You don’t belong here: explaining the excess of rare species in terms of habitat,space and time

Ecological communities are composed of a few common and several rare species. Many studies have evaluated the shape of abundance distribution curves, but few studies have assessed the causes of rarity. Using a dataset of stream macroinvertebrates, we investigated whether the excess of rare species in three focal communities of stones in riffles were common 1) in other habitats at the same stream site and period of sampling (environment), 2) in other stream sites in the same habitat and period of sampling (space), and 3) in other years in the same stream site and habitat (time). We observed that around 28% of the rare species were common in other habitats (environment), stream sites (space) or years (time). Among the three factors, rarity was mostly explained by habitat type, whereas a significant portion of the rare species in riffles were common in pools, submerged roots of terrestrial plants or in partially submerged moss patches. This result suggests that the presence in non‐optimum habitat is a strong determinant of the rarity observed in natural communities and most rare species are due to sampling artifacts or accidentally sampled transient species.     

Using rarity to infer how dendritic network structure shapes biodiversity in riverine communities

Dispersal of organisms connects physical localities, but the strength of connection varies widely. Variability in the influence of dispersal can be predictable in sharply defined networks like river systems because some sections of the network are more isolated, leading to different balances of local (i.e. environmental filtering, species interactions) and regional (i.e. dispersal‐driven) processes in structuring communities. We examined the influence of spatial isolation on the relative contributions of α‐ and β‐diversity to regional (γ) diversity, and examined how that influence differed between common and rare species in stream macroinvertebrate communities. One explanation for rarity on a regional scale is that common species are habitat generalists while rare species are specialists. Therefore, common species should be influenced more by dispersal‐driven processes while rare species should be more influenced by local processes. We predicted that for rare taxa, β‐diversity should represent a higher fraction of γ‐diversity in isolated headwaters but that differences between rare and common taxa with regard to the contribution of β‐diversity to γ‐diversity should be less distinct in well‐connected mainstem habitats. To test these predictions, we used macroinvertebrate communities from 634 sites across 22 watersheds. Regardless of rarity, β‐ and γ‐diversity were higher in headwaters compared to mainstems. However, α‐diversity was similar regardless of isolation for rare assemblages. But contrary to our predictions, common assemblages of predators and herbivores did exhibit differences in α‐diversity between locations. Our predictions were strongly supported for two guilds of consumers, the detritivores and collectors, but less so for herbivores and predators. However, these results make sense considering differences in life histories between the groups. For detritivores and collectors, species turnover (β‐diversity) was higher in isolated regions in river networks, and rarity exacerbated this effect, resulting in higher regional diversity of rare species, supporting the general theory that rarity reflects habitat specialization.     

Common and rare species respond to similar niche processes in macroinvertebrate metacommunities

Ecologists have long investigated why communities are composed of a few common species and many rare species. Most studies relate rarity to either niche differentiation among species or spatial processes. There is a parallel between these processes and the processes proposed to explain the structure of metacommunities. Based on a metacommunity perspective and on data on stream macroinvertebrates from different regions of Brazil, we answer two questions. 1) Are sets of common and rare species affected by similar niche and spatial processes? 2) How does the community composition of common and of rare species differ? The main hypothesis we test is that common species are mainly affected by environmental factors, whereas rare species are mostly influenced by dispersal limitation. We used variation partitioning to determine the proportion of variation explained by the environment and space in common and rare species matrices. Contrary to our expectations, evidence supported the idea that both common and rare species are affected mainly by environmental factors, even after controlling for the differing information content between common and rare species matrices. Moreover, the abundance of some common species is also a good predictor of variation in rare species matrices. Niche differences are unlikely to be the sole cause of patterns of rarity in these metacommunities. We suggest that sets of common and rare species react to similar major environmental gradients and that rare species also respond to processes that operate at a more fine‐grained spatial scale, particularly biotic interactions. We extend the view that species sorting is the dominant process structuring metacommunities and argue that future studies focusing on rarity would benefit from a metacommunity perspective.     

The role of transitional areas as avian biodiversity centres

Aim  With the ever-increasing threats to biodiversity, efforts are being directed towards identifying hotspots of special importance for conservation. In particular, there has been an effort to identify irreplaceable regions that are especially rich in rare species. Areas of transition between ecological systems in which multiple species coincide are expected, almost by definition, to be species-rich. Here, we examine whether this is simply a result of an overlap between two communities in boundary regions, or whether boundary areas also hold concentrations of rare (e.g. range-limited) species. We ask whether an analysis that includes areas of transition may be a useful contribution to the identification of biodiversity centres.
Location and methods  To address these questions, we examined the relationship between passeriform richness and range size rarity of approximately 2300 bird species in 4889 1° New World grid cells, and the distance of the cells to boundaries between adjacent plant-based ecoregions.
Results  Areas nearer to boundary regions between ecoregions not only had more bird species, but also scored more highly in terms of species rarity. The range centres of the rarest 10% of species were distributed significantly closer to boundaries between ecoregions than were species in general. This pattern persisted for rarity when we divided the New World into three latitudinal belts and analysed each separately, and when we excluded the Andes. It also persisted when compared with randomly generated ecoregion polygons.
Main conclusions  The findings of this work suggest that transitional environments harbour many rare species, in addition to high richness. Consequently areas of biotic transition should be highly valued as biodiversity centres and need to be included in future global conservation analyses and decisions.     

Early detection of potentially invasive invertebrate species in Mytilus galloprovincialis Lamarck, 1819 dominated communities in harbours

Constan?a harbour is a major port on the western coast of the semi-enclosed Black Sea. Its brackish waters and low species richness make it vulnerable to invasions. The intensive maritime traffic through Constan?a harbour facilitates the arrival of alien species. We investigated the species composition of the mussel beds on vertical artificial concrete substrate inside the harbour. We selected this habitat for study because it is frequently affected by fluctuating levels of temperature, salinity and dissolved oxygen, and by accidental pollution episodes. The shallow communities inhabiting it are thus unstable and often restructured, prone to accept alien species. Monthly samples were collected from three locations from the upper layer of hard artificial substrata (maximum depth 2?m) during two consecutive years. Ten alien macro-invertebrate species were inventoried, representing 13.5% of the total number of species. Two of these alien species were sampled starting the end of summer 2010, following a period of high temperatures that triggered hypoxia, causing mass mortalities of benthic organisms. Based on the species accumulation curve, we estimated that we have detected all benthic alien species on artificial substrate from Constan?a harbour, but additional effort is required to detect all the native species. Our results suggest that monitoring of benthic communities at small depths in harbours is a simple and useful tool in early detection of potentially invasive alien species. The selected habitat is easily accessible, the method is low-cost, and the samples represent reliable indicators of alien species establishment.     

Do persistent rare species experience stronger negative frequency dependence than common species?

Understanding why so many species are rare yet persistent remains a significant challenge for both theoretical and empirical ecologists. Yenni et al. (2012, Ecology, 93, 456–461) proposed that strong negative frequency dependence causes species to be rare while simultaneously buffering them against extinction. This hypothesis predicts that, on average, rare species should experience stronger negative frequency dependence than common species. However, it is unknown if ecological communities generally show this theoretical pattern. We discuss the implications of this phenomenon for community dynamics, and develop a method to test for a non‐random relationship between negative frequency dependence and relative abundance using species abundance data from 90 communities across a broad range of environments and taxonomic groups. To account for biases introduced by measurement error, we compared the observed correlation between species relative abundance and the strength of frequency dependence against expectations from a randomization procedure. In approximately half of the analysed communities, we found increasingly strong negative frequency dependence with decreasing relative abundance: rare species experienced stronger frequency dependence than common species. The randomization test never detected stronger negative frequency dependence in more common species. Our results suggest that strong negative frequency dependence is a signature of persistent, rare species in many communities.     

Determinants of species rarity: population growth rates of species sharing the same habitat

Determining differences between common and rare species is commonly used to identify factors responsible for rarity. Existing studies, however, suffer from two important drawbacks. First, studies compare species that are closely related phylogenetically but occupy different habitats. Second, these studies concentrate on single life history traits, with unknown relevance for population growth rates. Complete life cycles of one rare and one common Cirsium species sharing the same habitat were compared. Population growth rate was slightly lower in the rare species, translating into a large difference in local extinction probability. Seed predation intensity did not differ between species. However, it can be demonstrated that in connection with the data on complete demography, seed predation is the key factor causing a lower population growth rate in the rare species. These results are the first estimation of factors responsible for commonness or rarity of plants in terms of population growth rate without confounding differences in ecology. They demonstrate that conclusions based on single traits may be misleading and that only a comparison based on a complete life cycle can provide unequivocal evidence for concluding which factors are really those responsible for species commonness or rarity.     

Species abundance distributions as a proxy for the niche-neutrality continuum

Aims Species abundance distributions (SADs) are often used to verify mechanistic theories underlying community assembly. However, it is now accepted that SADs alone are not sufficient to reveal biological mechanisms. Recent attention focuses on the relative importance of stochastic dispersal processes versus deterministic processes such as interspecific competition and environmental filtering. Here, we combine a study of the commonness and rarity of species (i.e. the SAD) with mechanistic processes underlying community composition. By comparing the occurrence frequencies of each and every species with its abundance, we quantify the relative contributions of common and rare species to the maintenance of community structure. Essentially, we relate the continuum between commonness and rarity with that of niches and neutrality.Methods An individual-based, spatially explicit model was used to simulate local communities in niche spaces with the same parameters. We generated sets of assemblages from which species were eliminated in opposing sequences: from common to rare and from rare to common, and investigated the relationship between the abundance and frequency of species. We tested the predictions of our model with empirical data from a field experiment in the environmentally homogeneous alpine meadows of the Qinghai–Tibetan plateau.Important findings Our simulations support the widespread notion that common species maintain community structure, while rare species maintain species diversity, in both local and regional communities. Our results, both from theoretical simulations and from empirical observations, revealed positive correlations between the abundance of a particular species and its occurrence frequency. SAD curves describe a continuum between commonness and rarity. Removing species from the 'rare' end of this continuum has little effect on the similarity of communities, but removing species from the 'common' end of the continuum causes significant increases in beta diversity, or species turnover, between communities. In local communities distributed in a homogenous habitat, species located at the 'common' end of the continuum should be selected by environmental filtering, with niche space partitioning governed by interspecific competition. Conversely, species located at the 'rare' end of the continuum are most likely subject to stochastic dispersal processes. Species situated at intermediate locations on this continuum are therefore determined by niche and neutral processes acting together. Our results suggest that, in homogeneous habitats, SAD curves describing the common-rare continuum may also be used to describe the continuum between niches and neutrality.     

Investigating microbial associations from sequencing survey data with co‐correspondence analysis

Microbial communities, which drive major ecosystem functions, consist of a wide range of interacting species. Understanding how microbial communities are structured and the processes underlying this is crucial to interpreting ecosystem responses to global change but is challenging as microbial interactions cannot usually be directly observed. Multiple efforts are currently focused to combine next‐generation sequencing (NGS) techniques with refined statistical analysis (e.g., network analysis, multivariate analysis) to characterize the structures of microbial communities. However, most of these approaches consider a single table of sequencing data measured for several samples. Technological advances now make it possible to collect NGS data on different taxonomic groups simultaneously for the same samples, allowing us to analyse a pair of tables. Here, an analytical framework based on co‐correspondence analysis (CoCA) is proposed to study the distributions, assemblages and interactions between two microbial communities. We show the ability of this approach to highlight the relationships between two microbial communities, using two data sets exhibiting various types of interactions. CoCA identified strong association patterns between autotrophic and heterotrophic microbial eukaryote assemblages, on the one hand, and between microalgae and viruses, on the other. We demonstrate also how CoCA can be used, complementary to network analysis, to reorder co‐occurrence networks and thus investigate the presence of patterns in ecological networks.     

The chosen few—variations in common and rare soil bacteria across biomes

Soil bacterial communities are dominated by a few abundant species, while their richness is associated with rare species with largely unknown ecological roles and biogeography. Analyses of previously published soil bacterial community data using a novel classification of common and rare bacteria indicate that only 0.4% of bacterial species can be considered common and are prevalent across biomes. The remaining bacterial species designated as rare are endemic with low relative abundances. Observations coupled with mechanistic models highlight the central role of soil wetness in shaping bacterial rarity. An individual-based model reveals systematic shifts in community composition induced by low carbon inputs in drier soils that deprive common species of exhibiting physiological advantages relative to other species. We find that only a “chosen few” common species shape bacterial communities across biomes; however, their contributions are curtailed in resource-limited environments where a larger number of rare species constitutes the soil microbiome.Subject terms: Biodiversity, Microbial ecology, Microbial ecology, Soil microbiology     

Rarity and species/area relationships of vascular plants in deciduous woods, western Norway - applications to nature reserve selection

The Rabinowitz s model of rarity was applied to a vascular plant census list from 60 deciduous woods in western Norway By applying information from distribution maps and plant sociological literature from western Norway it was possible to obtain data on geographical distribution, habitat specificity, and maximum local population size at the regional-scale of western Norway This enabled a comparison between rarity at the local scale and rarity at the regional scale At the local scale rarity was primarily due to narrow geographic distribution At the regional scale, however, the most frequent form of rarity was due to restricted habitat specificity The species/area relationship and the SLOSS effect for the rare species at the regional scale are compared with patterns involving the total species list It is shown that a single large wood supports fewer regional-scale rare species than do combinations of two small woods of equal area The species/area relationship for species with small population sizes at the regional scale has a different slope from the species/area relationship for all species Area is a better predictor of regional-scale rarity than is the number of common species     

Functional rarity of plants in German hay meadows — Patterns on the species level and mismatches with community species richness

Functional rarity (FR) — a feature combining a species'' rarity with the distinctiveness of its traits — is a promising tool to better understand the ecological importance of rare species and consequently to protect functional diversity more efficiently. However, we lack a systematic understanding of FR on both the species level (which species are functionally rare and why) and the community level (how is FR associated with biodiversity and environmental conditions). Here, we quantify FR for 218 plant species from German hay meadows on a local, regional, and national scale by combining data from 6500 vegetation relevés and 15 ecologically relevant traits. We investigate the association between rarity and trait distinctiveness on different spatial scales via correlation measures and show which traits lead to low or high trait distinctiveness via distance‐based redundancy analysis. We test how species richness and FR are correlated, and use boosted regression trees to determine environmental conditions that are driving species richness and FR. On the local scale, only rare species showed high trait distinctiveness while on larger spatial scales rare and common species showed high trait distinctiveness. As infrequent trait attributes (e.g., legumes, low clonality) led to higher trait distinctiveness, we argue that functionally rare species are either specialists or transients. While specialists occupy a particular niche in hay meadows leading to lower rarity on larger spatial scales, transients display distinct but maladaptive traits resulting in high rarity across all spatial scales. More functionally rare species than expected by chance occurred in species‐poor communities indicating that they prefer environmental conditions differing from characteristic conditions of species‐rich hay meadows. Finally, we argue that functionally rare species are not necessarily relevant for nature conservation because many were transients from surrounding habitats. However, FR can facilitate our understanding of why species are rare in a habitat and under which conditions these species occur.     

The spatial variability of rare and common species in a gall-inhabiting Lepidoptera community

Determining the spatial variability in abundance structure of rare species is necessary to assess the validity of the often clarmed properties of rare species, I e as being both vulnerable to extinction and good indicators of environmental change The spatial concordance of the Lepidoptera species that inhabit a fungus-induced gall on Acacia karroo was examined across South Africa A positive relationship was found between species distribution and abundance The common and moderately common species in the community were highly concordant, although the rare species were diffusive As such, the vulnerability of the rare species in this community is difficult to assess and they are unlikely to make useful indicators of environmental change Although preliminary results suggest that the community is temporally concordant, establishing the level of temporal, in addition to spaual, concordance of rarity is necessary to determine the mechanisms responsible for the abundance structure of rare species in communities     

The contribution of rare species to community phylogenetic diversity across a global network of forest plots

Niche differentiation has been proposed as an explanation for rarity in species assemblages. To test this hypothesis requires quantifying the ecological similarity of species. This similarity can potentially be estimated by using phylogenetic relatedness. In this study, we predicted that if niche differentiation does explain the co-occurrence of rare and common species, then rare species should contribute greatly to the overall community phylogenetic diversity (PD), abundance will have phylogenetic signal, and common and rare species will be phylogenetically dissimilar. We tested these predictions by developing a novel method that integrates species rank abundance distributions with phylogenetic trees and trend analyses, to examine the relative contribution of individual species to the overall community PD. We then supplement this approach with analyses of phylogenetic signal in abundances and measures of phylogenetic similarity within and between rare and common species groups. We applied this analytical approach to 15 long-term temperate and tropical forest dynamics plots from around the world. We show that the niche differentiation hypothesis is supported in six of the nine gap-dominated forests but is rejected in the six disturbance-dominated and three gap-dominated forests. We also show that the three metrics utilized in this study each provide unique but corroborating information regarding the phylogenetic distribution of rarity in communities.     

Rare, threatened and alien species in the gastropod communities in the clay pit ponds in relation to the environmental factors (The Ciechanowska Upland, Central Poland)

The objectives of the present survey were to formulate a zoocenological analysis of the gastropod communities in clay pit ponds, as well as to determine the relationships between the gastropods and their environments, and to evaluate the water habitats in terms of their ecological-conservation value. The physical and chemical parameters of water, gastropod species and macrophytes occurring in the ponds indicate mesotrophic conditions. Principal Component Analysis (PCA) reveals a correlation between gastropod density and nitrates, a correlation between gastropod density and alkalinity, and additionally shows a correlation between gastropod density and chlorides. The pond surface area, nitrates, chlorides concentrate, alkalinity, and substratum have all affected these gastropod communities. The occurrence of the first permanent population of Ferrissia clessiniana (Jickeli, 1882) was recorded in Poland. Valvata naticina Menke 1845 has become a critically rare species (CR) due to the pollution of water environments. Five other species, e.g. Anisus vorticulus (Troschel, 1834) and Planorbis carinatus O.F. Müller, 1774 are recorded on the Polish Red List of Species. The clay pit ponds of the Ciechanowska Upland, because of their distinctive environmental features, provide a refuge where a number of rare, threatened and alien gastropod species live.     

Functional homogenization of bird communities along habitat gradients: accounting for niche multidimensionality

Aim To test whether functional homogenization of bird communities is promoted by anthropogenic landscape transformation, using specialization and habitat preference indices that account for the multidimensionality of niches. Location Catalonia, north‐east Iberian Peninsula. Methods We used data on bird species occurrences and landscape features in 2834 1‐km² squares. Three orthogonal landscape gradients, which were taken as niche dimensions, were defined by means of principal components analysis (PCA). Specialization and habitat preference indices were created for 103 terrestrial bird species on the basis of their frequency of occurrence variation along the landscape gradients. These indices, together with species rarity, were then averaged for bird communities. We then analysed the patterns of variation of communities’ mean specialization, mean rarity and mean habitat preference values along a gradient of agricultural–forest habitat mosaics. Results Wherever we found a significant variation in the degree of specialization along the agricultural–forest gradient, agricultural habitats held more specialized bird communities than did forest ones and bore, on average, rarer species. Thus, results contradicted our initial hypothesis that humanized areas would bear more functionally homogenized bird communities. Higher α‐diversity values tended to be associated with generalist communities and with those having rarer species. Main conclusions Estimations of bird community specialization for different niche dimensions can behave differently along certain landscape gradients, and some of these differences can be explained by the variation of mean habitat preferences. Thus, we argue that a multidimensional approach to assess average niche breadth of communities can be more informative than a unidimensional measure. Our results suggest that widespread land abandonment and current secondary forest expansion throughout the Mediterranean area are promoting functional homogenization of bird communities. It would be desirable to construct larger‐scale indicators of functional homogenization in order to monitor communities’ responses to widespread landscape changes.     

Life History Differences between Rare and Common Flowering Plant Species of California and the British Isles

Generalizations about rare and endangered species are important for the development of conservation management policy and for understanding of the nature of rarity. Therefore, we sought such generalizations by statistically comparing eight life history and reproductive traits of rare and common plant species in two better-studied but climatically and geographically distinct Holarctic floras-those of California and the British Isles. Trends were often similar in both floras. Rare and common species differ significantly for a number of characters. In both floras, a woody habit was significantly more frequent for the rare species than the common species. Also, in both floras, monocarpy was less frequent in the rare species, significantly so in California. The rare species of both floras were, on average, significantly shorter in stature than the common species. This trend in stature remained significant when nonwoody species were compared but did not do so for woody species. Rare and common species differed with regard to their frequency of inflorescence structure types, but these differences were not concordant for both floras. The rare species of the British Isles had significantly higher proportions of mixed and polymorphic flower colors; the trend was not significant in California. In both floras, rare species had a higher frequency of many-seeded fruits, significantly so in California. California's rare species had a significantly higher frequency of dehiscent fruits than common species; the trend was reversed and not significant for the British Isles. We found no significant differences for characters associated with fruit dispersal. Finally, in California, the median altitude of the range of the common species was significantly greater than that of the rare species. At present, these correlates cannot be assigned as possible causes or consequences of rarity. Nonetheless, they may represent "high-risk" traits that could be used to identify other species already at risk or potentially at risk of becoming rarer.     

Deconstructing richness patterns by commonness and rarity reveals bioclimatic and spatial effects in black fly metacommunities

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The taxonomic distribution of rare and common species among families in the vascular plant flora of Fennoscandia

Many plant traits are not randomly distributed among families. The question considered here is ‘are rarity and commonness of vascular plants in Fennoscandia randomly distributed among families?’ If more rare or more common species are found within a family, this may give some initial indications about which traits may predict rarity and commonness of species. A species was defined as rare or common based on its abundance and on the number of grid squares it occupies. 1521 naturally occurring species in 229 75×75 km grid squares were used. Permutation tests were performed to assess statistically if rarity and commonness are randomly distributed among families. Several families can be identified as having more rare or more common species than would be expected under a random allocation model. However, there are little deviations from what would be expected if rarity and commonness were randomly distributed among families in the whole Fennoscandian flora. It is proposed that the arbitrary geographical limits of the study area may account for the lack of any clear patterns of rarity and commonness among and between families.     

Factors influencing spatial distribution of fish communities on a fringing reef at Mauritius, S.W. Indian Ocean

This paper analyses the spatial patterns of fish communities on a narrow fringing reef of Mauritius and identifies some controlling factors. Canonical Correspondence Analysis revealed that the location in the reef ecosystem, the living coral coverage, and the proximity to a dredged area were the major factors controlling the distribution and abundance of fish species. Two distinct communities were observed across the fringing reef, representing a land-ocean gradient. The low diversity of fish species, and also of invertebrates such as corals, molluscs, and echinoderms is probably a consequence of the narrowness of the fringing reef and of anthropogenic impacts, notably the high pollution by nutrients.