Predicting the species abundance distribution using a model food web

A large number of models of the species abundance distribution (SAD) have been proposed, many of which are generically similar to the log-normal distribution, from which they are often indistinguishable when describing a given data set. Ecological data sets are necessarily incomplete samples of an ecosystem, subject to statistical noise, and cannot readily be combined to yield a closer approximation to the underlying distribution. In this paper, we adopt the Webworld ecosystem model to study the predicted SAD in detail. The Webworld model is complex, and does not allow analytic examination of such features; rather, we use simulation data and an approach similar to that of ecologists analysing empirical data. By examining large sets of fully described data we are able to resolve features which can distinguish between models but which have not been investigated in detail in field data. We find that the power-law normal distribution is superior to both the log-normal and logit-normal distributions, and that the data can improve on even this at the high-population cut-off.     

Sampling species abundance distributions: resolving the veil-line debate

Preston's classic work on the theory of species abundance distributions (SADs) in ecology has been challenged by Dewdney. Dewdney contends that Preston's veil-line concept, relating to the shape of sample SADs, is flawed. Here, I show that Preston's and Dewdney's theories can be reconciled by considering the differing mathematical properties of the sampling process on logarithmic (Preston) versus linear (Dewdney) abundance scales. I also derive several related results and show, importantly, that one cannot reject the log-normal distribution as a plausible SAD based only on sampling arguments, as Dewdney and others have done.     

Abundance,biomass and diversity of ground-beetles (Col. Carabidae) as indicators of climatic change effects over elevation strata in Tenerife (Canary Islands)

Species relative importance distribution pattern changes of the ground-beetle assemblages were analyzed along elevation strata of Tenerife Island. The species importance estimates were expressed in terms of (i) activity density, as total catching of ground-beetle adults obtained with pitfall traps over each elevation stratum for one year, and (ii) biomass, as the total number of specimens caught multiplied by a mean dry weight in milligrams for the species. The K-dominance curves indicated moderate or insignificant perturbances, and patterns were sigmoidal following a truncated log-normal slightly skewed to the right, by using the Kolmogoroff–Smirnov test. The results also showed perceptible deviations from the truncated log-normal pattern (p < 0.05) mainly with biomass data. The disturbance through successional progress and perturbances by environmental warming and cooling could be assumed by deviations from the log-normal distribution among species. Thus, assuming that the assemblages of strata exhibited generally low similarity, the results will be arranged around the following four tracks: (1) the assemblage progressed toward highest abundances, dominance and a low-diversity equilibrium state in the cloud montane stratum, (2) the assemblage was subject to severe warming and dryness, lowest abundances with dominance in biomass, such that log-normal pattern was not shown in the basal stratum, (3) a non-equilibrium state in summer-xeric montane stratum maintained the highest diversity and an archetypical log-normal pattern was described for assemblage, and (4) assemblage stressed by cold semi-arid climate showed a certain tendency to log-normality and decrease in the diversity for the summit stratum. These results indicate that variation in ground-beetle assemblages by way of advanced evolutionary and adaptive trade-offs can best be understood as consequences of selective pressures by adverse climatic changes – perturbances – or seasonal climatic fluctuations and population dynamics – disturbances – according to the elevation stratum, which can generate different deviations from the log-normal pattern; these are more directly related to magnitude and frequency of local natural disturbance regimes and the productivity of the ecosystem.     

Modern benthic foraminifera on Banco Chinchorro,Quintana Roo,Mexico

Benthic foraminiferal assemblages may be used as environmental indicators on Banco Chinchorro, an isolated carbonate platform off the eastern coast of the Yucatan Peninsula. Seventy-seven species from 44 genera were identified in 14 surface sediment samples, which were collected along an E–W windward-to-leeward transect across the platform. A total of 15,493 foraminiferal tests (max. 1,200 tests per sample) were investigated and served as the basis of this study. As many taxa range throughout several platform zones, assemblages are better environmental indicators as compared to individual species. Four foraminiferal assemblages were identified using statistical methods including (1) a Homotrema assemblage, which occurs at the windward platform margin, (2) an Archaias-Homotrema assemblage which is found on the leeward margin and on platform interior coral patch reefs, (3) a Quinqueloculininae-Archaias-Rosalina assemblage of the western platform, and (4) an Archaias-Quinqueloculininae assemblage characteristic of the eastern platform interior. Environmental factors which influence variation in foraminiferal distribution and diversity on Banco Chinchorro include exposure to waves and currents and substrate (plant and algal growth). Sediment transport does not play a major role in Banco Chinchorro based on the observation that there are only limited amounts of taxa found outside their typical habitats, and, that mean grain-size and sorting of foraminiferal tests do not exhibit clear patterns. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Phylogenetic and ecological correlates with male adult life span of rainforest butterflies

Adult life spans are an important life history variable in butterflies, but have rarely been investigated in cross-species comparisons. Using 377 captive specimens from a Bornean rainforest assemblage (wild catches with low wing wear, belonging to 102 species) under standardized feeding conditions, substantial differences in the average adult life spans of species were observed, ranging from few days to almost three weeks. Analyses were carried out on the 30 most common species (247 specimens, only males). They revealed that related taxa had similar life spans, with nymphalids and some lycaenid groups being generally longer-lived than other taxa. Two traits of adult feeding behaviour are strong predictors of longevity in multivariate, phylogeny-controlled analyses: Fruit-feeding (versus nectar feeding) is associated with longer life spans, whereas the occurrence of mud-puddling behaviour is associated with short adult life. Larval feeding, male territoriality and a number of morphological measures showed no independent relationships with life spans. Furthermore, there was no evidence that long-lived species have larger geographic distributions (i.e., are better dispersers). Explanatory hypotheses are put forward, which may be a starting point for further investigations. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Activity density versus biomass distribution patterns among ground-beetle species as bioindicator for conservation planning over a wide range of altitudes in Tenerife (Canary Islands)

The ground-beetle assemblage was examined as an ecological indicator on elevation gradients running from sea level to 2360 m in Southeastern Tenerife. The approach was tested by fitting for one sampling year a singly left-truncated log-normal distribution to activity density and biomass data of species sampled by pitfall trapping. Forty-one sampling plots were regularly located over the wide range of altitudes. Small samples of individuals were selected to estimate the average biomass of each species.This research tests, in the first place, the null hypothesis that the assemblage of species does not follow a singly left-truncated log-normal distribution as a result of pressure from anthropogenic disturbances. Secondly, the study also examines the hypothesis of the prevailing of K-selection species in undisturbed mature stages of ecological succession. By way of prediction, it is posited that the highest gamma diversity of ground-beetles would be at the biomass scale, as a result of reduction of dominance, since disturbance effects could affect more to the species with specialized strategies for highly developed and well-preserved stages of ecological succession. The results showed significant changes in the sequence of species, which depends on whether one analyzes the total biomass or total activity density. The results confirm that the observed distributions were consistent with a left-truncated log-normal distribution pattern. The diversity calculated as log-normal λ on the basis of activity density was higher than the diversity calculated on the basis of the biomass of species. Consequently, the Canarian terrestrial ecosystems along the elevation gradients was evolved and still well preserved with environments inhabited by species tending toward K-selection traits.     

Is there an ecological basis for species abundance distributions?

Community ecologists have attempted to explain species abundance distribution (SAD) shape for more than 80 years, but usually without relating SAD shape explicitly to ecological variables. We explored whether the scale (total assemblage abundance) and shape (assemblage evenness) of avifaunal SADs were related to ecological covariates. We used data on avifaunas, in-site habitat structure and landscape context that were assembled from previous studies; this amounted to 197 transects distributed across 16,000 km² of the box-ironbark forests of southeastern Australia. We used Bayesian conditional autoregressive models to link SAD scale and shape to these ecological covariates. Variation in SAD scale was relatable to some ecological covariates, especially to landscape vegetation cover and to tree height. We could not find any relationships between SAD shape and ecological covariates. SAD shape, the core component in SAD theory, may hold little information about how assemblages are governed ecologically and may result from statistical processes, which, if general, would indicate that SAD shape is not useful for distinguishing among theories of assemblage structure.     

How species richness and total abundance constrain the distribution of abundance

The species abundance distribution (SAD) is one of the most intensively studied distributions in ecology and its hollow‐curve shape is one of ecology's most general patterns. We examine the SAD in the context of all possible forms having the same richness (S) and total abundance (N), i.e. the feasible set. We find that feasible sets are dominated by similarly shaped hollow curves, most of which are highly correlated with empirical SADs (most R² values > 75%), revealing a strong influence of N and S on the form of the SAD and an a priori explanation for the ubiquitous hollow curve. Empirical SADs are often more hollow and less variable than the majority of the feasible set, revealing exceptional unevenness and relatively low natural variability among ecological communities. We discuss the importance of the feasible set in understanding how general constraints determine observable variation and influence the forms of predicted and empirical patterns.     

Artifactions in the Log-Transformation of Species Abundance Distributions

One of the most frequently studied pattern in ecology is the Species Abundance Distribution (SAD) that represents the frequency distribution of species abundances in an assemblage. Two main approaches to displaying such information have been employed: histograms constructed using exponentially increasing bin widths as pioneered by Preston (1948), and plots of ranked species abundances. While both techniques have been extensively used in the investigation of community ecology hypotheses, the Preston-style species-abundance histogram has become central to current debates concerning appropriate characterization of the SAD and the processes generating it. Here we point out an important issue in the Preston approach that has profound implications to this debate: by employing bins of exponentially increasing size, the resultant histogram may display a hump-shaped pattern that is not congruent with the shape of the untransformed distribution. Moreover, any distribution constructed from log-transformed abundances will necessarily reveal at least one internal mode, even when the non-transformed probability density function is strictly decreasing. We warn against misinterpretation of such transformed datasets, and suggest that rank-abundance plots, which are equivalent to the cumulative distribution functions extensively used in other branches of science, represent a more informative approach as they allow for better discrimination between a number of probability distributions. Ecologists should be aware that logarithmic transformation often generates a log-normal-like shape, and are encouraged to use rank abundance curves to visualize and analyze species-abundance patterns.     

Spatial and seasonal variations in benthic algal assemblages in streams in monsoonal Hong Kong

Samples from stone surfaces were collected in pools within four unpolluted hillstreams (two shaded and two unshaded) in monsoonal Hong Kong (lat. 23°N) to elucidate the extent of spatial (within and among streams) and temporal (seasonal) variations in algal biomass and assemblage composition. Sampling continued for over 12 months, incorporating the dry season when streams were at baseflow, and the wet season when spates were frequent. We anticipated that algal biomass would be lower in shaded streams and during the wet season, with associated seasonal differences in assemblage composition or relative abundance of different growth forms (e.g. erect versus prostrate). Benthic chlorophyll a (a proxy for algal biomass) varied among streams from an annual mean of 11.0–22.3 mg m⁻². Dry-season standing stocks were 18% higher than during the wet season when spate-induced disturbance reduced algal standing stocks. Algal biomass varied significantly at the stream scale, but not at the pool scale, and was lower in unshaded streams, where standing stocks may have been limited by high densities of algivorous balitorid loaches (mainly Pseudogastromyzon myersi). An overriding effect of grazers on algal biomass could also have reduced variations resulting from spate-induced disturbance. Significant differences in assemblage composition among streams, which were dominated by diatoms and cyanobacteria (totally 82 taxa) were not systematically related to shading conditions. Seasonal variations in algal assemblages were statistically significant but rather minor, and did not involve major shifts in composition or growth form caused by spate-induced disturbance. The abundance of filamentous cyanobacteria in all the streams may have been due to ‘gardening’ by balitorid loaches that removed erect or stalked diatoms and favoured cyanobacteria that persist through basal regeneration of filaments. This explanation requires validation through manipulative experiments. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Handling editor: Luis Mauricio Bini     

Distribution patterns of benthic foraminifera across the Ypresian–Lutetian Gorrondatxe section,Northern Spain: Response to sedimentary disturbance

We present a study of benthic foraminiferal assemblages from an Ypresian–Lutetian distal submarine fan system in the lower bathyal Gorrondatxe section (Basque-Cantabrian Basin, northern Spain). The objective of our study is to analyze the benthic foraminiferal distribution patterns and their response to sedimentary disturbance and related factors.Assemblages contain a high percentage of allochthonous taxa, such as asterigerinids and other shallow water taxa, which were transported downslope by turbidity currents.Detailed quantitative analyses, supported by R-mode cluster and Detrended Correspondence Analyses (after removing allochthonous taxa from the foraminiferal counts) allowed us to identify 6 assemblages that are divided into two groups related to the turbidite content in the Gorrondatxe section. Assemblages 1, characteristic of the turbidite-poor intervals with low sedimentary disturbance, include assemblage 1a (with highly diverse common middle–lower bathyal calcareous taxa) assemblage 1b (with common agglutinated taxa, mainly trochamminids), and assemblage 1c (characterized by calcareous taxa that are also common in the turbidite-rich interval).Assemblages 2, characterized by a high dominance, prevail in the turbidite-rich interval, and include assemblage 2a (characterized by the dominance of infaunal bolivinids and epifaunal cibicids), assemblage 2b (typified by moderate to low diversity and dominated by deep-infaunal Globobulimina species), and assemblage 2c (typified by very abundant suspension-feeding astrorhizids). The high abundance of bolivinids and Globobulimina species may be related to an enhanced input of low-quality organic matter transported by turbidity currents to the seafloor, representing different stages of recolonisation after disturbance and different energy regimes. High current activity was probably responsible for the abundance of cibicids, while moderate to low diverse and high dominance assemblages characterize the recolonisation of the substrate after disturbance.We conclude that sedimentary disturbance and other related factors such as current activity, resuspension of sediments at the seafloor, and supply of organic matter (and its quality) played an important role in the distribution of benthic foraminifera in the Gorrondatxe section. The identification of allochthonous taxa emerges as an essential aspect of the study of environments with sedimentary disturbance.     

THE TECHNIQUE OF LABELLED MITOSES: ANALYSIS BY AUTOMATIC CURVE-FITTING

An improved method is described for the analysis of data obtained by the technique of labelled mitoses. It is a development of the method described by Barrett (1966) in which theoretical curves are computed on the basis of a model which assumes that the phases G¹, S and G² are described by independent log-normal distributions; the analysis consists in finding a form of this model which gives a labelled mitoses curve which is the best fit to the available data. This fitting procedure has now been made automatic. No comprehensive indication of the goodness of fit can be given, although in the analysis of over fifty sets of data the method appears to have worked well.
A supplementary computer program is described which, on the basis of three separate assumed modes of cell loss, calculates the form of the age distributions and theoretical continuous labelling curves. This allows growth fraction to be calculated in a way which takes account of the distribution of phase durations and the non-rectangular age distributions of expanding cell populations. It also gives an opportunity to study the implications of continuous labelling data as regards the mode of cell loss.
A comparison is made between the present method of labelled mitoses curve analysis and the empirical rules which have often been used.     

A ‘fast-food approach’ to the standardization of quadratic diversity

Abstract

Intuitively, a community composed of ecologically dissimilar taxa is more diverse than a community composed of more similar taxa. However, since traditional diversity indices such as Shannon's entropy or Simpson's diversity are computed solely from the relative abundances of a given species assemblage, they cannot account for ecological differences between species. There have been recent developments regarding the use of quadratic entropy, a diversity index that incorporates both species relative abundances and a measure of the pairwise ecological differences between species. In this paper we firstly show that under some specific circumstances quadratic entropy can be additively decomposed into α- β- and γ-diversities, a property that renders it a desirable measure of diversity in the ecological practice. Next, we suggest a quick and simple method for obtaining a standardized version of quadratic entropy that may allow an easier interpretation of the resulting diversity values.     

Local distribution of macrophytes and consequences for sampling methods in large rivers

During the years 2003 and 2004, the distribution of macrophytes was studied at eight sites in two large rivers in the southwest of France (the Dordogne and Garonne). Using a pinpoint method, we obtained 7,083 observations and recorded physical parameters such as depth, distance from bank, water velocity, and substrate type. By using logistic regressions, we showed that a combination of these factors significantly influences the distribution of macrophytes. This enabled us to highlight transversal distribution patterns. Helophyte spermatophytes, free-floating taxa, and most of the nonanchored algae were characteristic of the shallow areas located near the banks. The deepest areas were characterized by a reduced number of species with a majority of submerged spermatophytes which are resistant to high velocity, anchored algae, and bryophytes. These results can be used to implement the Macrophyte Biological Index for Rivers (IBMR) for large rivers. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Handling editor: S. M. Thomaz     

The Atlantic elements in the Swiss flora: distribution, diversity, and conservation status

The purpose of this study was to examine the composition, distribution, ecology, and conservation status of the Atlantic elements of the Swiss flora. About 195 Atlantic and 80 Mediterranean–Atlantic vascular plant species of the European flora have been used as the basis for our analysis. The complete list of 3,143 taxa has been used as the reference for the Swiss flora. The distributions of the species are illustrated in coincidence maps based on the computer database of the Data Centre of the Swiss Flora in Geneva, Switzerland. Our study demonstrates clearly that the Atlantic flora of Europe requires a new biogeographical appraisal. The Swiss flora comprises 66 Atlantic and Mediterranean–Atlantic taxa, which are taxonomically and ecologically highly diverse. Switzerland contains 44% of all European Sub-Atlantic plants. This confirms the Sub-Atlantic geographical position of Switzerland. Only one Eu-Atlantic species growing in Switzerland, Vicia orobus, can be classified as native with certainty. This species is critically endangered and merits the highest conservation priority. Although a very alpine country, Switzerland has a relatively large number of Mediterranean–Atlantic species. The Atlantic and Mediterranean–Atlantic plants are a very threatened group in Switzerland, with wetland plants the most imperilled ecological group. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

On plotting species abundance distributions

1. There has been a revival of interest in species abundance distribution (SAD) models, stimulated by the claim that the log-normal distribution gave an underestimate of the observed numbers of rare species in species-rich assemblages. This led to the development of the neutral Zero Sum Multinomial distribution (ZSM) to better fit the observed data. 2. Yet plots of SADs, purportedly of the same data, showed differences in frequencies of species and of statistical fits to the ZSM and log-normal models due to the use of different binning methods. 3. We plot six different binning methods for the Barro Colorado Island (BCI) tropical tree data. The appearances of the curves are very different for the different binning methods. Consequently, the fits to different models may vary depending on the binning system used. 4. There is no agreed binning method for SAD plots. Our analysis suggests that a simple doubling of the number of individuals per species in each bin is perhaps the most practical one for illustrative purposes. Alternatively rank-abundance plots should be used. 5. For fitting and testing models exact methods have been developed and application of these does not require binning of data. Errors are introduced unnecessarily if data are binned before testing goodness-of-fit to models.     

Diversity: between neutrality and structure

Here I present an integrated framework for species abundance distributions (SADs) that goes beyond the neutral theory without relying on complex mechanistic models. I give some general mathematical results on the relationship between SADs and their underlying dynamics, and analyse an extensive set of marine phytoplankton data in order to test the neutral theory against this broader framework.
The main theoretical and empirical results are: (i) the logseries, which is the SAD produced by simple neutral models without migration, is quite robust in response to additional factors, including some forms of niche segregation; (ii) when there is a small but significant deviation from a logseries, the SAD will generally have the form of a power law, regardless of the specific mechanisms; (iii) when the deviation is moderate, the SAD will generally have the form of a lognormal, regardless of the specific mechanisms; (iv) although in a wide range of situations neutral and non-neutral dynamics cannot be distinguished from the SAD alone, some empirical SADs do have the fingerprint of non-neutrality: this is the case of marine dinoflagellates, in contrast to marine diatoms, which adjust to neutral theory predictions. The results for marine phytoplankton illustrate that both neutral and non-neutral mechanisms coexist in nature, and seem to have different weights in different groups of organisms.
In addition to the above findings, I discuss several related contributions and point out some important pitfalls in the literature.     

Comparison study of the modern ostracod associations in the Kara and Laptev seas: Ecological aspects

Recent ostracod assemblages were investigated from coretop sediment samples collected in the eastern Kara Sea from water depths down to 300 m. A total of 45 species were identified, 27 of them were reported for the Kara Sea for the first time. The Kara Sea data were compared with our results on the distribution of ostracods in the eastern Laptev Sea. The spatial distribution of recent taxa and the ecological groupings demonstrate a clear relation to dominant environmental factors which range from estuarine to full-marine conditions. Four assemblages related to average summer bottom water salinities were established: (1) a freshwater assemblage from the inner estuaries of the Ob' and Yenisei rivers with salinities less than 2 and from thermokarst lagoons of the southern Laptev Sea coast with strong salinization in winter; (2) a brackishwater assemblage of the outer estuaries of the Ob' and Yenisei rivers with salinities up to 26; (3) a mixed euryhaline–marine assemblage dominated by euryhaline species Paracyprideis pseudopunctillata and Heterocyprideis sorbyana from the inner shelf river-affected zone of the Kara and Laptev seas, where salinities range between 26 and 32; (4) a taxonomically diverse marine assemblage dominated by shallow-water marine taxa from the northern parts of the Kara and Laptev shelves and upper continental slope with stable bottom environments and a salinity higher than 32. Abundant euryhaline species found at greater water depths are identified as part of an ice-rafted assemblage. They are possibly entrained into the newly formed fast ice during autumn storms and freeze-up period and then transported to the distal open-sea areas during summer.     

Villafranchian-Galerian mammal faunas transition in South-Western Europe. The case of the late Early Pleistocene mammal fauna of the Frantoio locality,Arda River (Castell’Arquato,Piacenza, Northern Italy)

We investigated the fossil mammal assemblage from the late Early Pleistocene (early Galerian) site of the Arda River. Seven taxa were identified: one carnivore (Ursus dolinensis), five artiodactyls (Sus strozzii, Pseudodama farnetesis, Praemegaceros sp., Bison sp., and Hippopotamus sp.) and one perissodactyl (Stephanorhinus hundsheimensis). The Arda River faunal assemblage includes taxa already present in the Villafranchian, such as Pseudodama and Sus strozzii. The bear U. dolinensis and the bison, a more evolved form than Bison (Eobison), are taxa typical of the beginning of the Galerian mammal age. Paleontological, sedimentological and paleobotanical data point towards the presence of woodlands settled on an alluvial plain with patches of grassland dated around 1.0 Ma. The continental sediments of the Arda River represent one of the first steps of the forming of the alluvial Po valley.