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.     

Genetic diversity and population structure of endangered Isoetes coreana in South Korea based on RAPD analysis

Isoetes coreana Chung and Choi is on the list of critically endangered species in South Korea. Using randomly amplified polymorphic DNA (RAPD) markers, we investigated the genetic diversity within and between seven local populations of I. coreana. Ten RAPD primers produced a total of 94 bands, of which 59 (62.8%) were polymorphic. A low level of genetic diversity was recognized within the populations of I. coreana: polymorphic loci (P), with values ranging from 3.4% to 33.9%, and a mean value of 15.5% being observed. Analysis of molecular variance (AMOVA) showed that genetic diversity was greater among populations (81.6%) than within populations (19.7%) or among the three regions included in this study (Han River, Youngsan River, and Nakdong River). In addition, a high degree of genetic differentiation (θ^B = 0.742) was detected among the populations. These results indicate that genetic differentiation has occurred very rapidly. However, the rate of gene flow between populations was found to be as low as 0.059, irrespective of the genetic and geographical distances between the populations, which indicates that genetic drift must have played an important role in forming the present populations of I. coreana. Because a reduction of genetic diversity as a result of genetic drift is undesirable, increasing the gene flow between populations of Korean quillwort I. coreana should be considered as a conservation strategy.     

Genetic diversity and population structure of Armillaria luteo-virens (Physalacriaceae) in Qinghai-Tibet Plateau revealed by SSR markers

Armillaria luteo-virens is a type of ectomycorrhiza whose fruit body is widely used as an edible mushroom in the Qinghai-Tibetan Plateau. In total, 404 individuals of A. luteo-virens from 23 geographically separate populations were analyzed using eight pairs of SSR markers. The average number of alleles among nine populations was 28.65 with a range from 20 to 38. The mean observed (H_O) and expected (H_E) heterozygosity ranged from 0.446 to 0.501 and from 0.499 to 0.554, respectively. An analysis of molecular variance (AMOVA) showed that most genetic variation occurred within populations (83.32%). The mean value of F_ST (0.176) suggested low genetic differentiation among populations. The 23 studied populations were divided into two main clusters based on the NJ dendrogram, which was also confirmed by STRUCTURE analysis. This study may aid in not only the protection of this species but also the management of genetic resources for future artificial cultivation.     

Microsatellite analysis of the genetic structure of captive forest musk deer populations and its implication for conservation

Forest musk deer (Moschus berezovskii) are rare as a result of poaching for musk and habitat loss. Some captive populations of forest musk deer have been established for decades in China. However, little genetic information is available for conservation management. In this paper, genetic variations, population structures, and the genetic bottleneck hypothesis were examined using 11 microsatellite loci from captive populations in Miyalo, Jinfeng and Maerkang in Sichuan Province, China. Estimates of genetic variability revealed substantial genetic variation in the three populations. A total of 142 different alleles were observed in 121 forest musk deer and the effective number of alleles per locus varied from 6.76 to 12.95. The average values of observed heterozygosity, expected heterozygosity, and Nei's expected heterozygosity were 0.552, 0.899 and 0.894 respectively. The overall significant (P < 0.001) deficit of heterozygotes because of inbreeding within breeds amounted to 34.5%. The mean F_ST (P < 0.001) showed that approximately 90.2% of the genetic variation was within populations and 9.8% was across populations. The UPGMA diagram, based on Nei's unbiased genetic distance, indicated that the three populations were differentiated into two different groups and it agreed with their origin and history. Bottleneck tests indicated that all three populations have undergone a population bottleneck, suggesting a small effective population size. Acknowledging that the genetic structure of populations has crucial conservation implications, the present genetic information should be taken into account in management plans for the conservation of captive forest musk deer.     

Genetic diversity and population structure in Tunisian Lavandula stoechas L. and Lavandula multifida L. (Lamiaceae)

The genetic diversity and population structure of 20 Tunisian Lavandula stoechas L. and Lavandula multifida L. populations, from different bioclimates, were analysed by starch gel electrophoresis using seven isozymes. The genetic diversity within populations varied according to species. Variation in L. multifida was higher than that observed for L. stoechas, and exclusive alleles were detected for taxa.

A high differentiation among populations, for each species, estimated by Wright's F-statistics was revealed. The genetic structure of populations from the same bioclimate was substantial. Nei's, R. [1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89, 583–590] genetic distance among pairs of populations was low. The UPGMA cluster analysis of genetic distance values revealed that populations for each species were not strictly clustered together according to bioclimate or geographic proximity.

For each species, the low genetic divergence among populations and their substantial structure indicate their recent fragmentation due to anthropic pressures. The dendrogram generated from pairwise genetic distance among all populations showed two distinct clusters each corresponding to one species. The high genetic divergence between the two species, based on isozymes, corroborates their taxonomic status, as previously reported using morphological traits. The strategy for the management and conservation of populations should be made for each taxa according to its level of diversity and bioclimate.     

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.     

Multi-locus genomic analysis reveals the genetic diversity and population structure of the rock carp (Procypris rabaudi) in the upper Yangtze River

Rock carp [Procypris rabaudi (Tchang)] is an endemic species widely distributed throughout the upper reaches of the Yangtze River and its tributaries. Recently, the wild genetic resources of this species have markedly declined and it has been listed as vulnerable in China. Thus, conservation policies for this species are required urgently. However, information supporting decision-making on the conservation of this species is insufficient, especially at the genetic level. In this work, eight populations covering the entire natural range of the species were investigated using amplified fragments length polymorphism markers to determine the genetic diversity and population genetic structure. The results indicated that this species is characterized by moderate levels of genetic polymorphism (46.4% polymorphic loci) and genetic diversity (He = 0.163), and by moderate to high levels of differentiation among the geographical populations. Principal coordinate and Bayesian assignment analysis were used to investigate the genetic structure of this species. No genetically distinct groups among the individuals were detected. The results provided new genetic information and have wide implications for genetic assessment, fishery management and conservation of the rock carp.     

Genetic diversity and population structure of the Asian green mussel Perna viridis in South China Sea based on microsatellite markers

The green mussel, Perna viridis is ecologically and economically important in the coastal region of the South China Sea. Determining its population genetic structure at this fine geographic scale will help sustainable management of natural stocks. In this study, we examined the genetic diversity and population genetic structure of P. viridis from four locations in the South China Sea (n = 45–48) using nine microsatellite loci. The results showed moderate levels of genetic diversity in all four samples (mean A = 13.222–14.000, mean A_e = 7.092–7.571, mean A_r = 12.894–13.746, mean H_o = 0.596–0.656, mean H_e = 0.690–0.733) and a large effective population size estimate for the pooled sample (total N_e estimates = infinity, 95% CI = 1869.0-infinity). We did not detect any sign of recent bottleneck events in P. viridis populations in the South China Sea. The conventional and a model-based analysis reveal low, non-significant genetic divergence among the four samples (F_ST = − 0.001–0.005, P > 0.05/6). The results obtained from this study can provide valuable genetic information for the conservation and fishery management of P. viridis by retaining the high N_e estimates.     

Genetic diversity and population structure of Opisthopappus longilobus and Opisthopappus taihangensis (Asteraceae) in China determined using sequence related amplified polymorphism markers

The genetic diversity and structure of four Opisthopappus longilobus and nine Opisthopappus taihangensis populations from Mts. Taihang were analyzed using SRAP markers. The results showed that O. longilobus (PPB = 95.16%, H = 0.349, I = 0.517) and O. taihangensis populations (PPB = 94.58%, H = 0.332, I = 0.504) had high genetic diversity. The genetic diversity within populations varied according to two species. Low genetic differentiation was detected among O. longilobus (Φ_ST = 0.105) and O. taihangensis (Φ_ST = 0.188) populations, respectively. Significantly genetic variation was found between O. longilobus and O. taihangensis (Φ_ST = 0.232). The dendrogram generated from pairwise genetic distance among all populations showed two distinct clusters, each corresponding to one species. A Mantel test revealed insignificant positive correlation between genetic distances and geographic distances (r_{O. longilobus} = 0.3021; r_{O. taihangensis} = 0.3658; P > 0.05). Those results indicated that self-compatibility, effective gene flow, biological traits, and historical factors may be the main factors causing geographical differentiation in the structure of O. longilobus and O. taihangensis populations.     

Low genetic diversity and significant structuring in the endangered Mentha cervina populations and its implications for conservation

Eighteen populations of the endangered aromatic and medicinal plant Mentha cervina (Lamiaceae) were sampled across its natural range, in the western half of the Iberian Peninsula, and inter-simple sequence repeats (ISSRs) markers were used to assess genetic diversity and population structure. M. cervina populations exhibited a relatively low genetic diversity (percentage of polymorphic loci PPB = 14.2–58.3%, Nei's genetic diversity H_e = 0.135–0.205, Shannon's information index I = 0.08 − 0.33). However, the genetic diversity at species level was relatively high (PPB = 98.3%; H_e = 0.325; I = 0.23). The results of the analysis of molecular variance indicated very structured populations, with 50% of the variance within populations, 44% among populations and 6% between regions defined by hydrographic basins, in line with the gene differentiation coefficient (G_ST = 0.532). A Mantel test did not find significant correlation between genetic and geographic distance matrices (r = 0.064), indicating that isolation by distance is not shaping the present genetic structure. The levels and patterns of genetic diversity in M. cervina populations were assumed to result largely from a combination of evolutionary history and its unique biological traits, such as breeding system, low capacity of dispersion, small effective size and habitat fragmentation. The high genetic differentiation among populations indicates the necessity of conserving the maximum possible number of populations. The results also provide information to select sites for ex situ conservation. Optimal harvesting strategies, cultivation and tissue culture should also be developed as soon as possible to guarantee sustainable use of the species under study.     

Genetic diversity and structure of the epiphytic foliose lichen Lobaria pindarensis in the Himalayas depends on elevation

The epiphytic lichen Lobaria pindarensis is a Himalayan endemic species with little information on distribution, genetic diversity and structural complexity. During an intensive survey in the Nepal Himalayas, we collected 1256 thallus fragments from 45 phorophyte species to study their distribution and population genetics along an elevational gradient. We quantified genetic diversity and population structure of each symbiont at 17 fungus specific and 9 alga specific microsatellite loci. The Bayesian clustering identified three and two distinct gene pools for mycobiont and photobiont. We found that genetic diversity, allelic richness and gene pool composition and distribution were significantly influenced by elevation. We discovered both clonally and sexually reproduced repeated genotypes of the symbionts.     

中国首次发现黑脸琵鹭的繁殖地

1999年6月15日在中国黄海北部辽宁省大连市长海县石城乡一个无人居住的岛屿上,首次发现了3对黑脸琵鹭的繁殖个体(在观察时还见到另外3只黑脸琵鹭)。该岛屿位于石城乡东侧,北纬39°31′,东经123°02′,面积约025km2,海拔高46m。鸟的群落结构主要以黑尾鸥数量最多,约有800只左右,其次为黄嘴白鹭约400只左右,还有少量的银鸥、海鸥等在岛上繁殖。     

Genetic diversity and population structure of Buddleja crispa Bentham in the Himalaya-Hengduan Mountains region revealed by AFLP

Buddleja crispa Benth. is one of the most morphologically variable species in genus Buddleja, and it is widely distributed in the Himalaya-Hengduan Mountains (HHM) region. This study used AFLPs as a tool to examine the genetic variation among and within 25 populations of B. crispa. Analysis of population genetics of the species aimed to clarify morphological variation, current distribution patterns, strong adaptability to habitats, and the effects of geological factors in the HHM region. The genetic structure results, based on PCoA and NJ cluster analyses, revealed that the populations of B. crispa were divided into two genetic groups. Furthermore, the peripheral populations had lower genetic diversity than the populations in the center of the distribution areas (Three Parallel Rivers). We conclude that the gene flow (predominantly seed and pollen flow) and the population differentiation of B. crispa might be more affected by the barriers formed by rivers and mountains than by geographic distance.     

Genetic diversity and population structure of Leptosphaeria maculans isolates in Western Canada

Leptosphaeria maculans is a serious concern for canola production worldwide. For effective disease management, knowledge of the pathogen's genetic variability and population structure is a prerequisite. In this study, whole-genome sequencing was performed for 162 of 1590 L. maculans isolates collected in the years 2007–2008 and 2012–2014 in Western Canada. DNA variants in genome-wide and specific regions including avirulence (Avr) genes were characterized. A total of 31,870 high-quality polymorphic DNA variants were used to study L. maculans genetic diversity and population structure. Cluster analysis showed that 150 isolates were clustered into 2 main groups and 4 subgroups by DNA variants located in either Avr or small secreted protein-encoding genes and into 2 main groups and 6 subgroups by genome-wide variants. The analysis of nucleotide diversity and differentiation also confirmed genetic variation within a population and among populations. Principal component analysis with genome-wide variants showed that the isolates collected in 2012–2014 were more genetically diverse than those collected in 2007–2008. Population structure analysis discovered three distinct sub-populations. Although isolates from Saskatchewan and Alberta were of similar genetic composition, Manitoba isolates were highly diverse. Genome-wide association study detected DNA variants in genes AvrLm4-7, Lema_T86300, and Lema_T86310 associated with the years of collection.     

Assessment of genetic diversity and population structure of Bergenia stracheyi (Saxifragaceae) in the Western Himalaya (India)

Genetic diversity and population structure in Bergenia stracheyi, a threatened medicinal herb in the Western Himalaya of India was analysed using directed amplification of minisatellite DNA (DAMD) and inter simple sequence repeats (ISSR) markers. A total of 41 accessions of B. stracheyi representing three populations (Khillenmarg –KLM, Jalori Pass-JLP and Rohtang-RTG) were considered in the present study. The cumulative data analysis for 26 (10 DAMD + 16 ISSR) markers revealed 87.1% polymorphism. The maximum inter-population genetic distance was found between KLM and JLP, whereas the minimum genetic distance was found between RTG and JLP populations. The analysis of molecular variance (AMOVA) revealed maximum percentage of variation among individuals within populations (75%) than among the populations (25%). Clustering pattern of the three sample populations in STRUCTURE and PCoA analyses showed high genetic variation at population level. The present study revealed that distribution patterns, high altitudinal ranges, high habitat specificity, relatively high gene flow, small and isolated population size have shaped the current population structure of B. stracheyi in the Western Himalayan region. DAMD and ISSR markers have provided significant insights into characterization of B. stracheyi populations, and facilitate selection of appropriate accessions for further utilization in conservation and bioprospecting programmes.     

Genetic diversity and population structure analysis of Qinghai-Tibetan plateau schizothoracine fish (Gymnocypris dobula) based on mtDNA D-loop sequences

Gymnocypris dobula is a commercially important fishery species and mostly distributed in the freshwater of Tibetan plateau. In this study, genetic diversity and intraspecific population differentiation were examined by using mitochondrial DNA D-loop sequences in 97 individuals sampled from three localities (Pali, Lasa and Yanghu) in the Tibetan plateau. Two hundred and fourteen polymorphic sites and 50 haplotypes were defined among the three localities. Genetic diversity analysis showed that the highest genetic diversity level was found in Pali population. Phylogenetic relationships analysis results indicated that closer phylogenetic relationships were found between the Yanghu and Lasa populations. Genetic population differentiation analysis indicated that the majority of variation (84.91%) was attributed to variations among populations and the largest differentiation was found between Pali and Lasa localities (F_st = 0.874, Nm = 0.036). Moreover, the historical demographic events were assessed by implementing the mismatch distribution analysis, Fajima's D test and Fu's Fs test. The results indicated that the Pali population had undergone a demographic expansion, possibly within the last 0.163 MYA (Million Years Ago). Our study firstly identified the population genetic structure of the G. dobula, which could be helpful for artificial breeding, fishery stock identification and resource conservation for this species.     

黑龙江省张广才岭北部小飞鼠的遗传多样性与种群历史动态

小飞鼠 (Pteromys volans) 为树栖夜行滑行类啮齿动物,在森林种子传播和维持生态系统平衡等方面发挥着重要的生态学作用。本研究利用mtDNA Cytb、控制区和nDNA微卫星3种分子标记,对黑龙江省张广才岭北部的小飞鼠种群进行遗传多样性与历史动态分析。检测出Cytb全序列 (1 140 bp) 的平均单倍型多样性为0.909,平均核苷酸多样性为0.616%;控制区全序列 (1 066 bp) 的平均单倍型多样性为0.945,平均核苷酸多样性为1.698%;微卫星检测出种群平均等位基因数13.167个,观测杂合度0.727,期望杂合度0.864,近交系数0.159。结果表明,小飞鼠种群遗传多样性丰富,但存在一定程度的杂合度不足和近亲繁殖;未检测到种群近期遗传瓶颈效应,种群内无遗传分化。高比例的稀有单倍型 (≥ 60%) 、低频率等位基因与近亲繁殖,提示未来种群面临遗传多样性下降的风险,建议加大对该物种的关注和保护力度。基于Cyt b基因的系统进化关系结果表明,小飞鼠存在3个明显的遗传谱系：远东、欧亚大陆北部和日本北海道,本研究中张广才岭和大兴安岭的样本单倍型归属为远东谱系。     

Genetic diversity and population structure of the endangered medicinal plant Phellodendron amurense in China revealed by SSR markers

Phellodendron amurense is an endangered tree with important medicinal and economic value in China. In this study, eight nuclear SSR primer pairs were employed to assess the genetic diversity and structure of 22 natural populations, including 516 individuals. A total of 66 alleles were detected with an average of 8.3 alleles per locus ranging from 3 to 17. The expected heterozygosity (He) of each SSR locus varied from 0.347 to 0.877 (average 0.627). Analysis of molecular variance (AMOVA) revealed that the main variation component existed within populations (95.11%) rather than among populations (4.89%). The Wilcoxon's sign-rank tests did not show any recent bottleneck effect in any population. A Mantel test displayed a significant correlation between the geographic distances and genetic distances for all populations (r = 0.566, P = 0.0001), indicating conformity to the isolation by distance model. Bayesian clustering and UPGMA supported grouping the populations into two groups. The present genetic structure of P. amurense may be explained by geographical isolation. The lack of genetic structure and genetic diversity decreased with increasing latitude within the Northeast China group may be due to postglacial northward expansion from a single refugium. Proper conservation measures are proposed for this species.     

Genetic variation and population structure in Korean endemic species: III.Hosta minor (Liliaceae)

Hosta minor, an insect-pollinated and rhizomatous herbaceous perennial, occurs in eastern and southern Korean Peninsula. AlthoughH. minor is a Korean endemic species and most populations of the species are scattered, the species maintains considerably high levels of genetic variation within the species, with a moderate level of variation (14%) found among populations. Nineteen of the 29 putative loci resolved (66%) were polymorphic within the species, the mean number of alleles per locus was 2.10 across all populations and averaged 1.68 within populations. In addition, genetic diversity was a considerably higher (for species and population level, mean estimates of genetic diversity were 0.275 and 0.230, respectively) than the average for other long-lived herbaceous perennials. Indirect estimate of the number of migrants per generation (Nm=1.03, calculated from mean G_ST) was moderate. Factors contributing to the high levels of genetic diversity found within populations ofH. minor include population maintenance via sexual and asexual modes of reproduction, primarily outcrossing breeding system, long generation time, probable ancient polyploid origin of the species, and moderate levels of seed dispersal by wind. Human disturbance in South Korea such as road and apartment constructions appears to be the major threat to this genetically diverse species.     

圈养小熊猫遗传多样性与种群遗传结构分析

小熊猫是亚洲特有的珍稀濒危动物,目前受到栖息地减少、片断化和人类活动干扰等威胁。中国圈养小熊猫已经有60 多年历史,约55 个机构曾经饲养过小熊猫,现今圈养数量有400 多只,评估小熊猫圈养种群的遗传多样性和遗传结构对科学维持圈养种群和保存遗传种质资源意义重大。本研究利用19 个微卫星座位,对中国境内11 个小熊猫圈养种群的116 只个体进行了遗传多样性评估及遗传结构分析。结果显示11 个种群都具有较高的遗传多样性,平均基因丰富度3.505 ± 1.033 (北京)至4.026 ± 1.219 (冕宁),期望杂合度0.631 ± 0.225(黄山)至0.782 ±0.171 (温岭)。其中福州和无锡种群极显著偏离Hardy-Weinberg 平衡。整个圈养群体内各个种群遗传分化系数为0.055,呈显著分化,表明11 个种群遗传分化水平较高。Bayesian 遗传聚类分析将11 个种群聚为三个遗传簇,与野生种群的遗传聚类结果一致。结论:小熊猫圈养种群与野生种群相比,同样具有较高的遗传多样性。因此,圈养小熊猫遗传管理的重点不再是引进野生个体充实圈养种群,应制订科学的繁殖计划,避免近交,从而维持圈养种群的遗传多样性。