Incorporating differences between genetic diversity of trees and herbaceous plants in conservation strategies.

Reviews that summarize the genetic diversity of plant species in relation to their life history and ecological traits show that forest trees have more genetic diversity at population and species levels than annuals or herbaceous perennials. In addition, among-population genetic differentiation is significantly lower in trees than in most herbaceous perennials and annuals. Possible reasons for these differences between trees and herbaceous perennials and annuals have not been discussed critically. Several traits, such as high rates of outcrossing, long-distance pollen and seed dispersal, large effective population sizes (Ne ), arborescent stature, low population density, longevity, overlapping generations, and occurrence in late successional communities, may make trees less sensitive to genetic bottlenecks and more resistant to habitat fragmentation or climate change. We recommend that guidelines for genetic conservation strategies be designed differently for tree species versus other types of plant species. Because most tree species fit an LH scenario (low [L] genetic differentiation and high [H] genetic diversity), tree seeds could be sourced from a few populations distributed across the species' range. For the in situ conservation of trees, translocation is a viable option to increase Ne . In contrast, rare herbaceous understory species are frequently HL (high differentiation and low diversity) species. Under the HL scenario, seeds should be taken from many populations with high genetic diversity. In situ conservation efforts for herbaceous plants should focus on protecting habitats because the typically small populations of these species are vulnerable to the loss of genetic diversity. The robust allozyme genetic diversity databases could be used to develop conservation strategies for species lacking genetic information. As a case study of reforestation with several tree species in denuded areas on the Korean Peninsula, we recommend the selection of local genotypes as suitable sources to prevent adverse effects and to insure the successful restoration in the long term.

Incorporación de diferencias de diversidad genética entre árboles y plantas herbáceas en estrategias de conservación Resumen Las revisiones que resumen la diversidad genética de las plantas en relación con sus características ecológicas y biológicas muestran que los árboles forestales tienen más diversidad genética a nivel de población y de especie que las plantas anuales o las perennes herbáceas. Sumado a esto, la diferenciación genética entre poblaciones es significativamente más baja en los árboles que en la mayoría de las perennes herbáceas y las anuales. Hasta la fecha no se han discutido críticamente las posibles explicaciones de estas diferencias entre los árboles y las perennes herbáceas y las plantas anuales. Varias características, como las tasas altas de alogamia, la dispersión a gran distancia de polen y semillas, el gran tamaño de la población efectiva (Ne ), la estatura arbórea, la baja densidad poblacional, la longevidad, el solapamiento de generaciones y la presencia dentro de comunidades sucesionales tardías, pueden generar en los árboles una menor sensibilidad a los cuellos de botella genéticos y una mayor resistencia a la fragmentación del hábitat o al cambio climático. Recomendamos que las directrices para las estrategias de conservación genética estén diseñadas de manera diferente para las especies arbóreas que para otro tipo de plantas. Ya que la mayoría de las especies arbóreas encajan dentro de un escenario LH (baja [L] diferenciación genética y alta [H] diversidad genética), las semillas de los árboles podrían tomarse de unas cuantas poblaciones dispersas a lo largo del área de distribución de la especie. Por lo anterior, para la conservación in situ de los árboles, la translocación es una opción viable para incrementar la Ne . Al contrario de esta situación, las especies herbáceas raras del sotobosque con frecuencia son especies HL (alta diferenciación y baja diversidad). En el escenario HL, las semillas deberían ser recolectadas de muchas poblaciones con diversidad genética alta y los esfuerzos de conservación in situ para las plantas herbáceas deberían enfocarse en la protección del hábitat ya que las poblaciones típicamente pequeñas de estas especies son vulnerables a la pérdida de la diversidad genética. Las robustas bases de datos de diversidad genética aloenzimática podrían usarse para desarrollar estrategias de conservación para las especies que carecen de información genética. Como caso de estudio de reforestación con varias especies arbóreas en áreas deforestadas de la Península de Corea, recomendamos la selección de genotipos locales como fuente adecuada para prevenir los efectos adversos y para asegurar la restauración exitosa a largo plazo.

Comparative genetic structure between Sedum ussuriense and S. kamtschaticum (Crassulaceae), two stonecrops co-occurring on rocky cliffs.

• Premise of the study: Geographic isolation due to discontinuities of suitable habitat may have significant effects on the genetic structure of plant populations. Even within a few kilometers, physical barriers to gene flow may lead to considerable genetic differentiation among populations.• Methods: Sedum ussuriense is a boreal species that in Korea occurs only in four valleys separated by mountain ranges in Juwangsan National Park and its vicinity (a range of ∼15 km). Its congener S. kamtschaticum, by contrast, co-occurs in the four valleys but also on the intervening mountains. Using 12 allozyme loci, we comparatively assessed genetic variability and structure in 12 population pairs of the two stonecrops.• Key results: While we found high and comparable levels of within-population genetic variation for the two species, among-population divergence was significantly higher in S. ussuriense (FST = 0.261 vs. FST = 0.165). Sedum ussuriense also showed a much higher percentage of among-valley variation (19%) than S. kamtschaticum (4%).• Conclusions: High levels of genetic diversity in the two Sedum species are consistent with the previous hypothesis that mountains of the Korean Peninsula served as glacial refugia for many boreal species. Given that the two congeners have similar life-history traits, the lower among-population differentiation in S. kamtschaticum is attributable to its higher abundance and more continuous distribution in the study area. This study confirms the central role of geographic isolation in the genetic structure of plant species even at very small scales.

Contrasting levels of clonal and within-population genetic diversity between the 2 ecologically different herbs Polygonatum stenophyllum and Polygonatum inflatum (Liliaceae).

Comparative studies on clonal and genetic structure between ecologically contrasting congeners may provide valuable insights into the mechanisms promoting the maintenance of genetic diversity in clonal plant species. Polygonatum stenophyllum has long rhizomes (ca. 30-40 cm long) and largely occurs on sandy soils in open river banks, whereas its congener Polygonatum inflatum has short ones (ca. 5-10 cm long) and occurs on humic soils under deciduous forests. Using 21 allozyme loci, we comparatively assessed levels of clonal and genetic diversity in the 2 clonal species. Seven populations of P. stenophyllum consisted of single clones, and levels of within-population clonal and genetic variation were considerably lower than those of P. inflatum. However, when samples were pooled, P. stenophyllum harbored higher genetic variation than P. inflatum, which is due to higher among-population genetic differentiation in the former species compared with the latter (FST=0.636 vs. FST=0.165). Our data suggest that populations of P. stenophyllum have been mainly founded by a single seed or rhizome (through river water) or by a few seeds, whereas populations of P. inflatum would have been established through multiple, repeated seedling recruitment. Moderate levels of genetic diversity in a population of P. stenophyllum located at the foot of the Baekdudaegan Mountains and in all the populations of P. inflatum are consistent with the previous hypothesis that these mountains served as a glacial refugium for many boreal species of the Korean Peninsula.

Significant spatial aggregation and fine-scale genetic structure in the homosporous fern Cyrtomium falcatum (Dryopteridaceae).

Spores of homosporous ferns are small, wind-borne and thus have the potential for long-distance dispersal. This common perception has led to a prediction of near-random spatial genetic structure within fern populations. Spore dispersal and spore bank studies, however, indicate that most spores fall close to the maternal plant (< 5 m), supporting a prediction of significant fine-scale genetic structure (FSGS) within populations. To determine which of these two hypotheses is more likely to occur in nature, we measured inbreeding and quantified the spatial distribution of individuals and allozyme-based genotypes using spatial autocorrelation methods within four populations of the fern Cyrtomium falcatum in southern South Korea. Inbreeding levels were low, and all populations exhibited significant aggregation of individuals and strong FSGS. The present results support the second hypothesis, and the substantial FSGS in C. falcatum could reflect the unique features of most homosporous ferns (outcrossing mating systems that lead a majority of spores to occur at short distances and a very limited dispersal distance of male gametes). Although fern spores are physically analogous to orchid seeds, the intensity of FSGS exhibited in C. falcatum is four times stronger than that in 16 terrestrial orchid species.

Population history of the two carnivorous plants Drosera peltata var. nipponica and Drosera rotundifolia (Droseraceae) in Korea.

PREMISE OF THE STUDY: Drosera peltata var. nipponica, an element of the East Asia warm-temperate vegetation, and D. rotundifolia, a widely distributed boreal species, reach one of their northernmost and southernmost limits, respectively, on the Korean Peninsula. Because the Last Glacial Maximum (LGM)-Holocene dynamics of warm-temperate and boreal paleovegetation differed considerably on the Peninsula, the population history of these two sundews is expected to be different, leaving differential imprints in their genetic structure. METHODS: We investigated population genetic structure of D. peltata var. nipponica and D. rotundifolia in South Korea (10 populations of each for 20 allozyme loci) to infer their population history in this region. In addition, we compared the genetic variation harbored in the two sundews to those reported for other carnivorous and wetland plants. KEY RESULTS: Drosera peltata var. nipponica showed no genetic diversity, whereas D. rotundifolia exhibited extremely low within-population variation (He = 0.005) and considerable among-population divergence (FST = 0.817). CONCLUSIONS: Our results suggest that extant populations of D. peltata var. nipponica likely originated from a single ancestral population from southern Japan or southern China through postglacial dispersal. On the contrary, D. rotundifolia probably survived the LGM in situ, with extant populations derived from either one or several small source populations. We argue that separate conservation strategies should be employed, given that the two taxa have different ecological and demographic traits and harbor different levels of genetic diversity.

Was Jeju Island a glacial refugium for East Asian warm-temperate plants? Insights from the homosporous fern Selliguea hastata (Polypodiaceae).

PREMISE OF THE STUDY: We posed two hypotheses for broad scenarios of postglacial recolonization of Korea by the warm-temperate vegetation: (1) that extant Korean populations are derived from a single refugium, or (2) that they are derived from multiple refugia. We chose a homosporous fern typical of East Asian warm-temperate vegetation, Selliguea hastata, to test which of the two scenarios is more likely and to check whether Japan contained putative glacial refugia. METHODS: Using 16 allozyme loci, we obtained genotypes of 756 individuals from 20 populations, representative of the whole distribution area in Korea (including Jeju Island), Japan, and Taiwan. We assessed genetic variability within and among populations, Wright's F-statistics, and conducted analysis of molecular variance, model-based Bayesian clustering, and bottleneck tests. KEY RESULTS: We found no allozyme variation within populations of S. hastata in mainland Korea, whereas genetic polymorphism was detected for populations from Jeju Island, Japan (in particular a population from southeastern Shikoku), and Taiwan. The levels of inbreeding within populations were high, consistent with the potential of S. hastata for intragametophytic selfing. CONCLUSIONS: Data on allelic richness together with Bayesian clustering methods suggest a pattern of postglacial recolonization of mainland Korea from a single refugium, probably located either on Jeju Island or in Japan. Jeju Island should merit the highest priority for conservation biogeography, as it played a role as a Quaternary refugium for arctic-alpine, boreal, temperate as well as warm-temperate plants, as suggested here.

Genetic diversity in the Homosporous Fern Ophioglossum vulgatum (Ophioglossaceae) from South Korea: inference of mating system and population history.

It is generally believed that the members of Ophioglossaceae have subterranean, potentially bisexual gametophytes, which favor intragametophytic selfing. In Ophioglossaceae, previous allozyme studies revealed substantial inbreeding within Botrychium species and Mankyua chejuense. However, little is known about the mating system in species of the genus Ophioglossum. Molecular marker analyses can provide insights into the relative occurrence of selfing versus cross-fertilization in the species of Ophioglossum. We investigated allozyme variation in 8 Korean populations of the homosporous fern Ophioglossum vulgatum to infer its mating system and to get some insight into the population-establishment history in South Korea. We detected homozygous genotypes for alternative alleles at several loci, which suggest the occurrence of intragametophytic self-fertilization. Populations harbor low within-population variation (% P = 7.2, A = 1.08, and H (e) = 0.026) and a high among-population differentiation (F (ST) = 0.733). This, together with the finding that alternative alleles were fixed at several loci, suggests that the number and size of populations of O. vulgatum might have been severely reduced during the last glaciation (i.e., due to its in situ persistence in small, isolated refugia). The combined effects of severe random genetic drift and high rates of intragametophytic selfing are likely responsible for the genetic structure displayed by this homosporous fern. Its low levels of genetic diversity in South Korea justify the implementation of some conservation measures to ensure its long-term preservation.

Genetic variation and structure within 3 endangered Calanthe species (Orchidaceae) from Korea: inference of population-establishment history and implications for conservation.

It is thought that the warm-temperate vegetation of Korea, which at present is limited to southern coastal areas, was founded by individuals from glacial refugia putatively located in southern Japan and/or southern China. Two scenarios of postglacial recolonization can be hypothesized: 1) extant Korean populations are derived from multiple source populations or, 2) they originated from a single source. To test which of these scenarios is more likely, we surveyed patterns of genetic diversity in 3 congeneric terrestrial orchids that are typical of Korean warm-temperate vegetation, Calanthe discolor, C. sieboldii, and C. reflexa. In total, we studied 14 populations with 17 allozyme loci. To complement the study, we also tested the 2 scenarios with previous population-genetics data reported for other warm-temperate plant species native to Korea. Levels of genetic variation in the 3 Calanthe species were substantially higher than those typical of allozyme-based studies in other terrestrial orchid species, which clearly suggest a pattern of postglacial recolonization fitting the first scenario. However, previous studies with native Korean species showed equivocal patterns and suggest conflicting scenarios. The Calanthe species studied here and the previous genetic surveys conducted on other species indicate that the establishment of contemporary warm-temperate vegetation in Korea has been diverse since deglaciation. From a conservation perspective, C. reflexa should be regarded as endangered in Korea, needing special attention to preserve its current genetic diversity and to prevent further decreases in population sizes.

A review on Q ST-F ST comparisons of seed plants: Insights for conservation.

Increased access to genome-wide data provides new opportunities for plant conservation. However, information on neutral genetic diversity in a small number of marker loci can still be valuable because genomic data are not available to most rare plant species. In the hope of bridging the gap between conservation science and practice, we outline how conservation practitioners can more efficiently employ population genetic information in plant conservation. We first review the current knowledge about neutral genetic variation (NGV) and adaptive genetic variation (AGV) in seed plants, regarding both within-population and among-population components. We then introduce the estimates of among-population genetic differentiation in quantitative traits (Q ST) and neutral markers (F ST) to plant biology and summarize conservation applications derived from Q ST-F ST comparisons, particularly on how to capture most AGV and NGV on both in-situ and ex-situ programs. Based on a review of published studies, we found that, on average, two and four populations would be needed for woody perennials (n = 18) to capture 99% of NGV and AGV, respectively, whereas four populations would be needed in case of herbaceous perennials (n = 14). On average, Q ST is about 3.6, 1.5, and 1.1 times greater than F ST in woody plants, annuals, and herbaceous perennials, respectively. Hence, conservation and management policies or suggestions based solely on inference on F ST could be misleading, particularly in woody species. To maximize the preservation of the maximum levels of both AGV and NGV, we suggest using maximum Q ST rather than average Q ST. We recommend conservation managers and practitioners consider this when formulating further conservation and restoration plans for plant species, particularly woody species.

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.

Significant demographic and fine-scale genetic structure in expanding and senescing populations of the terrestrial orchid Cymbidium goeringii (Orchidaceae).

PREMISE OF THE STUDY: Fine-scale genetic structure (FSGS) in plants is influenced by variation in spatial and temporal demographic processes. To determine how demographic structure and FSGS change with stages of population succession, we studied replicate expanding and senescing populations of the Asian terrestrial orchid Cymbidium goeringii. METHODS: We used spatial autocorrelation methods (O-ring and kinship statistics) to quantify spatial demographic structure and FSGS in two expanding and two senescing populations, also measuring genetic diversity and inbreeding in each. KEY RESULTS: All populations exhibited significant aggregation of individuals and FSGS at short spatial scales. In expanding populations, this finding was associated with high recruitment rates, suggesting restricted seed dispersal. In senescing populations, recruitment was minimal, suggesting alternative mechanisms of aggregation, perhaps including spatial associations with mycorrhizal fungi. All populations had significant evidence of genetic bottlenecks, and inbreeding levels were consistently high. CONCLUSIONS: Our results indicate that different successional stages can generate similar patterns of spatial demographic and genetic structure, but as a consequence of different processes. These results contrast with the only other study of senescence effects on population genetic structure in an herbaceous perennial, which found little to no FSGS in senescing populations. With the exception of populations subject to mass collection by orchid sellers, significant FSGS is characteristic of the 16 terrestrial orchid species examined to date. From a conservation perspective, this result suggests that inference of orchid population history will benefit from analyses of both FSGS and demographic structure in combination with other ecological field data.

Climatic niche characteristics of native and invasive Lilium lancifolium.

One of the topics currently under discussion in biological invasions is whether the species' climatic niche has been conserved or, alternatively, has diverged during invasions. Here, we explore niche dynamic processes using the complex invasion history model of Lilium lancifolium, which is the first tested case of a native species (Korea) with two hypothesized spatial (regional and intercontinental) and temporal arrivals: (1) as an archaeophyte in East Asia (before AD 1500); and (2) as a neophyte in Europe, North America, Australia, and New Zealand (after AD 1500). Following a niche examination through both environmental and geographical spaces, the species in the archaeophyte range has apparently filled the ancestral native niche and, rather, would have increased it considerably. The species as a neophyte shows a closer climatic match with the archaeophyte range than with the native one. This pattern of niche similarity suggests that the neophyte range was probably colonized by a subset of archaeophyte propagules adapted to local climate that promoted the species' establishment. Overall, niche conservatism is proposed at each colonization step, from native to archaeophyte, and from archaeophyte to neophyte ranges. We detected signals of an advanced invasion stage within the archaeophyte range and traces of an early introduction stage in neophyte ranges.

Genetic diversity in the endangered terrestrial orchid Cypripedium japonicum in East Asia: Insights into population history and implications for conservation.

Little is known about levels and patterns of genetic diversity for the entire range of endangered orchids native to China, Korea, and Japan. In this study, we focus on Cypripedium japonicum and suggest three hypotheses: 1) that genetic drift has been a primary evolutionary force; 2) that populations in central and western China harbor higher levels of genetic variation relative to those from eastern China; and 3) that C. japonicum in China maintains the highest genetic variation among the three countries. Using ISSR and SCoT markers, we investigated genetic diversity in 17 populations to test the three hypotheses. As anticipated, we found low levels of genetic diversity at the species level with substantially high degree of genetic divergence, which can be mainly attributed to random genetic drift. Chinese populations harbor the highest within-population genetic variation, which tends to increase from east to west. We also found a close relationship between Korean populations and central/western Chinese populations. Historical rarity coupled with limited gene flow seems to be important factors for shaping genetic diversity and structure of C. japonicum. Our results indicate that the mountain areas in central and western China were likely refugia at the Last Glacial Maximum.

Comparison of genetic variation between northern and southern populations of Lilium cernuum (Liliaceae): Implications for Pleistocene refugia.

The so-called "Baekdudaegan" (BDDG), a mountain range that stretches along the Korean Peninsula, has been recently proposed as a major "southern" glacial refugium for boreal or temperate plant species based on palaeoecological and, especially, genetic data. Genetic studies comparing genetic variation between population occurring on the BDDG and more northern ones (i.e. in NE China and/or in Russian Far East) are, however, still too few to draw firm conclusions on the role of the BDDG as a refugium and a source for possible northward post-glacial recolonizations. In order to fill this gap, we selected a boreal/temperate herb, Lilium cernuum, and compared levels of allozyme-based genetic diversity of five populations from NE China with five populations from South Korea (home of its hypothesized refuge areas). As a complementary tool, we used the maximum entropy algorithm implemented in MaxEnt to infer the species' potential distribution for the present time, which was projected to different past climate scenarios for the Last Glacial Maximum (LGM). Permutation tests revealed that Korean populations harbored significantly higher levels of within-population genetic variation than those from NE China (expected heterozygosity = 0.173 vs. 0.095, respectively). Our results suggest that the lowered levels of genetic diversity in NE Chinese populations might be due to founder effects associated with post-glacial migration from southern regions. Congruent with genetic data, past distribution models showed higher probability of occurrence in southern ranges than in northern ones during the LGM. In addition, a positive correlation was detected between the expected heterozygosity and environmental LGM suitability. From a conservation perspective, our results further suggest that the southern populations in South Korea may be particularly worthy of protection.

Genetic structure of age classes in Camellia japonica (Theaceae).

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 (Moran's I), and coancestry measures to examine changes in genetic structure among seven age classes in a population (60-m x 100-m area) in southern Korea. In seedlings, weak but significant positive values of Moran's 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. Morisita's 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.

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.

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 population's successional status. To determine how demographic structure and fine-scale genetic structure (FSGS) change with stages in a population's 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 Wright's 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 H(E) = 0.281), landscape-level differentiation among sites was also high (F(ST) = 0.166) and all populations exhibited a significant deficit of heterozygotes relative to Hardy-Weinberg expectations (range F = 0.201-0.424, mean F(IS) = 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.

Fine-scale genetic structure among genetic individuals of the clone-forming monotypic genus Echinosophora koreensis (Fabaceae).

BACKGROUND AND AIMS: For rare endemics or endangered plant species that reproduce both sexually and vegetatively it is critical to understand the extent of clonality because assessment of clonal extent and distribution has important ecological and evolutionary consequences with conservation implications. A survey was undertaken to understand clonal effects on fine-scale genetic structure (FSGS) in two populations (one from a disturbed and the other from an undisturbed locality) of Echinosophora koreensis, an endangered small shrub belonging to a monotypic genus in central Korea that reproduces both sexually and vegetatively via rhizomes. METHODS: Using inter-simple sequence repeats (ISSRs) as genetic markers, the spatial distribution of individuals was evaluated using Ripley's L(d)-statistics and quantified the spatial scale of clonal spread and spatial distribution of ISSR genotypes using spatial autocorrelation analysis techniques (join-count statistics and kinship coefficient, F(ij)) for total samples and samples excluding clones. KEY RESULTS: A high degree of differentiation between populations was observed (phi(ST(g)) = 0.184, P < 0.001). Ripley's L(d)-statistics revealed a near random distribution of individuals in a disturbed population, whereas significant aggregation of individuals was found in an undisturbed site. The join-count statistics revealed that most clones significantly aggregate at < or = 6-m interplant distance. The Sp statistic reflecting patterns of correlograms revealed a strong pattern of FSGS for all four data sets (Sp = 0.072-0.154), but these patterns were not significantly different from each other. At small interplant distances (< or = 2 m), however, jackknifed 95% CIs revealed that the total samples exhibited significantly higher F(ij) values than the same samples excluding clones. CONCLUSION: The strong FSGS from genets is consistent with two biological and ecological traits of E. koreensis: bee-pollination and limited seed dispersal. Furthermore, potential clone mates over repeated generations would contribute to the observed high F(ij) values among genets at short distance. To ensure long-term ex situ genetic variability of the endangered E. koreensis, individuals located at distances of 10-12 m should be collected across entire populations of E. koreensis.

Patterns of hybridization and population genetic structure in the terrestrial orchids Liparis kumokiri and Liparis makinoana (Orchidaceae) in sympatric populations.

We investigated the potential for gene flow and genetic assimilation via hybridization between common and rare species of the terrestrial orchid genus Liparis, focusing specifically on sympatric and allopatric populations of the common Liparis kumokiri and the rare Liparis makinoana. We utilized analyses of genetic diversity, morphology, and the spatial distributions of individuals and genotypes to quantify the dynamics of interspecific gene flow at within- and among-population scales. High levels of allozyme genetic diversity (HE) were found in populations of the rare L. makinoana (0.317), whereas the common L. kumokiri (N = 1744 from 14 populations) revealed a complete lack of variation. This contrast may reflect different breeding systems and associated rates of genetic drift (L. makinoana is self-incompatible, whereas L. kumokiri is self-compatible). At the two known sympatric sites, individuals were found that recombined parental phenotypes, possessing floral characteristics of L. kumokiri and vegetative characteristics of L. makinoana. These putative hybrids were the only individuals found segregating alleles diagnostic of both parental species. Analysis of these individuals indicated that hybrid genotypes were skewed towards L. kumokiri and later generation recombinants of L. kumokiri at both sympatric sites. Furthermore, Ripley's bivariate L(r) statistics revealed that at one site these hybrids are strongly spatially clustered with L. kumokiri. Nonetheless, the relatively low frequency of hybrids, absence of ongoing hybridization (no F1s or first generation backcrossess), and strong genetic differentiation between morphologically 'pure' parental populations at sympatric sites (FST = 0.708-0.816) indicates that hybridization was not an important bridge for gene flow. The results from these two species suggest that natural hybridization has not played an important role in the diversification of Liparis, but instead support the view that genetic drift and limited gene flow are primarily responsible for speciation in Liparis. Based on genetic data and current status of the species, implications of the research for conservation are considered to provide guidelines for appropriate conservation and management strategies.