Bacterial Population Structure of the Jute-Retting Environment

Jute is one of the most versatile bast fibers obtained through the process of retting, which is a result of decomposition of stalks by the indigenous microflora. However, bacterial communities associated with the retting of jute are not well characterized. To investigate the presence of microorganisms during the process of jute retting, full-cycle rRNA approach was followed, and two 16S rRNA gene libraries, from jute-retting locations of Krishnanagar and Barrackpore, were constructed. Phylotypes affiliating to seven bacterial divisions were identified in both libraries. The bulk of clones came from Proteobacteria ( approximately 37, 41%) and a comparatively smaller proportion of clones from the divisions-Firmicutes ( approximately 11, 12%), Cytophaga-Flexibacter-Bacteroidetes group (CFB; approximately 9, 7%), Verrucomicrobia ( approximately 6, 5%), Acidobacteria ( approximately 4, 5%), Chlorobiales ( approximately 5, 5%), and Actinobacteria ( approximately 4, 2%) were identified. Percent coverage value and diversity estimations of phylotype richness, Shannon-Weiner index, and evenness confirmed the diverse nature of both the libraries. Evaluation of the retting waters by whole cell rRNA-targeted flourescent in situ hybridization, as detected by domain- and group-specific probes, we observed a considerable dominance of the beta-Proteobacteria (25.9%) along with the CFB group (24.4%). In addition, 32 bacterial species were isolated on culture media from the two retting environments and identified by 16S rDNA analysis, confirming the presence of phyla, Proteobacteria ( approximately 47%), Firmicutes ( approximately 22%), CFB group ( approximately 19%), and Actinobacteria ( approximately 13%) in the retting niche. Thus, our study presents the first quantification of the dominant and diverse bacterial phylotypes in the retting ponds, which will further help in improving the retting efficiency, and hence the fiber quality.     

Laplacian Eigenfunctions Learn Population Structure

Principal components analysis has been used for decades to summarize genetic variation across geographic regions and to infer population migration history. More recently, with the advent of genome-wide association studies of complex traits, it has become a commonly-used tool for detection and correction of confounding due to population structure. However, principal components are generally sensitive to outliers. Recently there has also been concern about its interpretation. Motivated from geometric learning, we describe a method based on spectral graph theory. Regarding each study subject as a node with suitably defined weights for its edges to close neighbors, one can form a weighted graph. We suggest using the spectrum of the associated graph Laplacian operator, namely, Laplacian eigenfunctions, to infer population structure. In simulations and real data on a ring species of birds, Laplacian eigenfunctions reveal more meaningful and less noisy structure of the underlying population, compared with principal components. The proposed approach is simple and computationally fast. It is expected to become a promising and basic method for population genetics and disease association studies.     

Spatial Population Structure of Yellowstone Bison

Abstract: Increases in Yellowstone National Park, USA, bison (Bison bison) numbers and shifts in seasonal distribution have resulted in more frequent movements of bison beyond park boundaries and development of an interagency management plan for the Yellowstone bison population. Implementation of the plan under the adaptive management paradigm requires an understanding of the spatial and temporal structure of the population. We used polythetic agglomerative hierarchical cluster analysis of radiolocations obtained from free-ranging bison to investigate seasonal movements and aggregations. We classified radiolocations into 4 periods: annual, peak rut (15 Jul-15 Sep), extended rut (1 Jun-31 Oct), and winter (1 Nov-31 May). We documented spatial separation of Yellowstone bison into 2 segments, the northern and central herds, during all periods. The estimated year-round exchange rate (4.85-5.83%) of instrumented bison varied with the fusion strategy employed. We did not observe exchange between the 2 segments during the peak rut and it varied during the extended rut (2.15-3.23%). We estimated a winter exchange of 4.85-7.77%. The outcome and effectiveness of management actions directed at Yellowstone bison may be affected by spatial segregation and herd affinity within the population. Reductions based on total population size, but not applied to the entire population, may adversely affect one herd while having little effect on the other. Similarly, management actions targeting a segment of the population may benefit from the spatial segregation exhibited.     

Genetic Structure of the Ancestral Population of Modern Humans

Neutral DNA polymorphisms from an 8-kb segment of the dystrophin gene, previously ascertained in a worldwide sample (n= 250 chromosomes), were used to characterize the population ancestral to the present-day human groups. The ancestral state of each polymorphic site was determined by comparing human variants with their orthologous sites in the great apes. The ``age before fixation' of the underlying mutations was estimated from the frequencies of the new alleles and analyzed in the context of these polymorphisms' distribution among 13 populations from Africa, Europe, Asia, New Guinea, and the Americas (n= 860 chromosomes in total). Seventeen polymorphisms older tan 100,000–200,000 years, which contributed ∼90% to the overall nucleotide diversity, were common to all human groups. Polymorphisms endemic to human groups or continentally restricted were younger than 100,000–200,000 years. Africans (six populations) with 13 such sites stood out from the rest of the world (seven populations), where only 2 population-specific variants were observed. The similarity of the frequencies of the old polymorphisms in Africans and non-Africans suggested a similar profile of genetic variability in the population before the modern human's divergence. This ancestral population was characterized by an effective size of about 10,000 as estimated from the nucleotide diversity; this size may describe the number of breeding individuals over a long time during the Middle Pleistocene or reflect a speciation bottleneck from an initially larger population at the end of this period. Received: 3 February 1998 / Accepted: 9 February 1998     

Changing Population Structure through the Use of Compound Chromosomes

Theoretical calculations and population cage data are presented to illustrate the use of compound chromosomes to change the genetic structure of insect populations.     

Influence of the Interaction for Fitness on the Population Structure

The incidence of non-allelic interaction for fitness in a diallelic digenic model is analyzed. Three types of interaction between the fitnesses are considered, namely: i) additive, ii) exponential and, iii) logarithmic. The model of MATHER and JINKS (1970) is applied in the computation of the interaction parameters. The theory of finite absorbing Markov chains (FELLER, 1968) is utilized in the representation of the genotypic structure of the selfing population over time. Expressions depending on the parameters of interaction are obtained for the mean number of generations that the process of genetic information flow delays in transitions among transient states. Also, a numerical example is studied in which the mean absorption times and the variances are calculated. Finally, the impact of fitness interaction on the genetic diversity of some populations is analyzed through the calculation of the genetic information neg-entropy (BRILLOUIN, 1959).     

On the Asymptotic Behaviour of the Population Number

We consider the stochastic model of an asexual population in which the number of couples formed in some generation is random variable depending on the number of individuals in that generation only. The conditions of convergence were obtained almost everywhere and in mean square of the normalized number of individuals in the n-th generation. These results may be considered as the generalization of some known statements about the models constructed on the basis of the branching processses theory.     

On the Population Dynamics of the Malaria Vector

A deterministic differential equation model for the population dynamics of the human malaria vector is derived and studied. Conditions for the existence and stability of a non-zero steady state vector population density are derived. These reveal that a threshold parameter, the vectorial basic reproduction number, exist and the vector can established itself in the community if and only if this parameter exceeds unity. When a non-zero steady state population density exists, it can be stable but it can also be driven to instability via a Hopf Bifurcation to periodic solutions, as a parameter is varied in parameter space. By considering a special case, an asymptotic perturbation analysis is used to derive the amplitude of the oscillating solutions for the full non-linear system. The present modelling exercise and results show that it is possible to study the population dynamics of disease vectors, and hence oscillatory behaviour as it is often observed in most indirectly transmitted infectious diseases of humans, without recourse to external seasonal forcing.     

Population Structure With Localized Haplotype Clusters

We propose a multilocus version of F_ST and a measure of haplotype diversity using localized haplotype clusters. Specifically, we use haplotype clusters identified with BEAGLE, which is a program implementing a hidden Markov model for localized haplotype clustering and performing several functions including inference of haplotype phase. We apply this methodology to HapMap phase 3 data. With this haplotype-cluster approach, African populations have highest diversity and lowest divergence from the ancestral population, East Asian populations have lowest diversity and highest divergence, and other populations (European, Indian, and Mexican) have intermediate levels of diversity and divergence. These relationships accord with expectation based on other studies and accepted models of human history. In contrast, the population-specific F_ST estimates obtained directly from single-nucleotide polymorphisms (SNPs) do not reflect such expected relationships. We show that ascertainment bias of SNPs has less impact on the proposed haplotype-cluster-based F_ST than on the SNP-based version, which provides a potential explanation for these results. Thus, these new measures of F_ST and haplotype-cluster diversity provide an important new tool for population genetic analysis of high-density SNP data.GENOME-WIDE data sets from worldwide panels of individuals provide an outstanding opportunity to investigate the genetic structure of human populations (Conrad et al. 2006; International Hapmap Consortium 2007; Jakobsson et al. 2008; Auton et al. 2009). Populations around the globe form a continuum rather than discrete units (Serre and Paabo 2004; Weiss and Long 2009). However, notions of discrete populations can be appropriate when, for example, ancestral populations were separated by geographic distance or barriers such that little gene flow occurred.F_ST (Wright 1951; Weir and Cockerham 1984; Holsinger and Weir 2009) is a measure of population divergence. It measures variation between populations vs. within populations. One can calculate a global measure, assuming that all populations are equally diverged from an ancestral population, or one can calculate F_ST for specific populations or for pairs of populations while utilizing data from all populations (Weir and Hill 2002). One use of F_ST is to test for signatures of selection (reviewed in Oleksyk et al. 2010).F_ST may be calculated for single genetic markers. For multiallelic markers, such as microsatellites, this is useful, but single-nucleotide polymorphisms (SNPs) contain much less information when taken one at a time, and thus it is advantageous to calculate averages over windows of markers (Weir et al. 2005) or even over the whole genome. The advantage of windowed F_ST is that it can be used to find regions of the genome that show different patterns of divergence, indicative of selective forces at work during human history.Another measure of human evolutionary history is haplotype diversity. Haplotype diversity may be measured using a count of the number of observed haplotypes in a region or by the expected haplotype heterozygosity based on haplotype frequencies in a region. Application of this regional measure to chromosomal data can be achieved by a haplotype block strategy (Patil et al. 2001) or by windowing (Conrad et al. 2006; Auton et al. 2009).One problem with the analysis of population structure based on genome-wide panels of SNPs is that a large proportion of the SNPs were ascertained in Caucasians, potentially biasing the results of the analyses. Analysis based on haplotypes is less susceptible to such bias (Conrad et al. 2006). This is because haplotypes can be represented by multiple patterns of SNPs; thus lack of ascertainment of a particular SNP does not usually prevent observation of the haplotype. On a chromosome-wide scale, one cannot directly use entire haplotypes, because all the haplotypes in the sample will almost certainly be unique, thus providing no information on population structure. Instead one can use haplotypes on a local basis, either by using windows of adjacent markers or by using localized haplotype clusters, for example those obtained from fastPHASE (Scheet and Stephens 2006) or BEAGLE (Browning 2006; Browning and Browning 2007a).Localized haplotype clusters are a clustering of haplotypes on a localized basis. At the position of each genetic marker, haplotypes are clustered according to their similarity in the vicinity of the position. Both fastPHASE and BEAGLE use hidden Markov modeling to perform the clustering, although the specific models used by the two programs differ.Localized haplotype clusters derived from fastPHASE have been used to investigate haplotype diversity, to create neighbor-joining trees of populations, and to create multidimensional scaling (MDS) plots (Jakobsson et al. 2008). It was found that haplotype clusters showed different patterns of diversity to SNPs, while the neighbor-joining and MDS plots were similar between haplotype clusters and SNPs.In this work, we apply windowed F_ST methods to localized haplotype clusters derived from the BEAGLE program (Browning and Browning 2007a,b, 2009). We consider population-average, population-specific, and pairwise F_ST estimates (Weir and Hill 2002). Population-average F_ST''s either assume that all the populations are equally diverged from a common ancestor, which is not realistic, or represent the average of a set of population-specific values. This can be convenient in that the results are summarized by a single statistic; however, information is lost. A common procedure is to calculate F_ST for each pair of populations, and these values reflect the degree of divergence between the two populations. Different levels of divergence are allowed for each pair of populations but each estimate uses data from only that pair of populations. On the other hand, population-specific F_ST''s allow unequal levels of divergence in a single analysis that makes use of all the data.We compare results from the localized haplotype clusters to those using SNPs directly. The results of applying localized haplotype clusters to population-specific F_ST estimation are very striking, showing better separation of populations and a more realistic pattern of divergence than for population-specific F_ST estimation using SNPs directly. We also use BEAGLE''s haplotype clusters in a haplotype diversity measure and investigate the relationship between this measure of haplotype-cluster diversity and the recombination rate.     

Genetic Structure of the Population of Alternaria solani in Brazil

Understanding the genetic structure of the population of Alternaria solani (AS) is an important component of epidemiological studies of early blight, a severe disease that affects potato (Po) and tomato (To) worldwide. Up to 150 isolates obtained from both hosts were analysed with RAPD and AFLP markers to estimate the amount and distribution of genetic variability of AS in Brazil. Using RAPD, gene diversity (h = 0.20) and scaled indices of diversity of Shannon (H′ = 0.66) and Stoddart and Taylor’s (G = 0.31) for the Po population were higher than those of the To (h = 0.07, H′ = 0.34, G = 0.17). For AFLP, the statistics for the Po (h = 0.17, H′ = 0.86, G = 0.49) and To (h = 0.17, H′ = 0.85, G = 0.36) populations were similar. For each RAPD and AFLP locus, the allele frequency for the overall population ranged from 0.006 to 0.988, and 0.007 to 0.993, respectively. Genetic differentiation was high (G_ST = 0.41 and θ = 0.59) and moderately high (G_ST = 0.23 and θ = 0.37) when estimated with RAPD and AFLP, respectively. Based on cluster analyses, there was strong evidence of association of pathogen haplotypes with host species. The null hypothesis of random association of alleles was rejected in the analysis of both RAPD (I_A = 13.1, P < 0.001) and AFLP (I_A = 2.2, P < 0.001) markers. The average number of migrants was estimated to be around one and two individuals per generation, using RAPD and AFLP, respectively. There was no correlation between genetic distance and geographical origin of AS haplotypes for RAPD (r = ?0.07, P = 0.84) and AFLP (r = ?0.03, P = 0.70). The AS population is clonal with high genetic variability, and there is genetic differentiation between the populations that affect To and Po.     

Population Structure of Anopheles gambiae in Africa

The population structure of Anopheles gambiae in Africa was studied using 11 microsatellite loci in 16 samples from 10 countries. All loci are located outside polymorphic inversions. Heterogeneity among loci was detected and two putative outlier loci were removed from analyses aimed at capturing genome-wide patterns. Two main divisions of the gene pool were separated by high differentiation (F(ST) > 0.1). The northwestern (NW) division included populations from Senegal, Ghana, Nigeria, Cameroon, Gabon, Democratic Republic of Congo (DRC), and western Kenya. The southeastern (SE) division included populations from eastern Kenya, Tanzania, Malawi, and Zambia. Inhospitable environments for A. gambiae along the Rift Valley partly separate these divisions. Reduced genetic diversity in the SE division and results of an analysis based on private alleles support the hypothesis that a recent bottleneck, followed by colonization from the NW populations shaped this structure. In the NW division, populations possessing the M rDNA genotype appeared to form a monophyletic clade. Although genetic distance increased with geographic distance, discontinuities were suggested between certain sets of populations. The absence of heterozygotes between sympatric M and S populations in the DRC and the high differentiation in locus 678 (F(ST)>0.28) contrasted with low differentiation in all other loci (-0.02相似文献   

A Model for Analysis of Population Structure

Arguments have been presented for the appropriateness of a multinomial Dirichlet distribution for describing single-locus genotypic frequencies in a subdivided population. This distribution is defined as a function of allele frequency, the average (over the entire population) inbreeding coefficient and the correlation between genotypes within a subdivision. Alternative parameterizations and their genetic interpretations are given.-We then show how information from a sample drawn from this subdivided population, in the absence of pedigrees, can be combined with the multinomial Dirichlet model to form a likelihood function. This likelihood function is then used as the basis for estimation and testing hypotheses concerning the genetic parameters of the model. Comparisons of this approach to the alternative procedure of Cockerham (1969) and (1973) are made using human data obtained from Tecumseh, Michigan and Monte Carlo simulations.-Finally, implications of these results to statistical inference and to mutation rates are presented.     

高寒植物长鞭红景天种群结构及数量特征

种群结构及数量特征的研究对揭示种群的形成机制和影响因素有着重要意义。在西藏林芝高山森林生态系统国家野外科学观测研究站所在的西藏色季拉山区,采用样地-样方法对研究站旁阳坡、大阴坡、观景台和山口公路上方的长鞭红景天种群进行了调查,共设76块样地、304个样方,进而对长鞭红景天种群结构及数量特征进行了分析研究。结果表明：长鞭红景天在色季拉山主要分布于6个群落类型：急尖长苞冷杉林（P1）、方枝柏林（P2）、薄毛海绵杜鹃灌丛（P3）、毛小叶垫柳灌丛（P4）、鳞腺杜鹃灌丛（P5）及硬叶柳灌丛（P6）。各群落中长鞭红景天平均密度大小顺序为：P3＞P1＞P2＞P4＞P6＞P5、平均基径为：P6＞P2＞P5＞P4＞P1＞P3、平均高度为：P6＞P2＞P5＞P1＞P3＞P4、平均花茎数为：P6＞P2＞P1＞P3＞P5＞P4、平均花茎环数为：P6＞P5＞P2＞P1＞P3＞P4、平均分枝数为：P6＞P1＞P3＞P2＞P4＞P5、重要值为：P5＞P4＞P3＞P2＞P1＞P6。不同群落类型中,长鞭红景天种群的基径、高度及花茎环数等结构系列均表现出不同程度的残缺现象,总体上也出现幼体数目少、成体和老体数目相对较多,但由于其种子繁殖存在一定周期性,并且在自然状态下也进行着无性繁殖,故其仍是增长型种群。对花茎环数的分析发现,长鞭红景天种群大量繁殖的周期是8~10年。长鞭红景天分枝数在5~8枝的植株数比例超过了50 %,分枝数最多的高达45枝,但这些分枝由于相互争夺从根吸收上来的有限营养的原因而生长相对较细。各枝花茎数情况方面,花茎数为1~2枝的所占比例为32.21%,这些主要是侧枝上的花茎;花茎数在7以上的植株占25.82 %,这主要是主轴上的花茎;总体上主轴上着生花茎多于侧枝上的花茎。基径与生长参数关系方面：长鞭红景天的生长参数都是随基径级增大而总体呈现出增大的趋势。研究结果可为进一步探讨长鞭红景天种群生存机制提供基础。     

Population Structure of Peronospora effusa in the Southwestern United States

Peronospora effusa is an obligate pathogen that causes downy mildew on spinach and is considered the most economically important disease of spinach. The objective of the current research was to assess genetic diversity of known historical races and isolates collected in 2014 from production fields in Yuma, Arizona and Salinas Valley, California. Candidate neutral single nucleotide polymorphisms (SNPs) were identified by comparing sequence data from reference isolates of known races of the pathogen collected in 2009 and 2010. Genotypes were assessed using targeted sequencing on genomic DNA extracted directly from infected plant tissue. Genotyping 26 historical and 167 contemporary samples at 46 SNP loci revealed 82 unique multi-locus genotypes. The unique genotypes clustered into five groups and the majority of isolates collected in 2014 were genetically closely related, regardless of source location. The historical samples, representing several races, showed greater genetic differentiation. Overall, the SNP data indicate much of the genotypic variation found within fields was produced during asexual development, whereas overall genetic diversity may be influenced by sexual recombination on broader geographical and temporal scales.     

濒危植物香果树（Emmenopterys henryi）种群结构与动态

香果树（Emmenopterys henryi）为我国特有种,属国家Ⅱ级重点保护植物。主要分布于江西、安徽等地亚热带中山或低山区的森林中。文中对武夷山自然保护区4个群落类型的香果树种群数量动态进行了系统研究,统计其径级结构、建立生命表,应用谱分析方法分析种群数量的动态变化,并对影响该种群结构的环境因子进行了分析。结果表明：（1）武夷山自然保护区香果树种群基本属于衰退型,幼苗少,中树、大树个体丰富。不同生境的种群密度存在差异,其中香果树纯林密度较大（8.45±0.818株·100 m^-2）,幼苗数量较多,更新较好（幼苗密度1.05±0.326株·100 m^-2）,针阔混交林中香果树密度较小（6.58±0.76株·100 m^-2）,无幼苗;（2）香果树种群中树死亡率较高,其他各级死亡率较低;（3）香果树种群自然更新过程存在明显的周期。（4）对影响香果树种群结构的13个环境因子通过主成分分析（PCA）发现,较高的光强、土壤含水量、弱酸性土壤、土壤有机质、大气湿度、大气温度和适量的人为干扰对种群增长发挥有利影响,而高海拔、阴坡、陡坡度和大的乔灌层盖度对香果树种群增长则发挥不利影响。（5）充分利用香果树幼树喜荫、大树喜光的特点,加强现有林分的就地保护,特别是具有结实能力的母树,并就地采种育苗,扩大人工种群数量。