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En Tunisie présaharienne les conséquences de la désertification sont progressivement devenues, au cours des dernières décennies, un problème environnemental majeur. On assiste à la dégradation continue du couvert végétal naturel, sous l'effet de diverses activités humaines. Ces activités mènent souvent au surpâturage, du fait de la régression de la superficie des parcours (suite à la mise en culture) et de l'augmentation de la pression pastorale, manifestée par la dégradation de la couverture végétale. Une telle dégradation quantitative et/ou qualitative s'accompagne de changements irréversibles de la flore et, en conséquence, des physionomies végétales marquées par la dominance des espèces délaissées par les animaux. Afin d'étudier les effets de l'interaction de la sécheresse saisonnière et du pâturage sur le recouvrement de la végétation et la diversité floristique, plusieurs transects permanents ont été installés à des distances variables autour de trois points d'eau situés en zone aride tunisienne. Le recouvrement et la richesse spécifique ont été mesurés durant deux saisons (automne et printemps) avec le recours à la méthode des points quadrats. Les principaux résultats de cette étude démontrent que l'effet du pâturage dans le sens d'une réduction du couvert végétal est plus remarquable au cours de l'automne. Le recouvrement global de la végétation peut être considéré comme un bon indicateur structural de l'état de l'écosystème. Les diversités alpha et bêta constituent à leur tour des bons indicateurs de structure de l'écosystème qui méritent d'être suivi dans des études similaires. In Presaharian Tunisia desertification has progressively become the major environmental problem during the last decades. Because of various human activities the natural vegetation is continuously degraded. These activities lead to overgrazing and decreasing plant cover, because of the regression of rangeland area (cropland extension) and the increase of the number of grazing animals. Such quantitative and/or qualitative degradation comes with irreversible changes of flora and, consequently, of the vegetation physiognomy marked by the dominance of unpalatable species. In order to study the interaction between seasonal drought and grazing on plant cover and diversity, many permanent transects were established at different distances around three watering points situated in the Tunisian arid zone. Plant cover and species richness dynamics were assessed and monitored during two seasons (fall and spring) using the quadrat — point method. The main results show that the impact of grazing in terms of reduction of the vegetation cover is more important during the fall. The vegetation cover can be considered to be a good structural indicator of the studied ecosystem. The alpha and beta diversities constitute good indictors for the ecosystem structure and are recommended to be estimated in future studies.

Aim This paper presents the statistical bases for temporal beta‐diversity analysis, a method to study changes in community composition through time from repeated surveys at several sites. Surveys of that type are presently done by ecologists around the world. A temporal beta‐diversity Index (TBI) is computed for each site, measuring the change in species composition between the first (T1) and second surveys (T2). TBI indices can be decomposed into losses and gains; they can also be tested for significance, allowing one to identify the sites that have changed in composition in exceptional ways. This method will be of value to identify exceptional sites in space–time surveys carried out to study anthropogenic impacts, including climate change. Innovation The null hypothesis of the TBI test is that a species assemblage is not exceptionally different between T1 and T2, compared to assemblages that could have been observed at this site at T1 and T2 under conditions corresponding to H0. Tests of significance of coefficients in a dissimilarity matrix are usually not possible because the values in the matrix are interrelated. Here, however, the dissimilarity between T1 and T2 for a site is computed with different data from the dissimilarities used for the T1–T2 comparison at other sites. It is thus possible to compute a valid test of significance in that case. In addition, the paper shows how TBI dissimilarities can be decomposed into loss and gain components (of species, or abundances‐per‐species) and how a B–C plot can be produced from these components, which informs users about the processes of biodiversity losses and gains through time in space–time survey data. Main conclusion Three applications of the method to different ecological communities are presented. This method is applicable worldwide to all types of communities, marine, and terrestrial. R software is available implementing the method. This paper describes a new method, temporal beta‐diversity analysis, to study the changes in community composition through time from repeated surveys at several sites. (a) A temporal beta‐diversity Index (TBI) is computed for each site, measuring the change in species composition between the first and second surveys. TBI indices can be tested for significance, allowing one to identify the sites that have changed in composition in exceptional ways. (b) It is often of interest to examine the species loss and gain components of the TBI indices because change through time is directional. Graphical procedures are demonstrated. Several examples from the ecological literature are provided.

Aim: The knowledge of biodiversity facets such as species composition, distribution and ecological niche is fundamental for the construction of biogeographic hypotheses and conservation strategies. However, the knowledge on these facets is affected by major shortfalls, which are even more pronounced in the tropics. This study aims to evaluate the effect of sampling bias and variation in collection effort on Linnean, Wallacean and Hutchinsonian shortfalls and diversity measures as species richness, endemism and beta-diversity. Location: Brazil. Methods: We have built a database with over 1.5 million records of arthropods, vertebrates and angiosperms of Brazil, based on specimens deposited in scientific collections and on the taxonomic literature. We used null models to test the collection bias regarding the proximity to access routes. We also tested the influence of sampling effort on diversity measures by regression models. To investigate the Wallacean shortfall, we modelled the geographic distribution of over 4000 species and compared their observed distribution with models. To quantify the Hutchinsonian shortfall, we used environmental Euclidean distance of the records to identify regions with poorly sampled environmental conditions. To estimate the Linnean shortfall, we measured the similarity of species composition between regions close to and far from access routes. Results: We demonstrated that despite the differences in sampling effort, the strong collection bias affects all taxonomic groups equally, generating a pattern of spatially biased sampling effort. This collection pattern contributes greatly to the biodiversity knowledge shortfalls, which directly affects the knowledge on the distribution patterns of diversity. Main conclusions: The knowledge on species richness, species composition and endemism in the Brazilian biodiversity is strongly biased spatially. Despite differences in sampling effort for each taxonomic group, roadside bias affected them equally. Species composition similarity decreased with the distance from access routes, suggesting collection surveys at sites far from roads could increase the probability of sampling new geographic records or new species.

Islands harbour evolutionary and ecologically unique biota, which are currently disproportionately threatened by a multitude of anthropogenic factors, including habitat loss, invasive species and climate change. Native forests on oceanic islands are important refugia for endemic species, many of which are rare and highly threatened. Long-term monitoring schemes for those biota and ecosystems are urgently needed: (i) to provide quantitative baselines for detecting changes within island ecosystems, (ii) to evaluate the effectiveness of conservation and management actions, and (iii) to identify general ecological patterns and processes using multiple island systems as repeated ‘natural experiments’. In this contribution, we call for a Global Island Monitoring Scheme (GIMS) for monitoring the remaining native island forests, using bryophytes, vascular plants, selected groups of arthropods and vertebrates as model taxa. As a basis for the GIMS, we also present new, optimized monitoring protocols for bryophytes and arthropods that were developed based on former standardized inventory protocols. Effective inventorying and monitoring of native island forests will require: (i) permanent plots covering diverse ecological gradients (e.g. elevation, age of terrain, anthropogenic disturbance); (ii) a multiple-taxa approach that is based on standardized and replicable protocols; (iii) a common set of indicator taxa and community properties that are indicative of native island forests’ welfare, building on, and harmonized with existing sampling and monitoring efforts; (iv) capacity building and training of local researchers, collaboration and continuous dialogue with local stakeholders; and (v) long-term commitment by funding agencies to maintain a global network of native island forest monitoring plots.

A major goal in ecology is to understand mechanisms that influence patterns of biodiversity and community assembly at various spatial and temporal scales. Understanding how community composition is created and maintained also is critical for natural resource management and biological conservation. In this study, we investigated environmental and spatial factors influencing beta diversity of local fish assemblages along the longitudinal gradient of a nearly pristine Neotropical river in the Colombian Llanos. Standardized surveys were conducted during the low-water season at 34 sites within the Bita River Basin. Physical, chemical, and landscape parameters were recorded at each site, and asymmetric eigenvector maps were used as spatial variables. To examine the relative influence of dispersal and environmental variables on beta diversity and its components, distance-based redundancy analysis (db-RDA) and variation partitioning analysis were conducted. We proposed that spatial scale of analysis and position within the river network would constrain patterns of beta diversity in different ways. However, results indicated that in this system, high beta diversity was consistent among species assemblages no matter the scale of analysis or position within the river network. Species replacement (turnover) dominated beta diversity, an indication of the importance of species sorting. These findings suggested that conservation of fish diversity in tropical rivers requires maintenance of both habitat heterogeneity (spatial variation in habitat conditions) and connectivity at the scale of entire river basins.

AIM: The variation in species composition among sites, or beta diversity, can be decomposed into replacement and richness difference. A debate is ongoing in the literature concerning the best ways of computing and interpreting these indices. This paper first reviews the historical development of the formulae for decomposing dissimilarities into replacement, richness difference and nestedness indices. These formulae are presented for species presence–absence and abundance using a unified algebraic framework. The indices decomposing beta play different roles in ecological analysis than do beta‐diversity indices. INNOVATION: Replacement and richness difference indices can be interpreted and related to ecosystem processes. The pairwise index values can be summed across all pairs of sites; these sums form a valid decomposition of total beta diversity into total replacement and total richness difference components. Different communities and study areas can be compared: some may be dominated by replacement, others by richness/abundance difference processes. Within a region, differences among sites measured by these indices can then be analysed and interpreted using explanatory variables or experimental factors. The paper also shows that local contributions of replacement and richness difference to total beta diversity can be computed and mapped. A case study is presented involving fish communities along a river. MAIN CONCLUSIONS: The different forms of indices are based upon the same functional numerators. These indices are complementary; they can help researchers understand different aspects of ecosystem functioning. The methods of analysis used in this paper apply to any of the indices recently proposed. Further work, based on ecological theory and numerical simulations, is required to clarify the precise meaning and domain of application of the different forms. The forms available for presence–absence and quantitative data are both useful because these different data types allow researchers to answer different types of ecological or biogeographic questions.

1. A fundamental aim in community ecology is to elucidate the processes structuring communities. The key to understanding community patterns is to account for species differences and similarities in how they respond to large-scale environmental gradients and partition local resources. Using phylogenetic relationships as a representation of species' ecological differences, we use phylogenetic beta-diversity (PBD) to examine how patterns of community relatedness change across space. 2. Specifically, we examine how PBD informs our understanding of the processes (spatial or environmental) directing species assembly along montane environmental gradients – in particular, whether patterns are consistent with niche conservatism. Also, we examine the depth of phylogenetic turnover to see where in evolutionary history shared environmental tolerances appear conserved. 3. For angiosperm communities situated to the east and west of the Continental Divide (CD) in the Rocky Mountain National Park in CO, USA, we compare nine beta-diversity indices (taxonomic, TBD: Jaccard, Bray–Curtis and Gower; PBD: PhyloSor, UniFrac, Dnn, Dpw, Rao's D and Rao's H) to changes in space, environment and environment controlling for space with the partial PROTEST method. 4. We find that PBD differs from taxonomic beta-diversity and some PBD metrics were redundant with one another (i.e. Rao's D & Dpw and UniFrac & PhyloSor). The indices' different sensitivities to evolutionary depth affected their responses to environmental and spatial gradients: TBD consistently associated greater with all factors (space, environment and environment controlled for space) than PBD metrics; PBD metrics more sensitive to recent changes were more highly correlated with all factors than those metrics sensitive to turnover deeper in the phylogeny. Generally, beta-diversity associated strongest with environment and least with space. 5. Synthesis. Taxonomic and phylogenetic beta-diversity complements each other to provide an enhanced perspective of the process governing community structure. Together, they depict patterns expected under niche conservatism for the Rocky Mountain angiosperm communities, that is, species' names change faster than their evolutionary relationships across space.

AIM: One of the main gaps in the assessment of biodiversity is the lack of a unified framework for measuring its taxonomic and functional facets and for unveiling the underlying patterns. LOCATION: Europe, 25 large river basins. METHODS: Here, we develop a decomposition of functional β‐diversity, i.e. the dissimilarity in functional composition between communities, into a functional turnover and a functional nestedness‐resultant component. RESULTS: We found that functional β‐diversity was lower than taxonomic β‐diversity. This difference was driven by a lower functional turnover compared with taxonomic turnover while the nestedness‐resultant component was similar for taxonomic and functional β‐diversity. MAIN CONCLUSIONS: Fish faunas with different species tend to share the same functional attributes. The framework presented in this paper will help to analyse biogeographical patterns as well as to measure the impact of human activities on the functional facets of biodiversity.

Environmental filtering is a major mechanism structuring ecological communities. However, it is still not clear how different abiotic drivers composing the environmental filter interact with each other to determine local species assemblage and create spatial patterns in species distribution. Here, we evaluated the effects of two strong and uncorrelated environmental variables (salinity and sediment properties) on the β-diversity of an estuarine macrobenthic community while accounting for spatial effects. Our results show that the benthic community composition has a strong spatial structure along the estuary, which can be greatly explained by salinity and sediment variation. Salinity is most associated with species replacement (turnover), whereas sediment is more important for species loss (nestedness). However, the effects of sediment variation on nestedness are mainly detected at a smaller spatial scale (estuarine sectors), whereas the effects of salinity on species turnover are stronger as spatial scale increases (entire estuary). Our findings suggest that environmental filters can drive both turnover and nestedness components of β-diversity, but that their relative importance depends on the spatial scale of investigation. Although abiotic drivers associated with detrimental effects (sediment) usually result in nestedness, larger spatial scales encompass abiotic drivers associated with different suitable conditions (salinity), increasing the relative importance of the replacement component of species β-diversity.