A method to incorporate the effect of taxonomic uncertainty on multivariate analyses of ecological data

Researchers in ecology commonly use multivariate analyses (e.g. redundancy analysis, canonical correspondence analysis, Mantel correlation, multivariate analysis of variance) to interpret patterns in biological data and relate these patterns to environmental predictors. There has been, however, little recognition of the errors associated with biological data and the influence that these may have on predictions derived from ecological hypotheses. We present a permutational method that assesses the effects of taxonomic uncertainty on the multivariate analyses typically used in the analysis of ecological data. The procedure is based on iterative randomizations that randomly re-assign non identified species in each site to any of the other species found in the remaining sites. After each re-assignment of species identities, the multivariate method at stake is run and a parameter of interest is calculated. Consequently, one can estimate a range of plausible values for the parameter of interest under different scenarios of re-assigned species identities. We demonstrate the use of our approach in the calculation of two parameters with an example involving tropical tree species from western Amazonia: 1) the Mantel correlation between compositional similarity and environmental distances between pairs of sites, and; 2) the variance explained by environmental predictors in redundancy analysis (RDA). We also investigated the effects of increasing taxonomic uncertainty (i.e. number of unidentified species), and the taxonomic resolution at which morphospecies are determined (genus-resolution, family-resolution, or fully undetermined species) on the uncertainty range of these parameters. To achieve this, we performed simulations on a tree dataset from southern Mexico by randomly selecting a portion of the species contained in the dataset and classifying them as unidentified at each level of decreasing taxonomic resolution. An analysis of covariance showed that both taxonomic uncertainty and resolution significantly influence the uncertainty range of the resulting parameters. Increasing taxonomic uncertainty expands our uncertainty of the parameters estimated both in the Mantel test and RDA. The effects of increasing taxonomic resolution, however, are not as evident. The method presented in this study improves the traditional approaches to study compositional change in ecological communities by accounting for some of the uncertainty inherent to biological data. We hope that this approach can be routinely used to estimate any parameter of interest obtained from compositional data tables when faced with taxonomic uncertainty.

Mapped cetacean habitat suitability and richness in the Azores, links to ArcGIS files

Marine spatial planning and ecological research call for high-resolution species distribution data. However, those data are still not available for most marine large vertebrates. The dynamic nature of oceanographic processes and the wide-ranging behavior of many marine vertebrates create further difficulties, as distribution data must incorporate both the spatial and temporal dimensions. Cetaceans play an essential role in structuring and maintaining marine ecosystems and face increasing threats from human activities. The Azores holds a high diversity of cetaceans but the information about spatial and temporal patterns of distribution for this marine megafauna group in the region is still very limited. To tackle this issue, we created monthly predictive cetacean distribution maps for spring and summer months, using data collected by the Azores Fisheries Observer Programme between 2004 and 2009. We then combined the individual predictive maps to obtain species richness maps for the same period. Our results reflect a great heterogeneity in distribution among species and within species among different months. This heterogeneity reflects a contrasting influence of oceanographic processes on the distribution of cetacean species. However, some persistent areas of increased species richness could also be identified from our results. We argue that policies aimed at effectively protecting cetaceans and their habitats must include the principle of dynamic ocean management coupled with other area-based management such as marine spatial planning.

Ecophysiology of Adonis distorta, a high-mountain species endemic of the Central Apennines

Morphological, anatomical and physiological plant and leaf traits of A. distorta, an endemic species of the Central Apennines on the Majella Massif, growing at 2,675 m a.s.l, were analyzed. The length of the phenological cycle starts immediately after the snowmelt at the end of May, lasting 128 ± 10 days. The low A. distorta height  (Hmax= 64 ± 4 mm) and total leaf area (TLA= 38 ± 9 cm2) associated to a high leaf mass area (LMA =11.8±0.6 mg cm−2) and a relatively high leaf tissue density (LTD = 124.6±14.3 mg cm−3) seem to be adaptive traits to the stress factors of the environment where it grows. From a physiological point of view, the high A. distorta photosynthetic rates (PN =19.6 ± 2.3 µmol m−2 s−1) and total chlorophyll content (Chla+b = 0.88 ± 0.13 mg g−1) in July are justified by the favorable temperature. PN decreases by 87% in September at the beginning of plant senescence. Photosynthesis and leaf respiration (RD) variations allow A. distorta to maintain a positive carbon balance during the growing season becoming indicative of the efficiency of plant carbon use. The results could be an important tool for conservation programmes of the A. distorta wild populations.

Modelling the niche for a marine vertebrate: A case study incorporating behavioural plasticity, proximate threats and climate change

[EN] The integration of satellite telemetry, remotely sensed environmental data, and habitat/environmental modelling has provided for a growing understanding of spatial and temporal ecology of species of conservation concern. The Republic of Cape Verde comprises the only substantial rookery for the loggerhead turtle Caretta caretta in the eastern Atlantic. A size related dichotomy in adult foraging patterns has previously been revealed for adult sea turtles from this population with a proportion of adults foraging neritically, whilst the majority forage oceanically. Here we describe observed habitat use and employ ecological niche modelling to identify suitable foraging habitats for animals utilising these two distinct behavioural strategies. We also investigate how these predicted habitat niches may alter under the influence of climate change induced oceanic temperature rises.

A recipe for scavenging in vertebrates - the natural history of a behaviour

Despite its prevalence, the importance of scavenging to carnivores is difficult to ascertain in modern day forms and impossible to study directly in extinct species. Yet, there are certain intrinsic and environmental features of a species that push it towards a scavenging lifestyle. These can be thought of as some of the principal parameters in optimal foraging theory namely, encounter rate and handling time. We use these components to highlight the morphologies and environments that would have been conducive to scavenging over geological time by focusing on the dominant vertebrate groups of the land, sea and air. The result is a synthesis on the natural history of scavenging. The features that make up our qualitative scale of scavenging can be applied to any given species and allow us to judge the likely importance of this foraging behaviour.

The 'rotiferologist' effect and other global correlates of species richness in monogonont rotifers

Global biodiversity patterns are often driven by diff erent environmental variables at diff erent scales. However, it is still controversial whether there are general trends, whether similar processes are responsible for similar patterns, and/or whether confounding eff ects such as sampling bias can produce misleading results. Our aim is twofold: 1) assessing the global correlates of diversity in a group of microscopic animals little analysed so far, and 2) inferring the infl uence of sampling intensity on biodiversity analyses. As a case study, we choose rotifers, because of their high potential for dispersal across the globe. We assembled and analysed a new worldwide dataset of records of monogonont rotifers, a group of microscopic aquatic animals, from 1960 to 1992. Using spatially explicit models, we assessed whether the diversity patterns conformed to those commonly obtained for larger organisms, and whether they still held true after controlling for sampling intensity, variations in area, and spatial structure in the data. Our results are in part analogous to those commonly obtained for macroorganisms (habitat heterogeneity and precipitation emerge as the main global correlates), but show some divergence (potential absence of a latitudinal gradient and of a large-scale correlation with human population). Moreover, the eff ect of sampling eff ort is remarkable, accounting for 50% of the variability; this strong eff ect may mask other patterns such as latitudinal gradients. Our study points out that sampling bias should be carefully considered when drawing conclusions from large-scale analyses, and calls for further faunistic work on microorganisms in all regions of the world to better understand the generality of the processes driving global patterns in biodiversity.

Bridging natural and social sciences: a framework for identify strategies and actions for the conservation of biodiversity.

The Atlantic Forest is one of the most diverse areas in the world and considered a hotspot. Several actions are needed for its preservation, among them the implementation of the Biodiversity Corridors. The Atlantic Forest has three biodiversity corridors and the Rio de Janeiro State, which harbors huge species diversity, is in the Serra do Mar Corridor. We developed socioeconomic, political and environmental indicators to present conservation strategies supported by a wide database. These indicators complemented the previous surveys of priority areas which emphasized biotic elements, and their integration allowed the elaboration of strategies for the conservation and management, regionally directed, to support actions to be implemented by the Government. The analysis was done considering three subjects: Anthropic Pressure, Physical and Biotic State, and Present Ability of Response. Data analysis followed a synthesis-aggregation schedule and the resulting database was taken to a workshop, where specialists proposed strategies and actions for the conservation. These strategies were discussed considering vegetation remnant distribution, biological relevance, environmental vulnerability, kind of anthropic pressure in the region and potential for success of the actions proposed, based on the ability of response. Rio de Janeiro State is very diverse in biotic, physical, political, socioeconomic and cultural aspects which demand specific actions for each region. So, depending on the present situation of the natural and anthropic environments and on the present and future sources of degradation, regionally directed actions are applicable. This specificity in conservation actions will enable that the State remnants will be more successfully protected.