Assessment of genetic diversity and population differentiation of Achyranthes bidentata (Amaranthaceae) in Dao Di and its surrounding region based on microsatellite markers

Identifying genetic diversity patterns is fundamentally important for effective species management and conservation. In this study, we used five microsatellite loci to investigate the genetic diversity and population differentiation of Achyranthes bidentata in Dao Di and its surrounding region. Our analysis of microsatellite data indicated the level of genetic diversity of A. bidentata (H_T = 0.333) was lower than other plants. The results showed no significant genetic diversity differences and population genetic differentiation between the Dao Di and surrounding region. Significant temperature differences (Bio2: mean diurnal range and Bio7: temperature annual range) were found between the Dao Di and surrounding region, which may improve the accumulation of medicinal ingredients of populations in the Dao Di. The populations of A. bidentata were divided into two genetic groups, which was caused by five temperature variables (Bio1, Bio4, Bio7, Bio9, and Bio11). This study thus provides an important case for over-collecting within limited ranges in affecting population diversity and bioclimate variables for different producing area in driving population differentiation.     

Genetic diversity and population differentiation of the Chinese soft-shelled turtle (Pelodiscus sinensis) in three geographical populations

The Chinese soft-shelled turtle (Pelodiscus sinensis) is one of the most important economical chelonians in the world. To understand the genetic variations of the Chinese soft-shelled turtle in China, 62 individuals were sampled from three localities and 18 polymorphic microsatellite loci tested were used to detect genetic diversity and population structure. Results showed that the genetic diversity of the wild P. sinensis was high. Except for the Wuhu populations, the majority of microsatellite loci are not deviation from Hardy–Weinberg equilibrium in the other two populations. AMOVA analysis indicated that genetic variations occurred mainly within populations (97.4%) rather than among populations (2.6%). The gene flow estimates (Nm) among three geographic populations demonstrated that strong gene flow existed (Nm > 1, mean 6). The present study supported that different habitats, breed turtles escaped, multiple paternity and long evolutionary history may be responsible for the current genetic diversity and differentiation in the wild Chinese soft-shelled turtle.     

An analysis of genetic diversity in Marphysa sanguinea from different geographic populations using ISSR polymorphisms

The genetic diversity of five wild populations of marine polychaete Marphysa sanguinea found in China was investigated using Inter-Simple Sequence Repeat-PCR (ISSR-PCR) polymorphisms. The results of the ISSR-PCR showed that 108 (90.8%) of the 119 ISSR loci tested were polymorphic. The Shannon's information index value was 0.4981, Nei's gene diversity was 0.3418, and the coefficient of gene differentiation (Gst) was 0.3671, which indicated that the among-population component accounted for 36.7% of the total variation, while the within-population component accounted for 63.3%. A UPGMA tree showed that the five populations clustered into two branches. Populations from Dalian, Xingcheng, and Rushan clustered together, while the two Guangxi populations, A and B, clustered into a unique group. The results indicated that the genetic diversity among the five populations of M. sanguinea is high, which will provide useful information for the protection of biodiversity among marine polychaetes.     

Extremely low genetic diversity and extensive genetic admixture at the northern range margins of Bombax ceiba

Understanding the evolutionary processes in species at the margins of their range is of great significance, because marginal populations may harbor local adaptations and will initiate further expansion in response to changes in the environment. Here we examined genetic variation in two nuclear genes and one chloroplast intergenic spacer in 13 northern marginal populations and one geographically central population of Bombax ceiba, a tree distributed mainly in tropical regions. Our results revealed an extremely low level of genetic diversity in each population at the northern margin of its range and strong genetic differentiation between southern China and South Asia. Cultivated and natural populations showed no significant differences in genetic variability. Genetic admixture in a nuclear gene was detected in 10 of the 13 populations at the northern margin of their range. The founder effect, in which a small number of individuals colonize the northern margins of its range, may explain the extremely low genetic diversity. During the establishment of new populations, different source populations may mix and undergo further genetic drift and differentiation. This study indicates that patterns of genetic diversity in tropical species at the margin of their range may also be severely influenced by founder effects.     

A simple derivation of the partitioning of genetic differentiation within subdivided populations

The genetic differentiation within a subdivided population can be partitioned into two proportions, one due to differentiation within sub-populations and the other due to differentiation among subpopulations. A simple mathematical derivation of this procedure, known as Nei's G _ST -statistics, is presented. The significance of considering the differing relative sizes of subpopulations is stressed. Possible fields of applications for breeders and conservationists who are concerned with the establishment of genetically diverse populations are mentioned.     

Strong intraspecific variation in genetic diversity and genetic differentiation in Daphnia magna: the effects of population turnover and population size

Theory predicts that genetic diversity and genetic differentiation may strongly vary among populations of the same species depending on population turnover and local population sizes. Yet, despite the importance of these predictions for evolutionary and conservation issues, empirical studies comparing high‐turnover and low‐turnover populations of the same species are scarce. In this study, we used Daphnia magna, a freshwater crustacean, as a model organism for such a comparison. In the southern/central part of its range, D. magna inhabits medium‐sized, stable ponds, whereas in the north, it occurs in small rock pools with strong population turnover. We found that these northern populations have a significantly lower genetic diversity and higher genetic differentiation compared to the southern/central populations. Total genetic diversity across populations was only about half and average within‐population diversity only about a third of that in southern/central populations. Moreover, an average southern population contains more genetic diversity than the whole metapopulation system in the north. We based our analyses both on silent sites and microsatellites. The similarity of our results despite the contrasting mutation rates of these markers suggests that the differences are caused by contemporary rather than by historical processes. Our findings show that variation in population turnover and population size may have a major impact on the genetic diversity and differentiation of populations, and hence may lead to differences in evolutionary processes like local adaptation, hybrid vigour and breeding system evolution in different parts of a species range.     

Simple sequence repeat marker diversity in cassava landraces: genetic diversity and differentiation in an asexually propagated crop

Cassava (Manihot esculenta) is an allogamous, vegetatively propagated, Neotropical crop that is also widely grown in tropical Africa and Southeast Asia. To elucidate genetic diversity and differentiation in the crop's primary and secondary centers of diversity, and the forces shaping them, SSR marker variation was assessed at 67 loci in 283 accessions of cassava landraces from Africa (Tanzania and Nigeria) and the Neotropics (Brazil, Colombia, Peru, Venezuela, Guatemala, Mexico and Argentina). Average gene diversity (i.e., genetic diversity) was high in all countries, with an average heterozygosity of 0.5358 ± 0.1184. Although the highest was found in Brazilian and Colombian accessions, genetic diversity in Neotropical and African materials is comparable. Despite the low level of differentiation [F_st(theta) = 0.091 ± 0.005] found among country samples, sufficient genetic distance (1-proportion of shared alleles) existed between individual genotypes to separate African from Neotropical accessions and to reveal a more pronounced substructure in the African landraces. Forces shaping differences in allele frequency at SSR loci and possibly counterbalancing successive founder effects involve probably spontaneous recombination, as assessed by parent-offspring relationships, and farmer-selection for adaptation.Communicated by H.C. Becker     

Comparative analysis of genetic diversity and population genetic structure in Abies chensiensis and Abies fargesii inferred from microsatellite markers

Abies chensiensis Tieghem and Abies fargesii Franchet are two closely related tree species of Pinaceae endemic to China. A. chensiensis is usually found scattered in small forest fragments, whereas A. fargesii is a dominant member of coniferous forest. To evaluate the genetic effect of fragmentation on A. chensiensis, a total of 24 populations were sampled from the whole distribution of the two species. Seven nuclear microsatellite loci were employed to analyze comparatively the genetic diversity and population genetic differentiation. Both A. chensiensis and A. fargesii have high level within-population genetic diversity and low inter-population genetic differentiation. Low microsatellite differentiation (2.1%) between A. fargesii and A. chensiensis was observed. But microsatellite marker was able to discriminate most populations of these two species. Compared to A. fargesii, A. chensiensi has lower allelic diversity and higher genetic differentiation among populations. It suggested the existence of negative genetic impacts of habitat fragmentation on A. chensiensis.     

竹叶眼子菜种群遗传多样性与群落物种多样性关系的研究

以洪湖中的沉水植物群落及其优势种竹叶眼子菜(Potamogeton wrightii Morong)为研究对象,利用AFLP分子标记结合野外调查的方法,分析保护区(干扰较小)与非保护区(干扰较大,敞水区)中沉水植物群落的物种多样性与竹叶眼子菜遗传多样性之间的相关性。结果显示:洪湖沉水植物群落物种丰富度(S)和物种多样性辛普森指数(D)在保护区和非保护区均未发现显著性差异;竹叶眼子菜的重要值(IV)在保护区(5.2%~23.2%)较非保护区(8.5%~73.3%)稳定。竹叶眼子菜的遗传多样性在两个区未发现显著差异,其遗传多样性与群落物种多样性这两个指标在保护区、非保护区及全湖水平均不相关,说明沉水植物群落的物种多样性和竹叶眼子菜的遗传多样性对不同环境干扰的响应有所差异。     

Genetic diversity and population differentiation of Capparis spinosa (Capparaceae) in Northwestern China

To explore the influence of vicariance on differentiation patterns of taxa in arid regions, we systematically assessed the genetic diversity and variability of Capparis spinosa, a typical xerophyte that is widely distributed in the Tianshan Mountains and adjacent areas. In total, 300 individuals from 25 populations were sampled, and 14 haplotypes were identified using two cpDNA sequences (rpS12-rpL20 and ndhF). A high level of total genetic diversity (H_T = 0.859) was detected, and this was attributed to the extensive distribution range, which included numerous large populations. The SAMOVA results suggested that the 25 populations were clustered into 4 major geographical groups; a similar divergence trend was found by constructing a BEAST phylogenetic tree and a network diagram. The AMOVA results revealed that significant genetic differentiation occurred among groups. Our results indicated a considerable correlation between genetic divergence and geographical distribution. Isolation due to complex mountain and desert geography might limit gene exchange between disjunct populations, resulting in high differentiation between geographical groups.     

Low genetic diversity and contrasting patterns of differentiation in the two monotypic genera Halacsya and Paramoltkia (Boraginaceae) endemic to the Balkan serpentines

Halacsya and Paramoltkia are two monotypic genera of the Balkan ultramafic outcrops, both classified as paleoendemics. They show close phylogenetic relationship, similar ecology and partially sympatric range, but contrasting life-history traits, patterns of distribution and chromosomal features. We performed a study to compare their infraspecific genetic structure using AFLP fingerprinting. Within-population heterozygosity (H_S) and total heterozygosity (H_T) were lower in diploid H. sendtneri than in polyploid P. doerfleri (0.121 and 0.142 vs. 0.165 and 0.178, respectively). Number of polymorphic loci was also higher in the latter species. Halacsya showed significant levels of among-population variation (14.5%) and population differentiation (F_ST = 0.145), as well as a structuring in four main geographic groups connected by low gene flow. Combined with inability for long-distance dispersal, these data suggest that present-day range fragmentation in this species is the result of historical losses of intervening populations and support its status of paleoendemic surviving in refugial serpentine “islands”. Populations of P. doerfleri were instead genetically very close (F_ST = 0.049), and variation was partitioned almost exclusively among individuals (95.1%). Lack of population groupings and higher levels of gene flow suggested a single, panmictic group, fitting more a metapopulation than a “classical” paleoendemic model.     

Seed and seedling diversity delimitation and differentiation of Indian populations of Melia dubia cav.

Melia dubia is one of the most important industrial tree species in the South East Asia. In last few decades, the populations of M. dubia has rapidly expanded in the Indian sub-continents, leading to an increase in the genetic diversity of species. However, very less information is available on intra-specific variation in Melia under the Indian subcontinent. Therefore, a present investigation was undertaken, to assess the level of diversity in seed and saplings of the Melia populations (ecotypes) collected from three agro-ecological regions of India. Results revealed that the seed and saplings of all the ecotypes are significantly different for all the traits, except for number of branches per plant, and the maximum variability was recorded in germination percentage, seed weight, internodal length, and sapling height of the species. The high heritability for seed weight (0.99), length (0.99), and width (0.97), and germination percentage (0.99) indicated that selection and genetic gain for these traits would be effective during the commencement of improvement program. Trait association analysis explained that higher seed weight significantly reduced sapling height, collar diameter, number of leaves per plant, internodal length, petiole length, and germination percentage (r = ?0.86; p < 0.001) that ultimately reduced the seedling vigor in Melia dubia. Interestingly, the number of branches per plant were not associated with any of the morphological traits. The first principal component explained 50.09% of the entire variation and all the traits contributed greatly to the variation for this principal component, except for number of branches, leaf width and seed length. The clustering approach assorted geographic variation of M. dubia populations into three main sub-clusters i.e. South, North, and North East populations each consisting of five, seven and one populations (including cultivar), respectively. Among different ecotypes, Bahumukhi, Varsha and US Nagar seed sources outperformed all others in seedling vigour (sapling height) and rest of the growth parameters. Overall, findings explained that considerable scope exists for the development of superior planting material of M. dubia through exploration of seeds and selection at the early seedling stage.     

Identification of a new Indian camel germplasm by microsatellite markers based genetic diversity and population structure of three camel populations

Camel invokes fascinating chapter of Indian desert history and is integral component of its ecosystem. Camel population has reached a crisis point after three decades of decline (75%) causing major concern to the policy makers. >28% of Indian camel is not yet characterized. It is imperative to describe country’s camel germplasm and its existing diversity for designing conservation plan. One such population is Sindhi, distributed along border with Pakistan. Twenty five microsatellite markers being valuable tool for estimating genetic diversity were selected to elucidate genetic variability and relationship of Sindhi with two registered camel breeds of India- Marwari and Kharai. The standard metrics of genomic diversity detected moderate variability in all the three populations. A total of 303 alleles with a mean of 8.116 ± 0.587 alleles per locus were found in total of 143 animals. Sindhi population had intermediate allelic diversity with 8.522 ± 1.063 alleles per locus. Corresponding values in Marwari and Kharai were 8.783 ± 0.962 and 7.043 ± 1.030, respectively. Genetic variability within the breeds was moderate as evidenced by the mean observed heterozygosity of 0.556 ± 0.025. Sindhi camel population harbors higher genetic variability (Ho = 0.594) as compared to the two registered camel breeds (Marwari, 0.543 and Kharai, 0.531). Mean expected heterozygosity under Hardy-Weinberg equilibrium was higher than the observed values across the three camel groups, indicating deviations from assumptions of this model. In fact, average positive F value of 0.084 to 0.206 reflected heterozygote deficiency in these populations. These Indian camel populations have not experienced serious demographic bottlenecks in the recent past. Differences among populations were medium and accounted for 7.3% of total genetic variability. Distinctness of three camel populations was supported by all the approaches utilized to study genetic relationships such as genetic distances, phylogenetic relationship, correspondence analysis, clustering method based on Bayesian approach and individual assignment. Sindhi camel population was clearly separated from two registered breeds of Indian camel. Results conclude Sindhi to be a separate genepool. Moderate genetic diversity provides an optimistic viewpoint for the survival of severely declining indigenous camel populations with appropriate planning strategies for conserving the existing genetic variation and to avoid any escalation of inbreeding.     

High genetic differentiation and cross-shelf patterns of genetic diversity among Great Barrier Reef populations of Symbiodinium

The resilience of Symbiodinium harboured by corals is dependent on the genetic diversity and extent of connectivity among reef populations. This study presents genetic analyses of Great Barrier Reef (GBR) populations of clade C Symbiodinium hosted by the alcyonacean coral, Sinularia flexibilis. Allelic variation at four newly developed microsatellite loci demonstrated that Symbiodinium populations are genetically differentiated at all spatial scales from 16 to 1,360 km (pairwise Φ_ST = 0.01–0.47, mean = 0.22); the only exception being two neighbouring populations in the Cairns region separated by 17 km. This indicates that gene flow is restricted for Symbiodinium C hosted by S. flexibilis on the GBR. Patterns of population structure reflect longshore circulation patterns and limited cross-shelf mixing, suggesting that passive transport by currents is the primary mechanism of dispersal in Symbiodinium types that are acquired horizontally. There was no correlation between the genetic structure of Symbiodinium populations and their host S. flexibilis, most likely because different factors affect the dispersal and recruitment of each partner in the symbiosis. The genetic diversity of these Symbiodinium reef populations is on average 1.5 times lower on inshore reefs than on offshore reefs. Lower inshore diversity may reflect the impact of recent bleaching events on Sinularia assemblages, which have been more widespread and severe on inshore reefs, but may also have been shaped by historical sea level fluctuations or recent migration patterns. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Communicated by Biology Editor Dr. Ruth Gates.     

The meaning of genetic variation within and between subpopulations

Summary Argumentation is presented which indicates that the additive decomposition of the total genetic variation of a population into variation within and between (among) its subpopulations suffers from conceptual inconsistency. While the measurement of variation between subpopulations can be shown to be identical to the measurement of subpopulation differentiation, the notion of variation within subpopulations, when viewed as a single measurement, cannot be derived as an independent and cogent concept. Rather, it appears to be merely technically defined as the arithmetic difference between the total variation and the variation between subpopulations, and this difference happens to be non-negative for concave measures of variation such as the (statistical) variance or certain measures of genetic diversity. In order to overcome the conceptual inconsistency, variation between subpopulations could be regarded as subpopulation differentiation and the notion of variation within subpopulations could be replaced by measurements of the degree to which the variation in the total population is represented within the subpopulations. A complementary situation with respect to total variation is thus realized once more, and appropriate measures can be directly derived from existing ones.     

High genetic diversity and strong differentiation in dramatically fluctuating populations of Zostera japonica (Zosteraceae): implication for conservation

Aims Seagrasses provide a variety of ecosystem goods and services, but they are subjected to frequently anthropogenic disturbances. In this study, we genotyped samples collected fromZostera japonicameadows with dramatic fluctuations in the area in order to understand the distribution of genetic variation within and among populations.     

Population genetic structure and interspecific differentiation between Acer davidii Franchi. and A. morrisonense Hayata (Aceraceae) based on SSR markers

Acer davidii Franch. and A. morrisonense Hayata are two important forest tree species (Aceraceae) endemic to mainland China and the Taiwan area, respectively. To investigate population structure and interspecific differentiation between them, we characterized a set of novel microsatellite markers using Illumina sequencing technology. The cross-species amplification analysis showed that 11 out of 21 polymorphic SSR primers of A. davidii also exhibited polymorphisms in A. morrisonense. At the species level, A. davidii has a slightly higher genetic diversity (mean observed heterozygosity, H_O = 0.180) than A. morrisonense (H_O = 0.119). AMOVA showed that most of the variations in A. davidii occurred among individuals within populations and within individuals. Bayesian clustering analyses demonstrated that the two maple species formed two clear genetic lineages. PCoA showed that A. davidii and A. morrisonense were significantly divided into two genetic groups. In addition, asymmetrical weaker gene flow was detected among the two forest tree species. These results suggest that the long term geographic isolation between the mainland and Taiwan may have resulted in a high level of genetic differentiation between these two important maple species.     

Genetic diversity and differentiation of masu salmon (Oncorhynchus masou masou) between and within cultured populations inferred from microsatellite DNA analysis

Masu salmon,Oncorhynchus masou masou,is one of the most valuable fishery species that has been introduced to China,though to date no studies on the genetic diversity and genetic relationship among hatchery populations has been performed with molecular markers.We undertook such a study and sampled 120 individuals from three hatchery stocks and analyzed 20 microsatellite loci.All loci were polymorphic and a total of 91 alleles were detected.A relatively low level of genetic diversity was revealed with effective number of allele of 3.1094,3.3299 and 3.1894 and expected heterozygosity of 0.6600,0.6648 and 0.6638 in the three stocks,respectively.Deviations from Hardy-Weinberg equilibrium were found due to heterozygote deficit.Accordingly,evidence of genetic bottlenecks were found in the three stocks.An individual assignment test demonstrated that 85% of individuals were correctly assigned into their original stocks.Pairwise Fst revealed that significant differentiation occurred between these three stocks.The results of the study indicated that disequilibrium of genetic structure and differentiation has occurred in all three stocks.This information collectively provides a basis for measures to avoid of loss of genetic diversity and introgression in Chinese aquaculture.     

姜状三七遗传多样性和遗传分化研究

利用5个DNA片段及12个微卫星标记（SSR）对姜状三七（Panax zingiberensis C.Y.Wu et K.W.Feng）的遗传多样性和遗传分化进行分析。结果显示，与其他人参属（Panax）植物相比：姜状三七具有相对较高物种水平的核苷酸多态性和等位基因数；在居群水平上，景谷居群具有最高的核苷酸多态性和等位基因数，而江城居群最低。AMOVA分析结果表明，姜状三七在物种水平上具有一定程度的遗传分化，但不显著；在居群水平，江城居群与其他居群间的分化程度最高，其他居群间遗传分化不明显。Structure分析结果也显示江城居群与其他居群被聚类到不同分组，且形态特征相近的样本并未聚到一起，同一分布点的样本遗传成分更相似。