Characterization of Staphylococcus species by SDS–PAGE of Whole-Cell and Extracellular Proteins

In this study, a total of fifteen staphylococcal strains belonging to different species were characterized by whole-cell and extracellular protein profiles using sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS–PAGE). The results are presented as dendrograms after quantitative analysis of the band patterns with a computer program. Visual inspection of protein bands and cluster analysis of protein patterns of to be used 15 strains, representing 10 Staphylococcus species, showed that whole-cell and extracellular protein profiles differed in several protein bands in Staphylococcus aureus, S. epidermidis, S. simulans, and other species of Staphylococcus; however, the differences were insufficient for reliable differentiation of Staphylococcus species by the SDS–PAGE method.     

A new digital method of data collection for spatial point pattern analysis in grassland communities

A major objective of plant ecology research is to determine the underlying processes responsible for the observed spatial distribution patterns of plant species. Plants can be approximated as points in space for this purpose, and thus, spatial point pattern analysis has become increasingly popular in ecological research. The basic piece of data for point pattern analysis is a point location of an ecological object in some study region. Therefore, point pattern analysis can only be performed if data can be collected. However, due to the lack of a convenient sampling method, a few previous studies have used point pattern analysis to examine the spatial patterns of grassland species. This is unfortunate because being able to explore point patterns in grassland systems has widespread implications for population dynamics, community‐level patterns, and ecological processes. In this study, we developed a new method to measure individual coordinates of species in grassland communities. This method records plant growing positions via digital picture samples that have been sub‐blocked within a geographical information system (GIS). Here, we tested out the new method by measuring the individual coordinates of Stipa grandis in grazed and ungrazed S. grandis communities in a temperate steppe ecosystem in China. Furthermore, we analyzed the pattern of S. grandis by using the pair correlation function g(r) with both a homogeneous Poisson process and a heterogeneous Poisson process. Our results showed that individuals of S. grandis were overdispersed according to the homogeneous Poisson process at 0–0.16 m in the ungrazed community, while they were clustered at 0.19 m according to the homogeneous and heterogeneous Poisson processes in the grazed community. These results suggest that competitive interactions dominated the ungrazed community, while facilitative interactions dominated the grazed community. In sum, we successfully executed a new sampling method, using digital photography and a geographical information system, to collect experimental data on the spatial point patterns for the populations in this grassland community.     

Two-dimensional pattern analysis on dominant species and community in subalpine meadow of Luya Mountain, Shanxi Province, China

The spatial pattern analysis of population and community is important to understand community structure and has become one key topic in modern plant ecology. There are many techniques for analyzing one-dimensional pattern in ecological literature. Two-dimensional pattern analysis is better than one-dimensional analysis in the study on community spatial characteristics and structure. However, it is hard to analyze these two-dimensional patterns due to poor effective methodology. The two-dimensional sampling using two transects that meet at right angles was applied to get quadrat data in this work. And then the data from the two transects were analyzed separately by one-dimensional pattern analysis method, two-term local quadrat variance. The length, width, and area of patches at different scales of pattern for populations were obtained from the analysis. For community pattern, detrended correspondence analysis (DCA) was employed to summarize the species information firstly, and then the first DCA axis scores were analyzed to check its pattern. The application of this method to the pattern analysis on dominant populations and community for subalpine meadow (Comm. Polygonum viviparum + Carex rigescens + Kobresia bellardii) in the Luya mountains showed that it could release the characteristics of spatial pattern clearly and was a very effective technique. The method is easy to use and saves time with obvious advantages, compared with the two-dimensional pattern analysis methods presented in the literatures. In the study meadow, the patterns of the main dominant species, Polygonum viviparum, Carex rigescens, and Kobresia bellardii, were apparent and comparatively regular in shape with large areas of patches at the same scale compared with other species such as Festuca sp. and Thalictrum petaloideum. There were two or three scales of patterns for each plant population studied. This was related to population features, the interaction with environmental factors, and their dominant position in the community. The two scales of patterns for the meadow community were clear. The pattern of community was closely correlated with that of the main dominant species. The patches of dominant species were inter-distributed and overlapped, and formed the community pattern together. This is beneficial for utilization of resources, and keeping the community stable. __________ Translated from Acta Ecologica Sinica, 2005, 25(6): 1264–1268 [译自: 生态学报]     

GENE FLOW IN CAVE ARTHROPODS: A QUALITATIVE AND QUANTITATIVE APPROACH

Slatkin's method (1981) for analyzing gene flow levels is applied to eleven species of cave arthropods. This provides insights into the strength of gene flow as a force affecting the evolution of cave organisms, while serving as a test of Slatkin's method. The results show that patterns of gene flow are consistent with the dispersal abilities and the ecological requirements of each species. Troglobites in general have lower gene flow values than troglophiles or trogloxenes. However, the geology of the area, its vegetation profile, and the geographic distance among the populations considered are also important in determining the gene flow levels. Gene flow patterns in three cave species, Ptomaphagus hirtus, Neaphaenops tellkampfii tellkampfii and Hadenoecus subterraneus, are compared in detail. These species inhabit the same highly interconnected karst area in south-central Kentucky but differ in their ecological requirements. The results suggest that gene flow levels are more dependent upon the intrinsic characteristics of each species than upon the availability of routes for dispersal. Overall estimates of gene flow were coupled with a more detailed population-structure analysis in four terrestrial cave arthropods: Speonomus delarouzeei, Hadenoecus cumberlandicus, Hadenoecus subterraneus and Euhadenoecus puteanus. The results stress the need for this type of analysis for subdivided species, in which estimates of the average gene flow can produce misleading results. Moreover, they show how these types of measures are more relevant in describing historical patterns of gene exchange than in indicating current levels of gene flow.     

Evaluation of random amplified polymorphic DNA (RAPD)-PCR as a method to differentiate Lactobacillus acidophilus,Lactobacillus crispatus,Lactobacillus amylovorus,Lactobacillus gallinarum,Lactobacillus gasseri,and Lactobacillus johnsonii

The technique random amplified polymorphic DNA (RAPD)-PCR was evaluated as a method to differentiate Lactobacillus acidophilus, Lactobacillus crispatus, Lactobacillus amylovorus, Lactobacillus gallinarum, Lactobacillus gasseri, and Lactobacillus johnsonii. Representative strains, including the type of each species, were selected from different clusters obtained by numerical analysis of total soluble cell protein patterns. Results obtained by RAPD-PCR corresponded well with results obtained by numerical analysis of total soluble cell protein patterns. The type strains of each species displayed different RAPD profiles. Strains with identical L(+)- nicotinamide adenine dinucleotide-dependent lactic dehydrogenase (nLDH) electrophoretic profiles could be distinguished on the basis of their RAPD profiles.     

Variability of Restriction Sites in Satellite DNA as a Molecular Basis of Taxonprint Method: Evidence from the Study of Caucasian Rock Lizards

The distribution of restriction sites in satellite DNA of 17 Caucasian rock lizard species of the genus Lacerta (Darevskia gen. nov., (Squamata, Lacertidae) was analyzed. The distribution patterns were shown to reflect the degree of satellite DNA evolutionary divergence, which could be revealed by taxonprint method, i.e., through the analysis of genomic DNA with a set of restriction endonucleases and subsequent computer-aided analysis. Thus, the taxonprint method offers an opportunity to examine the satellite DNA divergence in closely related species and infer the phylogeny of the species studied without reserting to costly and labor-consuming procedures. This is the advantage of using this technique at the early stages phylogenetic analysis of genomic DNA for rapid and effective estimation of relationships between closely related species as well as in the cases when DNA cloning and sequencing are too expensive or not feasible.     

Comparative phylogeography of five widespread tree species: Insights into the history of western Amazonia

Various historical processes have been put forth as drivers of patterns in the spatial distribution of Amazonian trees and their population genetic variation. We tested whether five widespread tree species show congruent phylogeographic breaks and similar patterns of demographic expansion, which could be related to proposed Pleistocene refugia or the presence of geological arches in western Amazonia. We sampled Otoba parvifolia/glycycarpa (Myristicaceae), Clarisia biflora, Poulsenia armata, Ficus insipida (all Moraceae), and Jacaratia digitata (Caricaceae) across the western Amazon Basin. Plastid DNA (trnH–psbA; 674 individuals from 34 populations) and nuclear ribosomal internal transcribed spacers (ITS; 214 individuals from 30 populations) were sequenced to assess genetic diversity, genetic differentiation, population genetic structure, and demographic patterns. Overall genetic diversity for both markers varied among species, with higher values in populations of shade‐tolerant species than in pioneer species. Spatial analysis of molecular variance (SAMOVA) identified three genetically differentiated groups for the plastid marker for each species, but the areas of genetic differentiation were not concordant among species. Fewer SAMOVA groups were found for ITS, with no detectable genetic differentiation among populations in pioneers. The lack of spatially congruent phylogeographic breaks across species suggests no common biogeographic history of these Amazonian tree species. The idiosyncratic phylogeographic patterns of species could be due instead to species‐specific responses to geological and climatic changes. Population genetic patterns were similar among species with similar biological features, indicating that the ecological characteristics of species impact large‐scale phylogeography.     

Mitochondrial DNA variation in pearl millet and related species

Summary Mitochondrial DNA (mtDNA) restriction endonuclease fragment patterns and patterns of mtDNA hybridized by mitochondrial gene probes were used to study phylogenetic relationships of seven Pennisetum species, including five P. americanum (pearl millet) ecotypes and a reference species from the distantly related genus, Panicum. The restriction patterns of the pearl millet ecotypes were uniform with the exception of the ecotype collected in Ethiopia. The probe hybridization method revealed more variability, with both the Rhodesian and Ethiopian ecotypes differing from the others and from each other. Considerable restriction pattern polymorphism was noted among different species of Pennisetum, and Panicum. Significant relationships were noted of Pennisetum polystachyon to P. pedicellatum and of P. purpureum to P. squamulatum using the restriction pattern method. In addition to those relationships, the hybridization method showed relationships of pearl millet to P. purpureum and to P. squamulatum. The relationships noted between species by the hybridization method agreed more closely to the cytological data than those indicated by the restriction pattern method. Therefore, the hybridization method appeared to be the preferred method for studying species relationships. The mitochondrial genome size of pearl millet was calculated to be 407 kb and the mitochondrial genome sizes of other Pennisetum species ranged from 341 to 486 kb.Florida Agricultural Experiment Station Journal Series No. 8485.     

Statistical analysis of the individual variability of 1D protein profiles as a tool in ecology: an application to parasitoid venom

Understanding the forces that shape eco‐evolutionary patterns often requires linking phenotypes to genotypes, allowing characterization of these patterns at the molecular level. DNA‐based markers are less informative in this aim compared to markers associated with gene expression and, more specifically, with protein quantities. The characterization of eco‐evolutionary patterns also usually requires the analysis of large sample sizes to accurately estimate interindividual variability. However, the methods used to characterize and compare protein samples are generally expensive and time‐consuming, which constrains the size of the produced data sets to few individuals. We present here a method that estimates the interindividual variability of protein quantities based on a global, semi‐automatic analysis of 1D electrophoretic profiles, opening the way to rapid analysis and comparison of hundreds of individuals. The main original features of the method are the in silico normalization of sample protein quantities using pictures of electrophoresis gels at different staining levels, as well as a new method of analysis of electrophoretic profiles based on a median profile. We demonstrate that this method can accurately discriminate between species and between geographically distant or close populations, based on interindividual variation in venom protein profiles from three endoparasitoid wasps of two different genera (Psyttalia concolor, Psyttalia lounsburyi and Leptopilina boulardi). Finally, we discuss the experimental designs that would benefit from the use of this method.     

Marine island biogeography. Response to comment on ‘Island biogeography: patterns of marine shallow‐water organisms’

In this response we have incorporated data on gastropod and seaweed biodiversity referred to by Ávila et al. (2016, Journal of Biogeography, doi: 10.1111/jbi.12816 ) to allow an updated analysis on marine shallow‐water biogeography patterns. When compared to the biogeography patterns reported in Hachich et al. (2015, Journal of Biogeography, 42 , 1871–1882), we find (1) no differences in the patterns originally reported for reef fish or seaweeds, (2) minor differences in gastropod species–area and species–age patterns and (3) a significant difference for the gastropod species‐isolation pattern. In our original work, we reported that there was limited evidence that gastropod species richness was influenced by island isolation; however, our new analysis reveals a power‐model relationship between these variables. Thus, we are now able to conclude that gastropod species diversity, whose dispersal capacity is intermediate between seaweeds (lowest) and reef fish (highest), is also influenced by island isolation.     

A CHROMATOGRAPHIC INVESTIGATION OF INTERSPECIFIC RELATIONSHIPS IN PINUS (SUBSECTION SYLVESTRES)

The foliage polyphenols of 16 Pinus species were compared by two-dimensional paper chromatography. The general patterns of chemical similarity were correlated with the geographic distributions of the species; sympatric species generally had greater chemical affinity than did allotropic species. This relationship did not always correspond to hybridization patterns and morphological similarities. The distinctive chromatographic patterns of the Southeast Asian species (P. insularis, P. luchuensis, P. merkusii) and their generally low affinities with species of Europe and the Asian mainland suggest that further investigation of the morphological relationships and the genetic compatibility of these species with other Sylvestres species is warranted. The chemical relationships of P. halepensis and P. heldreichii to other Sylvestres species were also unclear. The qualitative differences in polyphenols among species are consistent and of sufficient magnitude to enable the application of chromatographic analysis to studies of interspecific hybridization in Pinus.     

PCR-RFLP analysis of the IGS region of rDNA: a useful tool for the practical discrimination between species of the genus Debaryomyces

The amplification by PCR of the intergenic spacer region (IGS) of rDNA followed by restriction fragment length polymorphism (RFLP) analysis was evaluated as a potential method for discriminating the 16 species belonging to the genus Debaryomyces. The digestion of this region with some or all the enzymes used in this study (HapII, HhaI and MboI) produced species-specific patterns that permitted differentiation of the species in the genus. With the exception of Debaryomyces vanrijiae, the technique was also efficient for␣distinguishing the varieties in the species Debaryomyces hansenii (var. hansenii, var. fabryi), Debaryomyces occidentalis (var. occidentalis, var. persoonii) and Debaryomyces polymorphus (var. africanus, var. polymorphus), respectively. PCR-RFLP analysis of the IGS region of rDNA is proposed as a clear and reproducible technique for the practical discrimination of species of the yeast genus Debaryomyces.     

Temporal and spatial differentiation in seedling emergence may promote species coexistence in Mediterranean fire‐prone ecosystems

Mediterranean ecosystems are hotspots of species richness where fire is one of the key processes influencing their structure, composition and function. Post‐fire seedling emergence constitutes a crucial event in the life cycle of plants and species‐specific temporal and spatial patterns of seedling emergence have been hypothesized to contribute to the high diversity in these ecosystems. Here we study the temporal and spatial patterns of seedling emergence observed for the four dominant species (Cistus albidus, Ulex parviflorus, Helianthemum marifolium, Ononis fruticosa) after an experimental fire in a Mediterranean gorse shrubland. In a first analysis we compared the timing of emergence of each species using the Kaplan‐Meier method. The spatial component of seedling emergence and the spatiotemporal relationship between different cohorts of the same species were analyzed using recent techniques of spatial point pattern analyses. We found a bimodal temporal pattern of emergence. Emergence of Cistaceae species (H. marifolium and C. albidus) occurred predominantly early after the fire while Fabaceae (O. fruticosa and U. parviflorus) emerged mainly during the following autumn. Individually, all species showed an aggregated spatial pattern and, when testing for pair interactions, we found that the clusters of individual species were spatially segregated. Additionally, the clusters of individual species showed an internal spatial structure where seedlings of different cohorts were spatially segregated. Theoretical models predict that these patterns will promote species coexistence. We identified a number of mechanisms that all have the potential to contribute to the observed pattern formation. However, the potential interaction among these mechanisms are complex and not easy to predict. Our analyses take a significant step forward in studying seedling emergence in fire prone ecosystems since, to our knowledge, this is the first time that both spatial and temporal patterns of all dominant species have been studied together.     

Differentiation of Chlamydia Species by Combined Use of Polymerase Chain Reaction and Restriction Endonuclease Analysis

To differentiate Chlamydia spp., a primer pair designed to generate a genus-specific region of the major outer membrane protein (MOMP) gene was used in a PCR to amplify a single DNA fragment of 245-259 bp. In the PCR, the expected single DNA fragment was amplified from strains of Chlamydia trachomatis, C. psittaci, C. pneumoniae and C. pecorum, respectively. By restriction endonuclease analysis with AluI and PvuII, the amplified products exhibited four distinct patterns, corresponding to the four species. It is, therefore, concluded that one-step PCR followed by restriction endonuclease analysis as described in this study could be a valuable method for the detection and differentiation of Chlamydia species.     

The role of spatial scale and the perception of large-scale species-richness patterns

Despite two centuries of exploration, our understanding of factors determining the distribution of life on Earth is in many ways still in its infancy. Much of the disagreement about governing processes of variation in species richness may be the result of differences in our perception of species‐richness patterns. Until recently, most studies of large‐scale species‐richness patterns assumed implicitly that patterns and mechanisms were scale invariant. Illustrated with examples and a quantitative analysis of published data on altitudinal gradients of species richness (n = 204), this review discusses how scale effects (extent and grain size) can influence our perception of patterns and processes. For example, a hump‐shaped altitudinal species‐richness pattern is the most typical (c. 50%), with a monotonic decreasing pattern (c. 25%) also frequently reported, but the relative distribution of patterns changes readily with spatial grain and extent. If we are to attribute relative impact to various factors influencing species richness and distribution and to decide at which point along a spatial and temporal continuum they act, we should not ask only how results vary as a function of scale but also search for consistent patterns in these scale effects. The review concludes with suggestions of potential routes for future analytical exploration of species‐richness patterns.     

Can isotropy vs. anisotropy in the spatial association of plant species reveal physical vs. biotic facilitation?

In dryland ecosystems and other harsh environments, a large part of the vegetation is often clustered, appearing as ‘islands’. If ‘independent’ species, usually colonizers, can be distinguished from species which are ‘dependent’ on the presence of the colonizing species for successful establishment and/or persistence, the type of spatial pattern of the association ‐ isotropic (spatially symmetric) or anisotropic (spatially asymmetric) ‐ can give information on the underlying environmental factors driving the process of association. Modified spatial pattern analysis based on Ripley's K‐function can be applied to bivariate clustered patterns by cardinal direction in order to detect possible anisotropy in the pattern of association. The method was applied to mapped distribution patterns of two types of semi‐arid shrubland in southeastern Spain. In shrubland of Retama sphaerocarpa, low shrubs of Artemisia barrelieri were significantly clustered under the canopy of the Retama shrubs in all four cardinal directions, suggesting an isotropic facilitation effect. In low shrubland dominated by Anthyllis cytisoides and Artemisia barrelieri, Anthyllis shrubs occurred more frequently than expected on the eastern side (and downslope) of an Artemisia shrub. The possible environmental factors driving the two association patterns are discussed and recommendations for further applications of the analytical method are given.     

The bottom Oligochaeta communities in sand pits of different trophic status in Upper Silesia (Southern Poland)

Oligochaeta, occurring in the littoral zones of two sand pits, were sampled in order to determine the relationship between the oligochaete species and the waters’ trophic level. Differences between sand pits attributable to community structure and to an overall higher abundance of oligochaetes, especially tubificids, were observed in Dzierżno Małe. Multivariate analyses (correspondence analysis [CA] and canonical correspondence analysis [CCA]) reveal correlations between the distribution patterns of oligochaete species and the concentration of nitrates, phosphates and dissolved oxygen. Some species, e.g. Dero digitata, Limnodrilus hoffmeisteri, Potamothrix hammoniensis, Nais simplex, Limnodrilus claparedeanus, Limnodrilus udekemianus and Tubifex tubifex, were more abundant in eutrophic sites. The results of the study showed that the richness of Oligochaeta species is not a good method for estimating the trophic levels of the studied sand pits. Indicators based on the share of oligo-, meso- and eutrophic species in Oligochaeta communities are better for evaluating the water quality in the studied reservoirs.     

Comparative chiasma analysis using a computerised optical digitiser

A new computerised technique has been devised for measuring the distribution of chiasmata along diplotene bivalents. The method involves the introduction into the field of view of the microscope, of a fine light spot which can be accurately manipulated along the chromosomes of each bivalent. The data recorded include (a) the positions of the chiasmata along the bivalent in terms of their relative distances from the centromere and (b) the individual bivalent and cellular chiasma frequencies. — The method has been applied to the analysis of chiasma distribution patterns in the two known species of the genus Caledia, C. species nova 1 and C. captiva and in two chromosomal races of the latter. Statistical tests indicate that within bivalents at least 40% of the comparative distribution patterns of chiasmata between races and species are significantly different. Similar comparisons between populations within races reveal only 18% significant differences. — The observed distribution patterns of chiasmata in this genus suggest that chiasma formation is sequential from centromere to telomere. — The variation in the frequency and distribution of chiasmata between races and species suggests that the interference distances between successive chiasmata are, at least partially, independent of chiasma frequency and position. — The interracial and interspecific differences in chromosome structure are correlated with changes in chiasma pattern.