Estimation of density,survival rate and dilution rate ofMecostethus magister (Orthoptera: Acrididae) populations by the mark and recapture method

Population Ecology -     

A marking-and-recapture analysis of the adult population of a phytophagous lady-beetle,Epilachna sparsa orientalis

A marking-and-recapture study of a population of overwintered adults of Epilachna sparsa orientalis was carried out in a small farm containing potatoes and egg-plants. The experiment involved a single release and five recapture samplings during May–June. The data were analysed byLeslie's re-recapture method. Assumption of randomness of sampling proved to be well satisfied. Survival rate of the overwintered adult population was maintained as high as 90 per cent per week or more until early June, and then it declined rapidly towards the end of June. Initially overwintered adults exclusively lived on potato plants, but half of the population alive in mid June migrated to nearby egg-plants. Emigration out of the experimental field, however, seemed not to be occurring. Recapture data of marked individuals in the potato field indicate that majority of the individuals stayed within a radius of 3 m, at least for 2 weeks. Similar data taken from another field also suggest that their mobility was far restricted as compared with random movement within the field. Some comparisons were made between the population behaviours of overwintered adults of E. sparsa orientalis and E. vigintioctomaculata.     

A new method of sequential sampling to classify populations relative to a critical density

A method of sequential sampling for grading population level in relation to a critical density is proposed. The method is based on the relationship and can be used without restrictions on the distribution patterns. The formulae for simple random sampling as well as for two-stage sampling are given.     

A method to assess population changes in king penguins: the use of a Geographical Information System to estimate area-population relationships

During the last decades, king penguin (Aptenodytes patagonicus) populations have been reported to increase throughout most of their breeding range. In this study, we compared the results obtained from direct counts of incubating king penguins with the results yielded by the estimation of the change in area occupied by breeding birds at the Ratmanoff king penguin colony at the Kerguelen Islands. The area of the colony was determined using a Geographical Information System with a georeferencing extension on aerial pictures taken in 1963, 1985 and 1998. Individual king penguin were counted on the same pictures or pictures taken on the same day. The overall population increase between 1963 and 1998 was 733% while the colony area increased by 677%. This study indicates that monitoring change in colony size is a good indicator for detecting and monitoring large population changes in king penguins, in particular for remote colonies. The discrepancy between the two results may be from two different kinds of bias. Firstly, there could be a possible error in the estimation of the area occupied by the colony resulting from the georeferencing of oblique pictures, and secondly, the density of king penguins may also change with population number. This method, which only requires high-altitude pictures, also reduces the possible disturbance to breeding made by low- to medium-altitude flights. Accepted: 7 February 2000     

A Bayesian method to estimate the optimal threshold of a longitudinal biomarker

The objective of this study was to develop methods to estimate the optimal threshold of a longitudinal biomarker and its credible interval when the diagnostic test is based on a criterion that reflects a dynamic progression of that biomarker. Two methods are proposed: one parametric and one non‐parametric. In both the cases, the Bayesian inference was used to derive the posterior distribution of the optimal threshold from which an estimate and a credible interval could be obtained. A numerical study shows that the bias of the parametric method is low and the coverage probability of the credible interval close to the nominal value, with a small coverage asymmetry in some cases. This is also true for the non‐parametric method in case of large sample sizes. Both the methods were applied to estimate the optimal prostate‐specific antigen nadir value to diagnose prostate cancer recurrence after a high‐intensity focused ultrasound treatment. The parametric method can also be applied to non‐longitudinal biomarkers.     

A new method for estimating effective population sizes from a single sample of multilocus genotypes

Equations for the effective size ( N_e ) of a population were derived in terms of the frequencies of a pair of offspring taken at random from the population being sibs sharing the same one or two parents. Based on these equations, a novel method (called sibship assignment method) was proposed to infer N_e from the sibship frequencies estimated from a sibship assignment analysis, using the multilocus genotypes of a sample of offspring taken at random from a single cohort in a population. Comparative analyses of extensive simulated data and some empirical data clearly demonstrated that the sibship assignment method is much more accurate [measured by the root mean squared error, RMSE, of 1/(2 N_e )] than other methods such as the heterozygote excess method, the linkage disequilibrium method, and the temporal method. The RMSE of 1/(2 N_e ) from the sibship assignment method is typically a small fraction of that from other methods. The new method is also more general and flexible than other methods. It can be applied to populations with nonoverlapping generations of both diploid and haplodiploid species under random or nonrandom mating, using either codominant or dominant markers. It can also be applied to the estimation of N_e for a subpopulation with immigration. With some modification, it could be applied to monoecious diploid populations with self-fertilization, and to populations with overlapping generations.     

Functional response to host density in a parasitic wasp,with reference to population regulation

1. The functional response to, and preference for, the host density in a parasite were examined experimentally using an icheumon wasp, Exidechthis canescens, and its host Cadra cautella under controlled conditions.
2. Wasps were more active in host-searching at higher than lower host densities. Percent parasitism increased rapidly with initial increments in host density and then tended to increase more slowly at higher host densities. A sigmoid functional response curve is indicated, which implies that the parasite is able to control its host even at low densities.
3. Wasps actively selected areas of high host density in which to concentrate host-searching behavior.
4. Host-searching by E. canescens is stimulated by the odor of the host when present, and by food in which hosts have developed but have been removed.
5. Both the functional response and the host-density preference of the parasite are mediated by its host-searching behavior. This relationship is discussed in the context of population regulation.

     

一种含特异性侵染内共生菌Rickettisa massilia的烟粉虱种群建立方法

【目的】烟粉虱Bemisia tabaci(Gennadaius)广泛分布于全球除南极洲外各大洲的90多个国家和地区,其寄主范围广,危害严重,属于农业上的重要害虫。烟粉虱体内的内共生菌有助于其扩散传播,提高其寄主适合度,但其体内的内共生菌大都为次生内共生菌,很难进行体外培养,因此,加大了其内共生菌研究的难度。【方法】采集我国部分地区的烟粉虱种群,然后利用基于mt DNA COⅠ基因的种特异性引物进行种群生物型鉴定,再用内共生菌的特异性引物来鉴定含有特异性侵染内共生菌种群,确定个体含内生菌类型后,采取继代饲养方法建立种群。【结果】经鉴定烟粉虱的生物型为Q型(MED隐种),经过5代种群筛选后,可以建立稳定遗传的含特异性侵染内共生菌Rickettisa massilia菌的烟粉虱种群。【结论】通过本方法可以获得稳定的含有特异性侵染内共生菌Rickettisa massilia菌的烟粉虱种群。该方法对研究烟粉虱与体内内共生菌、植物三者之间以及烟粉虱体内某几种内共生菌之间的互作有重要意义,同时也为明确烟粉虱体内Rickettisa菌的作用研究打下基础。     

A new method of sequential sampling to obtain the population estimates with a fixed level of precision

A simple method of sequential sampling is developed which would make it automatically possible to secure, without excess sampling, a predetermined level of precision for a series of population estimates being required. It appears to have wide application to sampling field populations under various situations since it is simply based upon the relationship of variance to mean for which a comprehensive formula deduced for biological populations from the linearity in the regression of mean crowding on mean density could be adopted. Some problems that may arise in practical application of the method are also discussed.     

The dynamics of two viral infections in a single host population with applications to hantavirus

An SI epidemic model for a host with two viral infections circulating within the population is developed, analyzed, and numerically simulated. The model is a system of four differential equations which includes a state for susceptible individuals, two states for individuals infected with a single virus, one which is vertically transmitted and the other which is horizontally transmitted, and a fourth state for individuals infected with both viruses. A general growth function with density-dependent mortality is assumed. A special case of this model, where there is no coinfection and total cross immunity, is thoroughly analyzed. Several threshold values are defined which determine establishment of the disease and persistence at equilibrium for one or both of the infections within the host population. The model has applications to a hantavirus and an arenavirus that infect cotton rats. The hantavirus is transmitted horizontally whereas the arenavirus is transmitted vertically. It is shown through analysis and numerical simulations that both diseases can be maintained within a single host population, where individuals can be either infected with both viruses or with a single virus.     

A real-time PCR-based method to independently sample single simian immunodeficiency virus genomes from macaques with a range of viral loads

The generation of a diverse population of viral variants is a hallmark of simian immunodeficiency virus (SIV) infection. In order to address what role this diversity plays in disease progression, accurate sampling of the viral population is necessary. However, traditional PCR-based methods often rely on amplification of multiple genomes in one reaction, leading to resampling of viral genomes and potential errors in the estimations of viral diversity, especially when sequences from only one or a small number of PCRs are examined and/or viral copy number is low. Here we describe a method to amplify one viral envelope gene per PCR, thereby avoiding resampling. For this purpose we developed a highly accurate real-time PCR method to quantify SIV copy number, then used a single SIV template in a sensitive, high-fidelity full-length envelope PCR. Using this method, we have estimated the intra-animal viral diversity for a cohort of five pig-tailed macaques (Macaca nemestrina) infected with SIVMne variants, which displayed a broad range of viral loads at setpoint.     

A novel method to perform genomic walks using a combination of single strand DNA circularization and rolling circle amplification

Characterization of regions flanking a known sequence within a genome, known as genome walking, is a cornerstone technique in modern genetic analysis. In the present work we have developed a new PCR-dependent, directional genome walking protocol based on the unique circularization property of a novel DNA ligase, CircLigase. In the first step, PCR based primer extension is performed using a phosphorylated primer, designed to extend from the boundary of the known sequence, into the flanking region. This linear amplification results in the generation of single-stranded (ss) DNA, which is then circularized using CircLigase. Using the hyperbranching activity of Phi29 DNA polymerase, the circular ssDNA is then linearized by rolling circle amplification, resulting in copious amounts of double stranded concatameric DNA. Nested primers are used to amplify the flanking sequence using inverse PCR. The products are resolved on an agarose gel and the bands whose mobility change due to the nested location of the primer combination used are identified, extracted, and cloned into a plasmid vector for sequencing. Empirical proof for this concept was generated on two antimicrobial biosynthetic genes in Pseudomonas sp. LBUM300. Using the hcnB and phlD genes as starting points, ca 1 kb of flanking sequences were successfully isolated. The use of locus specific primers ensured both directionality and specificity of the walks, alleviating the generation of spurious amplicons, typically observed in randomly primed walking protocols. The presented genome walking protocol could be applied to any microbial genome and requires only 100-150 bp of prior sequence information. The proposed methodology does not entail laborious testing of restriction enzymes or adaptor ligation. This is the first report of a successful application of the novel ligase enzyme, CircLigase for genomic walking purposes.     

Validation of multiple single nucleotide variation calls by additional exome analysis with a semiconductor sequencer to supplement data of whole-genome sequencing of a human population

Background

Validation of single nucleotide variations in whole-genome sequencing is critical for studying disease-related variations in large populations. A combination of different types of next-generation sequencers for analyzing individual genomes may be an efficient means of validating multiple single nucleotide variations calls simultaneously.

Results

Here, we analyzed 12 independent Japanese genomes using two next-generation sequencing platforms: the Illumina HiSeq 2500 platform for whole-genome sequencing (average depth 32.4×), and the Ion Proton semiconductor sequencer for whole exome sequencing (average depth 109×). Single nucleotide polymorphism (SNP) calls based on the Illumina Human Omni 2.5-8 SNP chip data were used as the reference. We compared the variant calls for the 12 samples, and found that the concordance between the two next-generation sequencing platforms varied between 83% and 97%.

Conclusions

Our results show the versatility and usefulness of the combination of exome sequencing with whole-genome sequencing in studies of human population genetics and demonstrate that combining data from multiple sequencing platforms is an efficient approach to validate and supplement SNP calls.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-673) contains supplementary material, which is available to authorized users.     

On the reliability of a simple method for scoring phenotypes to estimate heritability: A case study with pupal color in Heliconius erato phyllis, Fabricius 1775 (Lepidoptera, Nymphalidae)

In this paper, two methods for assessing the degree of melanization of pupal exuviae from the butterfly Heliconius erato phyllis, Fabricius 1775 (Lepidoptera, Nymphalidae, Heliconiini) are compared. In the first method, which was qualitative, the exuviae were classified by scoring the degree of melanization, whereas in the second method, which was quantitative, the exuviae were classified by optical density followed by analysis with appropriate software. The heritability (h(2)) of the degree of melanization was estimated by regression and analysis of variance. The estimates of h (2) were similar with both methods, indicating that the qualitative method could be particularly suitable for field work. The low estimates obtained for heritability may have resulted from the small sample size (n = 7-18 broods, including the parents) or from the allocation-priority hypothesis in which pupal color would be a lower priority trait compared to morphological traits and adequate larval development.