Occupancy Frequency Distributions Research Articles

The spatial extent and the dispersal strategy of species shape the occupancy frequency distribution of stream insect assemblages.

Several theoretical models have been proposed as the underlying mechanisms behind occupancy frequency distribution (OFD) patterns. For instance, the metapopulation dynamic model predicts bimodal OFD pattern indicating the dominance of dispersal processes in structuring the assemblages, while the niche-based model predicts unimodal right-skewed OFD pattern, and thus assemblages are driven mostly by niche processes. However, it is well known that the observed OFD pattern reflects the interplay of several other factors (e.g. habitat heterogeneity, species specificity and sampling protocol parameters). It follows that the individual contribution of each factor to the OFD pattern is rather complicated to explore. Our main objective was to examine the role of the spatial extent of the sampling and the dispersal strategies of species in shaping OFD pattern. For this, we collected samples of stream insect assemblages inhabiting near-natural streams in the Pannon Ecoregion. We formed groups of species representing contrasting dispersal strategies (referred to as dispersal groups). Applying a computer program algorithm, we produced samples with different spatial extent. We found that with increasing spatial extent, the OFD pattern changed from bimodal to unimodal for active dispersers. Insect groups with different dispersal strategies differed in the strength of support for OFD patterns within all spatial extent. Furthermore, the strength of support for OFD patterns varied across dispersal groups differently as the spatial extent increased. Our results reflected underlying changes in mechanisms structuring assemblages along an increasing spatial extent. We also assumed that the stream insect dispersal strategy influences the relative role of dispersal and niche processes particularly as spatial extent increases from stream reaches to the extent of adjacent valleys. We could define spatial extents and dispersal strategies within which unique metacommunity processes could underlie the organisation of assemblages.

Temporally robust occupancy frequency distributions in riverine metacommunities explained by local biodiversity regulation

AbstractAimThe mechanisms determining the distribution of the number of sites species occupy, the occupancy frequency distribution (OFD), remain incompletely understood despite decades of research. To explore the dominant mechanisms responsible for the shape and temporal dynamics of empirical OFD, we develop a simple patch occupancy framework with intrinsically regulated local richness and fit the model to a highly replicated dataset describing macroinvertebrate, macrophyte and diatom occupancy.LocationEngland.Time periodUp to years between 1990 and 2020.Major taxa studiedMacroinvertebrates, macrophytes and diatoms.MethodsWe study the OFD in a highly replicated dataset of freshwater metacommunities in England across time. We consider temporal change in species richness, composition, and in the shape of the OFD. Goodness‐of‐fit of the steady state of a simple patch occupancy model—which predicts a log‐series OFD—to the empirical observations is assessed. Additionally, we test the capacity of the model to predict metacommunity‐scale processes.ResultsOur model provides a consistently good fit to empirical OFDs. It can additionally be used to predict metacommunity‐scale species turnover.Main conclusionsOur results support the view that metacommunity structure reflects a dynamic steady state controlled by local limits to coexistence.

Deterministic assembly processes shaping habitat‐specific glycoside hydrolase composition

AbstractAimGlycoside hydrolases (GHs) encoded by prokaryotes play a crucial role in the degradation of carbohydrates, which is a key step in the carbon cycle. However, their global distribution remains poorly understood. Here, we conducted a comprehensive investigation of the global biogeographic patterns of prokaryotic‐encoded GHs.LocationGlobal.Time periodPresent.Major taxa studiedProkaryotes.MethodsWe conducted a global survey of GH distribution based on 10,000 samples from the Earth Microbiome Project (EMP) and 17,923 completely sequenced prokaryotic genomes. The samples were retrieved from seven continents, covering all 17 EMP Ontology environments. We evaluated the assembly process and influencing factors of GH functional genes within prokaryotic communities, and analysed the rank abundance distributions (RADs), occupancy frequency distributions (OFDs), and taxonomic sources of GH families across various environments.ResultsThe median number of GH genes per thousand genes encoded by global prokaryotic communities was 9.11 (7.16–11.58), with a higher GH abundance in host‐associated communities than in free‐living communities. The median number of GH families in prokaryotic communities was 105 (86–121), with fewer families but tighter functional connections between families in host‐associated communities compared to free‐living communities. In any environment, the RAD of GH families followed a lognormal model, and their OFD was bimodal, with a strong positive correlation between the two. In addition, most GH families had complex and diverse taxonomic sources across different environments.Main conclusionsThis study provides a panoramic view of the functional potentials for carbohydrate degradation across prokaryotic communities under diverse environmental conditions. The composition of GHs encoded by prokaryotic communities exhibits clear habitat specificity, which is driven by a combination of biotic and abiotic factors and generated through highly deterministic assembly processes.

Occupancy-frequency distribution of birds in land-sharing and -sparing urban landscapes in Europe

Species richness is a widely used proxy for patterns of biodiversity variation in metacommunities. However, deeper analyses require additional metrics, such as the occupancy-frequency distributions (SOFD) of different local communities. The SOFD patterns indicate the number of shared species between study sites; therefore, they can provide new insights into the current debate on how to create more biodiversity-friendly cities. Breeding birds were counted from 593 point-count stations located in five 500 m × 500 m squares in land-sharing (LSH; low-density built areas interspersed with green spaces) and five similar nearby squares in land-sparing (LSP; densely built-up with set-aside, large-sized, continuous green spaces) landscapes in nine cities across Europe. High beta-diversity (with over 42% of the 103 species detected being restricted to a single city and only 7% found in all studied cities) showed the uniqueness of cities at the continental scale. Urban bird metacommunities followed the unimodal-satellite SOFD pattern at the European continental scale but a bimodal symmetric or asymmetric distribution at the city-level scale, suggesting that many common species occur in cities on a smaller scale. The LSP urban areas followed a unimodal satellite SOFD pattern with numerous rare species. In contrast, the LSH areas fit several types of bimodal SOFD patterns equally well, where communities share several common species. The findings also highlight the need to use multi-scale approaches to analyze the effects of LSH-LSP urban designs on urban bird diversity.

Macroinvertebrate species occupancy frequency distribution patterns in eutrophic lakes

Metacommunity models describe species occupancy frequency distribution (hereinafter ‘SOFD’). Our goal is to present how the differences in eight macroinvertebrate orders dispersal ability affect SOFD patterns. A total of 293 species from eight macroinvertebrate orders were observed in 14 eutrophic lakes in southern Finland. Species occupancy ranged from 1 to 14. About 30% (89 out of 293) of the species were found in only one lake, yielding a surprisingly high number of rare species. So, there were few widely distributed common species and numerous rare species with a restricted distribution. Combined data from eight macroinvertebrate orders supported the bimodal truncated SOFD pattern. Similarly, the low dispersal ability orders, watermites and mayflies, fitted the bimodal truncated SOFD pattern. However, bimodal symmetric SOFD pattern also fitted relatively well to the dragonflies and damselflies with high dispersal ability. It seems that differences in dispersal ability among different macroinvertebrate orders may partly explain observed differences. Moreover, our results supported slightly more a niche-based model rather than a metapopulation dynamics model in eutrophic lakes littoral macroinvertebrate metacommunities. Our results highlight that the dispersal ability is important trait for species conservation in patchily distributed habitat.

Macroecological distributions of gene variants highlight the functional organization of soil microbial systems.

The recent application of macroecological tools and concepts has made it possible to identify consistent patterns in the distribution of microbial biodiversity, which greatly improved our understanding of the microbial world at large scales. However, the distribution of microbial functions remains largely uncharted from the macroecological point of view. Here, we used macroecological models to examine how the genes encoding the functional capabilities of microorganisms are distributed within and across soil systems. Models built using functional gene array data from 818 soil microbial communities showed that the occupancy-frequency distributions of genes were bimodal in every studied site, and that their rank-abundance distributions were best described by a lognormal model. In addition, the relationships between gene occupancy and abundance were positive in all sites. This allowed us to identify genes with high abundance and ubiquitous distribution (core) and genes with low abundance and limited spatial distribution (satellites), and to show that they encode different sets of microbial traits. Common genes encode microbial traits related to the main biogeochemical cycles (C, N, P and S) while rare genes encode traits related to adaptation to environmental stresses, such as nutrient limitation, resistance to heavy metals and degradation of xenobiotics. Overall, this study characterized for the first time the distribution of microbial functional genes within soil systems, and highlight the interest of macroecological models for understanding the functional organization of microbial systems across spatial scales.

Spatial and temporal changes in occupancy frequency distribution patterns of freshwater macrophytes in Finland.

A useful method for characterizing biological numerous assemblages at regional scales is the species occupancy frequency distribution (SOFD). An SOFD shows the number or proportion of study sites each species occurred. Species that occur at only a few sites are termed satellite species, while species that occur at many sites are termed core species.This study is the first to document and assess SOFD patterns in aquatic macrophytes. It characterizes SOFD patterns of freshwater macrophyte assemblages in Finland at two spatial and two temporal scales. For this, I analyzed three published datasets on freshwater macrophyte distributions: two from studies conducted at a local scale and the third from large national surveys. One local study and the national study also included data on temporal variation in species occupancy frequencies.In the national study, the number of core and satellite species varied slightly between the older and the newer survey, respectively. Among the 113 waterbodies surveyed as part of the national study, the SOFD followed a unimodal satellite pattern. However, for the older dataset (from the 1930s), a bimodal symmetric pattern also fit the SOFD data well. At the local scale, I observed geographical variation in SOFD patterns. The dataset from southern Finland followed a unimodal satellite SOFD pattern; data from central Finland instead displayed a bimodal symmetric SOFD pattern, although they also fit equally well with a bimodal truncated pattern. Moreover, temporal patterns in central Finland seemed to demonstrate a shift from a bimodal symmetric to a bimodal asymmetric SOFD probably.Geographical variation in the SOFD pattern may be due to variation in the regional species pool. The temporal changes in SOFD pattern may be due to lake eutrophication and anthropogenic disturbance around waterbodies, which may increase number of macrophyte species.

Local and Geographic Factors Shape the Occupancy-Frequency Distribution of Freshwater Bacteria.

Species prevalence across the landscape is related to their local abundance, which is a result of deterministic and stochastic processes that select organisms capable of recolonizing sites where they were once extinct, a process known as the rescue effect. The occupancy-frequency distribution (OFD) describes these patterns and has been extensively used to understand organism's distribution but has been poorly tested on microorganisms. In order to test OFD on freshwater bacteria, we collected data from 60 shallow lakes distributed across a wide area in southeastern Brazil, to determine the bacterial operational taxonomic units (OTUs) that were present in all sites (core) and at only one site (satellite). Then, we analyzed the spatial abundance distributions of individual OTUs to understand the influence of local abundances on regional occupancy patterns. Finally, we tested the environmental factors that influenced occupancy and abundance. We found a significant bimodal OFD for freshwater bacteria using both OTUs (97% clustering) and amplicon sequence variants (ASVs, unique sequences), with 13 core OTUs and 1169 satellite OTUs, but only three core ASVs. Core organisms had a bimodal or gamma abundance distribution. The main driver of the core community was pH, while nutrients were key when the core community was excluded and the rest of the community (mild and satellite taxa) was considered. This study demonstrates the close relationship between local environmental conditions and the abundance and dispersion of microorganisms, which shapes their distribution across the landscape.

Odonate species occupancy frequency distribution and abundance-occupancy relationship patterns in temporal and permanent water bodies in a subtropical area.

This paper investigates species richness and species occupancy frequency distributions (SOFD) as well as patterns of abundance–occupancy relationship (SAOR) in Odonata (dragonflies and damselflies) in a subtropical area. A total of 82 species and 1983 individuals were noted from 73 permanent and temporal water bodies (lakes and ponds) in the Pampa biome in southern Brazil. Odonate species occupancy ranged from 1 to 54. There were few widely distributed generalist species and several specialist species with a restricted distribution. About 70% of the species occurred in <10% of the water bodies, yielding a surprisingly high number of rare species, often making up the majority of the communities. No difference in species richness was found between temporal and permanent water bodies. Both temporal and permanent water bodies had odonate assemblages that fitted best with the unimodal satellite SOFD pattern. It seems that unimodal satellite SOFD pattern frequently occurred in the aquatic habitats. The SAOR pattern was positive and did not differ between permanent and temporal water bodies. Our results are consistent with a niche‐based model rather than a metapopulation dynamic model.

Coordinated Metacommunity Assembly and Spatial Distribution of Multiple Microbial Kingdoms within a Lake.

Freshwater planktonic communities comprise a tremendous diversity of microorganisms. This study investigated the distribution patterns of microbial kingdoms (bacteria, fungi, protists, and microbial metazoans) within a lake ecosystem. Water samples were collected from 50 sites along the shoreline in a lake during an early eutrophication period, and MiSeq sequencing was performed with different marker genes. Metacommunity analyses revealed a bimodal occupancy-frequency distribution and a Clementsian gradient persisting throughout all microbial kingdoms, suggesting similar regional processes in all kingdoms. Variation partitioning revealed that environmental characteristics, macrophyte/macroinvertebrate composition, space coordinates, and distance-based Moran's eigenvector maps (dbMEM) together could explain up to 29% of the community variances in microbial kingdoms. Kingdom synchrony results showed strong couplings between kingdoms (R2 ≥ 0.31), except between Fungi and Metazoa (R2 = 0.09). Another variation partitioning revealed that microbial kingdoms could well explain their community variances up to 73%. Interestingly, the kingdom Protista was best synchronized with the other kingdoms. A correlation network showed that positive associations between kingdoms outnumbered the negative ones and that the kingdom Protista acted as a hub among kingdoms. Module analysis showed that network modules included multi-kingdom associations that were prevalent. Our findings suggest that protists coordinate community assembly and distribution of other kingdoms, and inter-kingdom interactions are a key determinant in shaping their community structures in a freshwater lake.

Temporally Stable Species Occupancy Frequency Distribution and Abundance–Occupancy Relationship Patterns in Urban Wintering Bird Assemblages

Urbanization is negatively affecting biodiversity worldwide and general ecological patterns may also differ between urban and more natural areas. The main aim of this study was to examine if urbanization has effects on the wintering species occupancy frequency distribution (SOFD) and species abundance-occupancy relationship (SAOR), and if the observed patterns varied between winters, different sizes of towns and regionally in Finland. In this study temporal variation of the SOFD and SAOR patterns were studied in 29 town and village centers along a 950 km (60-68˚ N) latitudinal gradient during mid-winters in Finland. Wintering bird were counted during three winters (1991-1992, 1999-2000, and 2009-2010) from the same study sites and with the same survey methods. A total of 35 wintering bird species and 13285 individuals were detected. The bimodal symmetric SOFD pattern explained best the distribution of species in the pooled data, and the observed pattern was constant between the study winters, different sized of towns and towns located in southern and northern Finland. Three species (Parus major, Pica pica and Passer domesticus) were core species during all winters, irrespective of the size of town or latitude. There was slightly higher number of species belonging in satellite species group in the southern than in the northern towns. No changes of species from the core- to satellite-species were detected, and vice versa. However, occupancy rate of some species belonging to the intermediate species group either moved towards satellite-species or core-species across winters. The SAOR pattern was positive and stable over study winters and did not differ between different sizes of towns or town location. Our results indicated that urbanization leads a structure of winter bird community, where there is few widely distributed sedentary core species and many partially migratory or migratory satellite species with a restricted distribution. Our results also demonstrated that urbanization stabilize between-winter community structure, probably because of intensive winter feeding activities. Our results give support to the meta-population model, which predicts a bimodal SOFD pattern.

Community structure of woody plants on islands along a bioclimatic gradient

Understanding patterns of community structure and the causes for their variation can be furthered by comparative biogeographic analyses of island biotas. We used woody plant data at the local scale to investigate variations in species rarity, alpha, beta, and gamma diversity within and between three islands from the oceanic archipelagoes of Azores, Canaries and Mascarene. We used standardized protocols to sample ten 50 m × 50 m forest plots in each of the three islands with contrasting climate and regional species pools: Terceira (Azores), Tenerife (Canaries), and Reunion (Mascarene Islands). Occupancy frequency distributions and species abundance distributions were used to investigate rarity. The partitioning of beta diversity in a distance-decay framework was used to test for spatial patterns of community composition. Rarity was much more pronounced in the highly diverse islands of Tenerife and Reunion than in the regionally poorer island of Terceira. The number of species rose faster with increasing sample area in both Tenerife and Reunion. The slope of the species rank abundance curve was steeper in Terceira whereas the richer island assemblages approached a lognormal model. Compositional changes according to spatial distance were mostly due to replacement of species in Terceira and Reunion. Our results point to important differences in the community structure of Terceira, which is the less diverse and temperate region in comparison to Tenerife and Reunion which are highly diverse.

Regional variations in occupancy frequency distribution patterns between odonate assemblages in Fennoscandia

AbstractOdonate (damselfly and dragonfly) species richness and species occupancy frequency distributions (SOFDs) were analyzed in relation to geographical location in standing waters (lakes and ponds) in Fennoscandia, from southern Sweden to central Finland. In total, 46 dragonfly and damselfly species were recorded from 292 waterbodies. Species richness decreased to the north and increased with waterbody area in central Finland, but not in southern Finland or in Sweden. Species occupancy ranged from 1 up to 209 lakes and ponds. Over 50% of the species occurred in &lt;10% of the waterbodies, although this proportion decreased to the north. In the southern lakes and ponds, none of the species occurred in all lakes, whereas in the north, many species were present in all of the studied waterbodies. The dispersal ability of the species did not explain the observed species occupancy frequencies, but generalist species with a large geographical range occurred in a higher percentage of the waterbodies. At Fennoscandia scale, we found that the unimodal satellite pattern was predominant. However, at smaller scale, we found geographical variations in odonate speciesSOFDpatterns. The most southern communities followed the unimodal satellite‐dominant pattern, whereas in other regions, communities fitted best with the bimodal core–satellite patterns. It seems that the richer species pool in the southern locations, and the larger distribution range of the northern species, skewed the unimodal pattern into a bimodal satellite‐dominant pattern.

Great theories of species diversity in space and why they were forgotten: The beginnings of a spatial ecology and the Nordic early 20th‐century botanists

AbstractSometimes, we stumble over literature revealing that well‐known and groundbreaking theories have previously been proposed by earlier researchers. Going back to the 1920s and a group of Nordic botanists, we discovered that they had already accomplished much of what theoretical ecologists and biographers, especially Americans, did half a century later. In order to restore their legacy and understand why the work of the early spatial ecologists in Scandinavia and Finland was forgotten, we examined their publications, recalculated some of their results from their original data and compared these to the more recent independent discoveries of these theories. These Nordic early 20th‐century botanists worked with sample areas (mainlands) as well as island systems, examining spatial patterns and foreseeing or even building probabilistic approaches to species–area relationships (SARs), occupancy‐frequency distributions (OFDs) and species‐to‐genus (S/G) ratios. Many theories in spatial ecology and biogeography are linked to the SAR, such as MacArthur and Wilson's equilibrium theory of island biogeography (based on colonization and extinction), Darlington's rule of thumb, Preston's canonical hypothesis, Diamond's rules of reserve design, and Coleman's random‐placement theory. However, many of the most important SAR‐based theories—as the mathematical shape of both mainland and island SARs as well as rules of thumb, colonization rates on islands, and the random‐placement theory—had already been discovered or discussed in the 1920s by members of the Stockholm group which included the Swedes Gunnar Romell, Olof Arrhenius, Harald Kylin, and The Svedberg, and a Finn, Widar Brenner. The notion of stochastic S/G ratios and the idea that distance affects colonization rates can be traced back to another Finn, Alvar Palmgren. Great theories like these may disappear, if they are, as these, buried in obscure journals or written in languages other than English. There was also almost no audience in the 1920s and 30s, as mathematical theories were less acceptable at that time. Perhaps even more importantly, a devastating dispute (“The Great Polemic”) arose between the Stockholm group of theoretically and mathematically inclined botanists and the Uppsala group of descriptive phytosociologists. The fight, in which the Uppsala group won, was more a political and sociological than an intellectual one. As a result, not only the budding discipline of spatial ecology faded into oblivion but also the researchers were lost to science, at least to spatial ecology and biogeography, and descriptive and taxonomic approaches came to dominate Nordic ecology right up to the 1960s.

Shared or distinct responses between intermediate and satellite stream fish species in an altered Amazonian River?

Environmental and spatial variables can distinctly influence the occupancy frequency distributions in stream fish. From a metacommunity context, we tested the following hypothesis, intermediate species are governed by dispersal and niche-based processes; in contrast, satellite species are governed by niche-based processes. To test this, we separately analyzed three data sets, the entire metacommunity, the intermediate species and the satellite species, using a forward selection of explanatory variables, and a partial Redundancy Distance Analysis. The fish and 31 variables of 52 stream reaches of a Brazilian river basin in the Western Amazon were collected during the dry period of 2012. The results for all of the data set revealed two different patterns: on one side, satellite species revealed that niche and dispersal-based processes were the most important; on the other side, for intermediate species and for all of the species set, only dispersal-based processes were the most important. For the data set including all of the species and the intermediate species, the variance was explained mainly by landscape scale variables. By contrast, the variance within the satellite species set was explained by local scale variables. Management efforts for intermediate species should be taking at larger scale, but they are usually less critical for the maintenance of aquatic biodiversity; on the other hand, management efforts for satellite species should be taken at smaller scale and based on specific biological and ecological information for the focal species.

Metapopulation theory identifies biogeographical patterns among core and satellite marine bacteria scaling from tens to thousands of kilometers.

Metapopulation theory developed in terrestrial ecology provides applicable frameworks for interpreting the role of local and regional processes in shaping species distribution patterns. Yet, empirical testing of metapopulation models on microbial communities is essentially lacking. We determined regional bacterioplankton dynamics from monthly transect sampling in the Baltic Sea Proper using 16S rRNA gene sequencing. A strong positive trend was found between local relative abundance and occupancy of populations. Notably, the occupancy-frequency distributions were significantly bimodal with a satellite mode of rare endemic populations and a core mode of abundant cosmopolitan populations (e.g. Synechococcus, SAR11 and SAR86 clade members). Temporal changes in population distributions supported several theoretical frameworks. Still, bimodality was found among bacterioplankton communities across the entire Baltic Sea, and was also frequent in globally distributed datasets. Datasets spanning waters with widely different physicochemical characteristics or environmental gradients typically lacked significant bimodal patterns. When such datasets were divided into subsets with coherent environmental conditions, bimodal patterns emerged, highlighting the importance of positive feedbacks between local abundance and occupancy within specific biomes. Thus, metapopulation theory applied to microbial biogeography can provide novel insights into the mechanisms governing shifts in biodiversity resulting from natural or anthropogenically induced changes in the environment.

Urbanization and species occupancy frequency distribution patterns in core zone areas of European towns

AbstractMore and more of the globe is becoming urbanized. Thus, characterizing the distribution and abundance of species occupying different towns is critically important. The primary aim of this study was to examine the effect of urbanization and latitude on the patterns of species occupancy frequency distribution (SOFD) in urban core zones of European towns (38 towns) along a 3850-km latitudinal gradient. We determined which of the three most common distributional models (unimodal-satellite dominant, bimodal symmetrical, and bimodal asymmetrical) provides the best fit for urban bird communities using the AICc-model selection procedure. Our pooled data exhibited a unimodal-satellite SOFD pattern. This result is inconsistent with the results from previous studies that have been conducted in more natural habitats, where data have mostly exhibited a bimodal SOFD pattern. Large-sized towns exhibited a bimodal symmetric pattern, whereas smaller-sized towns followed a unimodal- -satellite dominated SOFD pattern. The difference in environmental diversity is the most plausible explanation for this observation because habitat diversity of the study plots decreased as urbanization increased. Southern towns exhibited unimodal satellite SOFD patterns, central European towns exhibited bimodal symmetric, and northern towns exhibited bimodal asymmetric SOFD patterns. One explanation for this observation is that urbanization is a more recent phenomenon in the north than in the south. Therefore, more satellite species are found in northern towns than in southern towns. We found that core species in European towns are widely distributed, and their regional population sizes are large. Our results indicated that earlier urbanized species are more common in towns than the species that have urbanized later. We concluded that both the traits of bird species and characteristics of towns modified the SOFD patterns of urban-breeding birds. In the future, it would be interesting to study how the urban history impacts SOFD patterns and if the SOFD patterns of wintering and breeding assemblages are the same.

Deconstructing occupancy frequency distributions in stream insects: effects of body size and niche characteristics in different geographical regions

1. Occupancy frequency distributions (OFDs) are one means to study species distribution patterns, allowing the delineation of rare and common species. Very few studies have deconstructed entire assemblages by ecological or biological characteristics and subsequently examinedOFDsin subgroups of species.2. The effect of deconstruction of entire assemblages by niche breadth, niche position or body size classes onOFDsin stream insects in three drainage basins was examined. It was hypothesized thatOFDsshould not vary between different drainage basins, but they should be affected by deconstruction into different niche breadth, niche position or body size classes.3. TheOFDswere typically strongly right‐skewed in all drainage basins. The set of small‐sized species was strongly dominated by rare species, whereas the importance of rare species decreased with increasing body size. Further, while theOFDsof sets of species with marginal niche position or small niche breadth were strongly dominated by rare species, those of species with non‐marginal niche position or large niche breadth showed highly variable degrees of occupancy. TheOFDsof non‐marginal species were even uniform in the entire data and one drainage basin, providing partial support to thea priorihypothesis.4. Niche‐based explanations are likely to account for occupancies of marginal and small‐niched species, whereas the distributions of non‐marginal and broad‐niched species may be not only affected by niche‐based mechanisms but also by spatial dynamics. Deconstruction ofOFDsby ecological and biological traits thus showed that the patterns may vary between different subgroups of species.

Spatially-Explicit Estimation of Geographical Representation in Large-Scale Species Distribution Datasets

Much ecological research relies on existing multispecies distribution datasets. Such datasets, however, can vary considerably in quality, extent, resolution or taxonomic coverage. We provide a framework for a spatially-explicit evaluation of geographical representation within large-scale species distribution datasets, using the comparison of an occurrence atlas with a range atlas dataset as a working example. Specifically, we compared occurrence maps for 3773 taxa from the widely-used Atlas Florae Europaeae (AFE) with digitised range maps for 2049 taxa of the lesser-known Atlas of North European Vascular Plants. We calculated the level of agreement at a 50-km spatial resolution using average latitudinal and longitudinal species range, and area of occupancy. Agreement in species distribution was calculated and mapped using Jaccard similarity index and a reduced major axis (RMA) regression analysis of species richness between the entire atlases (5221 taxa in total) and between co-occurring species (601 taxa). We found no difference in distribution ranges or in the area of occupancy frequency distribution, indicating that atlases were sufficiently overlapping for a valid comparison. The similarity index map showed high levels of agreement for central, western, and northern Europe. The RMA regression confirmed that geographical representation of AFE was low in areas with a sparse data recording history (e.g., Russia, Belarus and the Ukraine). For co-occurring species in south-eastern Europe, however, the Atlas of North European Vascular Plants showed remarkably higher richness estimations. Geographical representation of atlas data can be much more heterogeneous than often assumed. Level of agreement between datasets can be used to evaluate geographical representation within datasets. Merging atlases into a single dataset is worthwhile in spite of methodological differences, and helps to fill gaps in our knowledge of species distribution ranges. Species distribution dataset mergers, such as the one exemplified here, can serve as a baseline towards comprehensive species distribution datasets.

Scale effect and bimodality in the frequency distribution of species occupancy

Community patterns in species-by-site matrices provide valuable clues for inferring ecological processes at work. One such pattern is the occupancy frequency distribution (OFD) depicting the frequency distribution of row sums (i.e., occupancy) with a quarter OFDs of bimodal forms. Another pattern that also reflects the structure of row sums is the ranked species occupancy curve (RSOC), and has been shown to imply a 50% of bimodality in OFDs. The use of RSOCs has been advocated in literature over the OFD based on two conclusions from a 6-model inference using only 24 matrices: (i) RSOCs have two general forms, with half representing bimodal OFDs; (ii) there are no effects of spatial and study scales on RSOCs of different forms. Using a much more representative dataset of 289 matrices, I cast doubt on these two conclusions. A missing but dominant RSOC model (the truncated power law) is added. The number of species and the nestedness of the community differ significantly among matrices of different RSOC forms; however, the number of sites and the taxa in the studies do not differ among RSOC or OFD forms. The quarter OFDs of bimodal forms is reassured, with the least frequent occupancy consistent with Raunkiaer’s law of frequency. Importantly, a RSOC is mathematically transferrable to an OFD, with the derivative of the occupancy ranking curve being equal to the negative reciprocal of the occupancy frequency. Based on the type of the community (null versus interactive) and site environment (homogenous versus heterogeneous), four scenarios are needed to identify pre-inferring assemblage mechanisms. The results highlight the need for shifting research from the emphasis of marginal sums to the analysis of matrix structure for an in-depth understanding of the community assemblage patterns and mechanisms.