Weber HQ632917 HQ633013 M.Möller MMO 06-916
Oreocharis magnidens Chun ex Pan HQ632930.1 HQ633026.1 PE-02052989
Oreocharis mileensis (W.T.Wang) Mich.Möller & A.Weber KM063145.1 KM063182.1 KUN-1385472
Oreocharis muscicola (Craib) Mich.Möller & A.Weber DQ912665 FJ501548 Kew (1995-2229)
Oreocharis nanchuanica (K.Y.Pan & Z.Y.Liu) Mich.Möller & A.Weber KM062924.1 KM063164.1 KUN-1385365
Oreocharis pankaiyuae Mich.Möller & A.Weber HQ632925 HQ633021 PE-02053064
Oreocharis primuliflora (Batalin) Mich.Möller & A.Weber HQ633019 HQ932923 PE-02053071
Oreocharis primuloides (Miq.) Benth. & Hook.f. ex Clarke FJ501546.1 FJ501364.1 PE-01270488
Oreocharis rhombifolia (K.Y.Pan) Mich.Möller & A.Weber GU350632 GU350664 PE-02053532
Oreocharis ronganensis (K.Y.Pan) Mich.Möller & A.Weber HQ633023 HQ632927 PE-00030693
Oreocharis rosthornii (Diels) Mich.Möller & A.Weber KM062928.1 KM063168.1 ZY0001346
Oreocharis rotundifolia Pan KM062911.1 KM063151.1 PE-00030861
Oreocharis saxatilis (Hemsl.) Mich.Möller & A.Weber KM062932.1 KM063172.1 JIU05295
Oreocharis sericea Léveillé KM232656.1 KJ475407.1 CSFI059560
Oreocharis sinensis (Oliv.) Mich.Möller & A.Weber HQ632912 HQ633008 IBSC-0548658
Oreocharis sinohenryi (Chun) Mich.Möller & A.Weber HQ632913.1 HQ633009.1 M.Möller MMO 07-1150
Oreocharis speciosa (Hemsl.) Mich.Möller & W.H. Chen KM062909.1 KM063149.1 K000858093
Oreocharis stewardii (Chun) Mich.Möller & A.Weber HQ632926 HQ633022 M.Möller MMO 06-917
Oreocharis urceolata (K.Y.Pan) Mich.Möller & A.Weber KM062920.1 KM063160.1 M.Möller MMO 09-1633
Oreocharis wangwentsaii Mich.Möller & A.Weber GU350658 GU350689 Liang R.H.YN-Qj
Oreocharis xiangguiensis W.T.Wang & K.Y.Pan HQ632932.1 HQ633028.1 JIU04686
Oreocharis dasyantha Chun MK587993 MK587954 S.Jun Ling 20181124-02
Oreocharis flavida Merr. MK587990 MK587947 S.Jun Ling 20181126-01
Oreocharis dasyantha Chun var. ferruginosa K.Y. Pan MK587992 MK587956 S.Jun Ling 20181124-05
Oreocharis sp. MK587948 MK587987 S.Jun Ling 20181205-01

Appendix 3

The results graph of the relationship between genetic and geographical distance for 12 populations based on the (a) ITS1/2 and (b) cpDNA

Appendix 4

Floral phenotypes in 16 characters of Oreocharis taxa in Hainan Island.

DW DE FT NG HM JF CH WZA WZB QX YG LM Total Variance Explained
corolla color, coded as (0) yellow with orange, (1) yellow, (2) orange 0 0 0 0 0 0 0 2 2 2 1 1 45.406%
corolla shape and type, coded as (0) conical, (1) thin tubular, (2) campanulate 0 0 0 0 0 1 0 2 2 2 1 1 34.040%
corolla size, coded as (0) <1.49 cm, (1) 1.5 cm<-<1.99 cm, (2) >2.0 cm 1 1 1 1 1 1 1 1 1 0 2 2 0
corolla mouse width, coded as (0) <0.5 cm, (1) >0.5cm 1 1 1 1 1 0 1 1 1 1 0 0 0
length of tube, coded as (0) <0.99 cm, (1) 1 cm <-<1.49 cm, (2) >1.5 cm 2 2 2 2 2 2 2 1 1 0 1 1 5.272%
length of sepal, coded as (0)short, (1) long 0 0 0 0 0 0 0 0 0 1 0 0 0
number of petal, coded as (0) five, (1) six 0 0 0 0 0 0 0 0 0 0 0 1 0
location of stamens, coded as (0) included, (1) throat and (2) exerted 2 2 2 2 2 0 2 0 0 0 1 1 0
types of stamens, coded as (0) equal length, (1) didynamous stamens 0 0 0 0 0 0 1 0 0 0 1 1 0
pollen presentation, coded as (0) simultaneous, (1) separated 0 0 0 0 0 0 1 0 0 0 0 0 0
anther shape, coded as (0) oval shape, (1) horseshoe stage 0 0 0 0 0 0 0 1 1 1 1 1 0
hair on stamen, coded as (0) absent, (1) exist 1 1 1 1 1 1 0 1 1 1 0 0 0
location of stigma, coded as (0) included, (1) throat and (2) exerted 2 2 2 2 2 1 2 0 0 0 0 0 9.293%
number of stigma, coded as (0) one, (1) two 0 0 0 0 0 0 0 0 0 0 1 1 0
serration pf leaves edge, ceded as (0) absent, (1) exist 0 0 0 0 0 0 0 1 1 1 1 1 3.280%
leaf epiderrmal hair on abaxial side , ceded as (0) absent, (1) exist 1 1 1 1 1 1 1 0 0 0 1 1 0