Chaney and Ruiz Revilla: Sampling Methods: Comment 1

The following comments pertain to Sampling Methods and Interpretation of Correlation: A Comparative Analysis of Seven Cross-Cultural Samples, Richard P. Chaney and Rogelio Ruiz Revilla, AA 71:597–633.     

Genome Wide Sampling Sequencing for SNP Genotyping: Methods,Challenges and Future Development

Genetic polymorphisms, particularly single nucleotide polymorphisms (SNPs), have been widely used to advance quantitative, functional and evolutionary genomics. Ideally, all genetic variants among individuals should be discovered when next generation sequencing (NGS) technologies and platforms are used for whole genome sequencing or resequencing. In order to improve the cost-effectiveness of the process, however, the research community has mainly focused on developing genome-wide sampling sequencing (GWSS) methods, a collection of reduced genome complexity sequencing, reduced genome representation sequencing and selective genome target sequencing. Here we review the major steps involved in library preparation, the types of adapters used for ligation and the primers designed for amplification of ligated products for sequencing. Unfortunately, currently available GWSS methods have their drawbacks, such as inconsistency in the number of reads per sample library, the number of sites/targets per individual, and the number of reads per site/target, all of which result in missing data. Suggestions are proposed here to improve library construction, genotype calling accuracy, genome-wide marker density and read mapping rate. In brief, optimized GWSS library preparation should generate a unique set of target sites with dense distribution along chromosomes and even coverage per site across all individuals.     

Quantifying Change Through Time in Spider Assemblages: Sampling Methods, Indices and Sources of Error

Using a sample dataset from six sites in the Southern Appalachian mountains in the United States, I evaluate the usefulness of diversity indices and similarity/difference indices for monitoring the changes in spider (Order Araneae) assemblages through time. The Shannon index, Brillouin index, Simpson's index and Margalef's index were correlated with each other and were able to detect successional changes in two old clear-cuts as well as disturbance to a Beech gap forest possibly due to Beech Bark Disease. Turnover, Bray-Curtis similarity, and Morisita-Horn similarity also detected successional differences between the forest types and indicated the short-term and long-term changes in a mature forest stand. Seasonal changes (early to late summer) in spider communities were consistently higher than yearly changes. I identify and discuss the implications of various sources of error that will adversely affect the accuracy and efficiency of a monitoring protocol: sensitivity of indices to sample size, sampler bias, inclusion of juveniles, taxonomic uncertainty and stochastic sampling effects. Although gross trends are still apparent in the sample data regardless of these errors, more subtle changes may be obscured. It is these subtle trends which may be more useful to managers attempting to identify disturbance before irreversible damage occurs.     

Evaluation of Common Methods for Sampling Invertebrate Pollinator Assemblages: Net Sampling Out-Perform Pan Traps

Methods for sampling ecological assemblages strive to be efficient, repeatable, and representative. Unknowingly, common methods may be limited in terms of revealing species function and so of less value for comparative studies. The global decline in pollination services has stimulated surveys of flower-visiting invertebrates, using pan traps and net sampling. We explore the relative merits of these two methods in terms of species discovery, quantifying abundance, function, and composition, and responses of species to changing floral resources. Using a spatially-nested design we sampled across a 5000 km² area of arid grasslands, including 432 hours of net sampling and 1296 pan trap-days, between June 2010 and July 2011. Net sampling yielded 22% more species and 30% higher abundance than pan traps, and better reflected the spatio-temporal variation of floral resources. Species composition differed significantly between methods; from 436 total species, 25% were sampled by both methods, 50% only by nets, and the remaining 25% only by pans. Apart from being less comprehensive, if pan traps do not sample flower-visitors, the link to pollination is questionable. By contrast, net sampling functionally linked species to pollination through behavioural observations of flower-visitation interaction frequency. Netted specimens are also necessary for evidence of pollen transport. Benefits of net-based sampling outweighed minor differences in overall sampling effort. As pan traps and net sampling methods are not equivalent for sampling invertebrate-flower interactions, we recommend net sampling of invertebrate pollinator assemblages, especially if datasets are intended to document declines in pollination and guide measures to retain this important ecosystem service.     

Comparative Estimation of Genetic Diversity in Population Studies using Molecular Sampling and Traditional Sampling Methods

Entomopathogenic nematodes (EPN) are efficient biological pest control agents. Population genetics studies on EPN are seldom known. Therefore, it is of interest to evaluate the significance of molecular sampling method (MSM) for accuracy, time needed, and cost effectiveness over traditional sampling method (TSM). The study was conducted at the Mohican Hills golf course at the state of Ohio where the EPN H. bacteriophora has been monitored for 18 years. The nematode population occupies an area of approximately 3700 m² with density range from 0.25-2 per gram soil. Genetic diversity of EPN was studied by molecular sampling method (MSM) and traditional sampling method (TSM) using the mitochondrial gene pcox1. The MSM picked 88% in compared to TSM with only 30% of sequenced cox 1 gene. All studied genetic polymorphism measures (sequence and haplotype) showed high levels of genetic diversity of MSM over TSM. MSM minimizes the chance of mitochondrial genes amplification from non target organisms (insect or other contaminating microorganisms). Moreover, it allows the sampling of more individuals with a reliable and credible representative sample size. Thus, we show that MSM supersedes TSM in labour intensity, time consumption and requirement of no special experience and efficiency.     

Qualitative Research Design: An Interactive Approach

Qualitative Research Design: An Interactive Approach. Joseph A. Maxwell. Thousand Oaks, CA: Sage Publications, 1996. 155 pp.     

Methods for Multiplex Template Sampling in Digital PCR Assays

The efficient use of digital PCR (dPCR) for precision copy number analysis requires high concentrations of target molecules that may be difficult or impossible to obtain from clinical samples. To solve this problem we present a strategy, called Multiplex Template Sampling (MTS), that effectively increases template concentrations by detecting multiple regions of fragmented target molecules. Three alternative assay approaches are presented for implementing MTS analysis of chromosome 21, providing a 10-fold concentration enhancement while preserving assay precision.     

Evaluation of Methods for Sampling, Recovery, and Enumeration of Bacteria Applied to the Phylloplane

Determining the fate and survival of genetically engineered microorganisms released into the environment requires the development and application of accurate and practical methods of detection and enumeration. Several experiments were performed to examine quantitative recovery methods that are commonly used or that have potential applications. In these experiments, Erwinia herbicola and Enterobacter cloacae were applied in greenhouses to Blue Lake bush beans (Phaseolus vulgaris) and Cayuse oats (Avena sativa). Sampling indicated that the variance in bacterial counts among leaves increased over time and that this increase caused an overestimation of the mean population size by bulk leaf samples relative to single leaf samples. An increase in the number of leaves in a bulk sample, above a minimum number, did not significantly reduce the variance between samples. Experiments evaluating recovery methods demonstrated that recovery of bacteria from leaves was significantly better with stomacher blending, than with blending, sonication, or washing and that the recovery efficiency was constant over a range of sample inoculum densities. Delayed processing of leaf samples, by storage in a freezer, did not significantly lower survival and recovery of microorganisms when storage was short term and leaves were not stored in buffer. The drop plate technique for enumeration of bacteria did not significantly differ from the spread plate method. Results of these sampling, recovery, and enumeration experiments indicate a need for increased development and standardization of methods used by researchers as there are significant differences among, and also important limitations to, some of the methods used.     

Measuring Spider Richness: Effects of Different Sampling Methods and Spatial and Temporal Scales

Assessing the richness of invertebrate taxa to aid conservation and management requires a better understanding of the potential sources of error. Patterns of richness for heathland spiders at the species and family levels were compared across three sampling methods, four spatial scales, and monthly intervals (for 16 months). A total of 33 families and 130 species was collected: pitfall traps collected 94% of species, sweep net, 25%, and visual search, 41%. The sampling methods produced variable results. Pitfall trap and sweep net techniques identified significant, yet contrasting spatial differences in the number of families and species at one spatial scale. Pitfall trap data reflected strong temporal variation that influenced spatial patterns in richness (across one spatial scale for families and two for species). The use of broader temporal scales introduced a potential failure to detect significant differences in the richness of ground active spiders, and this risk varied spatially. The sweep net is not recommended for this habitat, although a method that targets the foliage is required for a more complete faunal assessment. Visual searches detected no significant patterns in richness, yet given its potential and increasing use for rapid biodiversity surveys, ways to improve sampling efficiency are suggested.     

Freshwater Ecology and Eutrophication Meeting： Rationale, Objectives and Format

October 11-15 October 2008, Jinan University, Guangdong, China Limnology, although showing progress overall, still has many handicaps: there is a lack of understanding of process and functions, of animal and plant diversity, of taxonomy in some climatic regions like the tropics-subtropics, and the teaching of the discipline is lagging so far behind that in many countries that span several climatic zones,     

Assimilate Transport and Partitioning in Plants: Approaches,Methods, and Facets of Research

This review, dedicated to the 100th anniversary of A.L. Kursanov's date of birth, considers the development of phloem transport studies since his book, Assimilate Transport in the Plant, was published in 1976. This book and several other fundamental publications on phloem structure and functions basically shaped this physiological issue; as a result, several international meetings by scientists working in the area were induced, and the proceedings of these meetings were published at regular intervals. Six conferences have been held to date, and six corresponding collections of papers have been published and are reviewed here along with other experimental communications and reviews. This review considers the following topics: (1) the phloem structure and the ultrastructure of specialized phloem cells, (2) the physiological functions of phloem and their regulation, (3) photosynthesis and phloem loading with assimilates, (4) phloem unloading and the related processes of plant growth and development, (5) the mechanisms of sugar and amino acid transport, (6) the levels of transport, (7) transport compartments; (8) xylem–phloem and symplast–apoplast communication; (9) phloem transport vs. the integral plant physiology, (10) transport of xenobiotics, and (11) the trophic transport networks in symbionts.     

Questionnaires and Diaries as Research Instruments in Dream Research: Methodological Issues

Dream questionnaires are widely used in dream research to measure dream recall frequency and various aspects of dream life. The present study has investigated the intercorrelation between questionnaire and diary measures. 285 participants completed a dream questionnaire and kept a dream diary over a two-week period. Results indicate that keeping a dream diary increased dream recall in low and medium dream recallers but decreased dream recall in high dream recallers. The correlation coefficients between questionnaire items measuring aspects of dream content and diary data were large, except for a more complex scale (realism/bizarreness). In the low recall group, however, considerably lower coefficients were found indicating that recall and sampling processes affect the response to global items measuring dream content. Using the example of testing gender differences, the findings of the present study clearly indicate that the measurement technique affects the results. Whereas sufficient internal consistency and retest reliability have been demonstrated for various dream questionnaires, future research should focus on the aspects of validity by comparing questionnaire data to dream content analysis of at least 20 dreams per person.