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.     

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.     

Effect of colony size on the competitive outcome of encrusting colonial organisms

The relative importance of colony size ratio of interacting species was studied in Tomioka Bay, Japan. Six encrusting colonial species belonging to the following three different taxonomic groups were tested: Ascidia (three species), Bryozoa (two) and Porifera (one). Colonies of these organisms were grown in the community of sessile organisms developed on plastic panels. Logistic regression analysis was carried out to determine the effect of size ratio on the competitive outcome of interacting colonies. The results between all possible combinations among these six species did not show a significant size effect in competitive outcome (i.e. a larger colony size did not always prove important in the success of a competitive interaction with smaller colonies of other species). On the contrary, competitive success depends on the types of species interacting. Certain species such asDidemnum moseleyi (ascidian) andHaliclona sp. (sponge), in spite of being smaller in colony size, won in competitive interactions with larger colonies of other species such asDiplosoma mitsukurii (ascidian) andWatersipora subovoidea (bryozoan). These results contradict the one reported earlier: that the larger the colony size, the more chance the colony will have to win in competitive interactions.     

厦门湾大型底栖动物分类学多样性指数及分类充分性

以厦门湾为研究区域,收集2014—2015年大型底栖动物的调查数据,计算了大型底栖动物的分类学多样性指数,分析了分类学多样性指数与传统生物多样性指数的相关性和依从性,并从多个角度探讨大型底栖动物的分类充分性。结果表明,厦门湾大型底栖动物分类多样性指数(Δ)介于6.04—83.71之间,平均值为68.26,站位分布不均匀;分类差异性指数(Δ~*)介于74.27—99.54之间,平均值为84.23;平均分类差异指数(Δ~+)、分类差异变异指数(Λ~+)的理论平均值分别为86.82、345.0,个别站位落在95%置信区间外,表明局部区域环境受到了一定程度扰动。Δ、Δ~*与Margalef指数、Pielou均匀度指数、Shannon-Wiener指数、Simpson指数呈显著相关,而Δ~+、Λ~+与传统多样性指数间无显著相关;分类学多样性指数可作为传统生物多样性指数的补充。种级、属级和科级的同一多样性指数间呈显著线性相关,拟合度较高(多数R2﹥0.9);根据三个分类水平站位的nMDS二维排序图、2-STAGE的相似性和聚类图,种级、属级和科级的群落结构一致性强,属级较种级丢失的信息约8%、科级为20%,因此在条件有限的情况下,大型底栖动物的监测与评价可根据实际的条件和需求适当将生物鉴定放宽至属水平。     

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.     

RecPD: A Recombination-aware measure of phylogenetic diversity

A critical step in studying biological features (e.g., genetic variants, gene families, metabolic capabilities, or taxa) is assessing their diversity and distribution among a sample of individuals. Accurate assessments of these patterns are essential for linking features to traits or outcomes of interest and understanding their functional impact. Consequently, it is of crucial importance that the measures employed for quantifying feature diversity can perform robustly under any evolutionary scenario. However, the standard measures used for quantifying and comparing the distribution of features, such as prevalence, phylogenetic diversity, and related approaches, either do not take into consideration evolutionary history, or assume strictly vertical patterns of inheritance. Consequently, these approaches cannot accurately assess diversity for features that have undergone recombination or horizontal transfer. To address this issue, we have devised RecPD, a novel recombination-aware phylogenetic-diversity statistic for measuring the distribution and diversity of features under all evolutionary scenarios. RecPD utilizes ancestral-state reconstruction to map the presence / absence of features onto ancestral nodes in a species tree, and then identifies potential recombination events in the evolutionary history of the feature. We also derive several related measures from RecPD that can be used to assess and quantify evolutionary dynamics and correlation of feature evolutionary histories. We used simulation studies to show that RecPD reliably reconstructs feature evolutionary histories under diverse recombination and loss scenarios. We then applied RecPD in two diverse real-world scenarios including a preliminary study type III effector protein families secreted by the plant pathogenic bacterium Pseudomonas syringae and growth phenotypes of the Pseudomonas genus and demonstrate that prevalence is an inadequate measure that obscures the potential impact of recombination. We believe RecPD will have broad utility for revealing and quantifying complex evolutionary processes for features at any biological level.     

Development of hyperspectral imaging as a bio-optical taxonomic tool for pigmented marine organisms

Reflection spectra obtained from hyperspectral imaging can be used as a bio-optical taxonomic identification tool if the pigment composition and the corresponding optical absorption signatures of an organism are known. In this study we elucidate species-specific absorption and corresponding reflection signatures of marine organisms and discuss optical fingerprints from underwater hyperspectral imaging (UHI) for future automated identification of organisms on the seafloor. When mounted on underwater robots, UHI has the potential to be a time- and cost-efficient identification and mapping method covering large areas over a short time. Hyperspectral imaging in vivo and in situ were used to obtain species-specific reflection signatures (optical fingerprints). High performance liquid chromatography, liquid chromatography–mass spectroscopy and nuclear magnetic resonance were used for pigment identification and to obtain species-specific absorption signatures of four marine benthic species; the spoonworm Bonellia viridis, and the sponges Isodictya palmata, Hymedesmia paupertas and Hymedesima sp. Species-specific optical fingerprints based on a UHI-based reflectance signature were verified successfully in the organisms investigated.     

The measure of diversity

The measure of diversity is developed from axiomatic foundations, independently of any statistical considerations, and various examples of such measures cited. It is shown that almost all the more usual measures which have been used in the past are closely related to measures which satisfy our axioms; thus the general theory of diversity is unified and comparisons between the various measures can be made. Brillouin's measure, which does satisfy our axioms, turns out to be the only one satisfying a further axiom. Shannon's function (from information theory) is shown to occupy a central position in our development as the asymptotic limit of average diversity measures. Finally we extend the notion of the measure to allow for various degrees of difference between classes in a set.     

Patterns of taxonomic diversity among terrestrial isopods

The publication of the world catalog of terrestrial isopods some ten years ago by Schmalfuss has facilitated research on isopod diversity patterns at a global scale. Furthermore, even though we still lack a comprehensive and robust phylogeny of Oniscidea, we do have some useful approaches to phylogenetic relationships among major clades which can offer additional insights into isopod evolutionary dynamics. Taxonomic diversity is one of many approaches to biodiversity and, despite its sensitiveness to biases in taxonomic practice, has proved useful in exploring diversification dynamics of various taxa. In the present work, we attempt an analysis of taxonomic diversity patterns among Oniscidea based on an updated world list of species containing 3,710 species belonging to 527 genera and 37 families (data till April 2014). The analysis explores species diversity at the genus and family level, as well as the relationships between species per genera, species per families, and genera per families. In addition, we consider the structure of isopod taxonomic system under the fractal perspective that has been proposed as a measure of a taxon’s diversification. Finally, we check whether there is any phylogenetic signal behind taxonomic diversity patterns. The results can be useful in a more detailed elaboration of Oniscidea systematics.     

A similarity distance of diversity measure for discriminating mesophilic and thermophilic proteins

The successful prediction of thermophilic proteins is useful for designing stable enzymes that are functional at high temperature. We have used the increment of diversity (ID), a novel amino acid composition-based similarity distance, in a 2-class K-nearest neighbor classifier to classify thermophilic and mesophilic proteins. And the KNN-ID classifier was successfully developed to predict the thermophilic proteins. Instead of extracting features from protein sequences as done previously, our approach was based on a diversity measure of symbol sequences. The similarity distance between each pair of protein sequences was first calculated to quantitatively measure the similarity level of one given sequence and the other. The query protein is then determined using the K-nearest neighbor algorithm. Comparisons with multiple recently published methods showed that the KNN-ID proposed in this study outperforms the other methods. The improved predictive performance indicated it is a simple and effective classifier for discriminating thermophilic and mesophilic proteins. At last, the influence of protein length and protein identity on prediction accuracy was discussed further. The prediction model and dataset used in this article can be freely downloaded from http://wlxy.imu.edu.cn/college/biostation/fuwu/KNN-ID/index.htm.     

A new encrusting interstitial marine fauna from Brazil

Abstract. This paper reports the second occurrence of a sand‐grain encrusting interstitial epifauna dominated by bryozoans and polychaetes at a site thousands of kilometers from the first described occurrence of such a fauna 20 years ago. Such faunas seem to have gone almost unrecorded in the marine ecological literature, but they are potentially geographically widespread and ecologically significant, deserving recognition and further study by benthic ecologists. Although rooted‐erect and free‐living lunulitiform bryozoans can be abundant in soft‐bottom habitats, the presence of encrusting forms was, until recently, considered to be limited to patches of hard substrata. In 1985 and 1988, a new and seemingly unique habitat for encrusting bryozoans and other organisms on single grains of shell or sand was reported from the coastal waters of Florida, USA. Here we report a second discovery of an interstitial encrusting fauna from the continental shelf off the state of São Paulo, Brazil. In addition to the cupuladriid Discoporella umbellata, several species of bryozoans (9 cheilostomes, 3 ctenostomes, and 1 cyclostome) were found encrusting on or boring into sand grains from the 4 stations examined. Four species were found exclusively on sand to gravel size grains. The most abundant colonies, with ～1300–1500 colonies m^?2, belonged to a new species of Cleidochasma. New species of Trypostega and Reginella, each with up to 200–300 colonies m^?2, were also discovered. The grain‐encrusting bryozoans were characterized by their small size, and by the fact that sexual reproduction was initiated very early in colony growth; brood chambers (for the development of embryos into larvae) occurred in colonies having only a few zooids. Colonies of boring ctenostome and cheilostome bryozoans were even more abundant than those of grain encrusting forms, being present in almost every piece of shell (～5000–5500 colonies m^?2). The fauna also included representatives of other groups of encrusting organisms, especially tubeworms (11,000–13,000 tubes m^?2). Planned work on samples from additional stations on the São Paulo shelf will no doubt yield a larger number of species from various taxa and perhaps show some overlap in sand fauna species between the Brazilian and Floridian sites. In addition to the unique species of single grain encrusters, colonies of bryozoan species characteristic of larger subtidal hard substrata were also found on sand or gravel size grains, indicating that an interstitial refuge may be available to some epifaunal taxa and suggesting that this interstitial refuge, which remains almost completely unknown to benthic ecologists, may play a large role in determining distributions of those taxa.     

Insect taxonomic diversity in the Russian Far East

The insect fauna of the Russian Far East comprises 634 families from 31 orders. The estimated species number is 31500. The largest orders are Hymenoptera (76 families, 9000 estimated species), Diptera (120 families, 8000 estimated species), Coleoptera (114 families, 5500 estimated species), and Lepidoptera (81 families, 5000 estimated species). The fractions of the main insect orders in the fauna of the Russian Far East correspond to those in the Holarctic temperate zone. The high biodiversity of insects in the Russian Far East results from the position of this region extending across several climatic zones. There are four levels of diversity both for the families and for the species, corresponding to the tundra, taiga, the transitional area between taiga and broadleaved forests, and the broadleaved forest zone. The number of insect families increases by 3 times while that of species increases by 20 times from the tundra to the broadleaved forests. Differentiation of the insect fauna of the Russian Far East results from the recent climatic situation (the influence of the Pacific monsoon) and the geologic history (broadleaved forest refugia resulting from the absence of complete ice cover during Pleistocenic glaciation in the south of the Russian Far East); it reflects deep faunistic connections of the eastern Palaearctic with the Nearctic and Oriental Regions. The mountain areas in the North Pacific are the refugia of the Mesozoic and Tertiary insect faunas. The Pacific may have substantially reduced the Cenozoic aridization in the northern hemisphere, which was one of the important factors of formation of the recent biota in the Palaearctic and Nearctic regions.     

Multidecadal changes in functional diversity lag behind the recovery of taxonomic diversity

While there has been increasing interest in how taxonomic diversity is changing over time, less is known about how long‐term taxonomic changes may affect ecosystem functioning and resilience. Exploring long‐term patterns of functional diversity can provide key insights into the capacity of a community to carry out ecological processes and the redundancy of species’ roles. We focus on a protected freshwater system located in a national park in southeast Germany. We use a high‐resolution benthic macroinvertebrate dataset spanning 32 years (1983–2014) and test whether changes in functional diversity are reflected in taxonomic diversity using a multidimensional trait‐based approach and regression analyses. Specifically, we asked: (i) How has functional diversity changed over time? (ii) How functionally distinct are the community''s taxa? (iii) Are changes in functional diversity concurrent with taxonomic diversity? And (iv) what is the extent of community functional redundancy? Resultant from acidification mitigation, macroinvertebrate taxonomic diversity increased over the study period. Recovery of functional diversity was less pronounced, lagging behind responses of taxonomic diversity. Over multidecadal timescales, the macroinvertebrate community has become more homogenous with a high degree of functional redundancy, despite being isolated from direct anthropogenic activity. While taxonomic diversity increased over time, functional diversity has yet to catch up. These results demonstrate that anthropogenic pressures can remain a threat to biotic communities even in protected areas. The differences in taxonomic and functional recovery processes highlight the need to incorporate functional traits in assessments of biodiversity responses to global change.     

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.     

How to measure metabolic fluxes: a taxonomic guide for 13C fluxomics

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A unified index to measure ecological diversity and species rarity

Several indices have been created to measure diversity, and the most frequently used are the Shannon-Wiener (H) and Simpson (D) indices along with the number of species (S) and evenness (E). Controversies about which index should be used are common in literature. However, a generalized entropy (Tsallis entropy) has the potential to solve part of these problems. Here we explore a family of diversity indices (S_q; where q is the Tsallis index) and evenness (E_q), based on Tsallis entropy that incorporates the most used indices. It approaches S when q=0, H when q→1 and gives D when q=2. In general, varying the value of the Tsallis index (q), S_q varies from emphasis on species richness (q<1) to emphasis on dominance (q>1). Similarly, E_q also works as a tool to investigate diversity. In particular, for a given community, its minimum value represents the maximum deviation from homogeneity (E_q=1) for a particular q (herein named q*). It is remarkable that our analysis indicates that q* and its corresponding evenness, E_q*, are negatively affected by S when using simulated data. They may represent an index related to species rarity. Furthermore, S_q* (i.e. the value of S_q for a specific q*) is positively affected by richness that is an important property of any diversity index. In general, our findings indicate that the indices H, D, S, S_q*, E and E_q* are only part of a whole set of possibilities. In addition, the ecological properties of E_q* and S_q*, proposed here for the first time, show promise in ecology.