The pervasive influence of sampling and methodological artefacts on a macroecological pattern: the abundance–occupancy relationship

Aim   To investigate the influence of sampling and methodological artefacts on the correlation between abundance and occupancy.
Location   Global scope.
Methods   A fixed effects weighted regression model was fitted to standardized effect size for 175 examples of correlations between abundance and occupancy. A regression tree model with standard effect size as the dependent variable was also fitted to the data.
Results   Standard effect size, and therefore the correlation between abundance and occupancy, was found to be strongly influenced by the type of abundance measure used to characterize the abundance–occupancy relationship. Local mean abundance (also referred to as ecological mean abundance) was primarily responsible for negative correlations. Negative correlations also resulted from a mismatch in the sampling extents of abundance and occupancy measures.
Main conclusions   The combination of abundance and occupancy measures selected to characterize the abundance–occupancy relationship for a given set of data has a profound impact on the sign of the correlation between the selected measures. Previous attempts to understand the processes giving rise to the pattern represented by the abundance–occupancy relationship have confounded sampling artefacts (e.g. spatial extent of abundance and occupancy information) and methodological artefacts (e.g. combining a truncated abundance measure such as local mean abundance with an untruncated occupancy measure such as proportion of occupied samples). Thus, a revision of the approach currently used to define and evaluate competing explanatory models of the abundance–occupancy relationship appears to be necessary.     

Seed dispersal, seedling establishment and gap partitioning among tropical pioneer trees

1 We examined the abundance and distribution patterns of pioneer seeds in the soil seed bank, and of pioneer seedlings in 53 recently formed gaps, in a 50‐ha forest dynamics plot on Barro Colorado Island (BCI), Panama. The aim was to assess the importance of dispersal limitation (failure of seeds to arrive at all sites suitable for their germination) and establishment limitation (failure of seeds having reached a site to germinate successfully and establish as seedlings) in determining patterns of gap occupancy.
2 The abundance of seeds in the soil seed bank was strongly negatively correlated with seed size, but was not correlated with the abundance of reproductive‐sized adult trees in the plot. In contrast, the abundance of pioneer seedlings > 10 cm height in natural gaps was strongly correlated with adult abundance, but was not correlated with seed size.
3 Seedlings were non‐randomly distributed among gaps, but seedling abundance was not directly related to gap size, and there was no evidence of partitioning of the light environment of gaps by small seedlings. Large differences in growth and mortality rates among species were observed after 1 year, and this may result in the gap size partitioning previously found in saplings of the same species.
4 Seedlings of most species, particularly those with large seeds, were relatively more abundant than expected in gaps close to their conspecific adults. Proximity to reproductives, and by inference dispersal limitation, therefore exerts some effect on seedling distribution. None the less, large differences between seed and seedling abundances for some species, and low seedling occupancy rates in some gaps close to adult conspecifics, suggest that seedling emergence probabilities and species‐specific establishment requirements may also be important determinants of local abundance.     

Ligula intestinalis (L.) (Cestoda: Pseudophyllidea): plerocercoid-induced changes in the spleen and pronephros of roach, Rutilus rutilus (L.), and gudgeon, Gobio gobio (L.)

The effects of the plerocercoid of Ligula intestinalis (L.) (Cestoda: Pseudophyllidea) on the major lymphoid organs, the spleen and pronephros, of roach, Rutilus rutilus (L.), and gudgeon, Gobio gobio (L.), are described. The spleen of ligulosed roach showed a significant decrease in weight. Differential cell counts suggested this was due to a reduction in erythrocytes, despite significant increases in macrophages and vacuolated granulocytes. The spleen of gudgeon, which consisted almost entirely of erythrocytes, showed a slight reduction in weight in ligulosed fish. In both roach and gudgeon this decrease was independent of parasite burden. Differential cell counts of the pronephros from ligulosed roach revealed a significant decrease in neutrophils and increase in vacuolated granulocytes. In the pronephros of gudgeon, however, cell counts were unaffected by ligulosis. Ultrastructural observations included an apparent disintegration of vacuolated granulocytes and increased pinocytic activity in specialized endothelial cells in the spleens of ligulosed roach. Also, melano-macrophage centres and melano-macrophages increased in the spleen of ligulosed roach and gudgeon, respectively. The marked changes in spleen weight and differential cell counts in ligulosed roach and lack of such changes in ligulosed gudgeon correlate with the differential response to the parasite by these two fish species.     

Consumption of cyanobacteria by roach (Rutilus rutilus): useful or harmful to the fish?

1. The ability of roach to use cyanobacterial food is generally believed to be one reason for the dominance of roach over perch in eutrophic European lakes. The aim of this study was to test whether cyanobacteria really are a suitable food for juvenile roach. Special attention was paid to differences between the two cyanobacteria species Aphanizomenon and Microcystis which are common in eutrophic lakes and are ingested by roach there.
2. We performed growth and behaviour experiments with juvenile roach fed with zooplankton and the different cyanobacteria. Growth rate with Aphanizomenon was lower than with Daphnia but significantly higher than without food, whereas growth rate with Microcystis was as low as without food.
3. In cultivation experiments of roach faeces, Microcystis was found not to have been digested and grew exponentially after passing through the gut whereas Aphanizomenon stayed at low biomass. Differences in growth were not related to the toxin content of cyanobacteria. Investigations of roach motility showed no differences whether fed with Aphanizomenon or Microcystis .
4. In contrast to Microcystis , Aphanizomenon can be regarded as a suitable food source for juvenile roach probably because of its better digestability. We conclude that the ability to feed on cyanobacteria is not a general competitive advantage for roach, but the outcome depends on the species composition of the cyanobacteria.     

The effect of the acanthocephalan parasite (Pomphorhynchus laevis) on the drift of its intermediate host (Gammarus pulex)

SUMMARY 1. The drift of Gammarus pulex in a population in which approximately 20% of adults are infected with the acanthocephalan parasite Pomphorhynchus laevis was monitored at margin and mid-river sites in the River Teme, England over a 24-h period in mid-summer.
2. Drift densities showed a diurnal pattern with a large increase at night, independent of parasite burden.
3. There was no significant effect of site (margin or mid-river) on the proportion of parasitized and unparasitized G. pulex found in the drift or the benthos.
4. The drift of parasitized G. pulex was significantly greater than unparasitized animals. Gammarids harbouring only one parasite were found in significantly higher proportions in the drift than those with two or more parasites.
5. At both sites (margin and mid-river) the proportion of unparasitized adult G. pulex in the drift was significantly lower than that in the benthos. However, there was a significantly higher proportion of parasitized animals in the drift than in the benthos.     

Biological traits of stream macroinvertebrates from a semi-arid catchment: patterns along complex environmental gradients

1. The relationships between biological traits of macroinvertebrates and environmental characteristics were investigated in streams with contrasting physical, chemical or landscape level attributes. We used an ordination technique, RLQ analysis, which links an environmental table (R) with traits table (Q) through an abundance table (L) to investigate the relationship between habitat characteristics and biological traits.
2. A major environmental axis explaining the distribution of species and their distinctive biological features was obtained. This axis included variables of anthropogenic pressure (agricultural and urban uses) and natural variability (climatic and geologic) that are strongly intercorrelated in the study area, with a clear spatial component.
3. The attributes of species from frequently disturbed systems (small size, multivoltinism, diapause, ovoviviparity, etc.) were associated with semi-arid areas whereas traits common in more stable and favourable environments (large body size, semi-voltinism, isolated eggs, etc.) were found in upland forested areas.
4. The natural climatic variation was proposed as a disturbance axis of a theoretical habitat templet (driven by the intense hydrological disturbances typical of semi-arid streams), while anthropogenic pressure (mainly intensive agriculture) and high salinity, a natural consequence of geology, was proposed as an adversity axis. Different life-histories associated with contrasting environmental features were superimposed in this habitat templet.
5. The ecological–evolutionary scenario in which stream macroinvertebrates have evolved and by which their communities are organized, is closely linked to disturbance, environmental harshness and human pressure.     

Distribution of the cestode Caryophyllaeides fennica (Cestoda: Lytocestidae) in the population of cyprinid fish in the Rybinsk water reservoir

The distribution of the cestode Caryophyllaeides fennica in populations of the ide, roach, white bream and bream from the Rybinsk reservoir has been analyzed in regard to fish age. The relative abundance of C. fennica in populations of each host species was calculated as product of the helminthes abundance by the fish number in age groups. The highest prevalence and abundance of cestodes was found in the ide. All age classes of this species were infected, with the maximum in fishes of the age 3+ ... 5+. The roach is infected with C. fennica till only 10-year age; brean is infected till the age 4+. In the white bream C. fennica is an occasional parasite. The cestode number among hosts was as follows: bream--68%; roach--26%, ide--5%, white bream--1%. Different approaches to the estimation of the parasite abundance distribution among several host species (in terms of mean prevalence and intensity of the relative abundance of parasites) are discussed.     

Changes in distribution of an archaic moth, Micropterix calthella, in St Petersburg, Russia, between 1989 and 2005

Aim  This work aimed to assess changes in the number of suitable habitats and habitat occupancy by Micropterix calthella (L.) moths (Lepidoptera, Micropterigidae) in the city of St Petersburg between 1989 and 2005.
Location  The city of St Petersburg, Russia.
Methods  The study compares results of the survey conducted on 9–12 June 2005 with data collected in 1989 and is based on the assessment of the quality and occupancy of 103 habitats that were found potentially suitable for M. calthella in 1989. If habitats contained wet microsites with undisturbed litter and dense field layer vegetation with a high abundance of flowering Ranunculus sp., they were considered potentially suitable for M. calthella ; in these habitats, moths were searched for on flowers of Ranunculus – visually and/or by extensive sweep-netting.
Results  Both the number of habitats suitable for M. calthella and the number of habitats occupied by this species decreased since 1986 from 103 to 72 and from 58 to 34, respectively. The disappearance of habitats was primarily due to the building of residential blocks within the city (16 sites) and railway renovation (10 sites), while changes in habitat management, primarily in parks and recreation zones (five sites), were less important. The average distance from the city centre to the nearest population of M. calthella increased from 8.7 ± 1.5 to 12.9 ± 3.0 km (mean ± SE).
Main conclusion  The data for 2005 fit the prediction that M. calthella moths, which are unable to re-colonize potentially suitable habitats due to their low migratory ability, will disappear from the city. At the present rate of extinction, this process may take some 20–30 years to complete (or nearly complete).     

Effects of piscivore-mediated habitat use on growth, diet and zooplankton consumption of roach: an individual-based modelling approach

SUMMARY 1. We used an individual based modelling approach for roach to (i) simulate observed diel habitat shifts between the pelagic and littoral zone of a mesotrophic lake; (ii) analyse the relevance of these habitat shifts for the diet, activity costs and growth of roach; and (iii) quantify the effects of a hypothetical piscivore-mediated (presence of pikeperch) confinement of roach to the littoral zone on roach diet, activity costs and growth.
2. The model suggests that in the presence of pikeperch, roach shifts from zooplankton as the primary diet to increased consumption of less nutritious food items such as macrophytes, filamentous algae and detritus.
3. The growth of roach between May and October was predicted to be significantly higher in the absence of pikeperch, although the net activity costs were about 60% higher compared with the scenario where pikeperch were present.
4. These modelling results provide quantitative information for interpreting diel horizontal migrations of roach as a result from a trade-off between food availability and predation risk in different habitats of a lake.
5. Altering the habitat selection mode of planktivorous roach by piscivore stocking has the potential to reduce zooplankton consumption by fish substantially, and could therefore be used as a biomanipulation technique complementing the reduction of zooplanktivorous fish.     

Encounter rate between local populations shapes host selection in complex parasite life cycle

The present study aimed to understand how a parasite with a complex life cycle selects a given host succession when several potential hosts are present. Ligula intestinalis (Cestoda, Pseudophyllidea) was considered, which presents a life cycle with three hosts: copepod, fish, and piscivorous bird. Encounter probability between each pair of hosts was calculated for Lavernose-Lacasse gravel pit (France) using a sum of the product of the host abundances over time. Among four potential copepod hosts, two potential fish hosts, and six potential bird hosts, the results demonstrate that the copepod Eudiaptomus gracilis , the roach ( Rutilus rutilus ), and the great crested grebe ( Podiceps cristatus ) had a maximal encounter probability due to their abundance, but also due to the similarities of the temporal dynamics of their life cycles. These results agree with previous experiments and field work identifying a high specificity of L. intestinalis to E. gracilis , R. rutilus , and P. cristatus in the study site. This suggests that the abundance of potential hosts and the temporal dynamics of their life cycles act together to determine encounter rates between hosts and parasites, and thus could constitute a crucial determinant in local host selection by parasites with a complex life cycle.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 99–106.     

The decline of a roach Rutilus rutilus (L.) population in Chew Valley Lake

A series of nettings for roach in Chew Valley Lake carried out by members of the Zoology Department, Bristol University, has revealed a marked decline in the population between 1965 and 1968. Fish from the main Lake were found to be heavily parasitized with Ligula intestinalis (L.) while those from the inflow pool (Herriott's Pool) were practically free from infection. It is considered that the decline of the roach can be linked to the incidence of Ligula , but that clean fish from the inflow pool may provide breeding stock and maintain the production of fry, which serve as food for the trout.     

Biogeography of parasitism in freshwater fish: spatial patterns in hot spots of infection

Contrary to species occurrence, little is known about the determinants of spatial patterns of intraspecific variation in abundance, particularly for parasitic organisms. In this study, we provide a multi‐faceted overview of spatial patterns in parasite abundance and examine several potential underlying processes. We first tested for a latitudinal gradient in local abundance of the regionally most common parasite species and whether these species achieve higher abundances at the same localities (shared hot spots of infection). Secondly, we tested whether intraspecific similarity in local abundance between sites follows a spatial distance decay pattern or is better explained by variation in extrinsic biotic and abiotic factors between localities related to local parasite transmission success. We examined the infection landscape of a model fish host system (common and upland bullies, genus Gobiomorphus: Eleotridae) across its entire distributional range. We applied general linear models to test the effect of latitude on each species local abundance independently, including the abundance of each co‐infecting species as another predictor. We computed multiple regressions on distance matrices among localities based on abundance of each of the four most common trematode species, as well as for geographic distance, biotic and abiotic distinctness of the localities. Our results showed that the most widely distributed parasites of bullies also achieve the highest mean local abundances, following the abundance – occupancy relationship. Variation in local abundance of any focal parasite species was independent of latitude, the abundance of co‐occurring species and spatial distance or disparity in biotic attributes between localities. For only one parasite species, similarity of abundance between sites covaried with the extent of abiotic differences between sites. The lack of association between hot spots of infection for co‐occurring species reinforces the geographic mosaic scenario in which hosts and parasites coevolve by suggesting non‐deterministic, species‐specific variation in parasite abundance across space.     

Diversity, distribution and larval habitats of North Swedish blackflies (Diptera: Simuliidae)

1. Blackfly species richness and community structure were analysed at fifty-six sites in northern Sweden in two seasons. The sites were situated in a wide range of streams and rivers from small springbrooks, bog streams and lake-outlet streams to medium-sized forest rivers and large rivers draining montane regions.
2. Thirty-nine blackfly species were found, with between two and thirteen species per site. Neither species richness nor abundance could be related to the environmental variables measured.
3. An analysis of labral fan size of blackflies indicated a clear trend for the prevalence of larvae with small fans in large rivers and larvae with larger fan size in small streams. Similarly, fan size related to current velocities so that large fans were associated with slow current velocities and small fans with high velocities.
4. A strong relationship existed between species composition and habitat, as seen in ordination by non-metric multidimensional scaling. The relationship found between fan size and habitat size-related variables, such as channel width, depth, velocity and substratum particle size, along with longitude and altitude, in partial least squares regression analysis offered an explanation of the species composition–habitat relationship.
5. In addition to testing that distributions of blackfly larvae reflect morphological traits, we tested two general hypotheses pertaining to distribution patterns: (a) that blackfly communities show bimodal distributions; and (b) that their distributions are nested. Neither of these two hypotheses was supported by our observations. However, widespread blackfly species were locally more abundant than those found at relatively few sites, thus showing a positive abundance–occupancy relationship.     

Effects of snow cover on the benthic fauna in a glacier-fed stream

1. Alpine streams above the tree line are covered by snow for 6–9 months a year. However, winter dynamics in these streams are poorly known. The annual patterns of macroinvertebrate assemblages were studied in a glacial stream in the Austrian Alps, providing information on conditions under the snow.
2. Snow cover influenced water temperature, the content of benthic organic matter and insect development. Taxa richness and abundance of macroinvertebrates did not show a pronounced seasonal pattern. The duration of the autumn period with stable stream beds was important in determining the abundance and composition of the winter fauna.
3. There were significant differences in species composition between summer and winter. Two potential strategies in larval survival were evident: adaptation to the extreme abiotic conditions in summer (e.g. Diamesa spp.) or avoidance of these conditions and development during winter (e.g. Ephemeroptera and Plecoptera).
4. A comparison of a stream reach with continuous snow cover and a stream reach that remained open throughout winter showed that conditions under snow are suboptimal. At the open stream site, with higher water temperatures and greater food supply (benthic organic matter content), abundance and taxa richness was higher and larval growth was faster. Several taxa were found exclusively at this site.
5. Winter conditions did not provide an entirely homogeneous environment, abiotic conditions changed rapidly, especially at the onset of snowfall and at snowmelt. Continuous monitoring is necessary to recognize spatial and temporal heterogeneity in winter environments and the fauna of alpine streams.     

Occurrence and prevalence of Philometra filiformis (Stossich, 1896) on Pagellus erythrinus (Linnaeus, 1758) in the Southern Tyrrhenian Sea

In this paper the host‐parasite relationship between Philometra filiformis and the common pandora Pagellus erythrinus from the Southern Tyrrhenian Sea were studied. A total of 305 (257 females and 48 males) specimens of common pandora were sampled from June 2009 to April 2011 from commercial landings as well as from bottom trawl surveys. A total of 39 P. erythrinus were parasitized (mean prevalence, P = 12.80%; mean abundance, A = 0.19), with the parasite occurring throughout the study area and with wide fluctuations in prevalence values ranging from 0 to 28.60%. Prevalence increased with age of the host, with most parasites (27.78%) found in the older common pandora whereby P. filiformis parasitized only the females. A significant correlation between prevalence, abundance and maturity stages of the fish was evident, with most parasites found in mature/spawning specimens. The varying degrees of gonadic damage caused by this nematode reveal a serious threat to the reproductive success of P. erythrinus.     

Abundance–occupancy relationships

1.  The abundance and distribution of species tend to be linked, such that species declining in abundance often tend also to show declines in the number of sites they occupy, while species increasing in abundance tend also to be increasing in occupancy. Therefore, intraspecific abundance–occupancy relationships are commonly positive.
2.  The intraspecific pattern is mirrored by more general positive interspecific abundance–occupancy relationships: widespread species tend to be abundant, and narrowly distributed species rare.
3.  Here, we review recent research on these patterns based on the flora and fauna of the British Isles. We assess their generality, describe what is currently known about their structure, and summarize the results of tests of the several hypotheses proposed to explain their existence.
4.  The positive form generally exhibited by abundance–occupancy relationships, intraspecific or interspecific, has consequences for several areas of applied ecology, including conservation, harvesting, biological invasions and biodiversity inventorying. These implications are discussed briefly.     

Movement of two grassland butterflies in the same habitat network: the role of adult resources and size of the study area

Abstract. 1.  Movement patterns of two butterfly species (meadow brown Maniola jurtina L. and scarce copper Lycaenae virgaureae L.) were studied in a 172 ha area within a landscape with a high percentage of suitable habitats for mark–release–recapture experiments.
2.  Adult resource density, but not patch size or larval food plant abundance, influenced the numbers and the fractions of residents, emigrants, and immigrants.
3.  Differences between species were observed in movement frequency and maximum distances moved but not in mean distances moved.
4.  The scarce copper showed much greater movement ability than expected from the results of published studies. This is believed to be a result of the comparatively large size of the study area and the high cover of suitable habitat (>50%).
5.  The mean and maximum distances travelled by butterflies reflected differences in the size of the study area.     

Infection of the spined loach, Cobitis taenia (L.), by the digenean, Allocreadium transversale (Rud.)

The digenean Allocreadium transversale (Rud.) has been recorded once previously in Great Britain. During work on the feeding of Cobitis taenia (L.) it was found to be a frequently occurring gut parasite. Great variation occurred in its seasonal level of incidence and mean worm burden, indicating a rapid turnover and replacement of the parasite in the fish. No significant relationship could be shown between the level of infection and age of the fish; but a highly significant relationship occurred between incidence of infection and fish age.     

Improved abundance prediction from presence–absence data

Aim   Many ecological surveys record only the presence or absence of species in the cells of a rectangular grid. Ecologists have investigated methods for using these data to predict the total abundance of a species from the number of grid cells in which the species is present. Our aim is to improve such predictions by taking account of the spatial pattern of occupied cells, in addition to the number of occupied cells.
Innovation   We extend existing prediction models to include a spatial clustering variable. The extended models can be viewed as combining two macroecological regularities, the abundance–occupancy regularity and a spatial clustering regularity. The models are estimated using data from five tropical forest censuses, including three Panamanian censuses (4, 6 and 50 ha), one Costa Rican census (16 ha) and one Puerto Rican census (16 ha). A serpentine grassland census (8 × 8 m) from northern California is also studied.
Main conclusions   Taking account of the spatial clustering of occupied cells improves abundance prediction from presence–absence data, reducing the mean square error of log-predictions by roughly 54% relative to a benchmark Poisson predictor and by roughly 34% relative to current prediction methods. The results have high statistical significance.     

Distribution and abundance of parasite nematodes: ecological specialisation,phylogenetic constraint or simply epidemiology?

We investigate the patterns of abundance‐spatial occupancy relationships of adult parasite nematodes in mammal host populations (828 populations of nematodes from 66 different species of terrestrial mammals). A positive relationship between mean parasite abundance and host occupancy, i.e. prevalence, is found which suggests that local abundance is linked to spatial distribution across species. Moreover, the frequency distribution of the parasite prevalence is bimodal, which is consistent with a core‐satellite species distribution. In addition, a strong positive relationship between the abundance (log‐transformed) and its variance (log‐transformed) is observed, the distribution of worm abundance being lognormally distributed when abundance values have been corrected for host body size.
Hanski et al. proposed three distinct hypotheses, which might account for the positive relationship between abundance and prevalence in free and associated organisms: 1) ecological specialisation, 2) sampling artefact, and 3) metapopulation dynamics. In addition, Gaston and co‐workers listed five additional hypotheses. Four solutions were not applicable to our parasitological data due to the lack of relevant information in most host‐parasite studies. The fifth hypothesis, i.e. the confounded effects exerted by common history on observed patterns of parasite distributions, was considered using a phylogeny‐based comparison method. Testing the four possible hypotheses, we obtained the following results: 1) the variation of parasite distribution across host species is not due to phylogenetic confounding effects; 2) the positive relationship between mean abundance and prevalence of nematodes may not result from an ecological specialisation, i.e. host specificity, of these parasites; 3) both a positive abundance‐prevalence relationship and a negative coefficient of variation of abundance‐prevalence relationship are likely to occur which corroborates the sampling model developed by Hanski et al. We argue that demographic explanations may be of particular importance to explain the patterns of bimodality of prevalence when testing Monte‐Carlo simulations using epidemiological modelling frameworks, and when considering empirical findings. We conclude that both the bimodal distribution of parasite prevalence and the mean‐variance power function simply result from demographic and stochastic patterns (highlighted by the sampling model), which present compelling evidence that nematode parasite species might adjust their spatial distribution and burden in mammal hosts for simple epidemiological reasons.