A parametric diversity measure combining the relative abundances and taxonomic distinctiveness of species

Most ecological diversity indices summarize the information about the relative abundances of species without reflecting taxonomic differences between species. Nevertheless, in environmental conservation practice, data on species abundances are mostly irrelevant and generally unknown. In such cases, to summarize the conservation value of a given site, so‐called ‘taxonomic diversity’ measures can be used. Such measures are based on taxonomic relations among species and ignore species relative abundances. In this paper, bridging the gap between traditional biodiversity measures and taxonomic diversity measures, I introduce a parametric diversity index that combines species relative abundances with their taxonomic distinctiveness. Due to the parametric nature of the proposed index, the contribution of rare and abundant species to each diversity measure is explicit.     

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.     

An index of divergence from species to life-form diversity based on the notion of intrinsic diversity ordering

In this paper, we propose a measure of divergence from species tolife-form diversity based on the notion of intrinsic diversity ordering. First,species and life-form relative abundances within the analyzed community aredetermined. Next, community intrinsic diversity profile is computed both fromspecies and life-form relative abundances. Finally, the speed of decrease fromspecies to life-form diversity is obtained by comparing the area under thespecies diversity profile with the area under the corresponding life-formdiversity profile. Since life-forms classify plants into ecologically relevantgroups irrespective of their systematics, the proposed measure might be usefulto quantify the ecological similarity of different communities without loosinginformation on traditional taxonomic diversity figures. As an application fordemonstration, a small data set from a garigue community on ultramafic soils ofTuscany (central Italy) is used.     

Genetic diversity in European Pisum germplasm collections

The distinctness of, and overlap between, pea genotypes held in several Pisum germplasm collections has been used to determine their relatedness and to test previous ideas about the genetic diversity of Pisum. Our characterisation of genetic diversity among 4,538 Pisum accessions held in 7 European Genebanks has identified sources of novel genetic variation, and both reinforces and refines previous interpretations of the overall structure of genetic diversity in Pisum. Molecular marker analysis was based upon the presence/absence of polymorphism of retrotransposon insertions scored by a high-throughput microarray and SSAP approaches. We conclude that the diversity of Pisum constitutes a broad continuum, with graded differentiation into sub-populations which display various degrees of distinctness. The most distinct genetic groups correspond to the named taxa while the cultivars and landraces of Pisum sativum can be divided into two broad types, one of which is strongly enriched for modern cultivars. The addition of germplasm sets from six European Genebanks, chosen to represent high diversity, to a single collection previously studied with these markers resulted in modest additions to the overall diversity observed, suggesting that the great majority of the total genetic diversity collected for the Pisum genus has now been described. Two interesting sources of novel genetic variation have been identified. Finally, we have proposed reference sets of core accessions with a range of sample sizes to represent Pisum diversity for the future study and exploitation by researchers and breeders.     

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.     

A test of traditional diversity measures and taxonomic distinctness indices on benthic diatoms of soda pans in the Carpathian basin

Saline lakes are threatened all over the world and their conservation has been a key issue. Various diversity indices are available for ecological status assessments, however, with poorly explored relevance and applicability in saline, alkaline pans. Therefore, traditional diversity measures (species richness and Shannon diversity) and taxonomic distinctness indices (Average [AvTD] and Variance of Taxonomic Distinctness [VarTD]) were tested in more than 100 sampling sites of 39 soda pans in Central-Europe to find sufficient indicators of the ecological condition and simultaneously to facilitate their preservation according to the modern conservation practices. Results of the analyses showed that healthy soda pan ecosystems with high level of natural stress and reduced habitat heterogeneity are characterized by low diversity diatom assemblages. In soda pans where the stress can be extremely high from natural reasons, oligopoly of closely related species can develop: the average taxonomic distinctness appeared between genus and family level. The non-DNA-sequence based phylogenetic diversity measures (AvTD and VarTD), were generally sensitive to the trophic state of the lakes, in contrast to traditional diversity metrics, which were unequivocally indicative for the special physical and chemical parameters (e.g. conductivity, pH) of the soda pans. In some cases, when the response of the diversity measures for a given environmental variable (pH, temperature) overlapped, the AvTD was found to be a more precise indicator of the environmental changes (pH) than traditional ones. The decreasing tendency of the AvTD along the intensified natural impact may be explained by the long available time for the species to adapt to these special environments.     

Temporal turnover and the maintenance of diversity in ecological assemblages

Temporal variation in species abundances occurs in all ecological communities. Here, we explore the role that this temporal turnover plays in maintaining assemblage diversity. We investigate a three-decade time series of estuarine fishes and show that the abundances of the individual species fluctuate asynchronously around their mean levels. We then use a time-series modelling approach to examine the consequences of different patterns of turnover, by asking how the correlation between the abundance of a species in a given year and its abundance in the previous year influences the structure of the overall assemblage. Classical diversity measures that ignore species identities reveal that the observed assemblage structure will persist under all but the most extreme conditions. However, metrics that track species identities indicate a narrower set of turnover scenarios under which the predicted assemblage resembles the natural one. Our study suggests that species diversity metrics are insensitive to change and that measures that track species ranks may provide better early warning that an assemblage is being perturbed. It also highlights the need to incorporate temporal turnover in investigations of assemblage structure and function.     

Relational diversity

In biology, the measurement of diversity traditionally focusses on reporting number of unambiguously distinguishable types, thus referring to qualitative (discontinuously varying) traits. Inclusion of frequencies or other weights has produced a large variety of diversity indices. Quantitative (continuously varying) traits do not readily fit into this perspective. In fact, in the context of quantitative traits, the concept of diversity is not always clearly distinguished from the (statistical) notion of dispersion. In many cases the ambiguity even extends to qualitative traits. This is at variance with the broad spectrum of diversity issues ranging, e.g., from ecological and genetic aspects of diversity to functional, structural, systematic, or evolutionary (including phylogenetic) aspects. In view of the urgent need for a more consistent perspective, it is called to attention that all of these aspects, whether of qualitative or quantitative nature, can be gathered under the common roof of binary relations (for qualitative traits two objects are related, for example, if they share the same trait state). A comprehensive concept of (relational) diversity can be developed in two steps: (1) determine the number of unrelated pairs of objects among all admissible pairs as a measure of implicit (relative) diversity, (2) invoke the concept of effective number to transform the implicit measure of diversity into an explicit (absolute) measure. The transformation operates by equating the observed implicit diversity to the implicit diversity obtained for the ideal model of an equivalence relation with classes of equal size. The number of these classes specifies the effective number as an explicit measure of diversity. The wealth of problems that can be treated from this unified perspective is briefly addressed by classifying and interpreting established diversity indices in the light of relational diversity. Desirable applications to the above-mentioned aspects are specified with the help of types of relations such as order, hierarchical, and tree relations. Corresponding biological issues including taxonomic community diversity, mating system, food web, sociological, cladistic and phylogenetic, or hypercycle diversity are suggested for future consideration.     

Components of beta diversity in hierarchical sampling designs: A new approach

Diversity partitioning has been generally used to estimate the contribution of different levels of sampling hierarchy to landscape diversity. However, beta diversity values derived by partitioning strongly depend on focus and sample size and the partitioning is inadequate to express the contribution of landscape elements to community variation. Pairwise dissimilarities are also frequently used to express community turnover, but related approaches capture only limited aspects of it, especially for hierarchical sampling designs. To avoid these shortcomings, we suggest a procedure which quantifies the role of different levels of sampling hierarchy (relative beta diversity) and the share of landscape elements in the corresponding relative beta diversity (contribution value). Our novel method uses pairwise dissimilarities and is based on partitioning a dissimilarity matrix of sampling units. It is suitable to testing various null hypotheses via permutation techniques as demonstrated by artificial and actual data. The method is a valuable tool in ecology because it complements existing approaches while providing a unique way to understand community diversity in space.     

Taxonomic diversity as complementary information to assess plant species diversity in secondary vegetation and primary tropical deciduous forest

Question: Species diversity is commonly expressed as the number of species present in an area, but this unique value assumes that all species contribute equally to the area's biodiversity. Can taxonomic diversity be used as a complementary measure for species richness in order to assess plant biodiversity in remnants of primary forest and patches of secondary vegetation? Location: Veracruz, Mexico. Methods: Using data from six sampling transects of each vegetation type in an elevation gradient (400‐900 m a.s.l.), we compare the point, mean and cumulative floristic diversity of primary forest and secondary vegetation in a tropical deciduous landscape, using species richness and two measures of taxonomic diversity: average taxonomic distinctness (Δ+) and variation in taxonomic distinctness (Λ+). We performed a randomization test to detect differences in the observed taxonomic diversity, from the expected values derived from the species pool of each vegetation type. Results: We found that the species of secondary vegetation are more closely related at low taxonomic levels (lower Δ+ value) than the species of primary forest remnants. Also, in secondary vegetation the distribution of species is uneven among the taxonomic levels and units (high Λ+ value). These patterns are consistent for point, mean and cumulative taxonomic diversity. Families Asteraceae, Euphorbiaceae, Fabaceae and Poaceae are over‐represented, while families Bromeliaceae, Cactaceae, Orchidaceae and Pteridaceae are under‐represented in secondary vegetation. Conclusions: Although in a previous paper we concluded that secondary vegetation is more alpha‐diverse than primary forest (in terms of both cumulative and mean species richness), and beta‐diversity between vegetation types is notoriously high, we now provide a wider view by highlighting the importance of taxonomic diversity in primary forest remnants. Our data indicate that to measure biodiversity accurately, we should seek to capture its different facets. This will allow us to make conservation recommendations based on a broader view, and not on a single dimension.     

The structure of cross-cultural musical diversity

Human cultural traits, such as languages, musics, rituals and material objects, vary widely across cultures. However, the majority of comparative analyses of human cultural diversity focus on between-culture variation without consideration for within-culture variation. In contrast, biological approaches to genetic diversity, such as the analysis of molecular variance (AMOVA) framework, partition genetic diversity into both within- and between-population components. We attempt here for the first time to quantify both components of cultural diversity by applying the AMOVA model to music. By employing this approach with 421 traditional songs from 16 Austronesian-speaking populations, we show that the vast majority of musical variability is due to differences within populations rather than differences between. This demonstrates a striking parallel to the structure of genetic diversity in humans. A neighbour-net analysis of pairwise population musical divergence shows a large amount of reticulation, indicating the pervasive occurrence of borrowing and/or convergent evolution of musical features across populations.     

Multivariate dispersion as a measure of beta diversity

Beta diversity can be defined as the variability in species composition among sampling units for a given area. We propose that it can be measured as the average dissimilarity from individual observation units to their group centroid in multivariate space, using an appropriate dissimilarity measure. Differences in beta diversity among different areas or groups of samples can be tested using this approach. The choice of transformation and dissimilarity measure has important consequences for interpreting results. For kelp holdfast assemblages from New Zealand, variation in species composition was greater in smaller holdfasts, while variation in relative abundances was greater in larger holdasts. Variation in community structure of Norwegian continental shelf macrobenthic fauna increased with increases in environmental heterogeneity, regardless of the measure used. We propose a new dissimilarity measure which allows the relative weight placed on changes in composition vs. abundance to be specified explicitly.     

Of beta diversity,variance, evenness,and dissimilarity

The amount of variation in species composition among sampling units or beta diversity has become a primary tool for connecting the spatial structure of species assemblages to ecological processes. Many different measures of beta diversity have been developed. Among them, the total variance in the community composition matrix has been proposed as a single‐number estimate of beta diversity. In this study, I first show that this measure summarizes the compositional variation among sampling units after nonlinear transformation of species abundances. Therefore, it is not always adequate for estimating beta diversity. Next, I propose an alternative approach for calculating beta diversity in which variance is substituted by a weighted measure of concentration (i.e., an inverse measure of evenness). The relationship between this new measure of beta diversity and so‐called multiple‐site dissimilarity measures is also discussed.     

A novel multiple-site extension to pairwise partitioned taxonomic beta diversity

Our understanding of the causes of variation in taxonomic composition, or beta diversity, is progressing rapidly, thanks in part to recent methodological advances. For example, methods for partitioning beta diversity into its “replacement” and “richness” components have helped reveal patterns that had been undetected by traditional analyses. These partitioning methods are derived from pairwise dissimilarity measures, and are thus well suited to many conventional beta diversity analyses, including “distance decay” relationships. However, pairwise beta diversity measures have limitations, including their lack of information about taxa that are shared among three or more sites. Recently, a new suite of multiple-site counterparts to the pairwise partitioning measures of beta diversity was proposed, but the pairwise analogs upon which these were based were subsequently criticized, and compelling arguments were presented in favor of other partitioning approaches. Here, we introduce multiple-site partitioning measures that address these shortcomings, and illustrate their desirable properties using numerical simulations. We also provide an empirical example of their utility by analyzing the temporal beta diversity of breeding birds within the conterminous USA. We show that temporal beta diversity is predominantly driven by replacement rather than richness differences, and correspondingly, that correlations between temporal beta diversity and productivity and elevation are driven primarily by the replacement component. Furthermore, in contrast to existing multiple-site measures, we show that richness differences do play an important part in driving overall beta diversity patterns. Our new multiple-site measures therefore complement existing methods for analyzing beta diversity, and are especially suitable when compositional heterogeneity is the response of interest.     

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.     

Contrasting effects of mosaic structure on alpha and beta diversity of bird assemblages in a human‐modified landscape

Habitat loss and fragmentation are key processes causing biodiversity loss in human‐modified landscapes. Knowledge of these processes has largely been derived from measuring biodiversity at the scale of ‘within‐habitat’ fragments with the surrounding landscape considered as matrix. Yet, the loss of variation in species assemblages ‘among’ habitat fragments (landscape‐scale) may be as important a driver of biodiversity loss as the loss of diversity ‘within’ habitat fragments (local‐scale). We tested the hypothesis that heterogeneity in vegetation cover is important for maintaining alpha and beta diversity in human‐modified landscapes. We surveyed bird assemblages in eighty 300‐m‐long transects nested within twenty 1‐km² vegetation ‘mosaics’, with mosaics assigned to four categories defined by the cover extent and configuration of native eucalypt forest and exotic pine plantation. We examined bird assemblages at two spatial scales: 1) within and among transects, and 2) within and among mosaics. Alpha diversity was the mean species diversity within‐transects or within‐mosaics and beta diversity quantified the effective number of compositionally distinct transects or mosaics. We found that within‐transect alpha diversity was highest in vegetation mosaics defined by continuous eucalypt forest, lowest in mosaics of continuous pine plantation, and at intermediate levels in mosaics containing eucalypt patches in a pine matrix. We found that eucalypt mosaics had lower beta diversity than other mosaic types when ignoring relative abundances, but had similar or higher beta diversity when weighting with species abundances. Mosaics containing both pine and eucalypt forest differed in their bird compositional variation among transects, despite sharing a similar suite of species. This configuration effect at the mosaic scale reflected differences in vegetation composition among transects. Maintaining heterogeneity in vegetation cover could help to maintain variation among bird assemblages across landscapes, thus partially offsetting local‐scale diversity losses due to fragmentation. Critical to this is the retention of remnant native vegetation.     

Structural and taxonomic diversity predict above-ground biomass better than functional measures of maximum height in mixed-species forests

Aims: Mixed-species forests are known to be highly productive systems because of their high species diversity, including taxonomic diversity (species richness) and structural diversity. Recent empirical evidence also points to plant maximum height, as a functional trait that potentially drives forest above-ground biomass (AGB). However, the interrelations between these biotic variables are complex, and it is not always predictable if structural diversity attributes or functional metrics of plant maximum height would act as the most important determinant of stand biomass. Here we evaluated the relative importance of structural diversity attributes and functional metrics of plant maximum height (Hmax) in predicting and mediating AGB response to variation in species richness in mixed-species forests, while also accounting for fine-scale environmental variation. Location: Northern Benin. Methods: We used forest inventory data from mixed-species stands of native and exotic species. We quantified structural diversity as coefficient of variation of tree diameter at breast height (CVdbh) and of height (CVHt). For plant Hmax, we computed three metrics: functional range (FRHmax), functional divergence (FDHmax) and community-weighted mean (CWMHmax). We used topographical variables such as elevation and slope to account for possible environmental effects. Simple and multiple mixed-effects models, and structural equation models were performed to assess the direct and indirect links of AGB with species richness through structural diversity attributes and functional metrics of plant Hmax. Results: Species richness and CVdbh were positively related to AGB, while functional metrics of plant Hmax were not. Structural equation models revealed that species richness influenced AGB indirectly via CVdbh, which alone strongly promoted AGB. Elevation only had a positive direct effect on AGB. While increasing species richness enhanced CVdbh and functional measures of plant Hmax, there was no support for the latter mediating the effects of species richness on AGB. Conclusion: Structural diversity has a significant advantage in predicting and mediating the positive effect of species richness on AGB more so than functional measures of plant Hmax. We argue that structural diversity acts as a mechanism for the species richness–AGB relationship, and that maintaining high structural diversity would enhance biomass in mixed-species forests.     

Measuring beta‐diversity from taxonomic similarity

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 proposed 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‐di‐versity. 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 system's variation that is related to the higher‐order taxonomic structure of a pair of species plots.     

Maintained functional diversity in benthic communities in spite of diverging functional identities

Ecological studies based on time‐series often investigate community changes centered on species abundance or biomass but rarely expose the consequential functional aspects underlying such changes. Functional diversity measures have proven to be more accurate predictors for ecosystem functioning than traditional taxonomic approaches and hence gained much attention. There are only limited studies available that analyse the functional implications behind decadal changes of entire communities. We studied zoobenthic communities of two habitats, sheltered and exposed, of a coastal system subject to contrasting changes in community composition over the past four decades. Besides eutrophication and climate‐related impacts, the system has been invaded by a non‐native polycheate Marenzelleria spp., adding altered functional properties to the communities. The functional dispersion (FDis) metric was used as a measure for comparing the functional diversity of the contrasting habitats, with special focus on the role of Marenzelleria for the entire communities. We highlight changes in the functional identity of the communities, expressed as community‐weighted means of trait expression (CWM), using multivariate techniques, and investigate the relationship between taxonomic and functional changes. Despite contrasting community developments in the two habitats, with characteristics traditionally suggesting different environmental quality, we found that the FDis in both habitats remained similar and increased with the introduction of Marenzelleria. Although showing maintained functional diversity across time and space, the functional identity (CWM) of communities changed irrespective of taxonomical differences. Examples include inter alia alterations in palatability proxies, feeding position and sediment transportation types, indicating changed functionality of zoobenthos in coastal systems. We show, when focussing on qualitative functional changes of communities, it is important to evaluate the underlying functional identity, and not only rely on measures of the diversity of functions per se, as the quality indication of expressed functional traits can be concealed when using multi‐functionality approaches.     

分类多样性在大型底栖动物生态学方面的应用:以黄海底栖动物为例

根据文献资料,系统整理了黄海大型底栖动物物种名录,并得到了其平均分类差异指数和分类差异变异指数的理论平均值及95%置信区间漏斗图。结果表明,黄海共有大型底栖动物1,360种,分属于17门35纲91目368科842属。其平均分类差异指数的理论平均值为93.7,分类差异变异指数为213.6。将已知受到中度扰动的胶州湾部分站位真实值叠加到平均分类差异指数的95%置信区间漏斗图中,发现全部站位均显著低于95%置信区间,显示了平均分类差异指数在海洋污染监测方面的良好应用前景。