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.     

The consequences of using different measures of mean abundance to characterize the abundance–occupancy relationship

Aim To investigate the influence of choice of the measure of mean abundance on the abundance–occupancy relationship, and to examine the implications for identifying causal mechanisms. Innovation Simulations were performed to generate stochastic abundance–occupancy data sets covering a wide range of scenarios representative of empirical abundance–occupancy data. Two common measures of mean abundance were used: local mean abundance (mean abundance calculated using only data from occupied sites) and global mean abundance (mean abundance calculated using all sites or samples). I found that the choice of mean abundance measure had a strong effect on the correlation between abundance and occupancy. Local mean abundance was associated with a high proportion of negative correlations (mean percentage of negative correlations across 24 simulations = 44.39), while global mean abundance was strongly associated with positive correlations (mean percentage of negative correlations across 24 simulations = 0.02). Main conclusions The choice of abundance measure influences the correlation between abundance and occupancy. Negative correlations between local mean abundance and occupancy are an inherent and unavoidable consequence of using this measure of abundance. Efforts to identify causal mechanisms that give rise to the abundance–occupancy relationship have attempted to explain occasional negative correlations when the expectation was for positive correlations. This study shows that negative correlations arise from the choice of mean abundance measure and that this artefact confounds efforts to identify ecological causal mechanisms.     

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.     

An abundance–occupancy time-lag during the decline of an arctiid tiger moth

The positive interspecific abundance–occupancy relationship is one of the most general patterns in ecology. Positive intra specific relationships should also exist within species over time, and so a species should occupy more sites in years when it is more abundant. However, positive intraspecific relationships are not as ubiquitous as their interspecific counterparts. It has been hypothesized that low levels of temporal variation and time-lags between changes of abundance and occupancy within species make positive intraspecific relationships difficult to detect. We analyse 31 years of U.K.-wide data on the decline of an arctiid moth, Arctia caja , which provides the first empirical demonstration of an abundance–occupancy time-lag for any species. Such time-lags are probably common and we discuss their impact on the intraspecific abundance–occupancy relationship and their implications for conservation management. In A. caja , the time-lag indicates that the decline of the species is probably not driven by habitat loss.     

The anatomy of the interspecific abundance–range size relationship for the British avifauna: I. Spatial patterns

Data from the British Trust for Ornithology Common Birds Census and two atlases of breeding birds were used to examine the form of the interspecific abundance–range size relationship for the British avifauna. The relationship is positive for both farmland and woodland habitats and over two different periods, with some evidence of curvilinearity, using either proportion of occupied sites or numbers of occupied 10 × 10 km squares as measures of range size, and mean density at occupied sites as a measure of abundance. A log-linear plot gives the highest correlation. The relationship is stronger if based on maximum local densities than if based on average densities, but there is no relationship using minimum local densities. Relationships based on abundances at individual sites are uniformly positive for all sites, although the relationships for many sites also show evidence of curvilinearity, especially when range size is measured as the proportion of occupied sites. Species show significant concordance in their rank abundances across sites. We discuss some implications of these results.     

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.     

Abundance–range size relationships of macrolepidoptera in Britain: the effects of taxonomy and life history variables

1. A positive relationship between the local abundances and regional distributions of species in an assemblage has been observed for a wide variety of taxa, but its underlying mechanisms remain poorly understood.
2. Taxonomically controlled analyses of a group of the British macrolepidoptera (moths) find a strong, abundance–range size relationship.
3. Degree of polyphagy and habitat generalism explain significant within-taxon variation in both range size and abundance, with polyphages and habitat generalists having larger ranges and greater local abundances than specialists.
4. Taxa that feed in niches considered to be associated with a high diversity of parasitoids have significantly smaller range sizes than other taxa.
5. With the possible exception of body size, none of the life history variables examined explain significant variation around the range size–abundance relationship.     

Community-based processes behind species richness gradients: contrasting abundance–extinction dynamics and sampling effects in areas of low and high productivity

Aim  To consider the role of local colonization and extinction rates in explaining the generation and maintenance of species richness gradients at the regional scale.
Location  A Mediterranean biome (oak forests, deciduous forests, shrublands, pinewoods, firwoods, alpine heathlands, crops) in Catalonia, Spain.
Methods  We analysed the relative importance of direct and indirect effects of community size in explaining species richness gradients. Direct sampling effects of community size on species richness are predicted by Hubbell's neutral theory of biodiversity and biogeography. The greater the number of individuals in a locality, the greater the number of species expected by random direct sampling effects. Indirect effects are predicted by the abundance–extinction hypothesis, which states that in more productive sites increased population densities and reduced extinction rates may lead to high species richness. The study system was an altitudinal gradient of forest bird species richness.
Results  We found significant support for the existence of both direct and indirect effects of community size in species richness. Thus, both the neutral and the abundance–extinction hypotheses were supported for the altitudinal species richness gradient of forest birds in Catalonia. However, these mechanisms seem to drive variation in species richness only in low-productivity areas; in high-productivity areas, species richness was uncorrelated with community size and productivity measures.
Main conclusions  Our results support the existence of a geographical mosaic of community-based processes behind species richness gradients, with contrasting abundance–extinction dynamics and sampling effects in areas of low and high productivity.     

Is genomic diversity a useful proxy for census population size? Evidence from a species‐rich community of desert lizards

Species abundance data are critical for testing ecological theory, but obtaining accurate empirical estimates for many taxa is challenging. Proxies for species abundance can help researchers circumvent time and cost constraints that are prohibitive for long‐term sampling. Under simple demographic models, genetic diversity is expected to correlate with census size, such that genome‐wide heterozygosity may provide a surrogate measure of species abundance. We tested whether nucleotide diversity is correlated with long‐term estimates of abundance, occupancy and degree of ecological specialization in a diverse lizard community from arid Australia. Using targeted sequence capture, we obtained estimates of genomic diversity from 30 species of lizards, recovering an average of 5,066 loci covering 3.6 Mb of DNA sequence per individual. We compared measures of individual heterozygosity to a metric of habitat specialization to investigate whether ecological preference exerts a measurable effect on genetic diversity. We find that heterozygosity is significantly correlated with species abundance and occupancy, but not habitat specialization. Demonstrating the power of genomic sampling, the correlation between heterozygosity and abundance/occupancy emerged from considering just one or two individuals per species. However, genetic diversity does no better at predicting abundance than a single day of traditional sampling in this community. We conclude that genetic diversity is a useful proxy for regional‐scale species abundance and occupancy, but a large amount of unexplained variation in heterozygosity suggests additional constraints or a failure of ecological sampling to adequately capture variation in true population size.     

The relationships between abundance, range size and niche breadth in Central European tree species

Aim  Range size and niche breadth have been found to be positively related to abundance in many plant and animal groups. We tested these two relationships for the tree species flora of Central Europe; that is, for all 25 species that have their distribution centre in this region.
Location  Eurasia, with a focus on Central Europe.
Methods  We devised an abundance and niche variable classification system to transform the existing literature data into a semi-quantitative assessment of abundance and niche breadth (in terms of soil chemical and physical variables, and temperature) for each of the 25 tree species. Regression analyses between abundance, range size and niche breadth were conducted for the entire species sample and for subsets of species defined by their ecology or phylogeny.
Results  The relationship between abundance in the distribution centre and range size was weak for the Central European tree species. However, significant abundance–range size relationships were found for phylogenetically or ecologically more homogenous species groups (for example for trees of the order Rosales and for mid-successional tree species). Realized niche breadth was positively related to range size in the case of temperature, but not for soil-related variables. No relationship existed between niche breadth and abundance in the distribution centre.
Main conclusions  We hypothesize that the weak relationship between abundance and range size is primarily a consequence of substantial ecological and phylogenetic heterogeneity within this rather species-poor assemblage. The positive relationship between realized temperature niche breadth and range size emphasizes the strong influence of climatic variables on plant distribution patterns over continental or global scales.     

Behaviour of roach (Rutilus rutilus L.) altered by Ligula intestinalis (Cestoda: Pseudophyllidea): a field demonstration

1. We studied the influence of a cestode parasite, the tapeworm Ligula intestinalis (L.) on roach ( Rutilus rutilus L.) spatial occupancy in a French reservoir (Lake Pareloup, South-west of France).
2. Fish host age, habitat use and parasite occurrence and abundance were determined during a 1 year cycle using monthly gill-net catches. Multivariate analysis [generalized linear models (GLIM)], revealed significant relationships ( P  < 0.05) between roach age, its spatial occupancy and parasite occurrence and abundance.
3. Three-year-old roach were found to be heavily parasitized and their location toward the bank was significantly linked to parasite occurrence and abundance. Parasitized fish, considering both parasite occurrence and abundance, tended to occur close to the bank between July and December. On the contrary, between January and June no significant relationship was found.
4. These behavioural changes induced by the parasite may increase piscivorous bird encounter rate and predation efficiency on parasitized roach and therefore facilitate completion of the parasite's life cycle.     

Sampling effort, regression method, and the shape and slope of size–abundance relations

1. Despite a substantial body of work there remains much disagreement about the form of the relationship between organism abundance and body size. In an attempt at resolving these disagreements the shape and slope of samples from simulated and real abundance–mass distributions were assessed by ordinary least squares regression (OLS) and the reduced major axis method (RMA).
2. It is suggested that the data gathered by ecologists to assess these relationships are usually truncated in respect of density. Under these conditions RMA gives slope estimates which are consistently closer to the true slopes than OLS regression.
3. The triangular relationships reported by some workers are found over smaller mass and abundance ranges than linear relations. Scatter in slope estimates is much greater and positive slopes more common at small sample sizes and sample ranges. These results support the notion that inadequate and truncated sampling is responsible for much of the disagreement reported in the literature.
4. The results strongly support the notion that density declines with increasing body mass in a broad, linear band with a slope around −1. However there is some evidence to suggest that this overall relation results from a series of component relations with slopes which differ from the overall slope.     

Abundance-range size relationships in British birds: is unexplained variation a product of life history?

Positive interspecific relationships between local abundance and geographic range size are a common feature of animal assemblages However, range size typically explains only a moderate proportion of the variation m abundance, begging the question of whether species of differing life history deviate from the underlying relationship in any systematic fashion Using data for the avifauna of Britain, and applying a comparative method to control for the effects of phylogenetic association, we demonstrate that this does not appear to be the case Only adult survivorship, age at independence and incubation period explain significant variation in abundance once range size is controlled for statistically, and then only a few percent There are two probable reasons why this result is contrary to general expectation First, although many life history variables are expected to show simple correlations with abundance or range size It is not obvious how these might relate to variation about the abundance–range size relationship Second, intuitive ideas about the form such variation might take may be seriously confounded by phylogenetic non–independence     

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.     

Abundance – occupancy relationships in macrofauna on exposed sandy beaches: patterns and mechanisms

We studied the relationship between abundance and extent of occupancy of 158 species of macrofauna inhabiting 66 sandy beaches around the coast of Great Britain. We also used these data to test the predictions of two hypotheses proposed to explain positive abundance-occupancy relationships. We found a strong positive relationship between abundance and extent of occupancy; this pattern was apparent in taxonomic subsets of organisms which have contrasting reproductive and dispersal traits such as planktotrophic/lecithotrophic development in the plankton vs brood development under parental care. Moreover, the abundance-occupancy relationships in these taxonomic subsets had statistically indistinguishable slopes, and elevation. We propose that this lends support to the notion that differences in population structure such as the tendency to form metapopulations may not be primary determinants of the abundance-occupancy pattern in these taxa as proposed by the rescue/metapopulation hypothesis. To test the predictions of the niche-breadth hypothesis we derived values describing the range of sediment grain-sizes exploited by members of two taxonomic subgroups: amphipods and bivalves. We found a weak, statistically non-significant relationship between this niche-breadth measure and occupancy in bivalves which have been shown to respond to grain-size in previous studies, however this was negated after correction for possible artefacts of sampling effort. All other relationships between abundance or occupancy and grain-size range were non-significant. The consistency of the demonstrated abundance-occupancy relationship with those demonstrated in other studies of primarily terrestrial fauna indicates some shared mechanistic explanation, but our data fail to provide support for the two mechanistic hypotheses investigated.     

Occupancy-abundance relationships and sampling scales

The area of occupancy of a species and its abundance are dependent on the spatial scale at which they are measured. However, it is less obvious how the scale of sampling affects their correlation. This study investigated and modeled the effects of sampling unit size and a real extent on the interspecific occupancy-abundance relationships for a tropical tree species assemblage at a local scale and a temperate bird species assemblage at a regional scale. The results showed that both sampling unit size and study extent had profound quantitative effects on the occupancy-abundance relationship, although it remained positive. Several properties of the occupancy-abundance relationship can result from the effects of scale: 1) the linearity of the relationship decreases with the increase of sampling unit size; 2) for a given abundance, the area of occupancy increases with sampling unit size; and 3) variation in the area of occupancy increases with the increase of both sampling unit size and extent, and if the extent is large enough may be sufficient that no occupancy-abundance relationship is observed. Although the occupancy-abundance relationship can be satisfactorily modeled, the parameters depend on the scale used. This suggests that a model derived from one scale cannot be applied to another. In other words, to estimate the rarity or commonness of species using such a model, the estimation must be strictly done using the same sampling scale for all the species.     

Relationships between local population persistence, local abundance and regional occupancy of species: distribution patterns of diatoms in boreal streams

Aims We have two aims: (1) to examine the relationship between local population persistence, local abundance and regional occupancy of stream diatoms and (2) to characterize the form of the species–occupancy frequency distribution of stream diatoms. Location Boreal streams in Finland. There were three spatial extents: (1) across ecoregions in Finland, (2) within ecoregions in Finland, and (3) within a single drainage system in southern Finland. Methods Diatoms were sampled from stones (epilithon), sediment (epipelon) and aquatic plants (epiphyton) in streams using standardized sampling methods. To assess population persistence, diatom sampling was conducted monthly at four stream sites from June to October. The relationships between local population persistence, local abundance and regional occupancy were examined using correlation analyses. Results There was a significant positive relationship between local persistence and abundance of diatoms in epilithon, epipelon and epiphyton. Furthermore, local abundance and regional occupancy showed a significant positive relationship at multiple spatial extents; that is, across ecoregions, within ecoregions and within a drainage system. The relationships between occupancy and abundance did not differ appreciably among impacted and near pristine‐reference sites. The occupancy–frequency distribution was characterized by a large number of satellite species which occurred at only a few sites, whereas core species that occurred at most sites were virtually absent. Main conclusions The positive relationship between local population persistence and abundance suggested that a high local abundance may prevent local extinction or that high persistence is facilitated by a high local cell density. High local persistence and local abundance may also positively affect the degree of regional occupancy in stream diatoms. The results further showed that anthropogenic effects were probably too weak to bias the relationship between occupancy and abundance, or that the effects have already modified the distribution patterns of stream diatoms. The small number of core species in the species–occupancy frequency distribution suggested that the regional distribution patterns of stream diatoms, or perhaps unicellular microbial organisms in general, may not be fundamentally different from those described previously for multicellular organisms, mainly in terrestrial environments, although average global range sizes may differ sharply between these two broad groups of organisms.     

Random sampling, abundance–extinction dynamics and niche-filtering immigration constraints explain the generation of species richness gradients

Aim  The paradigm that species' patterns of distribution, abundance and coexistence are the result of adaptations of the species to their niches has recently been challenged by evidence that similar patterns may be generated by simple random processes. We argue here that a better understanding of macroecological patterns requires an integration of both ecological and neutral stochastic approaches. We demonstrate the utility of such an integrative approach by testing the sampling hypothesis in a species–energy relationship of forest bird species.
Location  A Mediterranean biome in Catalonia, Spain.
Methods  To test the sampling hypothesis we designed a metacommunity model that reproduces the stochastic sampling from a regional pool to predict local species richness variation. Four conceptually different sampling procedures were evaluated.
Results  We showed that stochastic sampling processes predicted a substantial part (over 40%) of the observed variation in species richness, but left considerable variation unexplained. This remaining variation in species richness may be better understood as the result of alternative ecological processes. First, the sampling model explained more variation in species richness when the probability that a species colonises a new locality was assumed to increase with its niche width, suggesting that ecological differences between species matter when it comes to explaining macroecological patterns. Second, extinction risk was significantly lower for species inhabiting high-energy regions, suggesting that abundance–extinction processes play a significant role in shaping species richness patterns.
Main conclusions  We conclude that species–energy relationships may not simply be understood as a result of either ecological or random sampling processes, but more likely as a combination of both.     

Scaling Occupancy Estimates up to Abundance for Wolves

Management of wildlife populations often requires reliable estimates of population size or distribution. Estimating abundance can be logistically difficult, and occupancy models have been used as a less expensive proxy for abundance estimation. Another alternative is to use independent estimates of home-range size and mean group size to directly scale occupancy estimates up to abundance. We used simulations to explore when scaling occupancy up to abundance is reliable, and as an example we applied an occupancy approach to estimate abundance of wolves (Canis lupus) from roadside snow-tracking surveys in northern Wisconsin, USA, in 2016 and 2018. Estimates of wolf abundance were plausible and compared favorably with independent estimates produced by territory mapping, and snow-tracking data requirements were lower than for territory mapping. Simulation results suggested that reasonable abundance estimates could be obtained under some conditions but also that severe positive bias could result under other conditions, especially when populations were small and dispersed, home range size was small, and areal sampling units were large. Positive bias in abundance estimates occurs because of closure assumption violations when tracks from a single wolf or pack are detected in >1 sample unit, and the sum of the sample unit areas where tracks were detected exceed the sum of the home range areas. Bias was minimized when sampling units were small relative to home range size or when sampling units were route segments that approximate point sample units, and when home ranges were highly aggregated. We conclude that, although caution is warranted when scaling occupancy estimates up to abundance, scaled occupancy models can provide feasible and reliable estimates of abundance, assuming home range size and mean group size are accurately known or estimated, sampling units are appropriately chosen, and covariates that aggregate home ranges can be used to accurately predict occupancy probability. © 2021 The Authors. The Journal of Wildlife Management published by Wiley Periodicals LLC on behalf of The Wildlife Society.     

Feather micro-organisms and uropygial antimicrobial defences in a colonial passerine bird

1.  The relationship between the composition of communities of micro-organisms and their hosts remains poorly understood. We conducted extensive field studies of feather-degrading bacteria, other cultivable bacteria, and fungi on the plumage of a migratory bird, the barn swallow Hirundo rustica Linnaeus, to understand the association between micro-organisms, host sociality and host antimicrobial defences, as reflected by the size of the uropygial gland.
2.  The abundance of feather-degrading bacteria, but not other cultivable bacteria or fungi, decreased with increasing size of the uropygial gland.
3.  Females had more feather-degrading bacteria than males.
4.  Barn swallows living in larger colonies had more feather-degrading bacteria than less social conspecifics.
5.  These findings suggest that the uropygial gland plays a specific role in regulating the abundance of feather-degrading bacteria that furthermore depends on the social environment of the host.