Mi Yoon Chung

Genetic structure of age classes in Camellia japonica (Theaceae)

Abstract.— Camellia japonica L. (Theaceae), an insect‐ and bird‐pollinated, broad‐leaved evergreen tree, is widely distributed in Japan and the southern Korean peninsula. The species has a relatively even age distribution within populations, which may influence the spatial genetic structure of different age classes relative to species with typical L‐shaped age distributions. To determine whether the internal spatial genetic structure found in seedlings and young individuals carries over into adults, we used allozyme loci, F‐statistics, spatial autocorrelation statistics (Morans I), and coancestry measures to examine changes in genetic structure among seven age classes in a population (60‐m × 100‐m area) in southern Korea. In seedlings, weak but significant positive values of Morans I‐statistics and coancestry measures were found for distances less than 14 m, which is consistent with a mechanism of limited seed dispersal combined with overlapping seed shadows. This spatial structure, however, dissipates in older age classes, and in adults genetic variation has an essentially random spatial distribution. Morisitas index of dispersion of individuals in each age class showed that seedlings and juveniles are more highly clustered than are older individuals. These results suggest that self‐thinning changes the spatial relationships of individuals, and thus genotypes. A multilocus estimate of FST (0.008) shows a small but statistically significant difference in allele frequencies among age classes. In summary, intrapopulation genetic structure within and among age classes of C. japonica was significant but weak. Despite presumably limited seed dispersal, weak spatial genetic structure in juveniles suggests overlapping seed shadows followed by self‐thinning during recruitment. The present study also demonstrates that studies of spatial genetic structure focusing on limited numbers of generations may not be sufficient to reveal the entire picture of genetic structure in populations with overlapping generations.

Spatial genetic structure in populations of the terrestrial orchid Cephalanthera longibracteata (Orchidaceae)

Orchid seeds are unusual for being the smallest among flowering plants. These dust-like seeds are wind-borne and, thus, would seem to have the potential for long-distance dispersal (a common perception); this perception has led to a prediction of near-random spatial genetic structure within orchid populations. Mathematical models (e.g., simple ballistic model) for wind-dispersed seeds and wind-tunnel experiments, in contrast, indicate that most seeds of orchids should fall close to the maternal plant (<6 m), supporting a prediction of significant fine-scale genetic structure within populations. In reality we do not know much about seed dispersion in orchids. To determine which of these two predictions is more appropriate, Wrights F statistics and spatial autocorrelation analysis were used to examine the genetic structure within two adult populations of the terrestrial orchid Cephalanthera longibracteata (Orchidaceae) in southern Korea. In results comparable to those of other self-compatible, mixed-mating plant species, C. longibracteata populations exhibited low levels of genetic diversity (mean H(e) = 0.036) and a significant excess of homozygosity (mean F(IS) = 0.330), consistent with substantial inbreeding via selfing and/or mating among close relatives in a spatially structured population. Spatial autocorrelation analysis revealed significant positive genetic correlations among plants located <10 m, with relatedness at <3 m comparable to that expected for half sibs and first cousins. This genetic structure supports the prediction that the majority of seed dispersal occurs over distances of less than 10 m and is responsible for generating substantial overlap in seed shadows within C. longibracteata populations.

Spatial genetic structure in a Neolitsea sericea population (Lauraceae)

Neolitsea sericea (Bl.) Koidz. (Lauraceae) is a dioecious, insect-pollinated, and broad-leaved evergreen tree with bird-dispersed seeds. We used allozyme loci, F-statistics, and spatial autocorrelation statistics (Moran’s I) to examine the changes in genetic structure among five age classes within a study population (60 m × 100 m area) in southern Korea. No significant differences in expected heterozygosity were found among the age classes. The mean F-values averaged over loci were similar among age classes and showed overall conformance of heterozygosities with Hardy–Weinberg proportions. Differences in allelic frequencies among age classes were small (mean GST=0.012), and statistically significant only for one locus (Pgd-2). The mean Moran’s I-values for each of five age classes indicated essentially random spatial distribution. The homogeneity of genetic structure and genetic diversity among the five age classes may reflect the occurrence of similar reproductive events, year after year. The results may reflect the attractive red drupes of N. sericea in that they cause various frugivorous birds to disperse the seed long distances and independently, which in turn may help N. sericea maintain higher levels of genetic diversity within populations.

Landscape-level spatial genetic structure in Quercus acutissima (Fagaceae)

Quercus acutissima (Fagaceae), a deciduous broad-leaved tree, is an important forest element in hillsides of South Korea. We used allozyme loci, Wrights F statistics, and multilocus spatial autocorrelation statistics to examine the distribution of genetic diversity within and among three local populations and the spatial genetic structure at a landscape scale (15 ha, 250 × 600 m) on Oenaro Island, South Korea. Levels of genetic diversity in Q. acutissima populations were comparable to mean values for other oak species. A moderate but significant deficit of heterozygotes (mean F(IS) = 0.069) was detected within local populations and low but significant differentiation was observed among populations (F(ST) = 0.010). Spatial autocorrelation analyses revealed little evidence of significant genetic structure at spatial scales of 100-120 m. The failure to detect genetic structure within populations may be due to intraspecific competition or random mortality among saplings, resulting in extensive thinning within maternal half-sib groups. Alternatively, low genetic differentiation at the landscape scale indicates substantial gene flow among local populations. Although wind-borne pollen may be the primary source of gene flow in Q. acutissima, these results suggest that acorn movement by animals may be more extensive than previously anticipated. Comparison of these genetic data for Oenaro Island with a disturbed isolated inland population suggests that population-to-population differences in internal genetic structure may be influenced by local variation in regeneration environment (e.g., disturbance).

Temporal aspects of the fine-scale genetic structure in a population of Cinnamomum insularimontanum (Lauraceae)

Cinnamomum insularimontanum Hayata (Lauraceae) is an insect-pollinated, broad-leaved evergreen tree with bird-dispersed seeds. We used allozyme loci, Wrights fixation index, spatial autocorrelation statistics (Morans I), and coancestry measures to examine changes in genetic structure among four age-classes within a recently founded study population (60×100 m area) in southern Korea. There were no significant differences in expected heterozygosity among age classes. However, significant genetic differentiation among age classes was detected (P<0.0001). Fixation indices within age classes showed significant deficits of observed heterozygosity, which may be caused by partial selfing. The homogeneity of genetic structure among four age-classes may reflect similar spatial patterns of seed immigration from surrounding populations occurring year after year. Finally, the average Morans I and coancestry estimates indicated essentially random spatial distributions of alleles for each of the four age-classes and between seedlings and 2–4 year juveniles vs adult trees. These findings are very similar to those observed in the same study area for another member of the Lauraceae, Neolitsea sericea, which has a very similar life history and ecological characteristics (ie, bird-dispersed fruits, insect pollination, and a similar age structure). Together, these results suggest that the fleshy drupes of lauraceous species represent an adaptation to aid in the independent dispersal of seed by birds, which in turn may increase the genetic diversity of founders colonizing new habitats.

Genetic Diversity in the Common Terrestrial Orchid Oreorchis patens and Its Rare Congener Oreorchis coreana: Inference of Species Evolutionary History and Implications for Conservation

We hypothesized that the main Korean mountain ranges provided many refugia for boreal plant species, where they likely found relatively stable habitats and maintained large population sizes. Under this scenario, high levels of genetic variation and low degree of differentiation among populations within these species were anticipated. To test this hypothesis, we examined levels of allozyme diversity (17 loci) in 12 populations of the common terrestrial montane orchid Oreorchis patens from the main ranges in Korea and 4 populations of its rare congener O. coreana, which is restricted to the Korean island of Jeju. As expected, O. patens harbored high levels of genetic variation within populations (%P = 62.8, A = 1.96, H (o) = 0.211, and H (e) = 0.237). Allele frequency differences among populations were low (F (ST) = 0.075), and the species also displayed a significant correlation between pairwise genetic differentiation and geographical distance. All these results suggest that extant populations were founded by multiple genetically diverse individuals and that most of this initial diversity would have been maintained in the stable mountainous conditions during Quaternary climatic oscillations. In contrast, we were unable to detect any genetic diversity in O. coreana, suggesting that contemporary populations likely originated from a single ancestral source population that had lost all genetic variability. From a long-term conservation genetics perspective, extreme rarity and small population sizes, coupled with its apparent genetic uniformity, place O. coreana at a high risk of extinction. Thus, both in situ and ex situ conservation efforts should be of particular importance for this species.

Spatial distribution of allozyme polymorphisms following clonal and sexual reproduction in populations of Rhus javanica (Anacardiaceae)

Rhus javanica L. (Anacardiaceae), a dioecious tree with both sexual reproduction and clonal growth, is widely distributed in warm temperate, subtropical, and tropical regions in east Asia. We used allozyme loci and spatial autocorrelation statistics to examine clonal structure and the spatial distribution of allozyme polymorphisms in two Korean populations. Populations of the species maintain moderate levels of allozyme variability (mean He=0.175, GST=0.060), and high levels of multilocus genotypic diversity (mean DG=0.971). Clone-pair distances ranged from 1.4 m to 57.4 m, and had high mean values of 24.0 m and 25.6 m in the two study populations. Approximate genetic patch widths were inferred to be 23–25 m. The results indicated that within populations there is moderate (one study population) or no (other study population) spatial genetic structure among sexually reproduced individuals, and vegetatively reproduced genotypes also are almost randomly distributed. The spatial genetic structure among sexually reproduced trees in the one case is probably caused by limited pollen dispersal in that population, and the lack of structure in the other probably results from the short time elapsed since founding. It appears that clonal reproduction also does not contribute substantially to genetic isolation by distance neither among the sexually reproduced individuals nor the total population. Ramets often establish long distances from their progenitors and thus do not substantially increase the degree of local consanguineous matings.

The complete chloroplast DNA sequence of Eleutherococcus senticosus (Araliaceae); comparative evolutionary analyses with other three asterids.

This study reports the complete chloroplast (cp) DNA sequence of Eleutherococcus senticosus (GenBank: JN 637765), an endangered endemic species. The genome is 156,768 bp in length, and contains a pair of inverted repeat (IR) regions of 25,930 bp each, a large single copy (LSC) region of 86,755 bp and a small single copy (SSC) region of 18,153 bp. The structural organization, gene and intron contents, gene order, AT content, codon usage, and transcription units of the E. senticosus chloroplast genome are similar to that of typical land plant cp DNA. We aligned and analyzed the sequences of 86 coding genes, 19 introns and 113 intergenic spacers (IGS) in three different taxonomic hierarchies; Eleutherococcus vs. Panax, Eleutherococcus vs. Daucus, and Eleutherococcus vs. Nicotiana. The distribution of indels, the number of polymorphic sites and nucleotide diversity indicate that positional constraint is more important than functional constraint for the evolution of cp genome sequences in Asterids. For example, the intron sequences in the LSC region exhibited base substitution rates 5–11-times higher than that of the IR regions, while the intron sequences in the SSC region evolved 7–14-times faster than those in the IR region. Furthermore, the Ka/Ks ratio of the gene coding sequences supports a stronger evolutionary constraint in the IR region than in the LSC or SSC regions. Therefore, our data suggest that selective sweeps by base collection mechanisms more frequently eliminate polymorphisms in the IR region than in other regions. Chloroplast genome regions that have high levels of base substitutions also show higher incidences of indels. Thirty-five simple sequence repeat (SSR) loci were identified in the Eleutherococcus chloroplast genome. Of these, 27 are homopolymers, while six are di-polymers and two are tri-polymers. In addition to the SSR loci, we also identified 18 medium size repeat units ranging from 22 to 79 bp, 11 of which are distributed in the IGS or intron regions. These medium size repeats may contribute to developing a cp genome-specific gene introduction vector because the region may use for specific recombination sites.

Allozyme diversity and population structure in Korean populations of Cymbidium goeringii (Orchidaceae)

Cymbidium goeringii (Orchidaceae). Mean observed population heterozygosity (Hop=0.181), expected heterozygosity (HeP=0.240), and total genetic diversity (HT=0.351) were all higher than average values for species with similar life-history characteristics. A considerable deficit of heterozygotes relative to Hardy–Weinberg expectations was detected (77% of fixation indices were positive) with a mean FIS of 0.278. On average, 90% of the total genetic diversity was found within populations (mean GST= 0.098). An indirect estimate of the number of migrants per generation (Nm=2.30, calculated from GST, Nm=8.48, calculated from the frequencies of unique alleles) indicated that gene flow has been extensive in C. goeringii. Results of a spatial autocorrelation analysis based on allele frequencies of 16 populations revealed a trend with respect to the distance classes (0<63 km, six significant positive values; beyond that distance, 12 significant negative values). It is highly probable that C. goeringii has a history of relative large, continuous populations that had greater chance for gene movement among adjacent populations via large numbers of small seeds, following the last Ice Age. Factors contributing to the high levels of genetic diversity found within populations of C. goeringii include its large and continuous populations, its long-lived perennial habit, its widespread geographical distribution, and its ability for relatively long distance seed movement by wind.

Effects of population succession on demographic and genetic processes: predictions and tests in the daylily Hemerocallis thunbergii (Liliaceae).

Spatial genetic structure within plant populations is influenced by variation in demographic processes through space and time, including a populations successional status. To determine how demographic structure and fine‐scale genetic structure (FSGS) change with stages in a populations successional history, we studied Hemerocallis thunbergii (Liliaceae), a nocturnal flowering and hawkmoth‐pollinated herbaceous perennial with rapid population turnover dynamics. We examined nine populations assigned to three successive stages of population succession: expansion, maturation, and senescence. We developed stage‐specific expectations for within‐population demographic and genetic structure, and then for each population quantified the spatial aggregation of individuals and genotypes using spatial autocorrelation methods (nonaccumulative O‐ring and kinship statistics, respectively), and at the landscape level measured inbreeding and genetic structure using Wrights F‐statistics. Analyses using the O‐ring statistic revealed significant aggregation of individuals at short spatial scales in expanding and senescing populations, in particular, which may reflect restricted seed dispersal around maternal individuals combined with relatively low local population densities at these stages. Significant FSGS was found for three of four expanding, no mature, and only one senescing population, a pattern generally consistent with expectations of successional processes. Although allozyme genetic diversity was high within populations (mean %P = 78.9 and HE = 0.281), landscape‐level differentiation among sites was also high (FST = 0.166) and all populations exhibited a significant deficit of heterozygotes relative to Hardy–Weinberg expectations (range F = 0.201–0.424, mean FIS = 0.321). Within populations, F was not correlated with the degree of FSGS, thus suggesting inbreeding due primarily to selfing as opposed to mating among close relatives in spatially structured populations. Our results demonstrate considerable variation in the spatial distribution of individuals and patterns and magnitude of FSGS in H. thunbergii populations across the landscape. This variation is generally consistent with succession‐stage‐specific differences in ecological processes operating within these populations.