Using generalized dissimilarity modelling to analyse and predict patterns of beta diversity in regional biodiversity assessment

Generalized dissimilarity modelling (GDM) is a statistical technique for analysing and predicting spatial patterns of turnover in community composition (beta diversity) across large regions. The approach is an extension of matrix regression, designed specifically to accommodate two types of nonlinearity commonly encountered in large-scaled ecological data sets: (1) the curvilinear relationship between increasing ecological distance, and observed compositional dissimilarity, between sites; and (2) the variation in the rate of compositional turnover at different positions along environmental gradients. GDM can be further adapted to accommodate special types of biological and environmental data including, for example, information on phylogenetic relationships between species and information on barriers to dispersal between geographical locations. The approach can be applied to a wide range of assessment activities including visualization of spatial patterns in community composition, constrained environmental classification, distributional modelling of species or community types, survey gap analysis, conservation assessment, and climate-change impact assessment.     

Australian land snails: a review of ecological research and conservation approaches

Land snails are an important yet often neglected component of Australia's biological diversity. Despite high levels of diversity within this group and the identification of many narrow range endemic species as being of conservation concern, there have been few detailed studies that document the ecology and conservation requirements of the group. A range of threats has been suggested, yet relatively few have been rigorously assessed. Whilst factors such as land clearing are readily apparent and have resulted in extinctions, other threats such as climate change are not well understood. This paper reviews studies conducted on terrestrial molluscs in Australia and highlights the need for further targeted ecological research, given the likely level of on-going threats. We urge researchers to apply rigorous approaches to data collection that will enable a deeper understanding of the factors governing distribution and abundance. Approaches used in other areas of conservation biology offer considerable scope for application to land snails and for the development of appropriate conservation strategies.     

Latitudinal and altitudinal diversity patterns and Rapoport effects in north-west European land snails and their causes

The latitudinal and altitudinal range sizes of north-west European land-snail species increase with increasing latitude/altitude. These Rapoport effects are not caused by northern/high-altitude species with wider latitudinal/altitudinal ranges and southern/low-altitude species with narrower latitudinal/altitudinal ranges, as predicted by the climatic variability hypothesis. They are instead caused mainly by different northern/upper borders of species occurring in the south part of the study area or at low and intermediate altitudes, respectively. This pattern indicates that the observed Rapoport effects are the result mainly of differential northward/upward expansion of species that were restricted to southern/low or intermediate altitude refugia during the glacials. Although all species occurring in a refugium experienced the same climatic conditions, there is stochastic variation in their climatic tolerance. Species with broader climatic tolerance were able to expand farer northwards/upwards postglacial. The altitudinal distribution of species richness in the analysed alpine faunas cannot be explained by the Rapoport-rescue hypothesis, because species richness peaks at intermediate altitudes and because there is no negative correlation between the number of range borders and altitude. The Rapoport-rescue hypothesis alone is probably also insufficient to explain the decrease in species richness with increasing latitude.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 87 , 309–323.     

Modelling the spatial distribution of beta diversity in Australian subtropical rainforest

Investigation of the spatial distribution of biodiversity among communities or across habitats (beta diversity) is often hampered by a scarcity of biological survey data. This is particularly the case in communities of high floristic diversity, such as the subtropical rainforests of eastern Australia. In contrast, there is excellent spatial coverage of environmental data for this region, such as geology, elevation and climate data. Generalized dissimilarity modelling was used in this study to combine biological survey data and environmental data grids for the investigation and prediction of floristic turnover among vegetation communities at a regional scale. Generalized dissimilarity modelling identified four environmental predictors of floristic turnover in the study region, all of which are linked with moisture stress: radiation of the driest quarter, precipitation of the driest period of the year, slope and aspect. Ten land classes representing largely homogeneous floristics and environment were identified and mapped for the region, allowing significantly greater discrimination than currently available mapping for this region. With increases in evapotranspiration and moisture stress predicted as a result of climate change, these results may allow future floristic shifts to be assessed in relation to regional‐scale gradients in floristic turnover.     

The relationship between species replacement,dissimilarity derived from nestedness,and nestedness

Aim Beta diversity can be partitioned into two components: dissimilarity due to species replacement and dissimilarity due to nestedness ( Baselga, 2010 , Global Ecology and Biogeography, 19 , 134–143). Several contributions have challenged this approach or proposed alternative frameworks. Here, I review the concepts and methods used in these recent contributions, with the aim of clarifying: (1) the rationale behind the partitioning of beta diversity into species replacement and nestedness‐resultant dissimilarity, (2) how, based on this rationale, numerators and denominators of indices have to match, and (3) how nestedness and nestedness‐resultant dissimilarity are related but different concepts. Innovation The rationale behind measures of species replacement (turnover) dictates that the number of species that are replaced between sites (numerator of the index) has to be relativized with respect to the total number of species that could potentially be replaced (denominator). However, a recently proposed partition of Jaccard dissimilarity fails to do this. In consequence, this partition underestimates the contribution of species replacement and overestimates the contribution of richness differences to total dissimilarity. I show how Jaccard dissimilarity can be partitioned into meaningful turnover and nestedness components, and extend these new indices to multiple‐site situations. Finally the concepts of nestedness and nestedness‐resultant dissimilarity are discussed. Main conclusions Nestedness should be assessed using consistent measures that depend both on paired overlap and matrix filling, e.g. NODF, whereas beta‐diversity patterns should be examined using measures that allow the total dissimilarity to be separated into the components of dissimilarity due to species replacement and dissimilarity due to nestedness. In the case of multiple‐site dissimilarity patterns, averaged pairwise indices should never be used because the mean of the pairwise values is unable to accurately reflect the multiple‐site attributes of dissimilarity.     

Hierarchical partitioning of ant diversity: implications for conservation of biogeographical diversity in arid and semi‐arid areas

Aim The scale of observation is important in detecting the spatial variation of biological assemblages, which should be taken into consideration for an appropriate plan of biogeographical conservation. We investigated whether (1) World Wildlife Fund’s ecoregion units are the appropriate scale for conserving ant diversity in Iran, (2) each ecoregion represents a distinct ant community composition and (3) patterns of diversity partitioning differ among four ecoregions. Location Iran, a sampling transect along four arid and semi‐arid ecoregions. Methods We applied hierarchical partitioning to data collected from a nested sampling design including four hierarchical levels: ‘local’, ‘landscape’, ‘ecoregional’ and ‘whole‐region’. Observed alpha and beta diversity components were compared with values of null distributions. Hierarchical cluster analysis was applied to evaluate similarity of ant species composition among ecoregions. Results Partitioning of whole‐region species richness showed that 85% of the species richness was generated by beta diversity among ecoregions and landscapes. The highest value of diversity was generated by beta diversity among ecoregions. Unlike whole‐region partitioning, separate partitioning within each ecoregion revealed that beta component among localities contributed to species richness of each ecoregion. Ecoregions showed different patterns of diversity partitioning. The alpha component contributed largely to the total diversity of two ecoregions, but for two other ecoregions, beta component contributed more than alpha component. Cluster analysis identified four discrete ant species compositions; however, it split landscapes of one ecoregion into two distinct groups. Main conclusions Whole‐region diversity partitioning indicates that ecoregions represent the appropriate scale for conserving ant diversity and that each ecoregion has a distinct ant fauna. However, different conservation strategies should be considered for different ecoregions owing to the differing scales of variation within them. Boundaries of ecoregions remain a subject for further studies. The influence of climate change on ecoregional boundaries should be considered and should be predicted with respect to future conservation maps.     

Species richness, environmental heterogeneity and area: a case study based on land snails in Skyros archipelago (Aegean Sea, Greece)

Aim To test the performance of the choros model in an archipelago using two measures of environmental heterogeneity. The choros model is a simple, easy‐to‐use mathematical relationship which approaches species richness as a combined function of area and environmental heterogeneity. Location The archipelago of Skyros in the central Aegean Sea (Greece). Methods We surveyed land snails on 12 islands of the archipelago. We informed the choros model with habitat data based on natural history information from the land snail species assemblage. We contrast this with habitat information taken from traditional vegetation classification to study the behaviour of choros with different measures of environmental heterogeneity. R² values and Akaike's information criterion (AIC) were used to compare the choros model and the Arrhenius species–area model. Path analysis was used to evaluate the variance in species richness explained by area and habitat diversity. Results Forty‐two land snail species were recorded, living in 33 different habitat types. The choros model with habitat types had more explanatory power than the classic species–area model and the choros model using vegetation types. This was true for all islands of the archipelago, as well as for the small islands alone. Combined effects of area and habitat diversity primarily explain species richness in the archipelago, but there is a decline when only small islands are considered. The effects of area are very low both for all the islands of the archipelago, and for the small islands alone. The variance explained by habitat diversity is low for the island group as a whole, but significantly increases for the small islands. Main conclusions The choros model is effective in describing species‐richness patterns of land snails in the Skyros Archipelago, incorporating ecologically relevant information on habitat occupancy and area. The choros model is more effective in explaining richness patterns on small islands. When using traditional vegetation types, the choros model performs worse than the classic species–area relationship, indicating that use of proxies for habitat diversity may be problematic. The slopes for choros and Arrhenius models both assert that, for land snails, the Skyros Archipelago is a portion of a larger biogeographical province. The choros model, informed by ecologically relevant habitat measures, in conjunction with path analysis points to the importance of habitat diversity in island species richness.     

Plant diversity patterns and their relationships with soil and climatic factors along an altitudinal gradient in the middle Tianshan Mountain area, Xinjiang, China

Patterns of plant diversity along the altitudinal gradient of Tianshan in central Xinjiang, China were examined. Plant and environment characteristics were surveyed from higher, south of Bogeda peak, to lower, north of Guerbantonggute desert. There were a total of 341 vascular plant, 295 herbage, 41 shrub, and seven tree species in the sampled plots. The plant richness of vegetation types generally showed a unimodal pattern along altitude, with a bimodal change of plant species number at 100-m intervals of altitudinal samples. The two belts of higher plant richness were in transient areas between vegetation types, the first in areas from dry grass to forest, and the second from forest to sub-alpine grass and bush. The beta diversity varied with altitudinal changes, with herbaceous species accounting for most species, and thus had similar species turnover patterns to total species. Matching the change of richness of plant species to environmental factors along altitude and correlating these by redundancy analysis revealed that the environmental factors controlling species richness and its pattern were the combined effects of temperature, precipitation, soil water, and nutrition. Water was more important at low altitude, and temperature at high altitude, and soil chemical and physical characters at middle altitudes. This study provides insights into plant diversity conservation of Bogeda Natural Reserve Areas in Tianshan Mountain. Nomenclatures: the scientific name for plants follows Flora of China (Compiling Committee of Flora of China).     

Estimating T-cell repertoire diversity: limitations of classical estimators and a new approach

A highly diverse T-cell receptor (TCR) repertoire is a fundamental property of an effective immune system, and is associated with efficient control of viral infections and other pathogens. However, direct measurement of total TCR diversity is impossible. The diversity is high and the frequency distribution of individual TCRs is heavily skewed; the diversity therefore cannot be captured in a blood sample. Consequently, estimators of the total number of TCR clonotypes that are present in the individual, in addition to those observed, are essential. This is analogous to the ‘unseen species problem’ in ecology. We review the diversity (species richness) estimators that have been applied to T-cell repertoires and the methods used to validate these estimators. We show that existing approaches have significant shortcomings, and frequently underestimate true TCR diversity. We highlight our recently developed estimator, DivE, which can accurately estimate diversity across a range of immunological and biological systems.     

Distribution patterns of land snails in Ugandan rain forests support the existence of Pleistocene forest refugia

Aim We investigated whether the biogeographical patterns expected if the East African fauna was affected by cycles of contraction to refugia and expansion of ranges, as has been previously hypothesized, can be found in the land snail fauna of rain forests in Uganda. Location The Albertine Rift region and the Lake Victoria forest belt in Uganda. Methods Snails and slugs were sampled in 60 plots in 13 rain forests, and small species were extracted from 5‐L leaf litter samples. Relative species richness was calculated by rarefaction. The influence of putative determinants of species richness was examined by bivariate correlation and multiple regression. Clustering and nestedness were tested by Monte Carlo simulations with a null model that considers the range size distribution, the species richness distribution of the forests, and the spatial autocorrelation of the occurrences of each species. Biotic elements were determined by model‐based Gaussian clustering. Results A total of 169 land snail species were recorded from 13 Ugandan rain forests. Relative species richness increases with rainfall and altitude, and decreases with evaporation and distance from the putative East Congolian refugia. Mean annual rainfall and distance from the putative East Congolian refugia were included in the best multiple regression model. The distribution areas of the Ugandan land snails are significantly clustered. Two montane, two lowland and a northern biotic element were found. The mean range extension increases with increasing distance from the putative East Congolian refugia. Moreover, the ranges of the Ugandan land snails are significantly nested. The centre of the sets of nested subsets is in the Virunga Mountains, close to the putative East Congolian refugia. Main conclusions The decrease of diversity with increasing distance from the putative East Congolian refugia, the clustering and nestedness of ranges, and the range size increase with increasing distance from the refugia indicate that the East African land snail fauna was affected by cycles of contraction to refugia and expansion of ranges. The significant clustering and nestedness cannot be explained by current environmental conditions. Given the environmental history, it can be supposed that the lowland elements expanded post‐glacially, whereas the ranges of the montane species are probably currently contracting.     

Diversity patterns of the terrestrial snail fauna of Nyungwe Forest National Park (Rwanda), a Pleistocene refugium in the heart of Africa

We investigated the land snail fauna of Nyungwe Forest National Park in south‐western Rwanda. Fifty plots at altitudes between 1718 and 2573 m were studied. In total, 3461 specimens were collected and were assigned to 102 land snail species. With respect to land snail species, Nyungwe Forest is the richest forest known in Africa. A comparison with other forests in the northern Albertine Rift indicates that land snail species richness in this region is significantly correlated with distance from Pleistocene forest refugia. The high beta diversity in Nyungwe is the result of a high species turnover between sites, which has biogeographical and ecological origins. Nyungwe Forest is situated on the Congo–Nile divide where species of different geographical origin may meet. Moreover, Nyungwe Forest offers a high diversity of habitats because it extends across a wide range of altitudinal zones. Species richness decreased with increasing altitude. It was also correlated with the presence of bare rocks that offer additional microhabitats and shelter. Although the occurrences of different land snail species in Nyungwe Forest were significantly clustered, only a minority of the species could be assigned to a group of species with similar occurrences. The majority of the species respond individualistically to environmental variables. The significant nestedness of the occurrences of the land snail species in Nyungwe was mainly correlated with altitude. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 363–375.     

High diversity and regional endemism in land snails of eastern Tanzania

In February/March 1995 we collected land snails (including slugs) at 12 stations in eastern Tanzania. A total of 571 person-hours yielded 9174 snails assigned to 159 morpho-species. The richest two sites each (<4ha of uniform forest) had 50 species (Amboni Cave) and 48 species (near Amani, Usambaras), nearly as great as the most species-rich sites known in the world; sieving of litter and soil would probably yield more species. In lowland (coastal) forests, both diversity and endemism seemed to decrease from north to south. Most snail species were found within only one of four coastal or one montane geographic regions, indicating substantial regional endemism. Only one species (Achatina fulica) appeared in all five regions, and 84% of all other species were found in only one (61%) or two regions (23%). The predatory streptaxids comprised about half the species and a third of the individuals at the Usambara site, an extremely high ratio of carnivores. Small snails (< 5mm greatest adult shell dimension) – many of which are probably undescribed species – comprise a substantial proportion of Tanzanian molluscan diversity; more surveys are needed, especially because of human pressures on the few forest patches remaining.     

Multiple scale patterns of shell and anatomy variability in land snails: the case of the Sicilian Marmorana (Gastropoda: Pulmonata, Helicidae)

Certain major aspects of phenotypic diversity are still largely unexplained. When phenotypic patterns do not relate to habitat variables, fine analysis of morphological patterns and their distribution sheds light on the origin of diversity. Among invertebrates, snails are an ideal model for studying the roles of the neutral processes and selection involved in creating diversity. To understand patterns and processes of variability on different scales (regional: areas; local: sites), morphological variability of two sets of characters (shell and genitalia) was quantified in a group of rock-dwelling land snails of the genus Marmorana (Pulmonata, Helicidae). To analyse shell variability, partitioning of the overall variation into size and shape components was analysed by a principal component-based approach. Shell shape and size variability is not significantly influenced by any environmental pressure. Variability at site scale is mainly attributed to shell size, which is a trait demonstrated to have a high degree of phenotypic plasticity. No sharp changes were observed for genitalia. Moreover, allometries between shell size and genitalia measurements involve a few populations. The observed multiple scale patterns are in line with the hypothesis that genital variance may be selectively controlled to maintain function.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 359–370.     

Patterns of beta diversity in Europe: the role of climate,land cover and distance across scales

Aim We test the prediction that beta diversity (species turnover) and the decay of community similarity with distance depend on spatial resolution (grain). We also study whether patterns of beta diversity are related to variability in climate, land cover or geographic distance and how the independent effects of these variables depend on the spatial grain of the data. Location Europe, Great Britain, Finland and Catalonia. Methods We used data on European birds, plants, butterflies, amphibians and reptiles, and data on British plants, Catalonian birds and Finnish butterflies. We fitted two or three nested grids of varying resolutions to each of these datasets. For each grid we calculated differences in climate, differences in land‐cover composition (CORINE) and beta diversity (β_sim, β_Jaccard) between all pairs of grid cells. In a separate analysis we looked specifically at pairs of adjacent grid cells (the first distance class). We then used variation partitioning to identify the magnitude of independent statistical associations (i.e. independent effects in the statistical sense) of climate, land cover and geographic distance with spatial patterns of beta diversity. Results Beta diversity between grid cells at any given distance decreased with increasing grain. Geographic distance was always the most important predictor of beta diversity for all pairwise comparisons at the extent of Europe. Climate and land cover had weaker but distinct and grain‐dependent effects. Climate was more important at relatively coarse grains, whereas land‐cover effects were stronger at finer grains. In the country‐wide analyses, climate and land cover were more important than geographic distance. Climatic and land‐cover models performed poorly and showed no systematic grain dependence for beta diversity between adjacent grid cells. Main conclusions We found that relationships between geographic distance and beta diversity, as well as the environmental correlates of beta diversity, are systematically grain dependent. The strong independent effect of distance indicates that, contrary to the current belief, a substantial fraction of species are missing from areas with a suitable environment. Moreover, the effects of geographic distance (at continental extents) and land cover (at fine grains) indicate that any species distribution modelling should take both environment and dispersal limitation into account.