Genetic diversity in the two endangered endemic species Kirengeshoma koreana (Hydrangeaceae) and Parasenecio pseudotaimingasa (Asteraceae) from Korea: Insights into population history and implications for conservation

As mountains have been hypothesized as harboring important Quaternary refugia for plants, one would expect high within-population genetic variation and low or moderate among-population differentiation for those species occurring there. We selected Kirengeshoma koreana and Parasenecio pseudotaimingasa, endemic to mountains of Korea to test the scenario that the main mountain ranges of the Peninsula would also have acted as refugia. We undertook a population genetic analysis using 15 and 12 putative allozyme loci of K. koreana and P. pseudotaimingasa, respectively. We found contrasting levels of genetic diversity in the two species; extremely low within-population genetic variation and high among-population divergence in K. koreana and high within-population genetic variation and moderate among-population divergence in P. pseudotaimingasa. We can conclude that, whereas Korean mountains would have provided large refugial areas (i.e., ‘macrorefugia’) for P. pseudotaimingasa, K. koreana would have endured the Quaternary climate oscillations in small, isolated populations (i.e., ‘microrefugia’). Given the lack of genetic diversity and the extremely low number of populations and individuals of K. koreana, a comprehensive conservation program is urgently needed for this rare and critically endangered species.     

伏牛山区连翘遗传多样性研究

利用2个叶绿体及1个核基因片段,对伏牛山区3个连翘野生种群30个个体进行了遗传多样性分析.结果表明,叶绿体基因数据得到4个单倍型(H1～H4),单倍型多样性指数(h)为0.545±0.066,核酸多样性指数π为0.001 72±0.000 21.核基因数据得到10个单倍型(A～J),单倍型多样性指数为0.501±0.076,核酸多样性指数π为0.002 53±0.000 49.核基因种群间遗传分化(ФST)为0.167,小于叶绿体基因ФST(0.886),种群间基因流(Nm)为1.250,显著大于叶绿体基因Nm(0.030).研究发现,伏牛山区野生连翘种群目前仍具有较高的遗传多样性,但部分人类活动较多的地区已经造成了连翘遗传多样性的降低.连翘种群间地理距离会限制种子介导的基因流,但在小区域范围内对花粉所介导的基因流影响不明显.     

Phylogenetic relationship,biogeography, and conservation genetics of endangered Fraxinus chiisanensis (Oleaceae), endemic to South Korea

Endemic plants are important for understanding phylogenetic relationships, biogeographical history, and genetic variation because of their restricted distribution and their role in conserving biodiversity. Here, we investigated the phylogenetic relationships of the Korean endemic Fraxinus chiisanensis by reconstructing the molecular phylogeny of Fraxinus based on two nuclear DNA (nrITS and phantastica) and two chloroplast DNA (psbA-trnH and rpl32-trnL) regions. Within our fossil-calibrated phylogenetic framework, we also inferred the biogeographical history of F. chiisanensis. To provide a scientific basis for the conservation of F. chiisanensis, we determined the levels of genetic diversity and genetic differentiation in this species. Combining information from nuclear and chloroplast DNA sequence data, our molecular phylogenetic analyses identified F. chiisanensis as a genetically distinct unit from its sister group, Fraxinus platypoda from Japan. Our molecular dating analyses using nuclear and chloroplast DNA data sets show F. chiisanensis diverged from its sister F. platypoda in the Early or Middle Miocene and differentiated in the Late Miocene on the Korean Peninsula. Our results suggest that the divergence of F. chiisanensis was associated with the submergence of the East China Sea land bridge and enhanced monsoons in East Asia. When compared to F. platypoda, F. chiisanensis exhibits low genetic diversity within populations and high genetic differentiation among populations. These results help us to understand the evolutionary history of F. chiisanensis and to develop a conservation strategy for this species.     

Genetic diversity of the endangered endemic Microcycas calocoma (Miq.) A. DC (Zamiaceae, Cycadales): Implications for conservation

The diversity and genetic structure of seven populations of Microcycas calocoma (Miq.) A. DC, were analyzed by gel electrophoresis using 19 allozymes. The mean number of alleles per locus (A) was 1.49 and the percentage of polymorphic loci was relatively high (P = 48.09). The mean observed (H_o) and expected heterozygosity (H_e) were 0.20 and 0.17, respectively. The F-statistics revealed a high population structure (F_st = 0.34). Mean gene flow between population pairs was Nm = 0.96. Results were compared with those of other cycad species, and indicate that M. calocoma populations have become fragmented due to increasing pressures of habitat conversion and disturbance. Also, geographical isolation among populations has generated allele loss in relation to altitude. The establishment and maintenance of protected areas for in situ conservation is critical to preserve the high genetic diversity of M. calocoma. Conservation strategy guidelines have been specified.     

Genetic diversity, population structure, and conservation of Sophora moorcroftiana (Fabaceae), a shrub endemic to the Tibetan Plateau

Sophora moorcroftiana is a perennial leguminous low shrub endemic to the middle reaches of Yarlung Zangbo River in Tibet. It is an important species to fix sand dunes and to avoid the formation of shifting sands; therefore, its progressive over-exploitation may enhance land desertification. The levels and distribution of genetic variability of this species were evaluated from 10 natural populations at 24 loci encoding 13 enzymes, using allozyme analysis by starch gel electrophoresis. Data obtained revealed moderate levels of genetic variation within populations (Pp=27.5%, Ap=1.5, Hep=0.122) and a considerable divergence among populations (FST=0.199). Significant positive correlations (r2=0.49, p<0.05; r2=0.46, p<0.05) were found between elevation and both mean number of alleles per locus (A) and gene diversity (He) in the studied populations of S. moorcroftiana. Lower genetic diversity in lower elevation populations might be due to the negative effects of human pressures and habitat fragmentation, to adaptation to high altitudes as a consequence of a peripatric speciation process, or to directional gene flow along the river basin from the source populations located in the west at higher altitudes. The evaluation of the degree of threat has led to the inclusion of this species in the category of EN ("endangered"), and conservation strategies for this endemic species are discussed on the basis of these findings.     

Genetic diversity and population structure of the endangered insect species Carabus variolosus in its western distribution range: Implications for conservation

Genetic variation was assessed in the endangered species C. variolosus (Coleoptera: Carabidae), which is listed in the European Habitats and Species Directive. Twelve populations from the north-western margin of its range in Germany and France to the border region between Slovenia and Croatia were investigated for variation at 16 allozyme loci. In general, genetic diversity was rather low as indicated by a mean allelic richness of 1.3 alleles per locus, a mean gene diversity (H _E ) of 0.071 and a mean proportion of polymorphic loci (P _95% ) of 16%. Genetic diversity did not change directionally from the margin towards the core of the range. Very high differentiation between populations (overall F _ST  = 0.465), the results of a Mantel test, and poor accordance between geographical and genetic distance suggest a high degree of isolation of the island-like distributed populations. High F _ST values and genetic distance measures, even between geographically close populations within the same drainage, confirm a very low dispersal power of this habitat specialist of headwater areas and swamps in woodlands, even in comparison with other flightless beetles. It is concluded that the majority of populations are demographically independent. Hierarchical F-statistics indicate that almost half of the genetic variance is found between regions and populations. Therefore, we recommend that conservation efforts consider every population as a management unit and aim to maintain as many populations as possible over as many regions as possible.     

Genetic diversity and population structure of endangered endemic Paeonia jishanensis in China and conservation implications

Paeonia jishanensis, one of the most important ancestral species of cultivated tree peonies, is an endangered ornamental and medicinal plant endemic to China. A total of 236 individuals of P. jishanensis from 10 extant populations were analysed using 21 EST-SSR markers to assess their genetic diversity and population structure. Moderate genetic diversity levels (H_E = 0.340) and high genetic differentiation among populations (F_ST = 0.335) were revealed. Combining the results of STRUCTURE, PCoA and neighbour-joining analyses, the 10 populations were divided into four genetic groups that were significantly related to their geographical origins, which was further supported by hierarchical AMOVA showing the highest variation of 17.9% among groups. The Mantel test showed a significant positive correlation between genetic distance and geographic distance among populations (r = 0.873, P < 0.0001). The genetic structure of P. jishanensis may be due to limited gene flow hindered by vicariance and its breeding system: facultative vegetative reproduction. This study carries significant implications for the conservation and utilization of this endangered species.     

Low genetic diversity in marginal populations of Bletilla striata (Orchidaceae) in southern Korea: Insights into population history and implications for conservation

The warm-temperate vegetation of Korea, currently limited to southern coastal areas, shifted southward during the Last Glacial Maximum towards glacial refugia putatively located in southern Japan and/or southern China. We hypothesized two scenarios of post-glacial re-colonization of warm-temperate species: (i) that extant Korean populations originated from a single source or (ii) that they are derived from multiple source populations. To test which of these scenarios is more likely, we investigated the patterns of genetic diversity in 16 populations of the warm-temperate terrestrial orchid Bletilla striata, employing 20 allozyme loci. Levels of genetic variation in B. striata were substantially lower than those reported in most other terrestrial orchids. However, the degree of genetic differentiation among populations was moderate. These results suggest a pattern of post-glacial re-colonization fitting the first scenario. Both in situ and ex situ conservation strategies are suggested to preserve the genetic variation of B. striata in Korea.     

Genetic diversity of Ophiocordyceps sinensis, a medicinal fungus endemic to the Tibetan Plateau: Implications for its evolution and conservation

Background  

Ophiocordyceps sinensis (syn. Cordyceps sinensis), endemic to alpine regions on the Tibetan plateau, is one of the most valuable medicinal fungi in the world. Huge commercial demand has led to excessive harvest and a dramatic decline in its numbers. The diversity of terrains and climates on the Tibetan Plateau and the broad insect host range (more than 50 species in the family Hepialidae) may have resulted in substantial intraspecific genetic diversity for this fungus. The objective of this study was to evaluate the population distribution of O. sinensis from geographically diverse regions of the Tibetan Plateau based on nrDNA ITS and MAT1-2-1 gene sequences. Understanding of the genetic diversity and genesis of O. sinensis will provide important information for the evolution and conservation of this fungus.     

山茶科3种中国特有濒危植物的遗传多样性研究

猪血木(Euryodendron excelsum)、圆籽荷(Apterosperma oblata)和杜鹃红山茶(Camellia changii)均为我国特有的山茶科珍稀濒危植物。本研究应用随机扩增多态性DNA(RAPD)检测方法,比较了这3个物种的遗传多样性。利用20－24个随机引物从猪血木、圆籽荷和杜鹃红山茶居群中分别获得206－305条RAPD谱带,多态位点百分率(PPL)分别为51.80％、80.26％和38.83％;居群间遗传分化指数G_ST分别为0.3566、0.1713、0.1242。结果显示：自然分布较广的圆籽荷的遗传多样性高于另外两种自然分布区狭窄的种类。3个物种的遗传变异均主要存在于居群内,但猪血木居群间的遗传分化明显高于圆籽荷和杜鹃红山茶,这可能与其生境的严重片断化有关。根据3个物种不同的遗传结构特点,建议加强现有自然居群的就地 保护,促进居群自然更新;收集不同分布点的种源,尽快建立广东山茶科珍稀濒危植物的保育中心,深入开展人工快繁研究,扩大这些种群的数量。     

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 history of golden monkeys (Rhinopithecus roxellana)

Golden monkey (Rhinopithecus roxellana), namely the snub-nosed monkey, is a well-known endangered primate, which distributes only in the central part of mainland China. As an effort to understand the current genetic status as well as population history of this species, we collected a sample of 32 individuals from four different regions, which cover the major habitat of this species. Forty-four allozyme loci were surveyed in our study by allozyme electrophoresis, none of which was found to be polymorphic. The void of polymorphism compared with that of other nonhuman primates is surprising particularly considering that the current population size is many times larger than that of some other endangered species. Since many independent loci are surveyed in this study, the most plausible explanation for our observation is that the population has experienced a recent bottleneck. We used a coalescent approach to explore various scenarios of population bottleneck and concluded that the most recent bottleneck could have happened within the last 15,000 years. Moreover, the proposed simulation approach could be useful to researchers who need to analyze the non- or low-polymorphism data.     

Genetic conservation and management of the California endemic,Torrey pine (Pinus torreyana Parry): Implications of genetic rescue in a genetically depauperate species

Rare species present a challenge under changing environmental conditions as the genetic consequences of rarity may limit species ability to adapt to environmental change. To evaluate the evolutionary potential of a rare species, we assessed variation in traits important to plant fitness using multigenerational common garden experiments. Torrey pine, Pinus torreyana Parry, is one of the rarest pines in the world, restricted to one mainland and one island population. Morphological differentiation between island and mainland populations suggests adaptation to local environments may have contributed to trait variation. The distribution of phenotypic variances within the common garden suggests distinct population‐specific growth trajectories underlay genetic differences, with the island population exhibiting substantially reduced genetic variance for growth relative to the mainland population. Furthermore, F1 hybrids, representing a cross between mainland and island trees, exhibit increased height accumulation and fecundity relative to mainland and island parents. This may indicate genetic rescue via intraspecific hybridization could provide the necessary genetic variation to persist in environments modified as a result of climate change. Long‐term common garden experiments, such as these, provide invaluable resources to assess the distribution of genetic variance that may inform conservation strategies to preserve evolutionary potential of rare species, including genetic rescue.     

Genetic diversity and population structure of Nuphar submersa (Nymphaeaceae), a critically endangered aquatic plant endemic to Japan,and implications for its conservation

Journal of Plant Research - Nuphar submersa (Nymphaeaceae) is a critically endangered freshwater macrophyte indigenous to central Japan, with only four small extant populations represented across...     

Genetic diversity and population structure in four Cirsium (Asteraceae) species

The present study considers genetic diversity of 38 populations in 4 Cirsium species of the genus Cirsium Mill. (Asteraceae), occurring in different ecological regions and tries to compare degree of genetic variability among the species with wide geographical distribution versus endemic C. pyramidale showing confined geographical distribution. The results showed that the endemic species has similar value of genetic diversity parameters as the species with wider distribution. We also studied the possible admixture nature of these populations and tried to understand the relation between genetic changes, geographical distribution and polyploidy level and chromosome pairing in these species. ISSR analysis showed population difference in allele composition and frequency. Clustering and PcoA ordination produced different groupings in each species, while STRUCTURE and reticulation analyses revealed high degree of genetic admixture and gene exchange among populations as well as allelic rearrangement. No significant correlation was observed between geographical distance and genetic distance of the populations and AMOVA test revealed no significant difference among populations in each species studied. However, high amount of within population variation occurred in all 4 species indicating their cross-pollination nature and high genetic admixture. The populations also varied in chiasma frequency and chromosome pairing as well as the occurrence of heterozygote translocations all creating more variability to be used by plants for local adaptation.     

Genetic diversity and population structure of Swertia tetraptera (Gentianaceae), an endemic species of Qinghai-Tibetan Plateau

Swertia tetraptera Maxim is an annual alpine herb endemic to the Qinghai-Tibetan Plateau (QTP). Its populations are locally scattered as isolated patches throughout this region. Genetic variation within and among thirty-four populations of this species was assessed using ISSR fingerprinting with 10 primers. High levels of genetic diversity exist within species (P = 98.9%, I = 0.3475; He = 0.2227), while the within-population diversity is low (P = 32.7%, I = 0.177; He = 0.12). High levels of genetic differentiation were detected among populations based on various statistics, including Nei’s genetic diversity analysis (G_ST = 0.4608), Bayesian analysis (θ^B = 0.476) and AMOVA (F_ST = 0.57). That is, populations shared low levels of genetic identity (I = 0.2622–0.0966). This genetic structure was probably due to severe genetic drift, breeding system and limited gene flow. The observed genetic structure of the populations implies that different populations across the distribution range of the species should be sampled to maintain high genetic diversity when a conservation strategy is implemented.