Population Genetic Analysis of Lobelia rhynchopetalum Hemsl. (Campanulaceae) Using DNA Sequences from ITS and Eight Chloroplast DNA Regions
DNA sequence data from the internal transcribed spacer of nuclear ribosomal DNA and eight chloroplast DNA regions were used to investigate haplotypic variation and population genetic structure of the Afroalpine giant lobelia, Lobelia rhynchopetalum. The study was based on eight populations sampled from two mountain systems in Ethiopia. A total of 20 variable sites were obtained, which resulted in 13 unique haplotypes and an overall nucleotide diversity (ND) of 0.281 ± 0.15 and gene diversity (GD) of 0.85 ± 0.04. Analysis of molecular variance (AMOVA) revealed a highly significant variation () among populations (), and phylogenetic analysis revealed that populations from the two mountain systems formed their own distinct clade with >90% bootstrap support. Each population should be regarded as a significant unit for conservation of this species. The primers designed for this study can be applied to any Lobelia and other closely related species for population genetics and phylogenetic studies.
Lobelia is the largest genus within the subfamily Lobelioideae of Campanulaceae family comprising over 350 species that range from small herbs to giant woody plants. Lobelia rhynchopetalum Hemsl., which belongs to the subgenus Tupa, section Rhynchopetalum , is one of the 21 giant lobelia species of eastern Africa that represent a premier botanical example of spectacular evolutionary radiations [2, 3]. It belongs to the most famous giant lobelia group exhibiting a giant-rosette growthform . Giant lobelias predated the formation of tall mountains in eastern Africa, and most evolution occurred in parallel up the mountains . These authors also suggested that an extinct forest species gave rise to several alpine giant lobelias, possibly from which L. rhynchopetalum has evolved. L. rhynchopetalum and other giant lobelias of eastern Africa have the same chromosome number () as that of their progenitor [5, 6] and, thus, their evolution has occurred without a change in chromosome number.
L. rhynchopetalum is a monocarpic perennial species endemic to the Ethiopian drained sites of the Afroalpine ecoregion (e.g. [1, 3]). The plant is frost tolerant and has an up to two-meter-tall unbranched stem with a large pith and thick and leathery leaves (e.g. ), which are suggested to be adaptations to the high altitude tropical environment . Once the plant has flowered and set seeds, it dies, leaving a tall hollow and dried-out stem. The seed capsules contain a huge number of tiny yellow seeds that can be easily dispersed by wind . L. rhynchopetalum is most prominent and noticeable in the Afroalpine part of the Bale and Simien mountain systems, commonly within an altitudinal range of 3600–4500 m asl, where it serves as a tourist attraction. The significance of this species is, therefore, not only ecological but also recreational and economic. Despite its significance, it is one of the least studied lobelia species at a molecular level and, to our knowledge, no DNA sequence data from this species is available in GenBank. Little is known about its population genetics, which makes it difficult to conserve at its full range of genetic diversity in the presence of threats from fire and overgrazing.
Fast evolving regions from nuclear and chloroplast genomes have been used to generate intraspecific DNA sequence data for plant population genetic studies [9–12], as it enables us to reveal the distribution of haplotypes, both within and among populations, and to identify species genetic diversity hotspots.
In the present study, DNA sequence data from the internal transcribed spacers (ITS) of nuclear ribosomal DNA (rDNA) and eight chloroplast DNA (cpDNA) regions were generated from L. rhynchopetalum with the objectives of (1) population genetic and phylogenetic analyses for its conservation and evolutionary significance, (2) evaluating the utility of these DNA regions for population genetic and phylogenetic analyses, particularly within the genus Lobelia, and (3) contributing DNA sequence data from this species to Genbank so that it can be used for broader phylogenetic and phylogeographic analyses in combination with DNA sequence data from other Lobelia species.
2. Materials and Methods
2.1. Plant Material
A total of eight populations of L. rhynchopetalum collected from the Bale (6°48′N–7°08′N and 39°45′E–39°57′E) and Simien (13°05′N–13°25′N and 37°50′E-38°30′E) mountain systems were used in this study (Table 1). Goba-1, -2, and -3 populations were from the Bale mountains whereas Debark-1-5 populations were from the Simien mountains. Each population was represented by five individual plants. Lobelia erinus L. was included as an outgroup species for the phylogenetic analysis of L. rhynchopetalum populations and for comparative assessment of the DNA regions used in this study (see Table 2).
2.2. DNA Extraction
DNA was extracted from silica-gel-dried young leaves using a modified CTAB procedure as described in  except that 100 mg of fine powder of leaf material was used instead of 300 mg. DNA quality and concentration were measured using a Nanodrop ND-1000 spectrophotometer (Saveen Werner, Sweden).
2.3. PCR and Sequencing
Target DNA regions (Table 2) were amplified using a GeneAMP PCR system 9700 thermocycler with the following temperature profiles: initial 3 min denaturing at 94°C and final 7 min extension at 72°C with the intervening 30 cycles of 1 min denaturing at 94°C, 1 min primer annealing at 48°C, and 2 min primer extension at 72°C. The ITS was amplified and sequenced using ITS5F and ITS4R primers [14, Table 2]. Eighteen new primers were designed to amplify and sequence the trnT-trnL, trnfM-trnS, petN-trnC, trnG-trnR, psbT-psbB, clpP intron-2, 3′trnK-matK, and psbD-trnT regions of cpDNA (Table 2) using the primer3 primer designing program . The primers were designed to the conserved regions based on the aligned DNA sequences of Trachelium caeruleum L. (Campanulaceae) and Helianthus annuus L. (Asteraceae) (accession numbers EU090187 and DQ383815, resp.). These primers were named (Table 2) based on their 5′ position (forward primers) and 3′ position (reverse primers) in the T. caeruleum complete chloroplast genome sequence.
The trnT-trnL intergenic spacer was amplified using primers 37258F and 37820R. The reverse primer, 37820R, was used to sequence this region. The trnfM-trnS region contains the trnfM gene, trnfM-trnG intergenic spacer, trnG gene, trnG-psbZ intergenic spacer, psbZ gene, psbZ-trnS integenic spacer, and trnS gene in that order. This region was amplified in two segments with a combination of four primers (Table 2). The first pair of primers (48992F and 49584R) amplified part of the trnfM gene and the full length of the trnG gene and the trnfM-trnG and the trnG-psbZ intergenic spacers. This part of the trnfM-trnS region was sequenced using primer 49584R. The second pair of primers (49595F and 50079R) amplified part of the psbZ gene and the psbZ-trnS intergenic spacer that were sequenced using primer 50079R. Similarly, part of the petN-trnC intergenic spacer was amplified and sequenced using primers 58099F and 58955R.
Primers 10002F and 10226R were used to amplify the trnG-trnR intergenic spacer (Table 2). The complete sequence of this spacer was obtained using the forward primer, 10002F. The psbT-psbB intergenic spacer was amplified using primers 26837F and 27102R and sequenced using the reverse primer, 27102R. Primers 111104F and 111454R were used to amplify intron-2 (the intron between exon-2 and exon-3) of the clpP gene, whose partial sequence was obtained by using primer 111454R. The 3′trnK-matK portion of the trnK intron was amplified using primers 1825F and 2195R, and the amplified fragment was sequenced using primer 1825F. Similarly, the psbD-trnT intergenic spacer was amplified using primers 53562F and 54107R. The reverse primer, 54107R, was used to obtain the partial sequence of this spacer (Table 2). The PCR products were purified by QIAquick PCR purification kit (Qiagen GmbH, Germany) using a microcentrifuge as recommended by the manufacturer. Eight microlitre of purified PCR product (50–100 ng) was mixed with 2 L of 5 M sequencing primer and sent to the sequencing facility at the University of Oslo (http://www.bio.uio.no/ABI-lab/), where DNA sequencing was carried out. The representative nucleotide sequences of ITS and the eight cpDNA regions of L. rhynchopetalum were submitted to nucleotide sequence database (NCBI GenBank), and their accession numbers are given in Table 2.
2.4. Sequence Alignment and Data Analyses
DNA sequences were edited using BIOEDIT version 7.0.5 , and the quality of the sequences was visually inspected using Sequence Scanner version 1.0 (Applied Biosystems). Sequences were aligned using Clustal X version 1.81 . PAUP* 4.0 Beta 10  was used to construct a bootstrap 50% majority rule consensus tree based on Kimura distance coefficient . Trees were generated using heuristic search with the tree-bisection-reconnection (TBR) branch swapping algorithm, and clade support was estimated using 1000 bootstrap replicates (starting trees were obtained via neighbor-joining, and initial Maxtree was set to 1000). Various population genetic analyses including gene and nucleotide diversity, analysis of molecular variance (AMOVA), haplotype distribution and interhaplotypic distance were conducted using Arlequin version 2 . The minimum spanning tree (MST) of haplotypes was also generated using Arlequin.
3.1. Some Sequence Characteristics of L. rhynchopetalum
In this study, full sequence length was obtained for the ITSs (ITS-1, 5.8S and ITS-2), trnGGCC gene, and trnfM-trnGGCC, trnGGCC-psbZ, and trnGUCC-trnR intergenic spacers. Partial sequences from the trnT-trnL, psbT-psbB, psbD-trnT, psbZ-trnS, petN-trnC intergenic spacers, trnfM, psbZ, and matK genes, and clpP intron-2 and 3′trnK-matK introns were also obtained. A total of 20 variable sites were obtained within L. rhynchopetalum, of which 3 are indel positions and the remaining 17 are substitutions. Indels were only obtained in the ITS and trnT-trnL regions. The trnT-trnL intergenic spacer sequences of all individuals from the Bale mountains were shorter by one nucleotide as compared to those from the Simien mountains. This single nucleotide long indel has clearly differentiated the populations according to their mountain system of origin.
The number of variable sites for each region of L. rhynchopetalum determined after coding indels according to the simple indel coding method of Simmons and Ochoterena  is given in the 5th column of Table 2. The highest number of variable sites within L. rhynchopetalum was obtained from ITS, as expected. Eleven variable sites were obtained in the entire ITS region, nine within ITS-1 and two within ITS-2. The psbT-psbB, psbD-trnT, trnfM-trnS, and clpP intron-2 sequences were the least variable regions, as only a single variable site per region was obtained within L. rhynchopetalum. In the case of the trnfM-trnS region, the variable site was located within the psbZ-trnS intergenic spacer. The average percent variable sites (%VS) of cpDNA regions and ITS within L. rhynchopetalum were 0.4% and 1.4%, respectively. These values were increased to 9% and 28%, in that order when the L. rhynchopetalum sequence was aligned with that of Lobelia erinus.
To evaluate the usefulness of the DNA regions used in this study for phylogenetic analysis, the DNA sequences of L. rhynchopetalum and L. erinus were aligned. Based on the aligned sequences of these species, different parameters of sequence variation of each DNA region were generated (Table 2). The %VS (without including indels) ranged from 2.1 (trnG-trnR) to 27.5 (ITS), of which 100% and 25.8% were parsimony informative, respectively. This analysis revealed a large number of parsimony informative variable sites in all DNA regions investigated in this study, with the exception of the trnG-trnR intergenic spacer (Table 2), suggesting their usefulness for phylogenetic analysis of the genus Lobelia and its various subgenera and sections.
3.2. Intrapopulation Genetic Analysis of L. rhynchopetalum
Genetic analyses of L. rhynchopetalum at the intra-population level were based on 20 polymorphic loci, which include both substitutions and indels. The number of haplotypes per population ranged from 1 to 5. No DNA sequence variation was obtained in the Goba-2, Goba-3, and Debark-2 populations. Since each of these populations carried a single haplotype, the estimates for their intra-population gene diversity and other related parameters were zero (see Table 1). Of the eight populations investigated in this study, Debark-1 was the most diverse, as the haplotype from each individual in the population was different. The haplotypes from the eight populations were in total 18, of which eight haplotypes were found in more than one population. Overall, 13 unique haplotypes were identified from the 40 individuals (Table 1). Five and eight of these haplotypes were unique to the Bale and Simien mountains, respectively.
Genetic diversity was estimated for each population and mountain system as gene diversity (GD; ) and nucleotide diversity (ND; [22, 23]). Nucleotide substitutions (transitions and transversions) are the major source of gene diversity within populations. The highest gene diversity (GD = 1.00) was obtained in the Debark-1 population with five haplotypes and six polymorphic sites, followed by Goba-1 (GD = 0.90) with 4 haplotypes and six polymorphic sites (Table 1). Population Goba-1 stood first in terms of nucleotide diversity (ND = 0.071), which is the average gene diversity over all loci under consideration (Table 1). Among the Simien mountain populations, the highest ND (0.038) was recorded in Debark-1. The estimates of ND were higher in the Bale mountains than in the Simien mountains (Table 1) while the estimates for GD were the same. Overall, GD and ND in L. rhynchopetalum were estimated to be 0.85 and 0.281, respectively.
The mean interhaplotypic distance (MIHD) was calculated based on the Kimura distance method . The highest estimate (0.081) was recorded in the Goba-1 population, which is almost twofold higher than the highest MIHD among the haplotypes in the populations from the Simien mountains. The mean number of pairwise differences () within populations ranged from 0.00 to 2.99, with the highest obtained in the Goba-1 population. The estimates for MIHD and were higher within the Bale mountains than within the Simien mountains (Table 1). Tajima’s test of selective neutrality (; ) was also applied to each population and mountain system. The estimates of this parameter (D) ranged from −1.33 to 1.22 (Table 1), which is not significantly different from zero. We obtained a similar insignificant deviation from zero when each DNA region was considered separately (data not shown). Theta (), a central parameter in population genetic models, summarizes the rate at which mutation and random genetic drift generate and maintain variation within a given DNA region. The estimates of three estimators (, and ) are given in Table 1. In this analysis, the estimate of was almost the same as that of π except the slight differences in standard deviation. The highest estimates for the three estimators were obtained in the Goba-1 population.
3.3. Interpopulation Genetic Analysis of L. rhynchopetalum
We quantified the population differentiation of haplotypes by using the analysis of molecular variance model  for all populations and for populations from each mountain system. The differentiation between the Bale populations and between the Simien populations was similar (). Overall, the analysis revealed that 85% of the variance in the distance matrix was accounted for by differences among populations and only 15% by diversity within populations (Table 3). When the significance of population differentiation was tested by 10000 permutations, populations were differentiated at a highly significant level () within geographic locations and overall. The hierarchical AMOVA also revealed a significant geographic differentiation of L. rhynchopetalum populations. In addition, the minimum spanning tree (Figure 1) and the distance-based 50% bootstrap majority rule consensus tree (Figure 2) obtained from the analyses of the sequence data demonstrated a clear geographic differentiation of this species.
4.1. The Utility of the DNA Regions for Population Genetic and Phylogenetics Studies
The presence of intraspecific variation in nuclear rDNA (e.g., [9, 11, 12]) and cpDNA (e.g., [10, 11, 26]) is well documented. Here, we used the internal transcribed spacers (ITSs) of nuclear rDNA and eight cpDNA regions for intra- and interpopulations genetic analyses of L. rhynchopetalum. In addition to information from published reports, our choice of the cpDNA regions used in this study was based on the aligned DNA sequences of Trachelium caeruleum and Helianthus annuus. The alignment of the sequences of these two species revealed mononucleotide repeat microsatellites and a large number of variable sites within the trnT-trnL, trnG-trnR, psbT-psbB, and psbD-trnT intergenic spacers, the 3′trnK-matK portion of the trnK intron, and the clpP intron-2. These regions were, therefore, targeted to identify polymorphic microsatellites within L. rhynchopetalum. However, no polymorphic microsatellites were found, and thus only variable sites due to nucleotide substitutions and indels were used.
The ITS region has been commonly used for plant molecular systematics at lower taxonomic levels and for intraspecific genetic studies since it was first used in phylogenetic inference . It has already become obvious that this region is much more variable than the fastest evolving regions of cpDNA. The result of this study is a further proof to this general understanding, as the ITS was over threefold more variable than the average variation obtained within the cpDNA regions in L. rhynchopetalum. The psbD-trnT region has been considered as one of the highly polymorphic regions of cpDNA  and proved to show some degree of polymorphism at the intraspecific level (e.g., ). The trnT-trnL, 3′trnK-matK, petN-trnC, psbT-psbB (as part of psbB-psbH), and trnfM-trnS regions are also among the fast evolving cpDNA regions . For example, the trnfM-trnS region was proved to be informative at the intraspecific level in Eritrichium nanum  and Vigna angularis . The trnG-trnR intergenic spacer and the clpP intron were not part of the 34 fast evolving cpDNA regions reported in  and may not have been used for systematics and population genetic studies.
The trnG-trnR region was revealed to be the least variable and parsimony informative in the aligned sequences of L. rhynchopetalum and L. erinus regardless of the fact that two variable sites were obtained within L. rhynchopetalum (see Table 2). On the other hand, when percent variable sites (%VS) and percent parsimony informative sites (%PIS) were considered, the clpP intron 2 was found to be as informative as previously reported fast evolving cpDNA regions  and hence can be safely used for low taxonomic level phylogenetic studies. Generally, this analysis revealed that all DNA regions included in this study, with the exception of the trnG-trnR intergenic spacer, have a large number of parsimony informative variable sites, which can be used for phylogenetic analysis of the genus Lobelia and its various subgenera and sections, as exemplified using L. erinus.
L. rhynchopetalum is more closely related to Lobelia aberdarica R. E. Fr. & T. C. E. Fr. than to most other east African giant lobelias, including Lobelia gibberoa Hemsl. . Thirty polymorphic sites were obtained within a 650 bp ITS aligned sequence of L. rhynchopetalum and L. aberdarica (accession number, AF163435). The alignment of the 3′trnK-matK intron partial sequences (309 bp) of L. rhynchopetalum and L. aberdarica (accession number, AF176898) revealed ten potentially informative sites. Similarly a 489 bp trnT-trnL aligned partial sequence of L. rhynchopetalum and L. giberroa (accession number, DQ285239) revealed 18 potentially informative sites. Hence, the combination of these cpDNA regions could sufficiently resolve the phylogenetic relationships between the east African giant lobelias and beyond.
4.2. Intra- and Interpopulation Genetic Analysis of L. rhynchopetalum
To develop conservation strategies that preserve maximum levels of genetic diversity of L. rhynchopetalum in situ and make reasonable decisions about sampling procedures of germplasm for their ex situ conservation, one should know how its genetic variation is distributed within the species and what their population genetic structure looks like. The DNA sequence data from ITS and eight cpDNA regions proved to be a useful tool for this purpose and successfully applied to reveal the genetic diversity and population genetic structure of this endemic giant lobelia, regardless of limited number of variable sites obtained. Of the eight populations, two populations showed high genetic variation while three populations showed no variation within population. These populations were from both mountain systems, suggesting that the extent of within-population diversity is not limited to geographic regions. However, Simien mountains appeared to be a more favorable habitat for L. rhynchopetalum than the Bale mountains, as four of its five populations showed intrapopulation haplotypic diversity.
Many natural ecosystems are subject to habitat fragmentation, which results in smaller and more isolated populations. Plant species remaining in fragmented habitats are of conservation concern due to impacts of decreased population size and increased isolation that threaten their viability due to genetic drift and consequently lower genetic diversity (e.g. ). The consequences of such isolation likely increase inbreeding, and in turn greater exposure to genetic drift, resulting in loss of genetic diversity. The absence of genetic variation in some L. rhynchopetalum populations may be best explained by genetic drift in relation to their small population size and limited gene flow between populations, as small isolated populations are highly likely to diverge from each other due to genetic drift, which causes fixation of alleles.
Population differentiation is driven by various evolutionary forces such as mutation, gene flow, genetic drift, and selection, and its extent depends on the relative strength of these individual forces in interaction with life history traits of the species. Theta () is a central parameter in population genetic models for the balance between mutation and random genetic drift. For haplotypic data, theta is measured as follow , where is effective population size and is a mutation rate per nucleotide site under neutral evolution theory model . Thus, summarizes the rate at which mutations and random genetic drift generate and maintain variation within a given DNA region, under conditions in which natural selection is not operating. There were only two variants per polymorphic site in our aligned DNA sequence data set, which fits to the assumption of the infinite-site model. Pi (π) is the other measure of sequence variability, which measures the pairwise differences between sequences. In this study, the estimates for and are similar. This suggests that the data fits with the infinite-site model, as these two parameters have equal expectation under this model (see ). Tajima’s test is the test for selective neutrality, and the parameter () is considered to be zero for neutral loci . In our analysis, was not significantly different from zero in all populations and groups. Therefore, we conclude that the neutral mutation hypothesis explains the DNA sequence variation obtained in this study.
Thirteen unique haplotypes were obtained by analyzing 40 individual plants. Only three of these, haplotypes were shared among populations of the same mountain systems. Analysis of molecular variance revealed that a high proportion (85%) of the genetic variation was found among populations, and within-population variation only accounted for 15% of the total variation. The 9 variable sites obtained from cpDNA regions were the major source of the highly significant population differentiation at all hierarchical levels, as only three of these sites were variable at the intrapopulation level. Such high population differentiation is not uncommon in endemic species with limited distribution and small population sizes, as a consequence of the pronounced effects of genetic drift (e.g., ). When populations are differentiated at a highly significant level, it is recommended to conserve representative samples ex situ from each population to reduce the risk of losing unique genetic variants. For in situ conservation, priority should be given to populations with relatively high genetic diversity. The results of this study and the ISSR-based study  are not in complete agreement as to which of these populations have high diversity, which makes it difficult to prioritize specific populations for in situ conservation. However, simultaneous consideration of the two data sets and environmental factors suggests Goba-1 and Debark-1 as good candidates for in situ conservation.
AMOVA revealed a highly significant differentiation not only between populations but also among the two mountain systems (Table 3). The differentiation of populations according to geographic areas was also clearly revealed in the 50% bootstrap majority rule consensus tree (Figure 2). Two major clades supported by high bootstrap values (>90%) were formed, in which the haplotypes from the two mountain systems were clearly separated. The result is in agreement with the ISSR-based study  in grouping populations according to mountain system of origin. Generally, all analyses revealed a significant differentiation of L. rhynchopetalum populations at various hierarchical levels. Such a high population differentiation can be partly explained by limited gene flow. Several factors, such as geographic distance between populations, pollen and seed dispersal mechanisms, and mode of reproduction, have a direct impact on the extent of gene flow between populations. For example, the significant differentiation between the two mountain systems can be partly explained by the Rift Valley as a barrier to gene flow. Similar results were previously reported in L. giberroa between these mountain systems . Such a limited gene flow between populations allows further population differentiation, which could lead to speciation.
Knox and Palmer  suggested that giant lobelias appear to have initially colonized the ancient upland in East Africa and then moved onto the tall mountains as they arose. Lobelia acrochila (E. Wimm.) Knox is the most closely related species to L. rhynchopetalum [3, 36]. The inclusion of L. acrochila in such type of studies will shed more light to the evolutionary radiation of giant lobelias in eastern Africa. The fact that the Simien mountains are the northernmost end of the distribution of giant lobelias in eastern Africa and the suggestion that giant lobelias were expanding from south towards north  may give more weight to the Bale mountains, than to the Simien mountains, as a likely place for the origin of this species. However, since populations from other mountains where this species may be found (though to a lesser extent) were not included in this study, further studies by including these populations are needed to support this suggestion.
This work has revealed the existing haplotypic variation and population genetic structure of L. rhynchopetalum. The combination of deterministic and stochastic factors and factors affecting gene flow seems to have played a significant role for the highly significant differentiations of the species at different hierarchical levels. With about 85% of the total genetic variation residing in between populations, each population should be regarded as an important contributor to the overall amount of genetic variation and a significant unit for conservation efforts of this species. Our recommendation is that representative populations from different altitudes and geographic locations should be targeted for conservation purposes, as it reduces the risk of losing unique genetic variants due to several factors. The DNA sequence data generated and submitted to GenBank and the nine pairs of new primers that can be applied to any Lobelia and other closely related species, both for population genetic and phylogenetic studies, are also a significant contribution of this work. Furthermore, since the cpDNA primers were designed based on the aligned sequences of Trachelium caeruleum (Campanulaceae) and Helianthus annuus (Asteraceae), they may be useful for similar studies not only in lobelias but also in various Campanulaceae and Asteraceae species.
This work was financed by the Swedish University of Agricultural Sciences to which the authors are highly grateful. The authors thank Mrs. Ann-Charlotte Strömdahl for her assistance in the laboratory-related work.
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