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.     

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.     

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.     

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.     

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.     

The ochotonids of Eurasia: Biochronology and taxonomic diversity

The ochotonid faunas of Eurasia and North America from the Oligocene to the present time are reviewed. The pika family (Ochotonidae Thomas 1897) belongs to the order Lagomorpha, which includes five families: Ochotonidae, Mimotonidae Li 1978, Leporidae Fischer 1817 (hares), Palaeolagidae Dice 1929, and Prolagidae Gureev 1960. The family Ochotonidae consists of two subfamilies: Sinolagomyinae Gureev, 1960 and Ochotoninae Thomas, 1897 and comprises a total of 17 genera. Originating in Central Asia at the beginning of the Late Oligocene, pikas flourished during the Late Oligocene. The highest taxonomic diversity of pikas can be found in the Miocene and Pliocene; towards the Pleistocene, the ochotonid fauna declined. Only one genus, Ochotona, remained extant by the end of the Pleistocene. The genus includes a total of 38 known extinct taxa and 28 extant species.     

Patterns in taxonomic and functional diversity of lake phytoplankton

1. Patterns in phytoplankton diversity in lakes and their relationships with environmental gradients have been traditionally based on taxonomic analyses and indices, even though measures of functional diversity (FD) might be expected to be more responsive to such gradients. 2. We assessed the influence of water column physical structure, and other components of the overall environment, on lake phytoplankton diversity using two taxonomically based indices [species richness (S) and the Shannon index (H’)] and a FD index, to determine whether these different measures respond in similar ways to habitat structure. The study encompassed 45 lakes in Eastern Canada, within two lake districts [the Eastern Townships Region (ETR) and Laurentians Region (LR)] that vary in geology and landscape and in lake morphometry and chemistry. 3. Across all lakes, S and H’ were higher in lakes having greater vertical temperature heterogeneity and higher susceptibility to wind mixing. In addition, H’ declined with total phosphorus concentration. FD was only related to maximum lake depth, a variable that integrates many other habitat features. 4. Further insight into the factors affecting phytoplankton diversity was obtained by contrasting the two regions. The taxonomically based diversity measures differed little between the regions, while FD was higher in the ETR where more trait variants were present and more evenly distributed amongst species. Whereas factors driving S did not differ between the regions, we found region‐dependent patterns in the relationships of H’ and FD with maximum lake depth: both indices decreased with maximum depth in the region with lakes more exposed to wind (ETR) but increased in the more hilly landscape where lakes are more sheltered from wind mixing (LR). 5. Our study demonstrates that, for phytoplankton communities, a FD index can show simpler and stronger responses to environmental drivers than a taxonomically based index, while shedding further light onto the functional traits that are important in particular lake categories.     

Dynamics of taxonomic diversity of bivalves in the Phanerozoic

Changes in the taxonomic composition of bivalves during the Phanerozoic are considered. Each period is characterized by a special set of taxa, in particular, families. Changes in taxonomic diversity, the episodes of maximum and minimum diversity are established and compared with those of other invertebrate groups. In general, the taxonomic diversity of bivalves gradually increased, except for a sharp decrease in the Early Triassic.     

Linguistic measure of taxonomic and functional relatedness of nucleotide sequences

The frequencies of "words", oligonucleotides within nucleotide sequences, reflect the genetic information contained in the sequence "texts". Nucleotide sequences are characteristically represented by their contrast word vocabularies. Comparison of the sequences by correlating their contrast vocabularies is shown to reflect well the relatedness (unrelatedness) between the sequences. A single value, the linguistic similarity between the sequences, is suggested as a measure of sequence relatedness. Sequences as short as 1000 bases can be characterized and quantitatively related to other sequences by this technique. The linguistic sequence similarity value is used for analysis of taxonomically and functionally diverse nucleotide sequences. The similarity value is shown to be very sensitive to the relatedness of the source species, thus providing a convenient tool for taxonomic classification of species by their sequence vocabularies. Functionally diverse sequences appear distinct by their linguistic similarity values. This can be a basis for a quick screening technique for functional characterization of the sequences and for mapping functionally distinct regions in long sequences.     

Evolution of the taxonomic diversity of Mongolian Ordovician-Silurian corals

Changes in the taxonomic diversity of Mongolian Ordovician-Silurian corals (Tabulatoidea, Heliolitoidea, Cyrtophyllida, Rugosa) are analyzed. Evolution of the taxonomic diversity is analyzed in two aspects: quantitative and qualitative changes. Changes in the diversity of Mongolian corals are caused by (1) evolutional developmental stage of the group and its adaptational possibilities (internal reason) and (2) changes in the environmental parameters, which reproduce regional and general global events (external reason).     

A taxonomic wish-list for community ecology

Community ecology seeks to explain the number and relative abundance of coexisting species. Four research frontiers in community ecology are closely tied to research in systematics and taxonomy: the statistics of species richness estimators, global patterns of biodiversity, the influence of global climate change on community structure, and phylogenetic influences on community structure. The most pressing needs for taxonomic information in community ecology research are usable taxonomic keys, current nomenclature, species occurrence records and resolved phylogenies. These products can best be obtained from Internet-based phylogenetic and taxonomic resources, but the lack of trained professional systematists and taxonomists threatens this effort. Community ecologists will benefit most directly from research in systematics and taxonomy by making better use of resources in museums and herbaria, and by actively seeking training, information and collaborations with taxonomic specialists.     

Biological diversity and the community structure of organisms

Biological diversity and the complexity of the community structure of benthic animals in different bodies of water are evaluated using the Shannon index. The literature data on the communities in Lake Krasnoye (Karelian Isthmus, Leningrad Oblast), Shchuchy Bay of Lake Ladoga, Neva Bay, and the eastern part of the Gulf of Finland have been analyzed. The extrema (maxima and minima) and the inflection point of the curve of functions are determined with the help of derivatives. The rate of the secondary succession is evaluated for the first time by the example of benthic communities. It is shown that the community structure of bottom animals in the Shchuchy Bay ecosystem formed in the process of succession proves to be more complex than in Lake Krasnoye and the Neva Bay communities that have been formed for a long time. Communities of bottom animals are less complex in polluted waters of the top of the eastern part of the Gulf of Finland. It has taken 12 years to reach the maximum diversity of the bottom animal communities in Shchuchy Bay, 16 years in Lake Krasnoye, and 7–10 years in Neva Bay. It is supposed that, under favorable conditions in the waterbodies of a moderate climate and in the absence of heavy pollution or eutrophication, it takes 12–14 years on average to form the most complex community structure of bottom animals (3–4 bit/spec.). The structure of communities in polluted waters remains simple.     

Glucanase gene diversity in prokaryotic and eukaryotic organisms

A number of bacteria and eukaryotes produce extracellular enzymes that degrade various types of polysaccharides including the glucans starch, cellulose and hemicellulose (xylan). The similarities in the modes of expression and specificity of enzyme classes, such as amylase, cellulose and xylanase, suggest common genetic origins for particular activities. Our determination of the extent of similarity between these glucanases suggests that such data may be of very limited use in describing the early evolution of these proteins. The great diversity of these proteins does allow identification of their most highly conserved (and presumably functionally important) regions.