Quantifying the effects of nutrient addition on the taxonomic distinctness of serpentine vegetation

Traditional diversity indices summarize the information about the relative abundances of species within a community without regard to differences between species. However, intuitively, a community composed of dissimilar taxa is more diverse than a community composed of more similar taxa. Therefore, useful indices of diversity should account for taxonomic relations among species. In this paper, a new parametric diversity index that combines species relative abundances and their taxonomic distinctiveness is used to quantify the way in which soil fertilization affects the diversity of a garigue community on ultramafic soils of Tuscany (central Italy). Results show that, while ultramafic soils generally host plant communities of limited taxonomic diversity with respect to similar communities on other substrates, fertilization significantly enhances the biomass production of species that are not exclusive to ultramafic soils. As a consequence, if diversity is measured combining species relative abundances with their taxonomic distinctiveness, nutrient addition tends to increase the diversity of ultramafic communities.     

An information-theoretical measure of taxonomic diversity

Traditional diversity indices are computed from the abundances of species present and are insensitive to taxonomic differences between species. However, a community in which most species belong to the same genus is intuitively less diverse than another community with a similar number of species distributed more evenly between genera. In this paper, we propose an information-theoretical measure of taxonomic diversity that reflects both the abundances and taxonomic distinctness of the species. Unlike previous measures of taxonomic diversity, such as Rao's quadratic entropy, in this new measure the analyzed taxonomic properties are associated with the single species instead of species pairs.     

Diversity measurement combining relative abundances and taxonomic distinctiveness of species

We discuss a diversity measure combining information of relative abundances and taxonomic distinctiveness suggested by Ricotta (2004). We show that Ricotta's measure violates weak species monotonicity, a condition that requires that the addition of a species should always increase a diversity index if abundances change only marginally. We suggest an alternative index satisfying weak species monotonicity and apply it to the 'Zeesserveld' forest reserve in the Netherlands.     

Strong requirements for weak diversities

Weikard et al . ( Diversity and Distributions , 12 , 215–217) show that the taxonomic diversity measure proposed by Ricotta (2004) violates 'weak species monotonicity'. This condition requires that the addition of a species to a given species set should always increase diversity if abundances change only marginally. They further propose a new taxonomic diversity index that overcomes this drawback. In this paper, some statistical properties of this new diversity index are briefly analysed.     

Phylogenetic diversity measures based on Hill numbers

We propose a parametric class of phylogenetic diversity (PD) measures that are sensitive to both species abundance and species taxonomic or phylogenetic distances. This work extends the conventional parametric species-neutral approach (based on 'effective number of species' or Hill numbers) to take into account species relatedness, and also generalizes the traditional phylogenetic approach (based on 'total phylogenetic length') to incorporate species abundances. The proposed measure quantifies 'the mean effective number of species' over any time interval of interest, or the 'effective number of maximally distinct lineages' over that time interval. The product of the measure and the interval length quantifies the 'branch diversity' of the phylogenetic tree during that interval. The new measures generalize and unify many existing measures and lead to a natural definition of taxonomic diversity as a special case. The replication principle (or doubling property), an important requirement for species-neutral diversity, is generalized to PD. The widely used Rao's quadratic entropy and the phylogenetic entropy do not satisfy this essential property, but a simple transformation converts each to our measures, which do satisfy the property. The proposed approach is applied to forest data for interpreting the effects of thinning.     

A phylogenetic perspective on the evolutionary processes of floristic assemblages within a biodiversity hotspot in eastern Asia

Abstract How to maximize the conservation of biodiversity is critical for conservation planning, particularly given rapid habitat loss and global climatic change. The importance of preserving phylogenetic diversity has gained recognition due to its ability to identify some influences of evolutionary history on contemporary patterns of species assemblages that traditional taxonomic richness measures cannot identify. In this study, we evaluate the relationship between taxonomic richness and phylogenetic diversity of angiosperms at genus and species levels and explore the spatial pattern of the residuals of this relationship. We then incorporate data on historical biogeography to understand the process that shaped contemporary floristic assemblages in a global biodiversity hotspot, Yunnan Province, located in southwestern China. We identified a strong correlation between phylogenetic diversity residuals and the biogeographic affinity of the lineages in the extant Yunnan angiosperm flora. Phylogenetic diversity is well correlated with taxonomic richness at both genus and species levels between floras in Yunnan, where two diversity centers of phylogenetic diversity were identified (the northwestern center and the southern center). The northwestern center, with lower phylogenetic diversity than expected based on taxonomic richness, is rich in temperate‐affinity lineages and signifies an area of rapid speciation. The southern center, with higher phylogenetic diversity than predicted by taxonomic richness, contains a higher proportion of lineages with tropical affinity and seems to have experienced high immigration rates. Our results highlight that maximizing phylogenetic diversity with historical interpretation can provide valuable insights into the floristic assemblage of a region and better‐informed decisions can be made to ensure different stages of a region's evolutionary history are preserved.     

Effects of livestock grazing on an Afromontane grassland bird community in the Bale Mountains of Ethiopia

Livestock grazing has been considered to be one of the major causes for biodiversity degradation worldwide. In this study, we examined this effect on Afromontane grassland birds by comparing their diversity between ungrazed and grazed grassland sites in the northern Bale Mountains, Ethiopia. We counted birds and recorded vegetation height and cover along 28 (14 in each land‐use type) 1 km transects. We used six different diversity measures (richness, evenness, Shannon diversity, taxonomic diversity and taxonomic distinctness) to express bird diversity and explored which of these measures better reveal the diversity pattern. Vegetation structure differed significantly between the two sites; the first two principal components accounted for 78% of the variation. Discriminant function analysis (DFA) showed bird diversity to differ significantly between the two sites; taxonomic diversity (Delta) contributed the most to the difference between the two sites, while species richness contributed the least. The results of ANOVA indicated that all diversity measures, except species richness, were significantly higher in the protected site compared to the unprotected site. In general, this study showed that grazing had negatively affected bird diversity in the study area and the use of taxonomic diversity measures had enabled us to reveal the impact better.     

Towards a unifying approach to diversity measures: bridging the gap between the Shannon entropy and Rao's quadratic index

The diversity of a species assemblage has been studied extensively for many decades in relation to its possible connection with ecosystem functioning and organization. In this view most diversity measures, such as Shannon's entropy, rely upon information theory as a basis for the quantification of diversity. Also, traditional diversity measures are computed using species relative abundances and cannot account for the ecological differences between species. Rao first proposed a diversity index, termed quadratic diversity (Q) that incorporates both species relative abundances and pairwise distances between species. Quadratic diversity is traditionally defined as the expected distance between two randomly selected individuals. In this paper, we show that quadratic diversity can be interpreted as the expected conflict among the species of a given assemblage. From this unusual interpretation, it naturally follows that Rao's Q can be related to the Shannon entropy through a generalized version of the Tsallis parametric entropy.     

The taxonomic distinctness of coastal bottom-dwelling fish communities of the North-east Atlantic

1. New techniques for identifying the average taxonomic range of species assemblages were applied to an extensive dataset of bottom-dwelling fish in the coastal waters of NW Europe. These taxonomic distinctness indices provided much greater resolution than traditional diversity indices as they incorporated information on taxonomic relationships into an index which measures species dominance. Unlike standard measures of species richness and diversity, the mean value of these statistics is independent of sampling effort, and this allows objective comparisons to be made between samples from studies where sampling effort is not standardized.
2. A reduction in the average taxonomic range between the fauna of western waters of the UK and that of the southern North Sea was consistent with the general decline in species richness observed between these regions, and suggests that these two factors may be spatially positively correlated. Indices calculated for individual samples of fish on a local scale, however, did not all fit this trend.
3. Much of the variability in taxonomic diversity within the coastal waters of NW Europe was caused by the variable geographical distribution of the elasmobranchs. Of all the families which comprise the fish communities, this group has life-history characteristics which make it most susceptible to impact by commercial trawl fisheries.
4. The use of taxonomic distinctness measures provided additional insights, of relevance to biodiversity assessment, suggesting that they might usefully be applied to other aquatic and terrestrial fauna.     

Conservation of Afrotropical antelopes: consequences and efficiency of using different site selection methods and diversity criteria

The consequences of different measures of biotic diversity for the selection of priority sites for conservation were investigated using a dataset on Afrotropical antelopes. Site networks were selected using species richness, taxonomic diversity and restricted-range diversity as selection criteria. Restricted-range diversity was the most efficient criterion at representing all the species in the dataset. However when only a few sites could be conserved (insufficient to include all species) restricted-range diversity was relatively poor at representing absolute numbers of species and also taxonomic diversity. Use of unweighted species richness rather than a taxonomically weighted score did not significantly reduce the amount of taxonomic diversity represented. As expected an iterative selection of sites was considerably more efficient at representing all aspects of diversity than selection of the top-scoring sites. However the efficiency of an iterative selection procedure was reduced when some areas were already part of the reserve network. Since none of the criteria for selecting reserves maximizes all aspects of biodiversity under all circumstances, it is necessary to be clear about the objectives of a reserve network when deciding on a method for site selection.     

Responses of taxonomic distinctness and species diversity indices to anthropogenic impacts and natural environmental gradients in stream macroinvertebrates

1. Many studies have shown traditional species diversity indices to perform poorly in discriminating anthropogenic influences on biodiversity. By contrast, in marine systems, taxonomic distinctness indices that take into account the taxonomic relatedness of species have been shown to discriminate anthropogenic effects. However, few studies have examined the performance of taxonomic distinctness indices in freshwater systems. 2. We studied the performance of four species diversity indices and four taxonomic distinctness indices for detecting anthropogenic effects on stream macroinvertebrate assemblages. Further, we examined the effects of catchment type and area, as well as two variables (pH and total phosphorus) potentially describing anthropogenic perturbation on biodiversity. 3. We found no indications of degraded biodiversity at the putatively disturbed sites. However, species density, rarefied species richness, Shannon's diversity and taxonomic diversity showed higher index values in streams draining mineral as opposed to peatland catchments. 4. Of the major environmental gradients analysed, biodiversity indices showed the strongest relationships with catchment area, lending further support to the importance of stream size for macroinvertebrate biodiversity. Some of the indices also showed weak linear and quadratic relationships to pH and total phosphorus, and residuals from the biodiversity index‐catchment area regressions (i.e. area effect standardized) were more weakly related to pH and total phosphorus than the original index values. 5. There are a number of reasons why the biodiversity indices did not respond to anthropogenic perturbation. First, some natural environmental gradients may mask the effects of perturbation on biodiversity. Secondly, perturbations of riverine ecosystems in our study area may not be strong enough to cause drastic changes in biodiversity. Thirdly, multiple anthropogenic stressors may either increase or decrease biodiversity, and thus the coarse division of sites into reference and altered streams may be an oversimplification. 6. Although neither species diversity nor taxonomic distinctness indices revealed anthropogenic degradation of macroinvertebrate assemblages in this study, the traditional species diversity and taxonomic distinctness indices were very weakly correlated. Therefore, we urge that biodiversity assessment and conservation planning should utilize a number of different indices, as they may provide complementary information about biotic assemblages.     

Taxonomic identification bias does not drive patterns of abundance and diversity in theropod dinosaurs

The ability of palaeontologists to correctly diagnose and classify new fossil species from incomplete morphological data is fundamental to our understanding of evolution. Different parts of the vertebrate skeleton have different likelihoods of fossil preservation and varying amounts of taxonomic information, which could bias our interpretations of fossil material. Substantial previous research has focused on the diversity and macroevolution of non-avian theropod dinosaurs. Theropods provide a rich dataset for analysis of the interactions between taxonomic diagnosability and fossil preservation. We use specimen data and formal taxonomic diagnoses to create a new metric, the Likelihood of Diagnosis, which quantifies the diagnostic likelihood of fossil species in relation to bone preservation potential. We use this to assess whether a taxonomic identification bias impacts the non-avian theropod fossil record. We find that the patterns of differential species abundance and clade diversity are not a consequence of their relative diagnosability. Although there are other factors that bias the theropod fossil record that are not investigated here, our results suggest that patterns of relative abundance and diversity for theropods might be more representative of Mesozoic ecology than often considered.     

Utilization of species checklist data in revealing the spatial distribution of fish diversity

Marine fish species checklists from six Chinese coastal waters were combined for the analysis of taxonomic diversity. The Genus-Family index (G-F index) ranged between 0.39 and 0.84, which generally indicated a decreasing trend with increasing latitude, with the exception of the southernmost area. Average taxonomic distinctness showed a slight increasing trend from northern to central study areas, but whether the taxonomic distinctness indices represent a latitudinal gradient of biodiversity requires further study. The multivariate analysis revealed a distinct latitudinal variation in fish assemblages. These results indicate that species checklist data are helpful in understanding the diversity distribution of fish species in the coastal zone. The potential of a species inventory should be exploited to fully understand biodiversity.     

The coverage of a random sample from a biological community.

A taxonomic group will frequently have a large number of species with small abundances. When a sample is drawn at random from this group, one is therefore faced with the problem that a large proportion of the species will not be discovered. A general definition of quantitative measures of "sample coverage" is proposed, and the problem of statistical inference is considered for two special cases, (1) the actual total relative abundance of those species that are represented in the sample, and (2) their relative contribution to the information index of diversity. The analysis is based on a extended version of the negative binomial species frequency model. The results are tabulated.     

Mammals on the EDGE: conservation priorities based on threat and phylogeny

Conservation priority setting based on phylogenetic diversity has frequently been proposed but rarely implemented. Here, we define a simple index that measures the contribution made by different species to phylogenetic diversity and show how the index might contribute towards species-based conservation priorities. We describe procedures to control for missing species, incomplete phylogenetic resolution and uncertainty in node ages that make it possible to apply the method in poorly known clades. We also show that the index is independent of clade size in phylogenies of more than 100 species, indicating that scores from unrelated taxonomic groups are likely to be comparable. Similar scores are returned under two different species concepts, suggesting that the index is robust to taxonomic changes. The approach is applied to a near-complete species-level phylogeny of the Mammalia to generate a global priority list incorporating both phylogenetic diversity and extinction risk. The 100 highest-ranking species represent a high proportion of total mammalian diversity and include many species not usually recognised as conservation priorities. Many species that are both evolutionarily distinct and globally endangered (EDGE species) do not benefit from existing conservation projects or protected areas. The results suggest that global conservation priorities may have to be reassessed in order to prevent a disproportionately large amount of mammalian evolutionary history becoming extinct in the near future.     

Functional dominance rather than taxonomic diversity and functional diversity mainly affects community aboveground biomass in the Inner Mongolia grassland

The relationship between biodiversity and productivity has been a hot topic in ecology. However, the relative importance of taxonomic diversity and functional characteristics (including functional dominance and functional diversity) in maintaining community productivity and the underlying mechanisms (including selection and complementarity effects) of the relationship between diversity and community productivity have been widely controversial. In this study, 194 sites were surveyed in five grassland types along a precipitation gradient in the Inner Mongolia grassland of China. The relationships between taxonomic diversity (species richness and the Shannon–Weaver index), functional dominance (the community‐weighted mean of four plant traits), functional diversity (Rao's quadratic entropy), and community aboveground biomass were analyzed. The results showed that (1) taxonomic diversity, functional dominance, functional diversity, and community aboveground biomass all increased from low to high precipitation grassland types; (2) there were significant positive linear relationships between taxonomic diversity, functional dominance, functional diversity, and community aboveground biomass; (3) the effect of functional characteristics on community aboveground biomass is greater than that of taxonomic diversity; and (4) community aboveground biomass depends on the community‐weighted mean plant height, which explained 57.1% of the variation in the community aboveground biomass. Our results suggested that functional dominance rather than taxonomic diversity and functional diversity mainly determines community productivity and that the selection effect plays a dominant role in maintaining the relationship between biodiversity and community productivity in the Inner Mongolia grassland.     

Combining richness and abundance into a single diversity index using matrix analogues of Shannon's and Simpson's indices

Shannon's and Simpson's indices have been the most widely accepted measures of ecological diversity for the past fifty years, even though neither statistic accounts for species abundances across geographic locales ("patches"). An abundant species that is endemic to a single patch can be as much of a conservation concern as a rare cosmopolitan species. I extend Shannon's and Simpson's indices to simultaneously account for species richness and relative abundances – i.e. extend them to multispecies metacommunities – by making the inputs to each index a matrix, rather than a vector. The Shannon's index analogue of diversity is mutual entropy of species and patches divided by marginal entropy of the individual geographic patches. The Simpson's index analogue of diversity is a modification of mutual entropy, with the logarithm moved to the outside of the summation, divided by Simpson's index of the patches. Both indices are normalized for number of patches, with the result being inversely proportional to biodiversity. These methods can be extended to account for time-series of such matrices and average age-classes of each species within each patch, as well as provide a measure of spatial coherence of communities.     

Patterns in freshwater diatom taxonomic distinctness along an eutrophication gradient

1. A variety of species richness measures have been used to assess the effects of environmental degradation on biodiversity. Such measures can be highly influenced by sample size, sampling effort, habitat type or complexity, however, and typically do not show monotonic responses to human impact. In addition to being independent of the degree of sampling effort involved in data acquisition, effective measures of biodiversity should reflect the degree of taxonomical relatedness among species within ecological assemblages and provide a basis for understanding observed diversity for a particular habitat type. Taxonomic diversity or distinctness indices emphasize the average taxonomic relatedness (i.e. degree of taxonomical closeness) between species in a community. 2. Eutrophication of freshwater ecosystems, mainly due to the increased availability of nutrients, notably phosphorus, has become a major environmental problem. Two measures of taxonomic distinctness (Average Taxonomic Distinctness and Variation in Taxonomic Distinctness) were applied to surface sediment diatoms from 45 lakes across the island of Ireland to examine whether taxonomic distinctness and nutrient enrichment were significantly related at a regional scale. The lakes span a range of concentrations of epilimnic total phosphorus (TP) and were grouped into six different types, based on depth and alkalinity levels, and three different categories according to trophic state (ultra‐oligotrophic and oligotrophic; mesotrophic; and eutrophic and hyper‐eutrophic). 3. The taxonomic distinctness measures revealed significant differences among lakes in the three different classes of trophic state, with nutrient‐rich lakes generally more taxonomically diverse than nutrient‐poor lakes. This implies that enrichment of oligotrophic lakes does not necessarily lead to a reduction in taxonomic diversity, at least as expressed by the indices used here. Furthermore, taxonomic distinctness was highly variable across the six different lake types regardless of nutrient level. 4. Results indicate that habitat availability and physical structure within the study lakes also exert a strong influence on the pattern of taxonomic diversity. Overall the results highlight problems with the use of taxonomic diversity measures for detecting impacts of freshwater eutrophication based on diatom assemblages.     

Common species have lower taxonomic diversity Evidence from the urban floras of Brussels and Rome

The species pool hypothesis claims that the large‐scale regional species pool is the chief parameter in determining small‐scale species richness through filtering of species that can persist within a community on the basis of their tolerance of the abiotic environment. Accordingly, different environmental conditions give rise to different species assemblages. From a taxonomic perspective, under the assumption of trait conservatism, co‐occurring species that experience similar environmental conditions are likely to be more taxonomically similar than ecologically distant species. The next step consists in understanding how commonness and rarity of individual species produce the observed taxonomic diversity. In this paper, the importance of environmental filtering in regulating the taxonomic structure of rare and common plant species in the urban floras of Brussels (Belgium) and Rome (Italy) is tested. First, we computed the taxonomic diversity of the rare and common species of Brussels and Rome based on the branching topology of the Linnaean taxonomic trees. Next, using a randomization procedure, we determined whether the taxonomic diversity of the rare species was significantly higher than the diversity of the common species. Results show that, for both urban floras, common species that shape the community matrix and experience similar environmental conditions have a taxonomic diversity that is significantly lower than that of the rare species that represent a relatively incidental set of species of more ‘disperse’ origin. Finally, from a conservation/management perspective our results imply that, given their high taxonomic heterogeneity, the protection of rare species is a central issue for preserving high levels of diversity in urban areas.