Comparison of attached algal communities on natural and artificial substrata along a thermal gradient

Colonization rate and community structure of periphyton assemblages was examined on aluminium and glass substrata and compared to populations on four submerged macrophyte species in three temperature zones in Cholla Lake, Arizona, U.S.A. Higher densities were achieved over shorter incubation intervals in the warmer zones (26–35° C). Representatives from the planktonic diatom community were first to colonize artificial substrata during the initial two hour incubation period in all temperature zones. Two periphyton diatom representatives, Amphora coffeiformis and Cocconeis placentula var. lineata were the numerical dominants after one week. Cocconeis placentula var. lineata was most competitive on natural substrata at temperatures <26°C, while Amphora coffeiformis dominated temperature zones >26°C with no significant preferences for artificial or natural substrata. The significance of temperature, specific conductance and availability of living hosts is discussed with respect to regulating populations of these two common periphytic diatom species in alkaline waters in southwestern U.S.A. Similarity indices (SIMI) were used to compare algal assemblages on various natural and artificial substrata pairs. Periphyton assemblages were very similar on all natural substrata within similar temperature zones, with little or no preference for macrophyte species displaying similar leaf morphology. Diatom assemblages were quite similar on aluminium and glass substrata throughout the incubation period in all temperature zones, while blue-green algal populations were significantly different, particularly in the higher temperature zones (>28°C). Natural periphyton communities were best represented after four weeks incubation with aluminium substrata in warmer temperature zones (>28°C) or where filamentous blue-green algae dominated. The selection of adequate incubation time when employing artificial substrata to evaluate natural assemblages for different environmental conditions and algal populations is discussed.     

Confidence intervals for the similarity between algal communities

While researchers commonly use similarity measures to compare algal communities, very few researchers have considered the variability of these estimated measures. This paper discusses a recent method for estimating the variance of and confidence intervals for similarity measures proposed by Johnson & Millie (1982, Hydrobiologia 89: 3–8). Applications of this method to data have produced confidence intervals that are too narrow. Two alternative methods, the jackknife method and the bootstrap, are shown to provide superior estimates of the variability.     

The occurrence of sub-ice algal aggregations off northeast Greenland

Massive growth of sub-ice algal assemblages was recorded at two stations under first-year ice off northeast Greenland using a Remotely Operated Vehicle equipped with cameras. The assemblages mainly consisted of the diatom Melosira arctica (Ehr.) Dickie. A station sampled at the beginning of June 1993 revealed two forms of growth, curtain-like and rope-like, but with many intermediate types along the entire 150 m transect. The algal distribution was patchy. No significant sympagic fauna was found close to the algal masses. At a station sampled in the middle of July, similar algal concentrations seemed to be disturbed by ice-melting processes. Two casts under multi-year ice flows failed to show any algal aggregations. The observation of algal assemblages under first-year ice is in contrast to earlier reports from the Barents Sea where they have been recorded exclusively under multi-year ice.     

Improved error bounds for genetic distances from DNA sequences

The genetic distance between two DNA sequences may be measured by the average number of nucleotide substitutions per position that has occurred since the two sequences diverged from a common ancestor. Estimates of this quantity can be derived from Markov models for the substitution process, while the variances are estimated using the delta method and confidence intervals calculated assuming normality. However, when the sampling distribution of the estimator deviates from normality, such intervals will not be accurate. For simple one-parameter models of nucleotide substitution, we propose a transformation of normal confidence intervals, which yields an almost exact approximation to the true confidence intervals of the distance estimators. To calculate confidence intervals for more complicated models, we propose the saddlepoint approximation. A simulation study shows that the saddlepoint-derived confidence intervals are a real improvement over existing methods.     

Use of confidence radii to visualise significant differences in principal components analysis: Application to mammal assemblages at locations with different disturbance levels

Multivariate statistical analysis is a powerful method of examining complex datasets, such as species assemblages, that does not suffer from the oversimplification prevalent in many univariate analyses. However, identifying whether data points on a multivariate plot are clustered is subjective, as there is no determination of significant differences between the points and no indication of the level of confidence in those points. The validity of drawing such conclusions may therefore be considered suspect. This paper describes a method of bootstrapping calculated principal components to estimate a confidence radius, similar to confidence intervals in univariate techniques. Plotting 3D scatterplots of the principal components, with the size of the spherical point representative of the level of confidence of the estimate, gives a clear and visual indication of significant difference between the points — where the spheres overlap there is no significant difference. We apply the technique to mammal assemblages at sites in Epping Forest (Essex, UK) that differ in the level of disturbance present and find that differences between some sites that appear large using traditional principal components analysis are actually not significantly different at the 95% confidence level, while other sites do differ significantly. Sites that differ most in anthropogenic disturbance are not significantly different in terms of assemblage structure.     

Coralline algae indicate Pleistocene evolution from deep,open platform to outer barrier reef environments in the northern Great Barrier Reef margin

Coralline algae from a drill core in Ribbon Reef 5 have been used to interpret changes in the depositional palaeoenvironments in the northern Australian Great Barrier Reef over the last 790 ka. Three main coralline algal assemblages, each dominated by members of a particular subfamily, have been distinguished by quantitative analysis: (1) mastophoroid assemblages, usually occurring as crusts on corals, are typical of the shallowest reef settings; (2) lithophylloid assemblages within algal nodules may represent shallow-water, cooler environments or deeper reef subenvironments; and (3) melobesioid assemblages are characteristic of deeper-water platform areas. The algal assemblages between 96 and 210 m b.s.f. (metre below sea floor) record a fluctuating but progressive shallowing-upwards from deep, outer-platform to shallower, non-reefal depositional environments. Two intervening episodes dominated by mastophoroids represent two phases of reef growth. The section above 96 m b.s.f. comprises several stacked reefs in which mastophoroid crusts similar to the present-day shallow-water assemblages predominate.Electronic Supplementary Material Supplementary material is available for this article at .Communicated by: Geological Editor P.K. Swart     

Comparison of populations as a function of confidence intervals of gene probability

A new method for population comparison has been developed in order to determine the most discriminating systems in relation to diverse populations. The method compares pairs of populations on the basis of confidence intervals for allelic frequencies and does not require any previous assumption, such as normality of the population. A data set of 12 populations studied for Polymarker Kit (Roche) genetic systems, 13 biallelic systems (LDLR, GYPA, D7S8) and two systems with three alleles each (HBGG, GC), was considered. The analysis produced a total of 144 confidence intervals (12 populations x 12 alleles). The raw data were then analyzed comparing pairs of populations, allele by allele, through their respective confidence intervals. The method calculates the matrix of similarity between pairs of populations for each allele and eventually for each genetic system. Finally, the 12 populations were classified depending on the number of nondiscriminating alleles. The results of this method are compared to those produced by such usual techniques as Principal Component Analysis.     

High assemblage persistence in heterogeneous habitats: an experimental test with stream benthic algae

1. The persistence of biological assemblages is positively affected by spatial heterogeneity. This influence may be indirect, through increased species richness. Another possibility is the increased availability of refuges from disturbances, which would prevent local loss. 2. We conducted a field experiment to test the hypothesis that greater roughness (a form of spatial heterogeneity) on the surface of substrata allows higher persistence of assemblages of stream benthic algae and that this relationship does not depend on species richness. Samples were taken on six occasions from smooth and rough artificial substrata used for algal colonisation. We calculated the persistence of assemblages using two analytical approaches: the mean distance to group centroid and the sum of the Euclidean distances between consecutive sampling occasions, both in a multivariate space. We also subsampled the data to take into account differences in species richness between treatments and thus to evaluate the effect of species richness on persistence. 3. Assemblages on rough substrata were more persistent than assemblages on smooth substrata. The effects detected were not due to the greater species richness on rough substrata, since a higher persistence of the assemblages on rough substrata remained after the subsampling procedures. 4. Our results indicate a strong positive relationship between substratum roughness and the persistence of stream benthic algal assemblages. We suggest that this is due to the presence of physical refuges in heterogeneous habitats.     

The role of recruitment in structuring patterns of small-scale spatial variability in intertidal and subtidal algal turfs

Recruitment is often important in structuring patterns of distribution and abundance of algal assemblages. Intertidal and subtidal turfing algal assemblages consistently vary on small spatial scales (tens of centimetres), and this variability may be due to patterns of recruitment varying on similar spatial scales. The validity of this model was evaluated by testing the hypothesis that the numbers and types of taxa recruiting to turfs would vary at small spatial scales within intertidal and within subtidal habitats. Abundances of algal recruits were estimated on sandstone plates that were placed at a number of spatial scales within intertidal and within subtidal habitats (centimetres to tens of metres). Significant differences in entire assemblages were found only between habitats. This was explained by abundances of individual taxa, which generally varied between intertidal and subtidal habitats or between sites within habitats. Only small proportions of the overall spatial variation (dissimilarity) could be explained at the scale of replicate recruitment plates that were centimetres apart. Results indicate that while recruitment may contribute to differences between intertidal and subtidal habitats, it cannot explain the small-scale spatial variability in established turfing algal assemblages within these habitats. There was some evidence to suggest that recruitment may contribute to variability in established turfing algal assemblages but only over longer time scales than examined here.     

Grazing effects in macroalgal communities depend on timing of patch colonization

Rocky macroalgal assemblages are typically composed of patches differing in age and species composition and grazing is generally a very important modifier of such assemblages. We hypothesized that patch colonization time determines its algal community and that grazing effects depend on the colonization time and vary with depth. We created patches by placing empty substrates at two sublittoral depths over five consecutive months, manipulated grazer entry and determined the algal species composition in each patch in the next growing season. Distinct algal colonization periods resulted in different algal assemblages. Although algal communities in our study area consist mainly of opportunistic species, thus being highly dynamic, the resulting macroalgal assemblages differed in species richness, diversity, composition, and total biomass even a year after first colonization. Substrates close to the water-surface supported a higher species richness and diversity than those in the deeper littoral. The community characteristics, total density, total biomass and species richness were only slightly, if at all affected by grazing. However, individual algal species or taxa showed varying and even contrasting responses to grazing, often differently between depths and depending on colonization time. In the deeper littoral, but not close to the water surface, grazing increased the density of filamentous brown algae while reducing the green alga Cladophora glomerata. In these taxa, grazing effects were strongest in patches colonized during the early growing season. Grazing at the colonization stage had lasting consequences for the density of several individual species.     

金沙江上段浮游藻类和着生藻类群落格局及其与环境因子的关系比较研究

比较河流浮游藻类和着生藻类群落的时空格局及其与环境因子关系的差异,有助于了解两类藻的区别与联系。然而,目前这方面的研究还不多。基于2019年秋季和2020年夏季金沙江上段干流17个样点藻类及水体理化指标的调查数据,分析了不同季节浮游藻类和着生藻类群落结构及其主要环境驱动因子,比较了两类藻的多样性格局及其与环境关系的异同。结果发现,调查河段的浮游藻类和着生藻类均以硅藻为主,其中浮游藻类以极小曲壳藻(Achnanthes minutissima)、钝脆杆藻(Fragilaria capucina)、适中舟形藻(Navicula accomoda)为主要优势种,着生藻类以极小曲壳藻(Achnanthes minutissima)、扁圆卵形藻(Cocconeis placentula)、橄榄绿色异极藻(Gomphonema olivaceum)为主要优势种。浮游藻类和着生藻类秋季平均密度分别为:2.41×10~5个/L、9.43×10~3个/cm~2,均明显高于夏季的平均密度(4.84×10~4个/L、4.84×10~3个/cm~2)。两类藻的群落格局表现出明显的季节变化,但只有着生藻分类单元...     

Improved confidence intervals in quantitative trait loci mapping by permutation bootstrapping

The nonparametric bootstrap approach is known to be suitable for calculating central confidence intervals for the locations of quantitative trait loci (QTL). However, the distribution of the bootstrap QTL position estimates along the chromosome is peaked at the positions of the markers and is not tailed equally. This results in conservativeness and large width of the confidence intervals. In this study three modified methods are proposed to calculate nonparametric bootstrap confidence intervals for QTL locations, which compute noncentral confidence intervals (uncorrected method I), correct for the impact of the markers (weighted method I), or both (weighted method II). Noncentral confidence intervals were computed with an analog of the highest posterior density method. The correction for the markers is based on the distribution of QTL estimates along the chromosome when the QTL is not linked with any marker, and it can be obtained with a permutation approach. In a simulation study the three methods were compared with the original bootstrap method. The results showed that it is useful, first, to compute noncentral confidence intervals and, second, to correct the bootstrap distribution of the QTL estimates for the impact of the markers. The weighted method II, combining these two properties, produced the shortest and less biased confidence intervals in a large number of simulated configurations.     

Confidence Intervals for Population Allele Frequencies: The General Case of Sampling from a Finite Diploid Population of Any Size

The estimation of population allele frequencies using sample data forms a central component of studies in population genetics. These estimates can be used to test hypotheses on the evolutionary processes governing changes in genetic variation among populations. However, existing studies frequently do not account for sampling uncertainty in these estimates, thus compromising their utility. Incorporation of this uncertainty has been hindered by the lack of a method for constructing confidence intervals containing the population allele frequencies, for the general case of sampling from a finite diploid population of any size. In this study, we address this important knowledge gap by presenting a rigorous mathematical method to construct such confidence intervals. For a range of scenarios, the method is used to demonstrate that for a particular allele, in order to obtain accurate estimates within 0.05 of the population allele frequency with high probability (%), a sample size of is often required. This analysis is augmented by an application of the method to empirical sample allele frequency data for two populations of the checkerspot butterfly (Melitaea cinxia L.), occupying meadows in Finland. For each population, the method is used to derive % confidence intervals for the population frequencies of three alleles. These intervals are then used to construct two joint % confidence regions, one for the set of three frequencies for each population. These regions are then used to derive a % confidence interval for Jost''s D, a measure of genetic differentiation between the two populations. Overall, the results demonstrate the practical utility of the method with respect to informing sampling design and accounting for sampling uncertainty in studies of population genetics, important for scientific hypothesis-testing and also for risk-based natural resource management.     

Colonization rates and community structure of diatoms on three different rock substrata in a lotic system

Diatom assemblages were monitored at weekly intervals over a 5 week period on Verde limestone, Supai sandstone, and Andesitic basalt substrata in a mountain stream in northern Arizona, U.S.A. Density, Shannon-Weiner diversity, evenness, and community similarity (SIMI) were used to compare colonization patterns and community structure between individual substratum types. Average standing crop values were nearly two-fold higher on sandstone than on either basalt or limestone substrata after the first week of the study. It is proposed that differences in micro-surface features between substrata and possibly the rate of substratum solubilization may cause these differences in density early in the colonization period. Following the initial week, standing crop and community structure were significantly similar on all substrata for the remainder of the study period. Maximum densities were attained by the third week and remained relatively constant on all substrata for the remainder of the study.

SEM micrographs demonstrated that surfaces of submerged substrata in streams are modified after the first week by the accumulation of organic aggregates. The establishment of an “organic matrix” early in the colonization process may provide relatively similar attachment surfaces for microbial invasion. This appears to reduce the initial microtopographic differences displayed by substrata and allows for a more uniform colonization pattern.     

On Parametric Confidence Intervals for the Cost‐Effectiveness Ratio

When comparing two competing interventions, confidence intervals for cost‐effectiveness ratios (CERs) provide information on the uncertainty in their point estimates. Techniques for constructing these confidence intervals are much debated. We provide a formal comparison of the Fieller, symmetric and Bonferroni methods for constructing confidence intervals for the CER using only the joint asymptotic distribution of the incremental cost and incremental effectiveness of the two interventions being compared. We prove the existence of a finite interval under the Fieller method when the incremental effectiveness is statistically significant. When this difference is not significant the Fieller method yields an unbounded confidence interval. The Fieller interval is always wider than the symmetric interval, but the latter is an approximation to the Fieller interval when the incremental effectiveness is highly significant. The Bonferroni method is shown to produce the widest interval. Because it accounts for the likely correlation between cost and effectiveness measures, and the intuitively appealing relationship between the existence of a bounded interval and the significance of the incremental effectiveness, the Fieller interval is to be preferred in reporting a confidence interval for the CER.     

Confidence Intervals in Qtl Mapping by Bootstrapping

The determination of empirical confidence intervals for the location of quantitative trait loci (QTLs) was investigated using simulation. Empirical confidence intervals were calculated using a bootstrap resampling method for a backcross population derived from inbred lines. Sample sizes were either 200 or 500 individuals, and the QTL explained 1, 5, or 10% of the phenotypic variance. The method worked well in that the proportion of empirical confidence intervals that contained the simulated QTL was close to expectation. In general, the confidence intervals were slightly conservatively biased. Correlations between the test statistic and the width of the confidence interval were strongly negative, so that the stronger the evidence for a QTL segregating, the smaller the empirical confidence interval for its location. The size of the average confidence interval depended heavily on the population size and the effect of the QTL. Marker spacing had only a small effect on the average empirical confidence interval. The LOD drop-off method to calculate empirical support intervals gave confidence intervals that generally were too small, in particular if confidence intervals were calculated only for samples above a certain significance threshold. The bootstrap method is easy to implement and is useful in the analysis of experimental data.     

Do tadpoles affect leaf decomposition in neotropical streams?

1. Of the relatively few studies that have examined consequences of amphibian declines on stream ecosystems, virtually all have focused on changes in algae (or algal‐based food webs) and little is known about the potential effects of tadpoles on leaf decomposition. We compared leaf litter decomposition dynamics in two neotropical streams: one with an intact community of tadpoles (with frogs) and one where tadpoles were absent (frogless) as a result of a fungal pathogen that had driven amphibians locally extinct. The stream with tadpoles contained a diverse assemblage (23 species) of larval anurans, and we identified five species of glass frog (Centrolenidae) tadpoles that were patchily distributed but commonly associated with leaf detritus and organic sediments in pools. The latter reached total densities of 0–318 tadpoles m^?2. 2. We experimentally excluded tadpoles from single‐species leaf packs incubated over a 40‐day period in streams with and without frogs. We predicted that decomposition rates would be higher in control (allowing access of tadpoles) treatments in the study stream with frogs than in the frogless stream and, in the stream with frogs, in the control than in the tadpole exclusion treatment. 3. In the stream with frogs, Centrolene prosoblepon and Cochranella albomaculata tadpoles were patchily distributed in leaf packs (0.0–33.3 m^?2). In contrast to our predictions, leaf mass loss and temperature‐corrected leaf decomposition rates in control treatments were almost identical in our stream with frogs (41.01% AFDM lost, k_{degree day} = ?0.028 day^?1) and in the frogless stream (41.81% AFDM lost, k_{degree day} = ?0.027 day^?1) and between control and tadpole exclusion treatments within each stream. Similarly, there were no significant differences in leaf pack bacterial biomass, microbial respiration rates or macroinvertebrate abundance between treatments or streams. Invertebrate assemblages on leaf packs were similar between treatments (SIMI = 0.97) and streams (SIMI = 0.95) and were dominated by larval Chironomidae, Simuliidae (Diptera) and larval Anchytarsus spp. (Coleoptera). 4. In contrast to dramatic effects of grazing tadpoles on algal communities observed previously, tadpoles had no major effects on decomposition. While centrolenid tadpoles were common in the stream with frogs, their patchy distribution in both experimental and natural leaf packs suggests that their effects on detrital dynamics and microbes are probably more localised than those of grazing tadpoles on algae.     

EPIPELIC AND EPILITHIC DIATOM ASSEMBLAGES IN MONTEZUMA WELL NATIONAL MONUMENT,ARIZONA1

Epipelic and epilithic diatom assemblages in Montezuma Well National Monument, Arizona, were identified and analyzed by H' (species diversity), species number, J' (evenness), relative abundance, SIMI (similarity index), and DI (dissimilarity index) values. The epipelic assemblage was found to be a tri-dominant association of Cyclotella pseudostelligera f. parva Czar. & Blinn, Cocconeis placentula var. lineata (Ehr.) V.H. and Achnanthes linearis (W. Sm.) Grun. The epilithic assemblage was a tri-dominant association of Rhoicosphenia curvata (Kütz.) Grun. ex Rabh., Cy. Pseudostelligera f. parva and Synedra ulna (Nitz.) Ehr. Both associations persisted throughout the year. Of the 83 taxa observed, 51 were common to both assemblages, 24 were restricted to the epipelon, and 8 were restricted to the epilithon. On a yearly basis, the epipelic assemblage exhibited less diversity (H') than the epilithon, even though the latter exhibited fewer taxa. The use of mean diversity values was also determined to be unacceptable. Cy. Pseudostelligera f. parva and S. ulna appeared more abundant under high light intensity and duration, Fragilaria construens var. venter (Ehr.) Grun. favored low light intensity and duration, whereas A. linearis, R. curvata and Co. placentula var. lineata were tolerant of a variety of intensities and durations. On a yearly basis, both assemblages exhibited slight similarity (SIMI, DI). The use of SIMI values for comparing assemblages with few highly abundant taxa was determined to be unacceptable and under these conditions, the use of DI was recommended.     

The importance of shore height and host identity for amphipod assemblages

The spatial distribution of organisms associated with marine intertidal macroalgae may be a direct result of their tolerance to air exposure or an indirect consequence of the distribution of their host. We compared amphipod assemblages from five intertidal macroalgae to investigate their relationship with algal identity. To test the effect of height regardless of algal characteristics, we transplanted coralline algal turfs to three different levels within the intertidal zone and compared amphipod assemblages after 1 and 14 days. Interstitial volume was positively correlated to the abundance of amphipods, suggesting that this attribute may correspond better to the potential space for their occupation when compared to algal biomass, thallus volume or the ratio between thallus and interstitial volume. Algal level determined the structure of the amphipod assemblages. Upper-level (Acanthophora spicifera and Caulerpa racemosa) and intermediate-level (coralline) algae host similar amphipod assemblages dominated by Apohyale media, but different from lower-level algae (Padina gymnospora and Sargassum cymosum), which were dominated by Hyale niger. Ten of the 15 amphipod species reported from natural communities were found in the transplanted plots. Distinct pools of amphipod species colonized coralline transplants at upper and lower levels after 1 day. However, regardless of the position on the shore, transplanted coralline turfs supported similar assemblages after 14 days, indicating that algal identity is also important for species assemblages. Our results suggest that both height on the shore and host identity combine to determine the vertical structure of amphipod assemblages in the rocky intertidal.     

Confidence intervals for a normal mean following a group sequential test

This paper presents methodology based on the likelihood-ratio test, developed for construction of confidence intervals for a normal mean, following a group sequential test. Examples show that the confidence intervals produced by this method have accurate nominal probability of coverage and have generally shorter average length than that produced by Tsiatis, Rosner, and Mehta (1984, Biometrics 40, 797-803).