Genetic relatedness and population differentiation of Himalayan hulless barley (Hordeum vulgare L.) landraces inferred with SSRs

A set of 107 hulless barley (Hordeum vulgare L. subsp. vulgare) landraces originally collected from the highlands of Nepal along the Annapurna and Manaslu Himalaya range were studied for genetic relatedness and population differentiation using simple sequence repeats (SSRs). The 44 genome covering barley SSRs applied in this study revealed a high level of genetic diversity among the landraces (diversity index, DI = 0.536) tested. The genetic similarity (GS) based UPGMA clustering and Bayesian Model-based (MB) structure analysis revealed a complex genetic structure of the landraces. Eight genetically distinct populations were identified, of which seven were further studied for diversity and differentiation. The genetic diversity estimated for all and each population separately revealed a hot spot of genetic diversity at Pisang (DI = 0.559). The populations are fairly differentiated (θ = 0.433, R _ST = 0.445) accounting for > 40% of the genetic variation among the populations. The pairwise population differentiation test confirmed that many of the geographic populations significantly differ from each other but that the differentiation is independent of the geographic distance (r = 0.224, P > 0.05). The high level of genetic diversity and complex population structure detected in Himalayan hulless barley landraces and the relevance of the findings are discussed.     

基于SSR分子标记的延胡索遗传多样性研究

采用SSR分子标记分析延胡索的遗传多样性,筛选出多态性高、稳定性好的12对引物,对19个居群360份延胡索样品进行了群体遗传分析。结果表明:(1)12对SSR引物共扩增出多态性位点227个,检测到4~9个等位基因,平均等位基因数目为5.25个,表现出丰富的多态性;延胡索居群具有较高的遗传多样性(Na=5.25,I=1.192 6,H=0.387 9),物种间遗传分化程度高(Fst=0.388 3),基因流较弱(Nm=0.393 8)。(2)UPGMA聚类分析和贝叶斯距离分析结果表明,19个居群明显聚为4大支;Mantle Test结果(r=0.326,P=0.01)表明,地理位置相近的种群亲缘关系更近。研究认为,延胡索的遗传结构是该物种自交为主的繁育系统、克隆生长、地理隔离以及居群间有限的基因流共同作用的结果,故对该物种的保护应以就地保护为主。     

Genetic diversity of insular natural populations of <Emphasis Type="Italic">Festuca pratensis</Emphasis> Huds.: RAPD analysis

In natural populations of Festuca pratensis Huds. from the islands of Onega Lake, the level of genetic diversity was evaluated. In three populations variability of 64 RAPD loci was tested. The level of genetic diversity (P _95% = 30.2; H _exp = 0.093) was low for a cross-pollinating plant species. Furthermore, genetic similarity between the plants from insular populations was found to be high (I _N = 0.887). It was demonstrated that genetic variation among the population accounted for at most 5.3% of total genetic diversity, which, however, was higher than the F _ST values for continental populations (F _ST = 0.022). It was suggested that specific features of the genetic structure of insular population, i.e., low gene diversity within the populations along with high differentiation among the populations, were caused by the gene flow attenuation, as a result of isolation, and intensification of inbreeding. These features had negative effect on total population adaptation.     

Differential effects of historical migration,glaciations and human impact on the genetic structure and diversity of the mountain pasture weed Veratrum album L.

Aim Today’s genetic population structure and diversity of species can be understood as the result of range expansion from the area of origin, past climatic oscillations and contemporary processes. We examined the relative importance of these factors in Veratrum album L., a toxic weed of mountain grasslands. Location Continental Europe. Methods Forty populations from the Asian border (Urals and Caucasus) to Portugal were studied using amplified fragment length polymorphisms (AFLPs) combined with selected plant and population measures. The data were analysed with phylogenetic, population genetic and regression methods inferring both genetic structure and diversity from geographic and ecological factors. Results Fragment frequency clines together with genetic distance clustering and principal coordinates analysis indicated an east–west direction in the genetic structure of V. album, suggesting ancient migration into Europe from a proposed Asian origin. However, the strong geographic pattern in the genetic structure, pronounced isolation by distance (R² = 0.74) and moderate overall population differentiation (F_ST = 0.13) suggests high historical gene flow, possibly during glacials, and vicariance into mountainous regions during interglacials. Occurrence of V. album during the last glaciation in several areas along the periphery of the Alps and recolonization of this mountain range from both eastern and central–western areas was indicated. Genetic diversity was highest in central Europe, a pattern that did not agree with the expectations from east–west migration into Europe. Furthermore, managed habitats showed higher levels of genetic diversity compared to unmanaged habitats. Stepwise linear regression determined shoot density and soil phosphorus as the main predictors of within‐population genetic diversity (R² = 0.40). Main conclusions Our results showed that V. album retained genetic imprints of historical range expansion into Europe, although this was alleviated by the influence of climatic oscillations and contemporary processes. For example, genetic population structure was strongly affected by post‐glacial vicariance while patterns of genetic diversity seemed mainly to be influenced by human land use. Our findings highlight the importance of applying a synthetic approach, testing the influence of both historical and contemporary processes on genetic structure and diversity in order to understand complex phylogeographic patterns. This may especially apply to widespread species, such as weeds. Implications of our findings for biological control are briefly discussed.     

RAPD–PCR Analysis of Genetic Diversity in the Manchurian Pheasant

The genetic diversity of a local population of the Manchurian pheasant Phasianus colchicus pallasi was studied using RAPD–PCR. Based on the DNA patterns obtained in PCR with five arbitrary decanucleotide primers, we assessed genetic polymorphism of this population, estimated genetic distances between individuals, and constructed an NJ phylogenetic tree, and an UPGMA dendrogram of genetic similarity. The population was shown to exhibit high average genetic polymorphism (P = 79.4%) and genetic distances (D = 0.267). Possible reasons for the high genetic diversity of this local population are discussed.     

The mango seed weevil Sternochetus mangiferae (Fabricius) (Coleoptera: Curculionidae) is characterized by low genetic diversity and lack of genetic structure

1. The mango seed weevil Sternochetus mangiferae (Fabricius) is distributed across the major mango-producing areas of the world and causes significant economic losses of mango fruit. Despite its importance as a crop pest, we have only limited information on the population genetics of the mango seed weevil.
2. Here, we examined the genetic diversity of this important pest using specimens intercepted by Beijing Customs District P. R. in China from 41 countries and regions. We used segments of the mitochondrial gene cytochrome c oxidase subunit I and the nuclear gene elongation factor 1-alpha to examine population genetic structure in this species.
3. Our results showed that genetic diversity is low in S. mangiferae, with a mean genetic distance of 0.095–0.14%. Other population genetic parameters also indicated a low level of genetic diversity among samples from a large geographic range. Analysis of molecular variance revealed little population genetic structure, and mismatch distribution analyses provided evidence of a population expansion, although other demographic metrics of population expansion were nonsignificant.
4. We suggest that the observed low level of genetic diversity and population genetic structure in S. mangiferae supports the hypothesis that the population genetics of this species has been impacted by anthropogenic transportation of mangoes and weevils.

     

Development and characterization of 24 microsatellite markers in Primula tosaensis,an endangered primrose,using MiSeq

Primula tosaensis (Primulaceae) is an endangered primrose endemic to Japan. In this study, 24 novel microsatellite markers were developed using Illumina MiSeq sequencing to facilitate conservation of this endangered species. The genetic diversity and polymorphisms of these novel markers were measured in 32 individuals from a wild P. tosaensis population. The number of alleles and expected heterozygosities ranged from 2 to 5 (mean = 2.8) and from 0.119 to 0.724 (mean = 0.395), respectively. All loci were in Hardy–Weinberg equilibrium. The markers developed in this study will provide a powerful and practical tool for investigating the population structure and genetic diversity of P. tosaensis.     

Population Genetic Structure of the Yangtze Finless Porpoise (Neophocaena phocaenoides asiaeorientalis): Implications for Management and Conservation

Understanding the population genetic structure is a prerequisite for conservation of a species. The degree of genetic variability characteristic of the mitochondrial DNA control region has been widely exploited in studies of population genetic structure and can be useful in identifying meaningful population subdivisions. To estimate the genetic profile of the Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis), an endangered freshwater population endemic to China, the complete mtDNA control region was examined in 39 individuals belonging to seven different stocks inhabiting the middle and lower reaches of the Yangtze River. Very low genetic diversity was found (nucleotide diversity 0.0011± 0.0002 and haplotypic diversity 0.65± 0.05). The mtDNA genetic pattern of the Yangtze population appears to indicate a founder event in its evolutionary history and to support the marine origin for this population. Analyses by F_st and Φ_st yielded statistically significant population genetic structure (F_st = 0.44, P < 0.05; Φ_st = 0.36, P < 0.05). These results may have significant implications for the management and conservation of the Yangtze finless porpoise in the future.     

Sexual reproduction, clonal diversity and genetic differentiation in patchily distributed populations of the temperate forest herb Paris quadrifolia (Trilliaceae)

Clonal plant species have been shown to adopt different strategies to persist in heterogeneous environments by changing relative investments in sexual reproduction and clonal propagation. As a result, clonal diversity and genetic variation may be different along environmental gradients. We examined the regional and local population structure of the clonal rhizomatous forest herb Paris quadrifolia in a complex of forest fragments in Voeren (Belgium). Relationships between population size (the number of shoots), shoot density (the number of shoots per m²) and local growth conditions were investigated for 47 populations. Clonal diversity and genetic variation within and among 19 populations were investigated using amplified fragment length polymorphism markers. To assess the importance of sexual reproduction, seed set, seed weight and germination success were determined in 18 populations. As predicted, local growth conditions largely affected population distribution, size and density of P. quadrifolia. Populations occurring in moist and relatively productive sites contained significantly more shoots. Here, shoots were also much more sparsely distributed compared to populations occurring in dry and relatively unproductive sites, where shoots showed a strongly aggregated distribution pattern. Clonal diversity was relatively high, compared with other clonal species (G/N ratio = 0.43 and Simpson’s D=0.81). Clonal diversity significantly (P<0.01) decreased with increasing shoot density while molecular genetic variation was significantly (P<0.01) affected by population size and local environmental conditions. Lack of recruitment and out-competition of less-adapted genotypes may explain the decreased genetic variation in dry sites. Analysis of molecular variance revealed significant genetic variation among populations (Φ _ST=0.42, P<0.001), whereas pairwise genetic distances were not correlated to geographic distances, suggesting that gene flow among populations is limited. Finally, the number of generative shoots, the number of seeds per fruit and seed weight were significantly and positively related to population size and local growth conditions. We conclude that under stressful conditions populations of clonal forest plant species can slowly evolve into remnant populations characterized by low levels of genetic variation and limited sexual reproduction. Conservation of suitable habitat conditions is therefore a prerequisite for effective long-term conservation of clonal forest plant species.     

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.     

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.     

珍稀濒危植物太行菊遗传多样性的ISSR分析

利用ISSR分子标记技术对太行山特有濒危物种太行菊11个自然居群的遗传多样性进行研究。用10个引物对11个居群的122个样品进行扩增,共得到150个扩增位点,其中多态性位点149个,多态位点百分率(PPL)为99.33%。POPGENE分析显示,太行菊具有较高的遗传多样性(H=0.2149,I=0.3455)。沁阳市大西天居群的遗传多样性水平最高(H=0.1910,I=0.2969),山西陵川县大双村居群的遗传多样性水平最低(H=0.1356,I=0.2155)。Nei’s遗传多样性分析表明,11个自然居群间出现了较高的遗传分化(基因分化系数Gst=0.2566,基因流Nm=1.4488)。生境的的片段化和基因流障碍可能是导致太行菊居群间遗传分化显著的主要原因。通过对太行菊居群遗传多样性和遗传结构的分析,该文提出了一些保护策略。     

Genetic variation and population structure in Korean populations of eurya japonica (Theaceae)

We investigated levels of genetic diversity, population genetic structure, and gene flow in Eurya japonica, a widespread and broad-leaved evergreen dioecious tree native to Japan, China, Taiwan, and the southern and southwestern coast of the Korean Peninsula. Starch-gel electrophoresis was conducted on leaves collected from 1,000 plants in 20 Korean populations. All 12 loci examined were polymorphic in at least one population, and the mean number of alleles per locus was 3.79. In addition, mean observed population heterozygosity (Ho_p = 0.425), expected heterozygosity (He_p = 0.462), and total genetic diversity (H_T = 0.496) were substantially higher than average values for species with similar life history traits. Although significant differences in allele frequency were detected between populations at all loci (P < 0.001), <7% of the genetic variation was found among populations (F_ST = 0.069). There was a significant negative correlation between genetic identity and distance between populations (r = -0.341; P < 0.05), but this explained only a small amount of the diversity among populations. Indirect estimates of the number of migrants per generation (Nm) (3.37, calculated from F_ST; 3.74, calculated from the mean frequency of eight private alleles) indicate that gene flow is extensive among Korean populations of E. japonica. Factors contributing to the high levels of genetic diversity found within populations of E. japonica include large and contiguous populations, obligating outcrossing (dioecious plant), high fecundity, and long generation time. Occasional seed dispersal by humans and pollen movement by domesticated honey bees may further enhance gene flow within the species.     

Genetic diversity and differentiation in natural and reintroduced populations of Bencomia exstipulata and comparisons with B. caudata (Rosaceae) in the Canary Islands: an analysis using microsatellites

Variation at five polymorphic microsatellite loci was used to investigate genetic diversity and differentiation of two tetraploid Canarian endemics, Bencomia exstipulata and B. caudata. Data were analysed and are discussed in terms of tetrasomic (autotetraploid) and disomic (allotetraploid) inheritance. In both cases, genetic diversity values were similar to those described in other tetraploid plant species. High genetic differentiation between the only two described natural populations of B. exstipulata was detected (F_ST = 0.411). Bayesian cluster analysis revealed a geographical structure with distinct genetic groups from each island. High genetic differentiation and low genetic diversity of the B. exstipulata population from Tenerife suggest a recent population bottleneck, perhaps caused by the most recent major volcanic eruption, for this natural locality. This may be heightened by possible inbreeding depression and the monoecy of these species. Polymorphic microsatellite loci were also tested across all species in the Bencomia alliance. These reliably amplified the target sequence, suggesting a high degree of conservation of the sequences flanking the microsatellites. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 160 , 429–441.     

Genetic diversity and morphological differentiation in Liatris helleri (Asteraceae), a threatened plant species

Liatris helleri (Asteraceae) is an insect-pollinated herbaceous perennial endemic to several high-elevation sites in the Blue Ridge Mountains of North Carolina. Allozymes were used to describe the genetic diversity and population structure in nine populations of this rare, federally listed species. Differences in leaf morphology were also examined for greenhouse-grown plants representing several populations. The proportion of the total genetic diversity found among populations, as indicated by the allozyme data, was 16%. Higher levels of population differentiation were found for differences in leaf shape; population of origin accounted for 37% of the variation in maximum leaf width, while families within populations accounted for 7%. In contrast to many endemic species, L. helleri maintains fairly high levels of genetic diversity. For the species, the percent polymorphic loci was 87.5, the average number of alleles at variable loci was 3.00 and the gene diversity was 0.276. Mean population values were percent polymorphic loci =58.4, mean number of alleles per polymorphic locus =2.59 and gene diversity =0.219. The estimated gene flow was low (Nm=0.85–1.32) and a relatively high correlation (r=0.55; p<0.005) was found between linear geographic and genetic distance. This suggests that the populations are partially isolated by distance, despite the limited range (<60 km) of the species. We recommend that population distinetiveness be maintained in restoration efforts.     

硬核资源遗传多样性的AFLP分析

为了解云南省硬核[Scleropyrum wallichianum（Wight et Arn.）Arn.]的遗传多样性,采用AFLP标记分析了7个居群84份种质材料的遗传变异。结果表明,从64对引物组合中挑选出多态性较好的引物8对,共扩增出1 728条带,其中多态性条带1 388条,多态性百分率为80.14%。硬核在物种水平的多样性指数分别为Na=1.416,Ne=1.179,H=0.137,I=0.225,在居群水平上分别为H=0.111,I=0.175;在遗传相似性系数为0.52时,这些种质材料可分为3组,其中易武居群具有丰富的遗传变异,大部分的遗传变异存在于居群内,而在0.05置信区间内居群间遗传变异仅为11.5%;居群间的遗传距离和地理距离无显著相关性（r=0.0323,P=0.5820）。因此,硬核资源可采用就地和迁地保护策略,以增加其遗传多样性。     

Consequences of prolonged clonal growth on local and regional genetic structure and fruiting success of the forest perennial Maianthemum bifolium

The balance between clonal propagation and sexual reproduction varies among species. Although theory predicts an impact of clonal growth on both‐ within‐ and between population genetic structure, most empirical evidence available to date does not reveal sharp differences between sexually reproducing and clonal species. This has been attributed mainly to the fact that even low levels of sexual recruitment can maintain high levels of genetic diversity. Here we study the effects of prolonged clonal growth and very low rates of sexual recruitment on the genetic structure of the perennial Maianthemum bifolium, an outcrossing understorey species of temperate forests. Average genotypic diversity (0.37) of the populations, as revealed by AFLP, was above the average values reported for species of similar characteristics, but some populations were extremely poor in genotypes. Fruiting success was positively correlated with genotypic diversity, probably as a result of shortage in mating types and compatible pollen in populations poor in genotypes. This was confirmed by a pollination experiment. Fruiting success increased by a factor three when individuals were hand‐pollinated with pollen from a nearby population compared to hand‐pollinations with pollen from the own population. Furthermore, the fruiting success after natural pollination (control individuals) was positively related to number of nearby populations which could act as pollen sources. Given the limited colonization capacity of the species (no seed flow), and the long time since fragmentation of the forest fragments studied, between‐population genetic differentiation was relatively low (Φ_st=0.14). Lack of genetic drift due to long generation times and very limited sexual recruitment is probably responsible for this. Our results show that prolonged clonal growth and lack of sexual recruitment may affect within‐ and between‐ population genetic structure and the capability for sexual reproduction.     

Effect of sire population on the genetic diversity and fitness of F1 progeny in the endangered Chinese endemic Sinocalycanthus chinensis

Sinocalycanthus chinensis Cheng et S. Y. Chang (Calycanthaceae), which has a unique systematic status, is listed as a national second‐class protected plant of China. In this study, the genetic diversity, performance, and fitness of F1 progeny from crosses between the Damingshan (DMS) population of S. chinensis and pollen parents from the Daleishan (DLS) and Longxushan (LXS) populations were examined. The DLS population has a relatively small population size, low genetic diversity, and considerable geographical and genetic distances from the DMS population relative to the LXS population. Compared with naturally occurring seeds, DLS‐sired seeds had the highest thousand‐seed weight, starch content, fat content, germination rate, germination index, and emergence rate, but the lowest protein content. Naturally occurring, open‐pollinated seeds had the lowest thousand‐seed weight, starch content, and fat content, but the highest protein content. Compared with natural F1 progeny, DMS × DLS seedlings had the highest genetic diversity, photosynthetic parameters, and growth characteristics, except for leaf mass ratio and stem mass ratio. Under strong light, DMS × DLS seedlings exhibited a F_v/F_m value of 0.75, while the other two seedling types exhibited F_v/F_m values of 0.65. DLS‐sired seeds had the most vigorous growth characteristics except for leaf mass ratio and stem mass ratio. These results suggest that genetic rescue by transplanting seedlings from the DLS population or hand pollination with pollen from the DLS population would be effective methods to reduce inbreeding depression and obtain strong offspring with high genetic diversity and fitness in the DMS population.     

ISSR primer screening and preliminary evaluation of genetic diversity in wild populations of Gycyrrhiza uralensis

Fourteen efficient inter-simple sequence repeat (ISSR) primers were screened and optimized for detecting the genetic diversity in wild populations of Glycyrrhiza uralensis Fisch. By using these primers, 249 polymorphic bands out of a total of 270 (92.2 %) were generated from 70 individuals of 4 wild G. uralensis populations sampled from Inner Mongolia Province of China. Nei’s gene diversity (h) and Shannon index (I) calculated from the data matrix of the ISSR phenotypes revealed a high level of genetic diversity with h = 0.268 and I = 0.415 within this plant. Analysis of molecular variation (AMOVA) showed that most of the genetic variation (81 %) occurred within the populations, whereas the variance among populations was only 19 %. The UPGMA tree based on Nei’s unbiased genetic diversity illustrated that populations from Bulage and Bayanwusu were genetically close related, while the population from Shanghaimiao was found to be the most diverse from the other three. The high genetic diversity implies that the wild resources of this species could be restored soon if an appropriate and efficient protection strategy was employed. Our results also provided an optimized method for evaluating genetic diversity of G. uralensis using ISSR markers which was useful for further investigation.     

Risso’s dolphins (<Emphasis Type="Italic">Grampus griseus</Emphasis>) in UK waters are differentiated from a population in the Mediterranean Sea and genetically less diverse

The Risso’s dolphin (Grampus griseus) has a worldwide distribution, but little is known about their population genetic structure. Local coastal populations are never known to be abundant, and are sometimes under anthropogenic impact. Therefore the question of regional differentiation by genetic drift and overall diversity levels is of conservation interest. Here we present preliminary data that clearly indicate genetic differentiation and lower genetic diversity of a population sampled in UK waters (primarily from the Western Isles, Scotland) compared to a Mediterranean sample. Significant differentiation was found in comparison with a sample from the Mediterranean for both microsatellite DNA markers (F _ST = 0.0296) and mtDNA sequence data (F _ST = 0.260; ϕ _ST = 0.542). Allelic diversity was lower in the UK for nearly all loci.