Genetic variation and population structure in Korean endemic species: IV.Hemerocallis hakuunensis (Liliaceae)

Hemerocallis hakuunensis, a Korean endemic species, maintains considerably higher levels of allozyme variation within populations (meanHe=0.253) and substantially lower levels of allozyme divergence among populations (meanG _ST=0.077) than average values reported for other insect-pollinated, outcrossing herbs. Indirect estimates of the number of migrants per generation (Nm=3.00, calculated fromG _ST;Nm=3.57, calculated from the frequency of nine alleles unique to single populations) indicate that gene flow has been extensive inH. hakuunensis. This is somewhat surprising when we consider the fact that no specialized seed dispersal mechanism is known, flowers are visited by bees, and the present-day populations of the species are discontinous and isolated. Results of a spatial autocorrelation analysis based on mean allele frequencies of 19 populations reveal that only 13% (95/720 cases) of Moran'sI values for the ten interpopulational distance classes are significantly different from the expected values and no distinct trend with respect to the distance classes is detected. Although it is unclear how the populations are genetically homogenous, it is highly probable thatH. hakuunensis might have a history of relatively large, continuous populations that had more chance for gene movement among adjacent populations after the last Ice Age. In addition, occasional hybridization withH. thunbergii in areas of sympatry in the central and southwestern Korean Peninsula may be one factor contributing the present-day high allozyme variation observed inH. hakuunensis.     

Clonal and fine-scale genetic structure in populations of a restricted Korean endemic, Hosta jonesii (Liliaceae) and the implications for conservation

BACKGROUND AND AIMS: In plant populations the magnitude of spatial genetic structure of apparent individuals (including clonal ramets) can be different from that of sexual individuals (genets). Thus, distinguishing the effects of clonal versus sexual individuals in population genetic analyses could provide important insights for evolutionary biology and conservation. To investigate the effects of clonal spread on the fine-scale spatial genetic structure within plant populations, Hosta jonesii (Liliaceae), an endemic species to Korea, was chosen as a study species. METHODS: Using allozymes as genetic markers, spatial autocorrelation analysis of ramets and of genets was conducted to quantify the spatial scale of clonal spread and genotype distribution in two populations of H. jonesii. KEY RESULTS: Join-count statistics revealed that most clones are significantly aggregated at < 3-m interplant distance. Spatial autocorrelation analysis of all individuals resulted in significantly higher Moran's I values at 0-3-m interplant distance than analyses of population samples in which clones were excluded. However, significant fine-scale genetic structure was still observed when clones were excluded. CONCLUSIONS: These results suggest that clones enhance the magnitude of spatial autocorrelation due to localized clonal spread. The significant fine-scale genetic structure detected in samples excluding clones is consistent with the biological and ecological traits exhibited by H. jonesii including bee pollination and limited seed dispersal. For conservation purposes, genetic diversity would be maximized in local populations of H. jonesii by collecting or preserving individuals that are spaced at least 5 m apart.     

Low Levels of Genetic Diversity within Populations of Hosta clausa (Liliaceae)

Abstract Genetic diversity of Korean populations in Hosta clausa was investigated using starch gel electrophoresis. Hosta clausa is widespread, grows only along streamsides, and has both sexual and asexual reproduction. Populations of the species are small and isolated. Thirty-two percent of the loci examined were polymorphic, and mean genetic diversity within populations (He_p=0.082) was lower than mean estimates for species with very similar life history characteristics (0.131), particularly for its congener H. yingeri (0.250). The mean number of multilocus genotypes per population was 8.7, and genotypic diversity index (D_G) was 0.84. Significant differences in allele frequencies among populations were found in all seven polymorphic loci (P < 0.001). About one-fifth of the total allozyme variation was among populations (G_ST=0.192). Indirect estimate of the number of migrants per generation (Nm=0.48, calculated from mean G_ST) and nine private alleles found indicate that gene movement among populations was low. The low levels of genetic diversity within populations and the relatively high levels of genetic diversity among populations suggest that strong moist habitat preferences, clonal reproduction, low level of gene flow among populations, genetic drift, and historical events may have played roles in the genetic structuring of the species.     

Genetic variation and population structure in Korean populations of sand dune speciesSalsola komarovi (Chenopodiaceae)

Salsola komarovi lljin is a herbaceous annual native to the sand dunes and beaches of Japan, northern China, Sakhalln and Korea. Starch-gel electrophoresis was conducted on leaves and stems collected from 300 plants in eight Korean populations. The mean number of alleles per locus (A _p=1.51), mean expected heterozygosity (He _p=0.116), and total genetic diversity (H _T=0.279) were comparable with those for species with similar life history and ecological traits. A general conformance of genotype frequencies to Hardy-Weinberg expectations (meanF _IS=−0.030) indicates thatS. komarovi is an outcrossing species. Slightly more than 20% of the genetic variation was found among populations (F _ST=0.204). In addition, significant differences in allele frequency were detected between populations at all 11 polymorphic loci (P<0.001). Nei's genetic identities range from 0.885 to 0.985 with a mean of 0.942. However, indirect estimates of the number of migrant per generation (0.97, calculated fromF _ST and 0.31, calculated from seven private alleles) indicate that the levels of gene flow is low among Korean populations. Although the species maintains a moderate level of genetic variation within populations, the small, isolated natural populations of the species have been severely destructed by human activities, particularly in summer season. If this is true, conservation efforts should be focused on those populations that currently maintain the most genetic diversity (e.g., populations of Cheju Island and coast of the southwestern Korean Peninsula).     

Genetic variation and population structure inOryza malampuzhaensis Krish.et Chand. endemic to Western Ghats, South India

Oryza malampuzhaensis Krish.et Chand. (2n = 4x = 48; Poaceae,Oryza) is endemic to Western Ghats, South India, and shows a highly localized distribution over a small geographical area in this region. This is the most poorly understood taxon in genusOryza and is often misidentified asO. officinalis owing to their close morphology. We assessed the nature and distribution of genetic variation among 11 populations ofO. malampuzhaensis using random amplified polymorphic DNA markers. The analysis revealed low genetic variation inO. malampuzhaensis. Cluster analysis of pairwise genetic distances of populations revealed three distinct clusters and the grouping of populations largely corresponded to their geographical proximity. Restricted gene flow and a geography-dependent differentiation were evident among populations. The altitude-influenced differences in ecological factors among the natural habitats of the populations seem to be the cause of the geography-dependent differentiation. Genetically isolated smaller populations and a narrow genetic base inO. malampuzhaensis point to its vulnerability to genetic drift and genetic depauperation. ThusO. malampuzhaensis appears to be under the threat of extinction and needs to be conserved by use of suitable methods. The present study also identified molecular markers diagnostic forO. malampuzhaensis.     

Genetic diversity and structure of the endemic Caesalpinia hintonii complex (Leguminosae: Caesalpinioideae) in Mexico

The Caesalpinia hintonii complex is formed by five endemic species (C. hintonii, C. laxa, C. macvaughii, C. melanadenia and C. epifanioi) occurring in central Mexico. This species complex is under incipient genetic divergence as by-product of local adaptations in reproductive and morphological traits to different habitats. We estimate the genetic variation and structure of populations of this species complex to assess the extent of genetic differentiation among populations and related species along its geographic distribution. Estimations of genetic diversity and structure were done based on ten enzymes and 18 loci. Mean number of alleles per locus ranged from 1.5 to 1.9. Polymorphic loci ranged from 42.1 to 68.4. Observed (H_o: range 0.191–0.275) and expected (H_e: range 0.205–0.317) heterozygosities in this complex were higher compared with other endemic and legume species. Neis genetic diversity estimates showed that most genetic variation was found within (H_S = 0.325) rather than among populations (D_ST = 0.085). Populations of the species C. hintonii showed a considerable genetic differentiation (F_ST = 0.207). The results of genetic diversity and structure within and among populations are in accord with the great morphological differentiation described for this species complex.     

Morphometric and Isozyme Analysis of the Genus Hosta (Liliaceae) in Korea

Abstract The hostas native to Korea have never been carefully reviewed taxonomically and their patterns of variability are not well understood. For morphological and electrophoretic studies, samples of rootstocks were taken from 45 Korean Hosta populations and from two populations of H. tsushimensis N. Fujita on Tsushima Island, Japan. For morphometric analysis, ten plants from each of twenty populations were grown and observed under greenhouse conditions. Fifty-one floral and vegetative characters were examined on each plant and the data were analyzed using principal components and cluster analysis. Six Korean species can be recognized: H. yingeri S. B. Jones (Taehuksan, Sohuksan, and Hong islands); H. capitata (Koidz.) Nakai (southern Korea); H. clausa Nakai (central and northern Korea); H. minor (Baker) Nakai (southeastern Korea including Wan and Kojae islands); H. venusta F. Maekawa (Cheju Island); and H. jonesii M. Chung (southern islands). Morphological features contributing to recognition of the natural groups were: ridges on the scape; the width of inner and outer floral lobes; bracts pappillous at apex; length and color of the bracts; length of inflorescences; the withering condition of the bracts; scabrous nerves on the lower leaf surface; and size of the leaves. Isozyme analyses indicate a recent origin of H. venusta from H. minor. Although hostas are easily hybridized, natural hybridization seems to be rare in Korea. The morphological and isozyme studies identified no hybrids and the species are well characterized by their distribution patterns, phenology, and habitats.     

Allozyme Diversity and Population Structure in Korean Populations of Cymbidium goeringii (Orchidaceae)

Cymbidium goeringii (Orchidaceae). Mean observed population heterozygosity (H _op=0.181), expected heterozygosity (H _eP=0.240), and total genetic diversity (H _T =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 F _IS of 0.278. On average, 90% of the total genetic diversity was found within populations (mean G _ST = 0.098). An indirect estimate of the number of migrants per generation (Nm=2.30, calculated from G _ST , 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. Received 18 June 1998/ Accepted in revised form 18 November 1998     

Genetic diversity and population differentiation of chestnut blight fungus, Cryphonectria parasitica, in China as revealed by RAPD

Seventeen Cryphonectria parasitica populations sampled from six regions in China were investigated using RAPD. Across all 169 isolates from the 17 populations evaluated, 52 of the 71 markers (73%) were polymorphic, total genetic diversity (h) was 0.1463, and Shannon’s index was 0.2312. Diversity within populations accounted for 74% of total genetic diversity, and genetic differentiation among populations was 0.26 (G _ST = 0.26). Gene flow was 1.4 among the populations; higher gene flow was found among populations within regions and among regions [N _m (G _SR) = 2.8 and N _m (G _RT) = 3.5]. The unweighted pair group mean analysis (UPGMA) dendrogram revealed two distinct clusters: the northern China group and the southern China group. The spatial autocorrelation analysis revealed that the variation at most loci was randomly distributed and lacked spatial structure, but several loci and closer distances were spatially structured. Human activity and habitat could also be important factors affecting genetic structure among C. parasitica populations in China. Genetic diversity was highest in Southwest China, descending in an orderly fashion to Northeast China. This pattern indicated that Southwest China might be the center of origin of C. parasitica in China. The present study provides useful information for understanding the origin and spread of chestnut blight fungus in China and valuable data for formulating relevant strategies for controlling the disease in China.     

Allozyme variation in Japanese species ofChionographis (Liliaceae)

Allozyme variation was examined in three diploid taxaChionographis japonica var.japonica, var.kurokamiana, andC. koidzumiana and three tetraploid taxaC. japonica var.kurohimensis, ssp.hisauchiana, and ssp.minoensis. Results show thatC. japonica var.kurokamiana is genetically closer toC. koidzumiana than to var.japonica. In the tetraploid taxa, fixed heterozygosities were found at several loci, and this supports the hypothesis that these taxa are allotetraploids. Furthermore, the tetraploid taxa have many unique alleles not found in the diploid taxa. This suggests that sufficient time has passed since the origin of tetraploids for new mutations to have been fixed.     

Population genetic structure of the Korean threadsail filefish (Stephanolepis cirrhifer) based on microsatellite marker analysis

The threadsail filefish Stephanolepis cirrhifer is one of the most important commercial fish resources in Korea. However, its natural populations have declined drastically over the last several decades. To investigate the genetic characteristics of the threadsail filefish for conservation and management purposes, its genetic variation was analyzed in Korean fishing grounds using 11 microsatellite loci. All populations showed moderate genetic diversity (mean number of alleles (N_A) = 8.6, expected heterozygosity (He) = 0.73), representing a slightly lower level of genetic variability than other congeneric species. The presence of a weak genetic population substructure was detected (F_ST = 0.023, R_ST = 0.030, P < 0.001), but this substructure did not feature significant isolation based on the distance between populations. This differentiation may be primarily attributable to genetic differences between populations from Geomundo and other localities, based on relative low level of gene flow, a high level of pairwise F_ST and R_ST or the position of this population in a phylogenetic tree. An analysis of molecular variance (AMOVA) also revealed a greater part of the variation within the population and genetic differentiation among the samples analyzed and identified two genetic clusters. The possibility of a recent genetic bottleneck was observed in some populations of S. cirrhifer. Given the prevailing ocean currents and the intensity of threadsail filefish harvesting activities in Korea, the possibility that human harvest and stock enhancement activities may have partially contributed to our detected genetic pattern cannot be excluded. Management strategies that take these findings into account might lower the risk of harmful genetic change in the species.     

Genetic diversity and multilocus genetic structure in the relictual endemic herb<Emphasis Type="Italic"> Japonolirion osense</Emphasis> (Petrosaviaceae)

Plant clonality may greatly reduce effective population size and influence management strategies of rare and endangered species. We examined genetic diversity and the extent of clonality in four populations of the monotypic herbaceous perennial Japonolirion osense, which is one of the most rare flowering plants in Japan. Allozyme analysis revealed moderate levels of genetic variation, and the proportion of polymorphic loci (P=66.7%) was higher than the value for species with similar life-history traits. With four polymorphic loci, 19 multilocus genotypes were observed among 433 aerial shoot samples and 10 (52%) were found only in single populations. The proportion of distinguishable genotypes (PD=0.10) and Simpson's index of diversity (D=0.52) also exhibited moderate levels of genotypic diversity compared to other clonal plants, with genotype frequencies at Hardy-Weinberg equilibrium. The distributions of genotypes were often localized and they were mostly found within a radius of 5 m. Spatial autocorrelation analysis showed that shoot samples located 4 m apart were expected to be genetically independent. The results suggest that the spatial extent of genets was relatively narrow and thus the clonality was not extensive.     

Genetic variation in nine Shorea species (Dipterocarpaceae) in Indonesia revealed by AFLPs

Shorea is the largest and most important genus of the Dipterocarpaceae. The genetic diversity and structure of nine Shorea species from two different locations, namely Nanjak Makmur in Sumatra and Sumalindo in Borneo, were evaluated using amplified fragment length polymorphism (AFLP) markers. A total of 274 trees were investigated at 85 polymorphic AFLP loci. Levels of genetic diversity of these species ranged from  = 0.100 for S. acuminata to  = 0.165 for S. blumutensis. The population of rare species S. blumutensis possessed the highest genetic diversity suggesting that geographically restricted species can have levels of genetic variation comparable to closely related widespread common congeners. Analyses of molecular variance revealed that the genetic variation was mainly found among species in both locations (57.7% in Sumatra; 56.3% in Borneo). The unweighted pairgroup method using arithmetic averages dendrogram of all samples revealed an almost complete separation of species. Thus, AFLP markers proved appropriate for phylogenetic studies of Shorea species. Specific markers have been detected showing high-frequency differences among species and between regions within species. Sequence information of these markers can be used to develop specific polymerase chain reaction markers for wood identification. The possibility of interspecific hybridization was discussed.     

云南中华按蚊的遗传变异和种群结构

为了掌握云南省各地中华按蚊种群间的遗传变异和种群结构特征,测序并分析了采自云南9个样本点5个种群组的89头中华按蚊的线粒体COII基因。结果表明这些中华按蚊种群的COII基因序列平均单倍型多样性指数和核苷酸多样性指数分别为h=0.933,π=0.00406,共有51个变异位点,占分析的739个碱基总数的6.9%;定义了39个单倍型,有2个频率最高的单倍型H1和H9,分别占个体序列数的20.2%和12.4%;系统发育分析表明单倍型与地理位置没有明显的对应关系,单倍型网络图显示大部分单倍型分布没有明显的亲缘地理格局,主要以单倍型H1、H9、H4、H33和H2为中心呈星状分布,但元江和元阳构成的种群组(YU)单倍型存在明显地域分布特征;AMOVA结果表明种群组间遗传变异为12.58%,达到显著水平(P=0.04888),地理种群组间具有明显种群遗传结构。不同地区两两种群组间的Fst值和Nm值显示大部分种群组间存在基因交流,没有形成明显的遗传分化,但YU种群组和其他种群组间缺乏明显的基因交流,这主要是因为哀牢山的阻隔,使云南东西部形成两种不同的气候,产生了明显的遗传分化;歧点分布图显示为明显单峰分布,中性检测结果均为显著负值,说明云南省的中华按蚊种群在近期经历过复杂的种群扩张事件。掌握中华按蚊遗传多样性及分化特征,对中华按蚊及疟疾控制具有重要的作用。     

Genetic structure of the Eurasian lynx population in north-eastern Poland and the Baltic states

We analyzed the genotypes of Eurasian lynx (Lynx lynx) from three populations in the westernmost part of the species main range. One population was situated at the distribution edge (NE Poland) and the two other (Latvia and Estonia) were located within the main, contiguous range of the species. The aim was to determine if the genetic composition varied among these populations and if there was evidence of isolation among them. Based on microsatellite allele frequencies, we found the allelic richness in Polish lynx to be lower than that in lynx from Latvia and Estonia. We also found significant differentiation among the lynx populations, with the NE Poland population forming a distinct genetic group relative to the two other populations (R _ST = 0.15 and 0.22, P < 0.0001). We suggest that genetic differentiation among lynx populations is the result of habitat insularisation that limits gene flow. This finding emphasizes the necessity to consider the lynx genetic differentiation in conservation planning of this species in Poland.     

Genetic variation in Lumnitzera racemosa, a mangrove species from the Indo-West Pacific

The genetic structure of 18 populations of Lumnitzera racemosa from the Indo-West Pacific, including South China, Malay Peninsula, Sri Lanka, and North Australia, was assessed by inter simple sequence repeat (ISSR) markers. Our results showed a relatively high level of genetic variation at the species level (P = 87.04%, H_e = 0.260). The value of G_st was 0.642, suggesting significant genetic differentiation among populations. At the population level, however, genetic diversity was low (P = 32.17%, H_e = 0.097). When populations were grouped according to geographic regions, i.e., South China Sea, the East Indian Ocean, and North Australia, it was inferred from AMOVA that more than half the total variation (55.37%) was accounted for by differentiation between regions. A UPGMA dendrogram based on genetic distance also revealed a deep split between populations from these regions, indicating that Malay Peninsula and the Indonesia archipelago may play an important part on the genetic differentiation in L. racemosa. The high degree of population differentiation between regions and low genetic variation within populations recorded here highlights the need for appropriate conservation measures for this species, both in terms of incorporating further populations into protected areas, and the restoration strategies for separate regions.     

Genetic diversity in the threatened insular endemic plantAster asa-grayi (Asteraceae)

Genetic diversity in an insular endemic plantAster asa-grayi was examined using enzyme electrophoresis. Distribution ofA. asa-grayi is restricted to only four subtropical islands of Japan, and this species is listed as vulnerable to extinction in the Red Data Book of Japanese wild plants. A total of 161 individuals were sampled from five populations on four islands. Genetic diversity values at the population level were very low, compared to other plant species with a similar life history. Genetic variability at the species level is comparable to the mean value of endemic species. Genetic differentiation among populations is extremely high (G_ST= 0.71), indicating that the gene flow among populations is highly impeded, and pollen and seed dispersal is limited due to the pollinators and the seed morphology. This is because the four islands are geographically isolated. Fixation indices suggested that most populations do not randomly cross. To conserve the genetic diversity of the species, artificial crossings among different island populations are necessary.     

Genetic diversity and population structure of the Black-faced Spoonbill (Platalea minor) among its breeding sites in South Korea: Implication for conservation

The endangered Black-faced Spoonbill Platalea minor has experienced drastic reductions in population size, geographic distribution, and habitat availability throughout East Asia. In the present study, we examined population genetic structure and genetic diversity of Black-faced Spoonbills inhabiting five sites off the west coast of South Korea encompassing a few of its major breeding sites. Ten microsatellite loci and the mitochondrial sequence were used to assess patterns of genetic variation based on 63 individuals. Three ND2 haplotypes were found among 61 individuals; the remaining two were identified as Eurasian Spoonbills, revealing an unexpected hybridization between these two species having different ecological niches in South Korea—the Eurasian Spoonbill overwinters in inland areas, whereas the Black-faced Spoonbill inhabits coastal areas during the summer. Analyses of microsatellite variation revealed no discrete population structure among the five breeding sites but very weak genetic differentiation among geographically distant regions. Assignment tests identified several possible migrants among sites. Our findings suggested that Black-faced Spoonbills from the five breeding sites could be managed as a single population and highlighted the importance of conserving the populations from Maedo, Suhaam, and Namdong reservoir, which are geographically close and have retained high levels of genetic diversity and large populations.     

Genetic diversity and population structure of spottedtail goby (Synechogobius ommaturus) based on AFLP analysis

Larval dispersal may have an important impact on genetic structure of benthic fishes. To examine population genetic structure of spottedtail goby Synechogobius ommaturus, samples from five different locations of China and Kunsan population in Korea were analyzed by using amplified fragment length polymorphism (AFLP) technology. A total of 253 bands were identified from 91 individuals by 5 primer combinations and the percentage of polymorphic bands was 43.87%. The average gene diversity was 0.0794 ± 0.1470 and Shannon’s information index was 0.1279 ± 0.2138. The pairwise F_st values ranged from 0.022 to 0.201. The results of AMOVA analysis indicated that 90.54% of the genetic variation contained within populations and 9.46% occurred among populations. The gene flow estimates (Nm) demonstrated that different gene flow existed among populations from 0.994 to 11.114. No significant genealogical branches or clusters were recognized on the UPGMA tree. The results support the hypothesis that larval dispersal ability can be responsible for the genetic diversity and population structuring.     

Genetic variation and population structure ofCarex breviculmis (Cyperaceae) in Korea

We determined the genetic diversity and population structures ofCarex breviculmis (Cyperaceae) populations in Korea, using genetic variations at 23 allozyme loci.C. breviculmis is a long-lived herbaceous species that is widely distributed in eastern Asia. A high level of genetic variation was found in 15 populations. Twelve enzymes revealed 23 loci, of which 11 were polymorphic (47.8%). Genetic diversity at the speciesand population levels were 0.174 and 0.146, respectively. Total genetic diversity (H_T = 0.363) and within-population genetic diversity (H_s = 0.346) were high, whereas the extent of the population divergence was relatively low (G_ST = 0.063). Deviation from random mating (Fis) within the 15 populations was 0.206. An indirect estimate of the number of migrants per generation(Nm = 3.69) indicated that gene flow was extensive among Korean populations of this species. Analysis of fixation indices revealed a substantial heterozygote deficiency in some populations and at some loci. Genetic identity between popu-lations was high, exceeding 0.956.