Determining adequate trapping effort and species richness using species accumulation curves for environmental impact assessments

Abstract Environmental impact assessments (EIA) require that the proponent indicates the potential impact that a development will have on the biodiversity of the area. As part of this assessment it is normal practice to inventory the vertebrate species in the area. We show here how species accumulation curves can be used as a tool by environmental consultants to indicate the adequacy of their trapping effort and predict species richness for a disturbance site. The shape of a species accumulation curve is influenced by the number of species in an assemblage and the proportional number of singletons (rarely caught species) in the survey sample. We provide guidelines for the number of individuals that need to be caught in a trapping program to achieve 80% and 90% of the species in a habitat, and we indicate how this number can be adjusted to accommodate variations in relative species abundance.     

Assessing biodiversity with species accumulation curves; inventories of small reptiles by pit‐trapping in Western Australia

Abstract We examined 11 non‐linear regression models to determine which of them best fitted curvilinear species accumulation curves based on pit‐trapping data for reptiles in a range of heterogeneous and homogenous sites in mesic, semi‐arid and arid regions of Western Australia. A well‐defined plateau in a species accumulation curve is required for any of the models accurately to estimate species richness. Two different measures of effort (pit‐trapping days and number of individuals caught) were used to determine if the measure of effort influenced the choice of the best model(s). We used species accumulation curves to predict species richness, determined the trapping effort required to catch a nominated percentage (e.g. 95%) of the predicted number of species in an area, and examined the relationship between species accumulation curves with diversity and rarity. Species richness, diversity and the proportion of rare species in a community influenced the shape of species accumulation curves. The Beta‐P model provided the best overall fit (highest r²) for heterogeneous and homogeneous sites. For heterogeneous sites, Hill, Rational, Clench, Exponential and Weibull models were the next best. For homogeneous habitats, Hill, Weibull and Chapman–Richards were the next best models. There was very little difference between Beta‐P and Hill models in fitting the data to accumulation curves, although the Hill model generally over‐estimated species richness. Most models worked equally well for both measures of trapping effort. Because the number of individuals caught was influenced by both pit‐trapping effort and the abundance of individuals, both measures of effort must be considered if species accumulation curves are to be used as a planning tool. Trapping effort to catch a nominated percentage of the total predicted species in homogeneous and heterogeneous habitats varied among sites, but even for only 75% of the predicted number of species it was generally much higher than the typical effort currently being used for terrestrial vertebrate fauna surveys in Australia. It was not possible to provide a general indication of the effort required to predict species richness for a site, or to capture a nominated proportion of species at a site, because species accumulation curves are heavily influenced by the characteristics of particular sites.     

A comparison of pitfall traps with bait traps for studying leaf litter ant communities.

A comparison of pitfall traps with bait traps for sampling leaf litter ants was studied in oak-dominated mixed forests during 1995-1997. A total of 31,732 ants were collected from pitfall traps and 54,694 ants were collected from bait traps. They belonged to four subfamilies, 17 genera, and 32 species. Bait traps caught 29 species, whereas pitfall traps caught 31 species. Bait traps attracted one species not found in pitfall traps, but missed three of the species collected with pitfall traps. Collections from the two sampling methods showed differences in species richness, relative abundance, diversity, and species accumulation curves. Pitfall traps caught significantly more ant species per plot than did bait traps. The ant species diversity obtained from pitfall traps was higher than that from bait traps. Bait traps took a much longer time to complete an estimate of species richness than did pitfall traps. Little information was added to pitfall trapping results by the bait trapping method. The results suggested that the pitfall trapping method is superior to the bait trapping method for leaf litter ant studies. Species accumulation curves showed that sampling of 2,192+/-532 ants from six plots by pitfall traps provided a good estimation of ant species richness under the conditions of this study.     

Assessment of the diversity and abundance of terrestrial mangrove arthropods in southern New South Wales,Australia

Abstract The diversity and abundance of arboreal and flying arthropods, in three mangrove patches along the south coast of New South Wales, Australia, was investigated to determine the degree of spatial variability in the assemblages among patches. Intercept traps and restricted canopy fogging were used to sample the communities at Minnamurra, Bonnievale and Kurnell. Twelve orders of arthropods were detected, incorporating 252 morphospecies. Abundance, species richness and species composition were very similar across all patches, the variation being much smaller than expected. These findings suggest that the composition of the arboreal and flying fauna associated with mangrove patches are very similar among patches, but preliminary results also showed that species composition could be highly variable within a patch. Variation between the trapping methods was large, as expected . Intercept trapping and restricted canopy fogging techniques were found to sample different suites of species and therefore complement each other well in sampling programs. Cumulative species curves differed between time periods but generally were flatter for intercept traps than for restricted canopy fogging. Results suggested, for a given level of effort, intercept traps caught a more representative sample of the species composition available to them.     

Parasitic worms: how many really?

Accumulation curves are useful tools to estimate species diversity. Here we argue that they can also be used in the study of global parasite species richness. Although this basic idea is not completely new, our approach differs from the previous ones as it treats each host species as an independent sample. We show that randomly resampling host–parasite records from the existing databases makes it possible to empirically model the relationship between the number of investigated host species, and the corresponding number of parasite species retrieved from those hosts. This method was tested on 21 inclusive lists of parasitic worms occurring on vertebrate hosts. All of the obtained models conform well to a power law curve. These curves were then used to estimate global parasite species richness. Results obtained with the new method suggest that current predictions are likely to severely overestimate parasite diversity.     

On the estimation of species richness based on the accumulation of previously unrecorded species

Estimation of species richness of local communities has become an important topic in community ecology and monitoring. Investigators can seldom enumerate all the species present in the area of interest during sampling sessions. If the location of interest is sampled repeatedly within a short time period, the number of new species recorded is typically largest in the initial sample and decreases as sampling proceeds, but new species may be detected if sampling sessions are added. The question is how to estimate the total number of species. The data collected by sampling the area of interest repeatedly can be used to build species accumulation curves: the cumulative number of species recorded as a function of the number of sampling sessions (which we refer to as “species accumulation data”). A classic approach used to compute total species richness is to fit curves to the data on species accumulation with sampling effort. This approach does not rest on direct estimation of the probability of detecting species during sampling sessions and has no underlying basis regarding the sampling process that gave rise to the data. Here we recommend a probabilistic, nonparametric estimator for species richness for use with species accumulation data. We use estimators of population size that were developed for capture‐recapture data, but that can be used to estimate the size of species assemblages using species accumulation data. Models of detection probability account for the underlying sampling process. They permit variation in detection probability among species. We illustrate this approach using data from the North American Breeding Bird Survey (BBS). We describe other situations where species accumulation data are collected under different designs (e.g., over longer periods of time, or over spatial replicates) and that lend themselves to of use capture‐recapture models for estimating the size of the community of interest. We discuss the assumptions and interpretations corresponding to each situation.     

Species diversity in vertical, horizontal, and temporal dimensions of a fruit-feeding butterfly community in an Ecuadorian rainforest

To test the hypotheses that fruit-feeding nymphalid butterflies are randomly distributed in space and time, a community of fruit-feeding nymphalid butterflies was sampled at monthly intervals for one year by trapping 6690 individuals of 130 species in the canopy and understory of four forest habitats: primary, higraded, secondary, and edge. The overall species abundance distribution was well described by a lognormal distribution. Total species diversity (γ-diversity) was partitioned into additive components within and among community subdivisions (α-diversity and β-diversity) in vertical, horizontal and temporal dimensions. Although community subdivisions showed high similarity (1 —β-diversity/γ-diversity), significant β-diversity existed in each dimension. Individual abundance and observed species richness was lower in the canopy than in the understory. However, rarefaction analysis and species accumulation curves revealed that canopy had higher species richness than understory. Observed species richness was roughly equal in all habitats, but individual abundance was much greater in edge, largely due to a single, specialist species. Rarefaction analysis and species accumulation curves showed that edge had significantly lower species richness than all other habitats. Samples from a single habitat, height and time contained only a small fraction of the total community species richness. This study demonstrates the feasibility, and necessity, of large-scale, long-term sampling in multiple dimensions for accurately measuring species richness and diversity in tropical forest communities. We discuss the importance of such studies in conservation biology.     

Ground-foraging ants (Hymenoptera: Formicidae) and rainfall effect on pitfall trapping in a deciduous thorn woodland (caatinga), Northeastern Brazil

The semi-arid Caatinga is the fourth largest biome of Brazil, which biota still remains one of the most poorly known, especially with regard to invertebrate groups. In this study, a ground-foraging ant assemblage was surveyed during one year and the effect of rainfall on pitfall trapping was assessed. The study was performed in an area located in the municipality of Pentecoste (3 degrees 48' S - 39 degrees 20' W), in the State of Ceará. A 200m transect with 20 equidistant sampling points was established. Transect sampling was performed once a month during 12 months, over the period August 2008-August 2009. At each sampling point, a pitfall trap partially filled with a mixture of ethanol and monoethylene glycol was placed at the beginning of each month and remained in the field for seven days. 39 species belonging to six subfamilies and 19 genera, plus two unidentified species, were collected, with Pheidole (10 spp.) and Camponotus (8 spp.) being the taxa with the most species. 23 species were frequent, being found in more than 50% of the 12 transect samplings. Five species had an intermediate frequency (25 to 50%), while 13 were relatively infrequent (less than 25%). Most of the species (22) showed low occurrence, being found in less than 10% of the 240 samples (20 samples each month, during 12 months). Only five species were collected in more than 50% of the samples, those species being also responsible for most of the total abundance (number of captured individuals of all species) observed each month. The species-accumulation curves (observed and estimated) indicated that sampling sufficiency was attained, and that about 92% of the estimated ground-foraging ant fauna had been collected. 40 and 29 species were collected in the dry and rainy season, respectively, with monthly species richness ranging from 13 to 28. The total ant abundance showed a drastic decrease during the rainy season, and a negative linear correlation was found between rainfall and total ant abundance (R2 = 0.68). A similar negative linear correlation was found for species occurrences against rainfall (R2 = 0.71), and for mean number of species per pitfall trap against rainfall (R2 = 0.71). However, some species showed equal abundance, occurrence and mean number of individuals per pitfall trap in both seasons, while others showed a much higher abundance and occurrence during the rainy season. Pitfall trapping as a method to sample ground-foraging ant assemblage of the Caatinga biome and potential factors responsible for lower pitfall trap performance during rainy season are discussed.     

Effect of species richness and relative abundance on the shape of the species accumulation curve

Abstract We explain how species accumulation curves are influenced by species richness (total number of species), relative abundance and diversity using computer‐generated simulations. Species richness defines the boundary of the horizontal asymptote value for a species accumulation curve, and the shape of the curve is influenced by both relative abundance and diversity. Simulations with a high proportion of rare species and a few abundant species have a species accumulation curve with a low ‘shoulder’ (inflection point on the ordinate axis) and a long upward slope to the asymptote. Simulations with a high proportion of relatively abundant species have a steeply rising initial slope to the species accumulation curve and plateau early. Diversity (as measured by Simpson's and Shannon–Weaver indices) for simulations is positively correlated with the initial slope of the species accumulation curve. Species accumulation curves cross when one simulation has a high proportion of both rare and abundant species compared with another that has a more even distribution of abundance among species.     

Estimating abundance from detection–nondetection data for randomly distributed or aggregated elusive populations

Estimating abundance is important in many ecological studies in order to understand the spatial and temporal dynamics of a population, which can assist in management and conservation. However, direct estimates of abundance can be difficult and expensive to obtain, particularly for wide-ranging, rare or elusive species. An alternative – estimating from detection-nondetection data – is a challenging but alluring concept to ecologists since the cost and effort of a study can be greatly reduced. This paper describes a method for estimating the abundance of randomly distributed or aggregated populations by using binary data where the probability of detection is less than one. The performances of the models were evaluated by computer simulations comprising 1620 cases. The results show that the accuracy of the abundance estimates increases as the sampling rate, efficiency of survey method, and the number of repeated surveys increase, whereas the accuracy declines as individuals become more aggregated. For a randomly distributed population, using a sampling rate of 0.05 in a survey method with a detection probability of 0.5, and repeating surveys three times provides sufficient accuracy of abundance. For an aggregated population, to achieve reasonably accurate abundance estimates the sampling rate should be doubled and each cell should be repeatedly surveyed on 4 to 6 occasions.     

Detecting temporal trends in species assemblages with bootstrapping procedures and hierarchical models

Quantifying patterns of temporal trends in species assemblages is an important analytical challenge in community ecology. We describe methods of analysis that can be applied to a matrix of counts of individuals that is organized by species (rows) and time-ordered sampling periods (columns). We first developed a bootstrapping procedure to test the null hypothesis of random sampling from a stationary species abundance distribution with temporally varying sampling probabilities. This procedure can be modified to account for undetected species. We next developed a hierarchical model to estimate species-specific trends in abundance while accounting for species-specific probabilities of detection. We analysed two long-term datasets on stream fishes and grassland insects to demonstrate these methods. For both assemblages, the bootstrap test indicated that temporal trends in abundance were more heterogeneous than expected under the null model. We used the hierarchical model to estimate trends in abundance and identified sets of species in each assemblage that were steadily increasing, decreasing or remaining constant in abundance over more than a decade of standardized annual surveys. Our methods of analysis are broadly applicable to other ecological datasets, and they represent an advance over most existing procedures, which do not incorporate effects of incomplete sampling and imperfect detection.     

Estimating trends of population decline in long-lived marine species in the Mediterranean Sea based on fishers' perceptions

We conducted interviews of a representative sample of 106 retired fishers in Italy, Spain and Greece, asking specific questions about the trends they perceived in dolphin and shark abundances between 1940 and 1999 (in three 20 year periods) compared to the present abundance. The large marine fauna studied were not target species of the commercial fleet segment interviewed (trawl fishery). The fishers were asked to rank the perceived abundance in each period into qualitative ordinal classes based on two indicators: frequency of sightings and frequency of catches (incidental or intentional) of each taxonomic group. The statistical analysis of the survey results showed that both incidental catches and the sighting frequency of dolphins have decreased significantly over the 60+ years of the study period (except for in Greece due to the recent population increase). This shows that fishers' perceptions are in agreement with the declining population trends detected by scientists. Shark catches were also perceived to have diminished since the early 1940s for all species. Other long-lived Mediterranean marine fauna (monk seals, whales) were at very low levels in the second half of the 20(th) century and no quantitative data could be obtained. Our study supports the results obtained in the Mediterranean and other seas that show the rapid disappearance (over a few decades) of marine fauna. We show that appropriately designed questionnaires help provide a picture of animal abundance in the past through the valuable perceptions of fishers. This information can be used to complement scientific sources or in some cases be taken as the only information source for establishing population trends in the abundance of sensitive species.     

Invertebrate communities on Western Australian eucalypts: A comparison of branch clipping and chemical knockdown procedures

Chemical knockdown and branch clipping procedures were used in wandoo (Eucalyptus wandoo) woodland and jarrah (E. marginata)/marri (E. calophylla) open-forest to sample arboreal invertebrate faunas on three species of Western Australian eucalypts. Jarrah was sampled in both habitats and had significantly lower invertebrate populations and a less diverse fauna than either wandoo or marri. The two procedures provided similar results with respect to the relative abundance of invertebrates on each plant species but the knockdowns sampled a more diverse fauna, including species sheltering in or on bark. Chemical knockdowns underestimated the abundance of sessile invertebrates, such as psyllids. Branch clipping sampled insufficient numbers of large, mobile, or cryptic invertebrates to estimate abundances, but provided a more accurate estimate of the abundance of sessile, leaf-dwelling organisms. Neither procedure provides a complete sample of arboreal invertebrates, but they are complementary. When used in conjunction with each other a more complete estimate of arboreal invertebrate abundance and diversity is obtained. Both procedures can be used concurrently with only a small increase in field time.     

Still a host of hosts for Wolbachia: analysis of recent data suggests that 40% of terrestrial arthropod species are infected

Wolbachia are intracellular bacteria that manipulate the reproduction of their arthropod hosts in remarkable ways. They are predominantly transmitted vertically from mother to offspring but also occasionally horizontally between species. In doing so, they infect a huge range of arthropod species worldwide. Recently, a statistical analysis estimated the infection frequency of Wolbachia among arthropod hosts to be 66%. At the same time, the authors of this analysis highlighted some weaknesses of the underlying data and concluded that in order to improve the estimate, a larger number of individuals per species should be assayed and species be chosen more randomly. Here we apply the statistical approach to a more appropriate data set from a recent survey that tested both a broad range of species and a sufficient number of individuals per species. Indeed, we find a substantially different infection frequency: We now estimate the proportion of Wolbachia-infected species to be around 40% which is lower than the previous estimate but still points to a surprisingly high number of arthropods harboring the bacteria. Notwithstanding this difference, we confirm the previous result that, within a given species, typically most or only a few individuals are infected. Moreover, we extend our analysis to include several reproductive parasites other than Wolbachia that were also screened for in the aforementioned empirical survey. For these symbionts we find a large variation in estimated infection frequencies and corroborate the finding that Wolbachia are the most abundant endosymbionts among arthropod species.     

A model of the species rank-abundance relation for a community in an open habitat

A mathematical model is proposed to describe the relationship between the abundance and the rank of species in order from the most abundant to the least in a community in an open habitat. This model is derived as a corollary of a species-area equation (Kobayashi , 1975) which could be expected in the case where the individuals of each species are uniformly distributed over a habitat area. Numerical simulation reveals that a rank-abundance curve for a universe results in different species-area or species-individual curves according to the spatial distribution of individuals, and that the relative abundance of each species in a sample varies with sample size unless the spatial distribution of individuals is uniform. A species-individual curve obtained bySanders 's (1968) rarefaction method agrees with that observed actually only for the spatially uniform distribution. Change in the pattern of rank-abundance curve with species diversity and with sample size is discussed in relation to the present model.     

Biology outside the classroom: the SNAB visit/issue report

Pitfall trap sampling of Carabid beetle species on roundabouts in Bracknell, Berkshire, was used to assess the biodiversity of this taxon by its use as an indicator. The aim of the study was to discover the role of traffic islands in the provision of refugia for invertebrate fauna in fragmented urban habitats. Sampling was performed on 15 roundabouts where a total of 24 species were recorded during four trapping periods over a total of 10 days. The resulting asymptotic curves indicated that the total number of species present on all but two of the sites had been represented in the samples taken. There was found to be a positive correlation between the area of the islands and the number of ground beetle species and between the log of the area and the number of individuals found. The log/log relationship between the area of the islands and the number of species was significant. The total abundance of the beetles present was also positively and significantly correlated with roundabout area when both variables were logged. The number of habitats on the islands was positively correlated with the total abundance and species richness. The relationship between species, area and habitat was also positively and significantly correlated. In conclusion, it is obvious that roundabouts of large area with higher numbers of habitat types are greater in Carabid beetle diversity than small, sparsely vegetated roundabouts. Thus, roundabouts can promote the maintenance of biodiversity in fragmented urban habitats.We present this study as an example of a simple method that could be used or easily adapted for educational use, and suggest how some of the perceived problems in its use may be overcome. We discuss how such a study could be useful in illustrating concepts such as biodiversity and species richness, and some of the factors that influence it, as well as demonstrating the level of biodiversity that can be found in urban environments.     

A comparison,by sweep sampling,of the insect fauna from corn and sweet potato monocultures and dicultures in Costa Rica

Summary The insect fauna of 80 day-old plots of corn and sweet potato monocultures and dicultures in Costa Rica were compared using sweep sampling. Six hundred sweeps were taken in each of the three habitats. There were 15% more total species in the diculture than either monoculture but approximately the same total number of individuals. There were 75% more species and approximately 100% more individuals of parasitic Hymenoptera in the diculture than the monocultures. The ratio of numbers of phytophagous individuals to predaceous/parasitic individuals was lowest in the diculture (2.5) and highest in the sweet potato monoculture (14.3). It is suggested that these patterns may be explained if phytophagous insects are limited basically by abundance and diversity of food so that a diculture is at best the sum of two monocultures. However if abundance and diversity of parasitic insects depends more on structural complexity, the result of putting together two monocultures would be synergistic in terms of numbers and species of insects.Two chrysomelid beetles and two leaf-hopper species that were extremely common in the monocultures were significantly less common or absent in the polyculture, and only one leaf-hopper that was rare in the monocultures was relatively more common in the diculture. Comparison of species similarity showed that the corn monoculture and the diculture were much more similar than the sweet potato monoculture and the diculture, and the two monocultures showed the least similarity.Statistically smoothed out species-subsample curves were constructed for each of the three habitats, the curves were fitted to a mathematical model, and they were then extended in order to predict the theoretical total number of species in all three communities sampled. Extrapolation of the curves suggests that approximately 33% of the total sweepable insect community was sampled in the three habitats.One year after the initial sweep samples were taken, the populations of two sweet potato pests, Diabrotica balteata and Diabrotica adelpha, were sampled ten times over a 120 day period in plots of corn and sweet potato monocultures and dicultures. Approximately 50 days after planting, the numbers of both beetles on sweet potato in monocultures were much higher than in dicultures. This trend continued the rest of the season, the difference reaching a maximum approximately 90 days after planting.These data suggest that indigenous agriculturalists are correct: increasing resource diversity in a cropping system may act as a form of biological control, by increasing the relative abundance and diversity of the predaceous parasitic fauna and decreasing the abundance of the major herbivores.     

Gradients in the number of species at reef-seagrass ecotones explained by gradients in abundance

Gradients in the composition and diversity (e.g. number of species) of faunal assemblages are common at ecotones between juxtaposed habitats. Patterns in the number of species, however, can be confounded by patterns in abundance of individuals, because more species tend to be found wherever there are more individuals. We tested whether proximity to reefs influenced patterns in the composition and diversity ('species density' = number of species per area and 'species richness' = number of species per number of individuals) of prosobranch gastropods in meadows of two seagrasses with different physiognomy: Posidonia and Amphibolis. A change in the species composition was observed from reef-seagrass edges towards the interiors of Amphibolis, but not in Posidonia meadows. Similarly, the abundance of gastropods and species density was higher at edges relative to interiors of Amphibolis meadows, but not in Posidonia meadows. However, species richness was not affected by proximity to reefs in either type of seagrass meadow. The higher number of species at the reef-Amphibolis edge was therefore a consequence of higher abundance, rather than species richness per se. These results suggest that patterns in the composition and diversity of fauna with proximity to adjacent habitats, and the underlying processes that they reflect, likely depend on the physiognomy of the habitat.     

日本千曲川河中游成年水生昆虫羽化后的沿边扩散与沿岸植被的关系

Adults of aquatic insects emerge fromstreamslive inthe nearby riparian zone where they can select streamsidevegetations as preferred sites in order to(a)completemetamorphosis,(b)rest while awaiting proper swarmingtime,(c)feedin order to produce eggs,or(d)mate toreproduce[1—3].Most adult aquatic insect dispersal studies have fo-cused on quantifying the degree of upstream move-ment[4,5].Some researchers have shown distinct patternsof upstreammovement related to post-mating ovipositionalbehavior…