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Species Presence/absence Data (species + absence_data)
Selected AbstractsMethods to account for spatial autocorrelation in the analysis of species distributional data: a reviewECOGRAPHY, Issue 5 2007Carsten F. Dormann Species distributional or trait data based on range map (extent-of-occurrence) or atlas survey data often display spatial autocorrelation, i.e. locations close to each other exhibit more similar values than those further apart. If this pattern remains present in the residuals of a statistical model based on such data, one of the key assumptions of standard statistical analyses, that residuals are independent and identically distributed (i.i.d), is violated. The violation of the assumption of i.i.d. residuals may bias parameter estimates and can increase type I error rates (falsely rejecting the null hypothesis of no effect). While this is increasingly recognised by researchers analysing species distribution data, there is, to our knowledge, no comprehensive overview of the many available spatial statistical methods to take spatial autocorrelation into account in tests of statistical significance. Here, we describe six different statistical approaches to infer correlates of species' distributions, for both presence/absence (binary response) and species abundance data (poisson or normally distributed response), while accounting for spatial autocorrelation in model residuals: autocovariate regression; spatial eigenvector mapping; generalised least squares; (conditional and simultaneous) autoregressive models and generalised estimating equations. A comprehensive comparison of the relative merits of these methods is beyond the scope of this paper. To demonstrate each method's implementation, however, we undertook preliminary tests based on simulated data. These preliminary tests verified that most of the spatial modeling techniques we examined showed good type I error control and precise parameter estimates, at least when confronted with simplistic simulated data containing spatial autocorrelation in the errors. However, we found that for presence/absence data the results and conclusions were very variable between the different methods. This is likely due to the low information content of binary maps. Also, in contrast with previous studies, we found that autocovariate methods consistently underestimated the effects of environmental controls of species distributions. Given their widespread use, in particular for the modelling of species presence/absence data (e.g. climate envelope models), we argue that this warrants further study and caution in their use. To aid other ecologists in making use of the methods described, code to implement them in freely available software is provided in an electronic appendix. [source] Contribution of native and non-native species to fish communities in French reservoirsFISHERIES MANAGEMENT & ECOLOGY, Issue 3-4 2004P. Irz Abstract Previous studies showed that only 20% of the variability in fish community structure in French reservoirs could be explained by site characteristics. In addition, no relationship was found between the relative abundance of species and stocking effort. Therefore, deliberate or uncontrolled introductions are likely to be the source of a great part of the observed communities. The objective of this study was to assess the importance of species introductions in French reservoirs. Fifty-one reservoirs were sampled to obtain species presence/absence data. Local native (LNaR) and non-native (LNNR) species richness were negatively correlated. LNaR was strongly correlated to the lake surface area, depth and catchment area, whereas LNNR was independent of environmental variables. Furthermore, LNaR was positively correlated to regional native richness. Conversely, local total richness was independent of regional total richness, but was related to the reservoirs' environmental characteristics. It was hypothesised that the native fish communities in French reservoirs are unsaturated and species introductions lead to saturated communities. [source] Assembly rules and functional groups at global biogeographical scalesFUNCTIONAL ECOLOGY, Issue 5 2002D. R. Bellwood Summary 1The taxonomic and functional composition of reef fish assemblages are quantified in three biogeographical regions: Great Barrier Reef, French Polynesia and Caribbean. Assemblages are described in three habitats of differing wave exposure. Functional abilities are estimated based on published analyses linking fin morphology and swimming performance. 2Two questions were addressed: (1) To what extent are labrid assemblages similar among habitats and regions? (2) To what extent are functional characteristics of fish assemblages shaped by differences in biodiversity, evolutionary history and species composition? 3All three regions display highly congruent patterns of habitat use, in terms of assemblage structure and functional characteristics, despite a five-fold difference in species richness, limited or no species overlap, and a 3·2-Myear history of isolation. Exposed reef crest assemblages were dominated by fishes with fins reflecting lift-based high-speed locomotion. In contrast to abundance-based patterns, species presence/absence data were uninformative. 4The relationship between swimming ability and habitat use reveals underlying assembly rules at a functional level, emphasizing the utility of functional attributes as a metric for comparing system-level properties in taxonomically distinct faunas. [source] Fish assemblages of the Casiquiare River, a corridor and zoogeographical filter for dispersal between the Orinoco and Amazon basinsJOURNAL OF BIOGEOGRAPHY, Issue 9 2008Kirk O. Winemiller Abstract Aim, The aim of this study was to determine whether the Casiquiare River functions as a free dispersal corridor or as a partial barrier (i.e. filter) for the interchange of fish species of the Orinoco and Negro/Amazon basins using species assemblage patterns according to geographical location and environmental features. Location, The Casiquiare, Upper Orinoco and Upper Negro rivers in southern Venezuela, South America. Methods, Our study was based on an analysis of species presence/absence data and environmental information (11 habitat characteristics) collected by the authors and colleagues between the years 1984 and 1999. The data set consisted of 269 sampled sites and 452 fish species (> 50,000 specimens). A wide range of habitat types was included in the samples, and the collection sites were located at various points along the entire length of the Casiquiare main channel, at multiple sites on its tributary streams, as well as at various nearby sites outside the Casiquiare drainage, within the Upper Orinoco and Upper Rio Negro river systems. Most specimens and field data used in this analysis are archived in the Museo de Ciencias Naturales in Guanare, Venezuela. We performed canonical correspondence analysis (CCA) based on species presence/absence using two versions of the data set: one that eliminated sites having < 5 species and species occurring at < 5 sites; and another that eliminated sites having < 10 species and species occurring at < 10 sites. Cluster analysis was performed on sites based on species assemblage similarity, and a separate analysis was performed on species based on CCA loadings. Results, The CCA results for the two versions of the data set were qualitatively the same. The dominant environmental axis contrasted assemblages and sites associated with blackwater vs. clearwater conditions. Longitudinal position on the Casiquiare River was correlated (r2 = 0.33) with CCA axis-1 scores, reflecting clearwater conditions nearer to its origin (bifurcation of the Orinoco) and blackwater conditions nearer to its mouth (junction with the Rio Negro). The second CCA axis was most strongly associated with habitat size and structural complexity. Species associations derived from the unweighted pair-group average clustering method and pair-wise squared Euclidean distances calculated from species loadings on CCA axes 1 and 2 showed seven ecological groupings. Cluster analysis of species assemblages according to watershed revealed a stronger influence of local environmental conditions than of geographical proximity. Main conclusions, Fish assemblage composition is more consistently associated with local environmental conditions than with geographical position within the river drainages. Nonetheless, the results support the hypothesis that the mainstem Casiquiare represents a hydrochemical gradient between clearwaters at its origin and blackwaters at its mouth, and as such appears to function as a semi-permeable barrier (environmental filter) to dispersal and faunal exchanges between the partially vicariant fish faunas of the Upper Orinoco and Upper Negro rivers. [source] | ||||||||||