Quantitative genetic diversity and conservation strategies for an allogamous annual species,Dasypyrum villosum (L.) Candargy (Poaceae)

Dasypyrum villosum (L.) Candargy is a weedy annual diploid (2n = 14, VV genomes) allogamous grass species (Poaceae, Triticeae). Genetic variation for 12 traits was studied in 43 natural populations (31 from Italy and 12 from Croatia and Montenegro of former Yugoslavia) grown in a common field environment in California. Although 7 of 12 traits followed the theoretical prediction that a larger proportion of genetic variation was distributed within populations than among populations, exceptions were found for spike length, plant height, and days to flag-leaf emergence, heading, and anthesis. Covariate analysis showed that developmentally closely related characters were more likely correlated at both population and family within population levels. Geographically closer populations shared more genetic similarity than distant populations as indicated by mean coefficients of variation and cluster analysis of the Euclidean distances among populations. As few as five populations, each population with five or more half-sib seeds taken randomly from 5 plants, is expected to capture more than 95% of the total genetic variation of this species in the region sampled, but sampling a much larger number of seeds per population (> 1000) for long-term storage would supply research and plant breeding needs for several decades. If seed regeneration is required, populations can be sampled from clusters having similar genetic variation, and grown in reproductive isolation or bulked seed samples from all populations of each cluster group can be grown in isolation. The former is recommended if population integrity is desired while the latter is sufficient to provide genetic resources for plant-breeding purposes.     

High genetic diversity in fragmented Iris pumila L. populations in Ukrainian steppe enclaves

Habitat fragmentation can prevent gene flow between plant populations and lead to a loss of genetic diversity. However, such impact of fragmentation has not always been consistently confirmed by previous studies and the issue still needs further research. Particularly little is known about the impact of fragmentation on steppe plants. Steppe once covered vast, continuous areas, and nowadays is among the most fragmented biomes. In Ukraine, remnants of this habitat survived in large but few nature reserves and loess ravines as well as on kurgans (burial mounds of ancient nomadic people), which, despite their small size, are still numerous and scattered throughout the landscape.We studied the impact of fragmentation on the genetic diversity and structure of Iris pumila, a typical species of European steppes. Our main focus was to compare the genetic characteristics between kurgan populations (n = 8), and populations from larger refugia (n = 6). We assessed the genetic diversity of the studied populations with Universal Rice Primers.Our analyses revealed high genetic diversity across all investigated populations (mean He: 0.233; mean PPB: 58.57). However in kurgan populations genetic diversity was significantly higher than in larger refugia. Genetic diversity (He) was negatively correlated with population size. Most of the molecular variance (82%) was represented within populations, whereas genetic differentiation among populations was moderate (Φ_ST = 0.160), and low among refugia types (Φ_RT = 0.026).The maintenance of high genetic diversity despite two centuries of fragmentation may be related to the moderate disturbance occurring on kurgans, which enhances the sexual reproduction of the species. Moreover, we assume that species traits such as longevity and polyploidy might counterbalance genetic drift, while its self-incompatibility and presence of a soil seed bank allows for the replenishment of the gene pool. Overall, our results suggest that kurgans can protect genetic diversity of steppe species.     

Effects of landscape structure on genetic diversity of Geum urbanum L. populations in agricultural landscapes

Plant species in fragmented populations are affected by landscape structure because persistence within and migration among inhabited patches may be influenced by the identity and configuration of surrounding habitat elements. This may also be true for species of the semi-natural vegetation in agricultural landscapes. To determine the effect of landscape elements we analyzed Wood Avens (Geum urbanum L.) populations within three 4×4 km² agricultural landscapes in Germany, Switzerland and Estonia, which differ in levels of land use intensity and habitat fragmentation. Genetic variation was determined in 15 randomly selected populations in each landscape using 10 microsatellite loci. The landscape structure was assessed at two circles around each population, with radii defined by the range limits of spatial genetic autocorrelation. Multiple regression analysis was used to determine the influence of landscape structure variables for inter- and intrapopulation genetic diversity. Gene diversity was equally high in Germany (H_e=0.27) and Switzerland (H_e=0.26) but lower in Estonia (H_e=0.16). A high overall inbreeding coefficient (F_IS=0.89) was found, as expected for a selfing breeding system in G. urbanum. Genetic differentiation among populations was high (overall F_ST=0.43, 0.48, and 0.45 in Estonia, Switzerland and Germany, respectively), and did not differ among the three landscapes. Only a moderate influence of individual land use types on genetic diversity within and among populations was found with some idiosyncratic relationships. Genetic variation within populations was correlated to the amount of hedgerows positively in Estonia but negatively in Switzerland. The study demonstrates that the distribution of individual land use types affects the genetic pattern of a common plant species. However, different variables were identified to influence the genetic structure in three different landscapes. This indicates a major influence of landscape-specific land use history and stochastic processes determining gene flow and plant population structure.     

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.     

Population structure and genetic diversity of black redhorse (Moxostoma duquesnei) in a highly fragmented watershed

Dams have the potential to affect population size and connectivity, reduce genetic diversity, and increase genetic differences among isolated riverine fish populations. Previous research has reported adverse effects on the distribution and demographics of black redhorse (Moxostoma duquesnei), a threatened fish species in Canada. However, effects on genetic diversity and population structure are unknown. We used microsatellite DNA markers to assess the number of genetic populations in the Grand River (Ontario) and to test whether dams have resulted in a loss of genetic diversity and increased genetic differentiation among populations. Three hundred and seventy-seven individuals from eight Grand River sites were genotyped at eight microsatellite loci. Measures of genetic diversity were moderately high and not significantly different among populations; strong evidence of recent population bottlenecks was not detected. Pairwise F_ST and exact tests identified weak (global F_ST = 0.011) but statistically significant population structure, although little population structuring was detected using either genetic distances or an individual-based clustering method. Neither geographic distance nor the number of intervening dams were correlated with pairwise differences among populations. Tests for regional equilibrium indicate that Grand River populations were either in equilibrium between gene flow and genetic drift or that gene flow is more influential than drift. While studies on other species have identified strong dam-related effects on genetic diversity and population structure, this study suggests that barrier permeability, river fragment length and the ecological characteristics of affected species can counterbalance dam-related effects.     

Loss of genetic diversity and fitness in Common Toad (Bufo bufo) populations isolated by inimical habitat

Measures of genetic diversity (including heterozygosity), survival and developmental homeostasis were found to be significantly lower in small, urban populations of the Common Toad (Bufo bufo) than in larger, rural populations of the same region. The autecology and genetic analysis of this relatively sedentary species suggested that the causal mechanism was genetic drift, arising from barriers to migration created by urban development. The pre-metamorphic survival of larvae cultured in identical conditions increased positively with the mean number of alleles at a locus and the percentage of polymorphic loci. Observed heterozygosity in urban garden and rural populations was correlated inversely with the number of observed physical abnormalities (used as a measure of developmental homeostasis) in the developing tadpoles. Genetic distances between town sites of mean 2.2 km separation were significantly higher than those between rural sites of mean 37 km separation. Genetic data were based on allozyme analysis of 27 loci in 8 urban and 4 rural populations. A subset of these sites (3 urban, 2 rural) were also assessed at 3 minisatellite loci and a positive correlation found between the average number of alleles per locus detected by the two methods. Estimates of Nei's 1972 genetic distance, derived separately from the DNA and protein data, were not, however, correlated. The reduction in genetic diversity and fitness observed in these urban toads provides an example of the effect on population persistence that longer term depletion in numbers and habitat fragmentation can have in the wider environment.     

区域变动尺度上不同生境类型及环境因子对西双版纳蝴蝶多样性的影响

【目的】生境类型和环境因子对物种分布和维持具有重要的影响。本研究通过分析不同生境类型对蝴蝶群落多样性及其群落结构影响的差异,以及环境因子对蝴蝶物种丰富度和多度的影响,为区域变动尺度蝴蝶多样性维持机制的研究奠定基础。【方法】于2019年8月和10月,在西双版纳地区采用样线法,调查了天然林、次生林、复合生境、人工林和农田5种生境中蝴蝶的物种,分析了蝴蝶群落多样性、群落结构相似性及物种丰富度和多度与环境因子的关系。【结果】2019年从西双版纳共采集蝴蝶2 226头,隶属于11科98属175种,在西双版纳州级尺度上蝴蝶物种丰富度高于县域尺度。在西双版纳州级尺度上,蝴蝶的物种丰富度和多度在5种生境间存在显著差异,而在县域尺度上,物种丰富度、多度和Chao 1物种丰富度估计值没有一致性规律。群落结构相似性结果显示,在西双版纳州级尺度上,蝴蝶群落结构在不同生境类型间存在极显著差异,在县域尺度上,仅勐腊区域蝴蝶群落结构在不同生境类型间存在显著差异。蝴蝶物种丰富度和多度不仅受到生境类型的影响,还受到温度、年均降水和海拔的影响。【结论】本研究结果表明,在区域变动尺度上,生境类型对西双版纳蝴蝶的多样性的影响较大,而温度、年均降水和海拔是维持蝴蝶物种多样性的重要因素。这些发现对当前人类导致的生境丧失和气候变化时代生物多样性的保护具有重要意义。     

Consequences of harvesting for genetic diversity in American ginseng (<Emphasis Type="Italic">Panax quinquefolius</Emphasis> L.): a simulation study

American ginseng, Panax quinquefolius L., is one of the most heavily traded medicinal plants in North America. The effect of harvest on genetic diversity in ginseng was measured with a single generation culling simulation program. Culling scenarios included random harvest at varying levels, legal limit random harvest and legal limit mature plant harvest. The legal limit was determined by the proportion of legally harvestable plants per population (% mature plants per population). Random harvest at varying levels resulted in significant loss of genetic diversity, especially allelic richness. Relative to initial levels, average within-population genetic diversity (H _e) was significantly lower when plants were culled randomly at the legal limit (Mann–Whitney U=430, p<0.001) or when only mature plants were culled (Mann–Whitney U=394, p<0.01). Within-population genetic diversity was significantly higher with legal limit mature plant harvest (H _e=0.068) than when plants were culled randomly at the legal limit (H _e=0.064; U=202, p<0.01). Based on these simulations of harvest over one generation, we recommend that harvesting fewer than the proportion of mature plants could reduce the negative genetic effects of harvest on ginseng populations.     

Assessment of the genetic variation of chamomile (Matricaria chamomilla L.) populations using phytochemical,morphological and ISSR markers

Inter simple sequence repeat (ISSR) markers were used to assess the genetic diversity of 23 populations of chamomile. Ten primers were applied, producing 193 polymorphic bands. The polymorphic bands were analysed using Simple Matching (SM) similarity index and UPGMA cluster analysis. The resulting dendrogram consisted of four major groups which were in accordance to the geographical regions from which the populations had originated. Populations from North-western (NW), South-Eastern (SE), Central (C) Iran and Europe tended to be classified separately into groups. The highest gene diversity was observed in populations from the Central regions of Iran (0.25). Principal coordinate analysis (PCoA) confirmed the results of cluster analysis, while morphological classification was not related to molecular results. The population from Hungary had the greatest yield of essential oil (0.88 gr/dw), whereas for Iranian ones the greatest and the lowest essential oil yields belonged to NW (Aza = 0.6 and Ard = 0.7) and C (Isf 4, Isf 5 and Isf 6 = 0.44) regions, respectively. The results of the present study could contribute to a better understanding and management of conservation and exploitation of the chamomile germplasm.     

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.     

Using genetic structure data and phylogenetic criteria in attributing prioritization scores for conservation of spontaneous Capparis spinosa L. populations from Tunisia

In Tunisia, the increasing pharmacological demand for spontaneous capers is actually leading to progressive forest overexploitation and genetic erosion of the species that is actually represented by scattered populations. Therefore, inventories with emphasis on the characterization, management and conservation of this medicinal plant are becoming a great need.In this work, genetic and phylogenetic criteria based on isozyme markers were used for the prioritization of spontaneous Capparis spinosa L. populations for conservation according to Vane-Wright and collaborators taxic method.Enzymatic loci varied in their ability to detect variation and population analyses indicated that most of the variation is partitioned between rather than within populations. Fst, gene flow values, PCA and cluster analysis also revealed significant differentiation between all populations.When combing phylogenetic and genetic criteria we were able to prioritize some of the populations for conservation. Therefore, the standardization and the summatory of all indices indicated that the populations Nebeur, Nahli and Dyr rank as a priority for conservation.So far, results of the present study appear to justify the in situ conservation strategy, where core areas completely free from perturbation would be defined for the populations with the highest priority for conservation, with the populations presenting unique alleles. This would guarantee the maintenance of most of the species’ genetic variation. The ex situ conservation management strategy would imply the setting up of specialized nurseries and national collections that are still missing in the country to counteract population fragmentation, demographic loss and genetic erosion threatening such spontaneous populations.     

Genetic diversity and population genetic structure of six dromedary camel (camelus dromedarius) populations in Saudi Arabia

Camels are an integral and essential component of the Saudi Arabian heritage. The genetic diversity and population genetic structure of dromedary camels are poorly documented in Saudi Arabia so this study was carried out to investigate the genetic diversity of both local and exotic camel breeds. The genetic diversity was evaluated within and among camel populations using 21 microsatellite loci. Hair and blood samples were collected from 296 unrelated animals representing 4 different local breeds, namely Majaheem (MG), Maghateer (MJ), Sofr (SO), and Shaul (SH), and two exotic breeds namely Sawahli (SL) and Somali (SU). Nineteen out of 21 microsatellite loci generated multi-locus fingerprints for the studied camel individuals, with an average of 13.3 alleles per locus. Based on the genetic analyses, the camels were divided into two groups: one contained the Saudi indigenous populations (MG, MJ, SH and SO) and the other contained the non-Saudi ones (SU and SL). There was very little gene flow occurring between the two groups. The African origin of SU and SL breeds may explain their close genetic relationship. It is anticipated that the genetic diversity assessment is important to preserve local camel genetic resources and develop future breeding programs to improve camel productivity.     

Genetic diversity within and among the wild populations of Murraya koenigii (L.) Spreng., as revealed by ISSR analysis

Murraya koenigii (L.) Spreng., commonly known as curry leaf plant, is found in the different hilly regions of India. In the present study, fifty-nine accessions representing eight wild populations of M. koenigii were analyzed using thirteen ISSR primers. A total of 152 bands were amplified, out of which, 136 were polymorphic corresponding to 89.47% polymorphism across the accessions. The pairwise population genetic distances were calculated for all the populations that varied from 0.05 to 0.13 between the populations of M. koenigii. AMOVA and Nei’s genetic diversity analysis revealed higher genetic variations within populations than among the populations. The clustering of populations in the dendrogram was not in congruence with geographical affiliations. The results indicate that the ISSR method is sufficiently informative and powerful to estimate the genetic diversity in M. koenigii populations. As M. koenigii is an important wild plant genetic resource, therefore, information on genetic variability might be a potential source as breeding material for development of commercially valuable traits in M. koenigii plants.     

Genetic and morphologic diversity of European fan palm (Chamaerops humilis L.) populations from different environments from Sicily

Chamaerops humilis is decreasing in abundance in Mediterranean Europe, which has induced the European community to call for its protection in Special Areas of Conservation. However, information about its genetic and morphological variability, which is crucial to the development of any conservation strategies, is insufficient. The present study aimed to investigate the genetic and morphological variability of C. humilis in Sicily, which was selected as a model because of the high number of dense populations. The relationships between morphological traits and climatic variables were studied to highlight patterns of adaptation to the environment, along with the genetic similarity among the populations. Ten natural populations were sampled, analyzed using 28 specifically designed SSR primers, and evaluated based on 29 morphological traits. The populations were clustered similarly based on genetic and morphological traits. Heterozygosity was high and inbreeding coefficients were low. These results, along with higher intra‐ than inter‐population differentiation, suggest that C. humilis populations in Sicily differentiated from a common ancestor and that inter‐population variation arose from secondary evolution processes induced by ecological adaptation. The correlations between climatic variables and morphological traits suggest that the morphological adaptation to arid environments depends more on summer temperatures than on evapotranspiration or rainfall and that autumn and winter temperatures are determinants of the species establishment at new sites. Considering the response of C. humilis to seasonal temperatures, the present results indicate this species as a candidate for tracking climatic changes in Europe. Further studies are needed to highlight the adaptation of C. humilis to cold environments. Palaeo‐climatological and ‐ecological studies could help clarify its strategies for the colonization of new sites. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176 , 66–81.     

山西不同地域菜粉蝶RAPD遗传多样性

采用RAPD技术分析了山西省菜粉蝶5个地域种群间的遗传多样性和遗传关系,用筛选出的12对引物扩增共得到143条带,其中127(88.8%)条带具有多态性,5个种群变异程度由大到小的顺序为:大同的(76.3%)＞太原的(74.7%)＞长治的(74.5%)＞代县的(73.7%)＞夏县的(70.7%).Shannon's信息指数分析结果显示大多数变异发生在种群内(73.7%).种群间的Nei's遗传距离较低(均＜0.1).用UPGMA和 Neighbor-joining做的基于RAPD标记的Nei's遗传距离的聚类图显示,各种群内的个体首先聚在一起,种群之间有一定分化,5个地域种群间较远距离的代县种群与夏县种群遗传关系最近并优先相聚.经过对试验结果的分析讨论认为:环境类型及其生态条件对山西省菜粉蝶地域种群的遗传多样性和遗传变异产生了重要的影响,其中农药的施用对菜粉蝶种群遗传结构的影响有可能是深刻的.     

Genetic structure and diversity of natural and domesticated populations of Citrus medica L. in the Eastern Himalayan region of Northeast India

Citron (Citrus medica L.) is a medicinally important species of citrus native to India and occurs in natural forests and home gardens in the foothills of the eastern Himalayan region of northeast India. The wild populations of citron in the region have undergone rapid decline due to natural and anthropogenic disturbances and most of the remaining individuals of citron are found in fragmented natural forests and home gardens in the region. In order to assess the genetic structure and diversity of citron in wild and domesticated populations, we analyzed 219 individuals of C. medica collected from four wild and eight domesticated populations using microsatellite markers. The genetic analysis based on five polymorphic microsatellite loci revealed an average of 13.40 allele per locus. The mean observed and expected heterozygosity values ranged between 0.220–0.540 and 0.438–0.733 respectively among the wild and domesticated populations. Domesticated populations showed close genetic relationships as compared to wild populations and pairwise Nei's genetic distance ranged from 0.062 to 2.091 among wild and domesticated populations. Analysis of molecular variance (AMOVA) showed higher genetic diversity among‐ than within populations. The analysis of population structure revealed five groups. Mixed ancestry of few individuals of different populations revealed exchange of genetic materials among farmers in the region. Citron populations in the region show high genetic variation. The knowledge gained through this study is invaluable for devising genetically sound strategies for conservation of citron genetic resources in the region.     

Genetic and allelopathic differences between populations of daisy fleabane Erigeron annuus (L.) Pers. (Asteraceae) from disturbed and stable habitats

The interactions between invasive plants and their habitats may vary at different phases of the invasion process and depend on the phenotypic plasticity or local adaptations of each species. In this study, we investigated whether habitat changes during the invasion process are related to variations in the physiological traits (allelopathic properties) and genetic differentiation of daisy fleabane (Erigeron annuus (L.) Pers.). E. annuus is a winter annual invasive species that originated in North America and is now distributed throughout Europe. Genetic and genotypic diversity analyses were performed for 37 populations of E. annuus based on inter simple sequence repeat (ISSR) polymorphisms. In total, 684 plants were analyzed; 342 were from stable habitats and 342 were from disturbed habitats. The genetic differences among the populations from the different habitats were studied using a Bayesian cluster analysis and an analysis of molecular variance (AMOVA) and by calculating the genetic and genotypic diversity parameters. A germination test using the juglone index was employed to examine the potential allelopathic properties of the plants from the different habitats. Bayesian cluster analysis, AMOVA and allelopathic effects evaluation revealed differences in the allelopathic potential and genetic structure of the E. annuus populations from the disturbed and stable habitats. This differentiation of populations could be associated with founder effects or with different selection pressures among habitats.     

Diet diversity and breeding of top predators are determined by habitat stability and structure: a case study with the Eurasian otter (<Emphasis Type="Italic">Lutra lutra</Emphasis> L.)

A study on Eurasian otter was conducted in order to establish if feeding ecology and breeding of this European freshwater top predator were affected by the habitat complexity or stability. The work was based on the comparison of contrasting environmental settings. Significant gradients were found for otter diet parameters and breeding, both also changing according to habitat gradient patterns (water capacity and permanence during droughts, habitat stability, and habitat complexity). The otter diet was less diverse in the most stable (and complex) habitats, eating more fish. Otters also breed more regularly in such more stable courses, with more suitable fish availability. The step toward lower habitat stability can put otters in a less advantageous position in front of generalist predators, foraging more frequently outside or in the edge of aquatic ecosystems. Implications for otters and other similar top predator’s conservation are discussed.