Giovanni Bacaro

Accounting for uncertainty when mapping species distributions: The need for maps of ignorance

Accurate mapping of species distributions is a fundamental goal of modern biogeography, both for basic and applied purposes. This is commonly done by plotting known species occurrences, expert-drawn range maps or geographical estimations derived from species distribution models. However, all three kinds of maps are implicitly subject to uncertainty, due to the quality and bias of raw distributional data, the process of map building, and the dynamic nature of species distributions themselves. Here we review the main sources of uncertainty suggesting a code of good practices in order to minimize their effects. Specifically, we claim that uncertainty should be always explicitly taken into account and we propose the creation of maps of ignorance to provide information on where the mapped distributions are reliable and where they are uncertain.

Old and new challenges in using species diversity for assessing biodiversity

Although the maintenance of diversity of living systems is critical for ecosystem functioning, the accelerating pace of global change is threatening its preservation. Standardized methods for biodiversity assessment and monitoring are needed. Species diversity is one of the most widely adopted metrics for assessing patterns and processes of biodiversity, at both ecological and biogeographic scales. However, those perspectives differ because of the types of data that can be feasibly collected, resulting in differences in the questions that can be addressed. Despite a theoretical consensus on diversity metrics, standardized methods for its measurement are lacking, especially at the scales needed to monitor biodiversity for conservation and management purposes. We review the conceptual framework for species diversity, examine common metrics, and explore their use for biodiversity conservation and management. Key differences in diversity measures at ecological and biogeographic scales are the completeness of species lists and the ability to include information on species abundances. We analyse the major pitfalls and problems with quantitative measurement of species diversity, look at the use of weighting measures by phylogenetic distance, discuss potential solutions and propose a research agenda to solve the major existing problems.

Computing diversity from dated phylogenies and taxonomic hierarchies: does it make a difference to the conclusions?

Recently, dated phylogenies have been increasingly used for ecological studies on community structure and conservation planning. There is, however, a major impediment to a systematic application of phylogenetic methods in ecology: reliable phylogenies with time-calibrated branch lengths are lacking for a large number of taxonomic groups and this condition is likely to continue for a long time. A solution for this problem consists in using undated phylogenies or taxonomic hierarchies as proxies for dated phylogenies. Nonetheless, little is known on the potential loss of information of these approaches compared to studies using dated phylogenies with time-calibrated branch lengths. The aim of this study is to ask how the use of undated phylogenies and taxonomic hierarchies biases a very simple measure of diversity, the mean pairwise phylogenetic distance between community species, compared to the diversity of dated phylogenies derived from the freely available software Phylomatic. This is illustrated with three sets of data on plant species sampled at different scales. Our results show that: (1) surprisingly, the diversity computed from dated phylogenies derived from Phylomatic is more strongly related to the diversity computed from taxonomic hierarchies than to the diversity computed from undated phylogenies, while (2) less surprisingly, the strength of this relationship increases if we consider only angiosperm species.

The role of regional and local scale predictors for plant species richness in Mediterranean forests

Abstract Both local and regional predictors play a role in determining plant community structure and composition. Climate, soil features as well as different local history and management affect forest understorey and tree species composition, but to date their specific role is relatively unknown. Few studies have addressed the importance of these predictors, especially in the Mediterranean area, where environmental conditions and human impacts have generated heterogeneous forest communities. In this study, the relationships between environmental variables and species richness of different groups of vascular plants (vascular species, woody species and open habitat species) and bryophytes were investigated in Tuscan forests. A total of 37 environmental variables were used by generalised linear model fitting in order to find parsimonious sub-sets of environmental factors (predictors) that are able to explain species diversity patterns at the local scale. Moreover, the role of regional and local variable groups on species richness of the considered plant groups was estimated by using the variance partitioning approach. We found that local variables, such as forest management and structure, explained more variance than regional variables for total species richness, open habitat species richness and bryophyte species richness. On the other hand, regional variables (such as elevation) played a central role for woody species richness.

Using taxonomic data to assess and monitor biodiversity: are the tribes still fighting?

In this article we review the problems encountered during the use of taxonomic information for the purpose of monitoring biodiversity. These problems encompass the nature of taxonomic data that requires human interpretation in order to be recognised in the field and grouped into well-defined classes such as species. We then briefly discuss some methods that may be utilized in order to minimise these problems.

Coastline Dune Vegetation Dynamics: Evidence of No Stability

Coastal dune ecosystems are subjected to severe stress and disturbance factors that are particularly high in the beach-foredune environment and generally decrease with distance from the coast. The present study aimed to link plant species composition of coastal foredunes with the physical dynamical processes of the coastline in central Italy. A random hierarchical sampling design, based on two spatial scales (quadrant and parcel), was applied to estimate the variation in plant community composition. Permutational multivariate analysis of variance (PERMANOVA) revealed an approximately similar amount of variation with respect to both the coastal dynamic class and the parcel level. In addition, principal coordinate analyses showed that three taxa – Ammophila arenaria, Elymus farctus and Otanthus maritimus subsp. maritimus – were mainly linked to the coastal dynamics: A. arenaria increases its abundance where erosion of the shoreline is very high, while E. farctus and O. maritimus are more abundant in the prograding coast. Finally, similarity percentages analysis (SIMPER) highlighted that where the erosive processes were strongest, the number of the species contributing to the total similarity was the highest. This is likely to indicate instability and a strong disturbance of plant communities that results in an unstable equilibrium. These findings have important implications for management and conservation actions.

Scale dependence of plant species richness in a network of protected areas

Despite the widely recognised importance of reserve networks, their effectiveness in encompassing and maintaining biodiversity is still debated. Species diversity is one of the most affordable measures of biodiversity, but it is difficult to survey such data over large scales. This research aimed to perform a sample-based assessment of species richness of groups of plants with different conservation value (alien species, protected species, and all species) within a reserve network, testing the use of partitioning as a tool for assessing diversity at different spatial scales, from the plot to the entire network. Plant diversity patterns differed for the groups of species for most of the investigated spatial scales. Despite these patterns assumed divergent tendencies when different species groups were considered, most of the species richness within the network was given by larger scale β-diversity for both alien and protected species, as well for all species. Diversity partitioning proved an effective tool to quantify the role of spatial scales in structuring the total species richness of the network, and is helpful in planning reserve networks.

Measuring beta-diversity from taxonomic similarity

Abstract Question: The utility of beta (β-) diversity measures that incorporate information about the degree of taxonomic (dis)similarity between species plots is becoming increasingly recognized. In this framework, the question for this study is: can we define an ecologically meaningful index of β-diversity that, besides indicating simple species turnover, is able to account for taxonomic similarity amongst species in plots? Methods: First, the properties of existing measures of taxonomic similarity measures are briefly reviewed. Next, a new measure of plot-to-plot taxonomic similarity is presented that is based on the maximal common subgraph of two taxonomic trees. The proposed measure is computed from species presences and absences and include information about the degree of higher-level taxonomic similarity between species plots. The performance of the proposed measure with respect to existing coefficients of taxonomic similarity and the coefficient of Jaccard is discussed using a small data set of heath plant communities. Finally, a method to quantify β-diversity from taxonomic dissimilarities is discussed. Results: The pro posed measure of taxonomic β-diversity incorporates not only species richness, but also information about the degree of higher-order taxonomic structure between species plots. In this view, it comes closer to a modern notion of biological diversity than more traditional measures of β-diversity. From regression analysis between the new coefficient and existing measures of taxonomic similarity it is shown that there is an evident nonlinearity between the coefficients. This nonlinearity demonstrates that the new coefficient measures similarity in a conceptually different way from previous indices. Also, in good agreement with the findings of previous authors, the regression between the new index and the Jaccard coefficient of similarity shows that more than 80% of the variance of the former is explained by the community structure at the species level, while only the residual variance is explained by differences in the higher-order taxonomic structure of the species plots. This means that a genuine taxonomic approach to the quantification of plot-to-plot similarity is only needed if we are interested in the residual systems variation that is related to the higher-order taxonomic structure of a pair of species plots.

High Plant Diversity of Grasslands in a Landscape Context: A Comparison of Contrasting Regions in Central Europe

Some regions and habitats harbour high numbers of plant species at a fine scale. A remarkable example is the grasslands of the White Carpathian Mountains (Czech Republic), which holds world records in local species richness; however, the causes are still poorly understood. To explore the landscape context of this phenomenon and its relationships to diversity patterns at larger scales, we compared diversity patterns in grasslands and other vegetation types in the White Carpathians with those in nearby regions lacking extremely species-rich grasslands, using data from vegetation plots and flora grid mapping of entire landscapes. Although small-scale species richness of grasslands and ruderal/weed vegetation of the White Carpathians was higher than in the nearby regions, the number of grassland and ruderal/weed species in the regional flora of the White Carpathians was not. Diversity of forests was not higher in this region at any scale. Thus the remarkably high local species richness of the White Carpathian grasslands does not result from a larger grassland species pool in the region, but from the fine-scale co-occurrence of many grassland species in this landscape, which results in the formation of grassland communities that are locally rich but with similar species composition when comparing different sites (i.e. high alpha but low beta diversity). This pattern can be partly attributed to the large total area of these grasslands, which reduces random extinctions of rare species, low geological diversity, which enables many species to occur at many sites across the landscape, and high land-cover diversity, which supports mixing of species from different vegetation types.

Phenology of Dryopteris affinis ssp. affinis and Polystichum aculeatum: modeling relationships to the climatic variables in a Mediterranean area

The phenology of leaves and stages from immature sori to spore release were studied in natural populations of two perennial herbaceous ferns, Dryopteris affinis ssp. affinis and Polystichum aculeatum, for 2 years in Italy. The Generalized Additive Model for Location, Scale and Shape (GAMLSS) was used to predict a particular phenological event from the climatic variables. Both fern species are evergreen with leaf lifespan of 13–14 months in D. affinis ssp. affinis and 15–24 months in P. aculeatum. Their leaf production is seasonal with most flushed in spring. In D. affinis ssp. affinis the decaying of old leaves is sudden whereas in P. aculeatum it is gradual, and in both types the decaying is accelerated just as the new leaves emerge. Temperature is the best predictor for the development of sori and spore release. The end of spore release and leaf emergence are positively affected by temperature and negatively affected by rainfall and snow cover for P. aculeatum. An almost similar response to climatic factors of emergent and senescent leaves and their phenology supportsthe hypothesis that old leaves serve as nutrient storage organs for new leaf growth. Comparison the phenological patterns between the 2 years indicated that the time lapses between each phenological event were the same within seasons for D. affinis ssp. affinis but show some differences for P. aculeatum. We also hypothesize that endogenous factors may play an important role in the phenology of P. aculeatum.