Genetic diversity and structure of Cordyceps sinensis populations from extensive geographical regions in China as revealed by inter-simple sequence repeat markers

Cordyceps sinensis is one of the most valuable medicinal caterpillar fungi native to China. However, its productivity is extremely limited and the species is becoming endangered. The genetic diversity of eighteen C. sinensis populations across its major distributing regions in China was evaluated by inter-simple sequence repeat (ISSR) markers. A total of 141 markers were produced in 180 individuals from the 18 populations, of which 99.3% were polymorphic. The low average of Shannon (0.104) and Nei index (0.07) of the 18 populations indicates that there are little genetic variations within populations. For all 18 populations, estimates of total gene diversity (H_T), gene diversity within populations (H_S), coefficient of genetic differentiation (G_ST), and gene flow (Nm) were 0.170, 0.071, 0.583, and 0.357, respectively. This pattern suggests that the genetic diversity of C. sinensis is low and most of the ISSR variations are found among populations with little gene exchange. The 18 populations are divided into five groups based on the genetic distance and the grouping pattern matches with the geographic distribution along the latitudinal gradient. The five groups show obvious difference in the G_ST and Nm values. Therefore, the genetic diversification of C. sinensis populations may be determined by geographic isolation and the combined effects of life history characters and the interaction with host insect species. The information illustrated by this study is useful for selecting in situ conservation sites of C. sinensis.     

ISSR variation in the endemic and endangered plant Cycas guizhouensis (Cycadaceae)

BACKGROUND AND AIMS: Cycas guizhouensis (Cycadaceae) is a rare and endangered species endemic to the southwest of China. An investigation was undertaken into the genetic variation of wild populations. METHODS: ISSR markers were used to determine the genetic variation within and between 12 extant populations of this species. KEY RESULTS: Low genetic diversity (at population level, P = 14.21 %, H(E) = 0.0597; at species level, P = 35.90 %, H(T) = 0.1082) and a high degree of differentiation among populations (G(ST) = 0.4321) were detected. CONCLUSIONS: This genetic structure is considered to be due to the combined effects of slow biochemical evolution, genetic drift, inbreeding and limited gene flow between populations. Based on these findings, strategies are proposed for the genetic conservation and management of the species.     

Phylogeographic analysis of Anatolian bats highlights the importance of the region for preserving the Chiropteran mitochondrial genetic diversity in the Western Palaearctic

Identification of intraspecific conservation units and incorporating the distribution of genetic diversity into management plans are crucial requirements for assessing effective protection strategies. This study investigates the phylogeographic structures of 33 bat species present in the Near East in order to evaluate the conservation implications of their intraspecific genetic diversity both at regional and large-scale levels. To compare Anatolian populations with the European ones, we utilized two commonly used mitochondrial markers, Cytb and ND1, and analysed them together with the available sequences from GenBank. The management requirements of the identified clades and their taxonomical relations were evaluated by analysing their distributions and the levels of their genetic differentiations. In 12 species and the large Myotis complex, we identified a total of 15 genetically distinct populations found in the Near East, some of which might represent biologically distinct taxa. Comparing the phylogeographic patterns of different taxa indicates that three regions, the Balkans, the Caucasus, and the southern Anatolia, harbour genetically divergent populations and should have higher priority in conservation practices. Considering that Turkey has one of the richest bat fauna in the Mediterranean region and the Anatolian populations of various species are genetically distinct, protecting populations in Turkey is critically important for preserving the genetic diversity of the bats in the Western Palaearctic. Both regional and large-scale conservation strategies, which incorporate the distribution of genetic diversity, should be assessed and further ecological studies are needed to clarify the taxonomic relations of the identified clades.     

武夷山地伯乐树种群遗传多样性的ISSR分析

伯乐树（Bretschneidera sinensis Hemsl.）为我国特有单型科珍稀濒危植物,具重要的科研价值。本研究采用ISSR分子标记对武夷山脉分布的5个伯乐树天然种群和1个移栽种群进行遗传多样性分析。结果表明伯乐树物种水平遗传多样性较高（PPB：75.70%;H_ES：0.304 5;H：0.450 1）,种群水平则较低（PPB：60.13%;H_EP：0.238 1;H：0.347 5）,MJY种群和BSZ种群分别是所有种群中遗传多样性最高和最低的。5个地理种群间遗传分化程度较高（G_st=0.218 1）,原因可能源于伯乐树的繁殖方式及生境片段化,Mantel检验也证实了地理距离与遗传距离具有显著相关性（r=0.626 7,P＜0.05）。针对伯乐树种群遗传多样性现状,建议加强现有自然种群的就地保护,促进种群自然更新。     

滇牡丹遗传多样性的ISSR分析

应用ISSR标记对中国西南地区特有植物滇牡丹(Paeonia delavayi)的遗传多样性进行了研究。从100个引物中筛选出10个用于正式扩增,在取自16个自然居群和1个迁地保护居群的511个个体中,检测到92个多态位点。在居群水平上,多态位点百分率（PPB）为44.61%,Nei′s基因多样性指数（H）和Shannon信息指数（I）分别为0.1657和0.2448。在物种水平上,多态位点百分率（PPB）为79.31%,Nei′s基因多样性指数（H）和Shannon信息指数（I）分别为0.2947和0.4355。居群间的遗传分化系数(G_ST)达0.4349。结果表明：滇牡丹遗传多样性水平较高,居群间遗传分化较大。结合以前的研究结果,对滇牡丹的现状进行评估的结果显示,滇牡丹并不濒危。     

中日5个岛屿山茶种群遗传多样性研究

运用ISSR分子标记法对中、日两国5个岛屿天然山茶种群共150个个体进行遗传多样性分析。结果表明:筛选出的20条引物扩增得到205条清晰条带,其中183条为多态性条带,多态位点百分比(PPB)为89.27%。经POPGENE软件分析,山茶种群平均多态位点百分比(PPB)为72.00%,Nei’s基因多样性指数(HE)为0.2743,Shannon信息多态性指数(H)为0.4023,种群水平遗传多样性较高。基因分化系数Gst=0.2033,表明遗传变异主要存在于种群内个体间。Mantel检验(r=0.7989,P<0.05)和UPGMA聚类表明岛屿地理隔离对山茶种群遗传分化具有重要影响。基于岛屿山茶种群遗传结构的分析,建议加强我国岛屿自然种群的就地保护力度。     

DNA marker technology for wildlife conservation

Use of molecular markers for identification of protected species offers a greater promise in the field of conservation biology. The information on genetic diversity of wildlife is necessary to ascertain the genetically deteriorated populations so that better management plans can be established for their conservation. Accurate classification of these threatened species allows understanding of the species biology and identification of distinct populations that should be managed with utmost care. Molecular markers are versatile tools for identification of populations with genetic crisis by comparing genetic diversities that in turn helps to resolve taxonomic uncertainties and to establish management units within species. The genetic marker analysis also provides sensitive and useful tools for prevention of illegal hunting and poaching and for more effective implementation of the laws for protection of the endangered species. This review summarizes various tools of DNA markers technology for application in molecular diversity analysis with special emphasis on wildlife conservation.     

Genetic characterization of a newly discovered Finnish Arctic charr (Salvelinus alpinus; Salmoniformes) population: Stocked or natural?

Like many salmonid species, Arctic charr (Salvelinus alpinus) is currently threatened by human-induced perturbations. From a conservation perspective, it is important to characterize the genetic diversity of populations so that genetically distinct units worthy of conservation effort can be identified. Here, we used microsatellite markers to assess whether a recently discovered Finnish population of lacustrine charr found in Lake Karhunpesälampi is of natural origin. We also aimed to reveal the colonization history of this lake. To this end, we quantified genetic diversity and distance of this population to other charr populations inhabiting Fennoscandia including all sources used in official Finnish stocking programs. The population was found to be genetically differentiated from all other populations analysed. This, together with the remote location of the lake and other population genetic information, indicates that the population is likely of natural origin. The population deserves to be acknowledged as a genetically distinct unit worthy of conservation.     

Inter-simple sequence repeat (ISSR) diversity within Monarda fistulosa var. brevis (Lamiaceae) and divergence between var. brevis and var. fistulosa in West Virginia

Inter-simple sequence repeat (ISSR) banding patterns were used to examine genetic diversity within and among populations ofMonarda fistulosa var.brevis, a rare taxon restricted to several populations in limestone glades and barrens in eastern West Virginia and Virginia. More than 34% of the total ISSR diversity in var.brevis occurred among populations, which is high when compared to the few other rare species that have been examined for ISSR variation. Prior studies demonstrated that var.brevis is morphologically distinct from the more widespread var.fistulosa, and that the differences are maintained when the two varieties are grown together in a uniform environment. The present study utilizing ISSR markers indicated that the two varieties are distinct, though quite similar genetically, and this is concordant with prior investigations documenting their morphological and habitat differences. However, the ISSR results suggest that the two varieties have diverged relatively recently and/or there is a low level of gene flow between them.     

Conservation Genetics of Jacquemontia reclinata (Convolvulaceae), an Endangered Species from Southern Florida: Implications for Restoration Management

Guidelines designed to aid in the restoration of rare species have been previously proposed using two primary strategies to select individuals for augmentation and reintroduction: mixing progeny from different populations or separating individuals from different populations. Understanding the genetic structure and diversity of an endangered species can offer insights into conservation management strategies. We used random amplified polymorphic DNA markers to assess the genetic structure and diversity of Jacquemontia reclinata , a federally endangered species endemic to Southeastern Florida. We sampled 20 percent of total number of individuals from eight of the ten known wild populations. Across individuals high levels of polymorphic loci (94.7%) were found and larger populations had greater genetic diversity. Cluster and ordination analyses found that one population was genetically differentiated from all the others; this population grows in a unique habitat. Most genetic variation (77.5%) was found within populations, and genetic distances between populations were not explained by their geographic distances. We recommend the use of two management units in restoration programs for J. reclinata , one consisting of the genetically differentiated population and the second consisting of the other seven populations sampled.     

Genetic diversity and population structure in the Brazilian Cattleya labiata (Orchidaceae) using RAPD and ISSR markers

Brazilian orchids are currently threatened with extinction due to habitat loss and, because of their high ornamental value, intense collecting pressure. Genetic diversity can play a key role in the survival of endangered orchid species. Here we provide the first data on genetic diversity and structure of wild populations in the genus Cattleya, in particular C.?labiata, using random amplified polymorphic DNA (RAPD) and intersimple sequence repeat (ISSR) markers. We studied 130 individuals, 117 belonging to Cattleya?labiata and 13 from 10 other species in the same genus. Data generated from 12 ISSR and 12 RAPD primers were used to determine genetic variability via a model-based Bayesian procedure (Structure) and molecular variance analysis. In addition, Shannon index, genetic diversity and Jaccard coefficients were also estimated. The marker data indicated that C. labiata has a high level of polymorphism, and five reconstructed populations were identified by Structure. The unweighted pair group method with arithmetic mean dendrogram did not group the samples by origin, which was also confirmed by Bayesian analysis, demonstrating the complex genetic structure of C.?labiata. Other Cattleya species showed no relationship with any C.?labiata sample. This genetic characterization of Cattleya from northeast Brazil contributes to knowledge of the genetic structure of the species and can be used to define strategies for conservation and breeding programmes.     

Inter-Simple Sequence Repeat Data Reveals High Genetic Diversity in Wild Populations of the Narrowly Distributed Endemic Lilium regale in the Minjiang River Valley of China

Lilium regale E.H. Wilson is endemic to a narrow geographic area in the Minjiang River valley in southwestern China, and is considered an important germplasm for breeding commercially valuable lily varieties, due to its vigorous growth, resistance to diseases and tolerance for low moisture. We analyzed the genetic diversity of eight populations of L. regale sampled across the entire natural distribution range of the species using Inter-Simple Sequence Repeat markers. The genetic diversity (expected heterozygosity= 0.3356) was higher than those reported for other narrowly distributed endemic plants. The levels of inbreeding (F _st = 0.1897) were low, and most of the genetic variability was found to be within (80.91%) than amongpopulations (19.09%). An indirect estimate of historical levels of gene flow (N _m =1.0678) indicated high levels of gene flow among populations. The eight analyzed populations clustered into three genetically distinct groups. Based on these results, we recommend conservation of large populations representing these three genetically distinct groups.     

Can physiographic regions substitute for genetically-determined conservation units? A case study with the threatened plant, <Emphasis Type="Italic">Silene spaldingii</Emphasis>

Protecting genetic diversity throughout the range of a species is important for conservation, as doing so provides for long-term evolutionary potential and persistence under a changing environment. Conservation of diversity at the intraspecific level requires identification of all genetically distinct population segments within species; i.e., conservation units (CUs). Silene spaldingii occurs in grasslands of the Columbia Plateau region of western North America and is listed as threatened under the Federal Endangered Species Act. The recovery plan identified five physiographic regions across the range of the species to use as surrogates for genetic CUs. We collected leaf samples from an average of 26 plants from each of 19 of the largest populations across all five physiographic regions and used variable microsatellite and chloroplast DNA markers to determine how genetic variation is distributed across the range of the species and how well physiographic regions reflect population structure within this species. Results of several multivariate analyses clustered our samples into four genetic groups which did not correspond well with the physiographic regions. We observed little genetic differentiation among populations in the main range of the species which encompasses nearly all of four contiguous physiographic regions. However, three other distinct genetic groups were identified: two in the disjunct northeast corner and one at the southeast edge of the main range. Modification of the CUs to reflect the genetic groups rather than the physiographic regions would result in CUs which better reflect historical patterns of population structure. Moreover, use of the genetic units to inform translocation and genetic rescue efforts could improve our ability to mimic natural patterns of gene flow. Our results suggest that physiographic regions may not always be an accurate reflection of population structure for threatened or endangered species.     

MtDNA haplotypes, sequence divergence, and morphological variation in Gray-breasted Wood Wrens (Henichorina leucophrys) and their conservation implications

ABSTRACT.   To reveal more clearly the places that are critical for generating and sustaining species diversity, the distribution of genetic diversity is informative for conservation. Evolutionary significant units (ESUs) represent distinct lineages within a species and are defined by genetic and morphological differences. We examine morphometrics and mitochondrial DNA sequences of two coastal and three Andean populations of Gray-breasted Wood Wrens ( Henicorhina leucophrys ) in Ecuador to determine if any populations are ESUs. Coastal Wood Wrens diverged genetically by 2.4%, 3.5%, and 4.4% from Andean populations of the northwest (Bellavista), southwest (Sural-Caucha), and southeast (Romerillos), respectively. The five populations (34 individuals) exhibited nine haplotypes. Both genetic and ecological results indicate that coastal Wood Wrens found in the Colonche Hills are ESUs, as are the Andean populations. In contrast with temperate regions, where large reserves connected by corridors may be effective, preservation of biodiversity in tropical South America may require protection of more localized areas.     

丹霞梧桐群体遗传结构及其遗传分化

丹霞梧桐(Firmiana danxiaensis)是分布于我国韶关地区北部丹霞地貌的特有物种, 其分布范围狭窄, 种群数量小。本文利用EST-SSR分子标记位点, 分析丹霞梧桐群体(丹霞山组群和南雄组群)的遗传多样性和遗传结构, 研究群体的分化历史, 探讨该物种的可能分布和科学保护策略。结果表明: 丹霞梧桐总的遗传多样性中等(Ht = 0.631), 群体内遗传多样性较高(Hs = 0.546), 遗传变异主要存在于群体内(79.66%), 但不同地理组群间存在显著的遗传分化(F_ST = 0.150)。长期地理隔离和现代人为干扰是形成丹霞梧桐当前遗传变异模式的主要原因。STRUCTURE分析可将研究群体划分为清晰的两个基因库(gene pool), 其遗传结构与系统发育地理格局之间有密切关系。丹霞梧桐不同地理群体经历了独立的进化路线, 但丹霞山群体的杂合性高, 遗传背景更为复杂。近似贝叶斯运算法(Approximate Bayesian Computation, ABC)分析表明, 丹霞山和南雄地理群体在10万年前由同一个祖先群体分化而来, 分化时有效群体大小分别为7,290和5,550。结合丹霞梧桐的遗传变异和生态位信息, 可推测丹霞梧桐曾广泛分布于南岭地区, 受第四纪第三次亚冰期的影响, 南岭北部的丹霞梧桐群体因气候剧烈变化而灭绝, 仅在南岭南部适宜的环境中得以保存并繁衍至今, 丹霞山和南雄是丹霞梧桐最主要的两个冰期避难所。在全面掌握丹霞梧桐的自然分布, 开展就地保护的基础上, 通过建立种质资源圃、人工种苗扩繁、自然回归试验等措施, 对于该物种的异地保护、种群恢复和开发利用具有重要意义。     

中国卵叶海桑遗传多样性的ISSR研究

卵叶海桑 (Sonneratiaovata)是海桑科濒危红树植物 ,在我国仅分布于海南文昌清澜自然保护区内。采用简单序列重复区间扩增 (ISSR)分子标记技术对该天然居群和东寨港红树林自然保护区引种的人工居群共 3个居群 3 9个个体进行了遗传变异分析。 1 1个引物共扩增出 1 85条带 ,其中 1 2 7条具多态性 ,多态位点百分率为 68.65 %。在居群水平上相对较低 ,多态位点百分率 3 6.76%～ 5 4.5 9% ,平均值为 47.2 1 %。Nei的基因多样性、Shannon信息指数在物种水平上分别为 0 .1 41 1和 0 .2 2 92 ;在居群水平上平均值分别为 0 .1 2 0 9和0 .1 91 0。Nei的遗传分化系数Gst表明 :87.5 8%遗传变异分布在居群内 ,1 2 .42 %的遗传变异分布在居群间。居群间的遗传一致度达 0 .970 7。东寨港迁地保护的人工居群有效地保护了卵叶海桑的遗传多样性。     

濒危植物蒙古扁桃不同地理种群遗传多样性的ISSR分析

采用 ISSR 分子标记对蒙古扁桃(Prunus mongolica)6个自然种群的遗传多样性进行了分析.12条ISSR引物共扩增出200条带,其中199条具多态性,多态位点比率为99.5％.在种群水平上多态位点百分率平均为55.3％.Nei's基因多样性、Shannon's信息指数在种群水平上分别为0.3241和0.4875,在物种水平上分别为0.3105和0.4722.根据基因分化系数,测得基因流值Nm为0.8266.UPGMA聚类分析结果表明:乌海千里沟种群和东升庙那仁乌拉种群遗传一致度最大,遗传关系最近.ISSR检测结果表明,包头萨拉齐种群的遗传多样性最丰富,在制定原位种质保护计划时,应优先保护包头萨拉齐周边地区的蒙古扁桃.     

Genetic diversity of the endangered Chinese endemic herb Primulina tabacum (Gesneriaceae) revealed by amplified fragment length polymorphism (AFLP)

Primulina tabacum Hance, is a critically endangered perennial endemic to limestone area in South China. Genetic variability within and among four extant populations of this species was assessed using AFLP markers. We expected a low genetic diversity level of this narrowly distributed species, but our results revealed that a high level of genetic diversity remains, both at population level (55.5% of markers polymorphic, H _E = 0.220, I _S = 0.321), and at species level (P = 85.6% of markers polymorphic, H _E = 0.339, I _S = 0.495), probably resulting from its refugial history and/or breeding system. High levels of genetic differentiation among populations was apparent based on Nei’s genetic diversity analysis (G _st=0.350). The restricted gene flow between populations is a potential reason for the high genetic differentiation. The population genetic diversity of P. tabacum revealed here has clear implications for conservation and management. To maintain present levels of genetic diversity, in situ conservation of all populations is necessary.     

Low genetic diversity and high genetic differentiation in the critically endangered Omphalogramma souliei (Primulaceae): implications for its conservation

Omphalogramma souliei Franch. is an endangered perennial herb only distributed in alpine areas of SW China. ISSR markers were applied to determine the genetic variation and genetic structure of 60 individuals of three populations of O. souliei in NW Yunnan, China. The genetic diversity at the species level is low with P=42.5% (percentage of polymorphic bands) and Hsp=0.1762 (total genetic diversity). However, a high level of genetic differentiation among populations was detected based on different measures (Nei's genetic diversity analysis: Gst=0.6038; AMOVA analysis: Fst=0.6797). Low level of genetic diversity within populations and significant genetic differentiation among populations might be due to the mixed mating system in which xenogamy predominated and autogamy played an assistant role in O. souliei. The genetic drift due to small population size and limited current gene flow also resulted in significant genetic differentiation. The assessment of genetic variation and differentiation of the endangered species provides important information for conservation on a genetic basis. Conservation strategies for this rare endemic species are proposed.     

Two genetically distinct units of Sinomanglietia glauca (Magnoliaceae) detected by chloroplast PCR-SSCP

Sinomanglietia glauca is a critically endangered species described from Jiangxi Province in the 1990s. Recently two populations were discovered from Yongshun County of west Hunan Province, about 450 km away from those in Jiangxi. Because of the new findings and the poor reproducibility inherent to RAPD and ISSR markers of previous studies, the population structure of this rare species was reanalyzed with chloroplast PCR-SSCP (single-stranded conformation polymorphism), including all of four recorded populations. The results showed that two distinct haplotypes characterized Jiangxi and Hunan populations separately, with no genetic variation occurring within regions. We postulated that this surprising pattern might result from habitat fragmenta-tion and demographic bottlenecks during and/or after the Quaternary glaciation. On the basis of the pronounced genetic structure, two evolutionarily significant units (ESUs) were recommended for effective conservation of S. glauca.