Functional diversity of protein C-termini: more than zipcoding?

The carboxylated (C)-terminus of proteins, which includes the single terminal alpha-carboxyl group and preceding residues, is uniquely positioned to serve as a recognition signature for a variety of cell-biological processes, including protein targeting, subcellular anchoring and the static and dynamic formation of macromolecular complexes. The terminal sequence motifs can be processed by posttranslational modifications, thereby providing a means to increase sequence diversity and to regulate interactions. Several classes of protein domains have been identified that are either designed for or are capable of interacting with protein C-termini - these include PDZ and TPR domains. The interactions between these protein domains and various terminal epitopes play an important role in specifying cell-biological functions. The combination of diversity and the plasticity of the chemistry of C-termini provides mechanisms for spatial and temporal specificity that are exploited by a variety of biological processes, ranging from specifying prokaryotic protein degradation to nucleating mammalian neuronal signaling complexes. Understanding the diverse functions of protein C-termini might also provide an important indexing criterion for functional proteomics.     

Songs versus colours versus horns: what explains the diversity of sexually selected traits?

Papers on sexual selection often highlight the incredible diversity of sexually selected traits across animals. Yet, few studies have tried to explain why this diversity evolved. Animals use many different types of traits to attract mates and outcompete rivals, including colours, songs, and horns, but it remains unclear why, for example, some taxa have songs, others have colours, and others horns. Here, we first conduct a systematic survey of the basic diversity and distribution of different types of sexually selected signals and weapons across the animal Tree of Life. Based on this survey, we describe seven major patterns in trait diversity and distributions. We then discuss 10 unanswered questions raised by these patterns, and how they might be addressed. One major pattern is that most types of sexually selected signals and weapons are apparently absent from most animal phyla (88%), in contrast to the conventional wisdom that a diversity of sexually selected traits is present across animals. Furthermore, most trait diversity is clustered in Arthropoda and Chordata, but only within certain clades. Within these clades, many different types of traits have evolved, and many types appear to have evolved repeatedly. By contrast, other major arthropod and chordate clades appear to lack all or most trait types, and similar patterns are repeated at smaller phylogenetic scales (e.g. within insects). Although most research on sexual selection focuses on female choice, we find similar numbers of traits (among sampled species) are involved in male contests (44%) and female choice (55%). Overall, these patterns are largely unexplained and unexplored, as are many other fundamental questions about the evolution of these traits. We suggest that understanding the diversity of sexually selected traits may require a shift towards macroevolutionary studies at relatively deep timescales (e.g. tens to hundreds of millions of years ago).     

Regional hotspots of butterfly diversity in a protected area: Are they indicators of unique assemblages and areas with more species of conservation concern?

The implementation of biodiversity studies to set conservation priorities assumes that the different criteria used in prioritisation are correlated. Based on butterfly data, we examined whether high total diversity (species density and richness), unique species assemblages, and high numbers of different categories of Species of European Conservation Concern (SPEC) were co-located in the same habitats in the Picos de Europa National Park, Spain. Species density (number of species per sample) declined with elevation and was significantly higher in Genista shrublands on southern slopes (Southern Genista shrubland). We found unique species assemblages for Southern Genista shrublands, heathlands, mown meadows and subalpine meadows, whereas Genista shrubland on northern slopes (Northern Genista shrubland) and pastures were occupied by more habitat generalist species. We also found an effect of elevation on species composition. Species with global distributions concentrated in Europe (SPECs 4b) tended to be associated with Southern Genista shrubland, whereas species with global distributions restricted to Europe (SPECs 4a) were associated with higher elevations. Thus, we suggest a higher conservation value for butterfly assemblages located both on Southern Genista shrublands and at high elevations as they contain unique assemblages with a higher number of SPECs. By comparing our data with a previous study on carabid beetles, we found a low coincidence between butterflies and beetles for habitats with high species diversity and unique assemblages. Our study suggests that preserving areas in the landscape supporting higher butterfly diversity only partially preserves those species of greater conservation concern, and that butterflies cannot be used as a reliable indicator of other priority taxa for conservation, such as carabid beetles.     

Are stacked species distribution models accurate at predicting multiple levels of diversity along a rainfall gradient?

We use observed patterns of species richness and composition of ant communities along a 1000 mm rainfall gradient in northern Australian savanna to assess the accuracy of species richness and turnover predictions derived from stacked species distribution models (S‐SDMs) and constrained by macroecological models (MEMs). We systematically sampled ants at 15 sites at 50 km intervals along the rainfall gradient in 2012 and 2013. Using the observed data, we created MEMs of species richness, composition and turnover. We built distribution models for 135 of the observed species using data from museum collections and online databases. We compared two approaches of stacking SDMs and three modelling algorithms to identify the most accurate way of predicting richness and composition. We then applied the same beta diversity metrics to compare the observed versus predicted patterns. Stacked SDMs consistently over‐predicted local species richness, and there was a mismatch between the observed pattern of richness estimated from the MEM, and the pattern predicted by S‐SDMs. The most accurate richness and turnover predictions occurred when the stacked models were rank‐ordered by their habitat suitability and constrained by the observed MEM richness predictions. In contrast with species richness, the predictions obtained by the MEM of community similarity, composition and turnover matched those predicted by the S‐SDMs. S‐SDMs regulated by MEMs may therefore be a useful tool in predicting compositional patterns despite being unreliable estimators of species richness. Our results highlight that the choice of species distribution model, the stacking method used, and underlying macroecological patterns all influence the accuracy of community assembly predictions derived from S‐SDMS.     

How does spatio-temporal disturbance influence species diversity in a hierarchical competitive system? Prospective order of species coexistence and extinction

To address how habitat destruction and hierarchical competition among species affect the spatio-temporal dynamics of a multi-species community, we present a compartment model in which multiple species undergo dispersal and competitive interactions in a patchy habitat arranged in a two-dimensional lattice. We assume that disturbances are periodically imposed on some parts of the lattice in a block, followed by a period free of disturbance. For convenience, species are ranked in order of competitive ability. We further assume that the intrinsic growth rate of species i, _i , and the dispersal ability, D _i , increase in decreasing order of rank. Our model can analytically determine the exact number of surviving species when disturbance is absent. In the presence of disturbance, we numerically examine how spatio-temporal changes in environmental heterogeneity affect species coexistence and extinction, for the case in which the value of _i /D _i monotonically increases or decreases with rank. The results demonstrate that (1) when the interspecific competition is smaller than the intraspecific competition, we can provide predictions on the prospective order of species to be driven extinct and the order of potential species to revive with increasing extents of disturbance; (2) when the interspecific competition is stronger than intraspecific competition, a small difference in the disturbance level can lead to drastic changes in the species composition, their densities and the order of species extinction. In addition, comparison with other similar models reveals that differences in species interaction in local population dynamics critically affect the disturbance-mediated species diversity.     

Biodiversity and ecosystem services−A case study for the assessment of multiple species and functional diversity levels in a cultural landscape

The expansion of large-scale plantations has a major impact on landscapes in the Tropics and Subtropics. Crops like soy bean, oil palm and rubber have led to drastic changes in land cover over the past decades, thereby altering ecosystem functions and services (ESS). Associated shifts in ESS such as climate regulation, erosion and water cycles, biodiversity as well as soil fertility or the provisioning of raw materials have been assessed through several models and software solutions (InVEST, ARIES, MIMES). However, suitable methods for the integration of a range of biodiversity assessments in agricultural landscapes are scarce.With this study, we introduce a methodology for incorporating multiple levels of species diversity into models to allow an integrated evaluation of ESS. We collected data sets from both published and unpublished sources on the distribution of vascular plants, selected pollinator groups, ground beetles, ungulates as well as amphibians, mammals, reptiles and birds in rubber-dominated landscapes, with a focus on our study sites in Southwest China and Thailand. Based on this information, we developed a common classification scheme that enables the integration of different facets of biodiversity (species diversity and functional diversity) to complement an interdisciplinary ESS assessment.Species diversity data were normalized against the most divers habitats reported (using habitat scores) to assess the impact of rubber cultivation on multiple levels of biodiversity. This resulted in a comparable matrix of different land use types and their suitability as habitat for the respective species groups allowing the aggregation of very diverse indicators. The findings were applied to two alternative land use scenarios in southern China to highlight the potential effects of land use and management decisions on species and functional diversity. Our results highlighted that the conservation oriented scenario did score higher for habitat suitability in both total species (+5%) as well as IUCN Red List species (+6%) assessments compared to the current state or business as usual scenarios (-2% and −3% compared to current state).The process presented here allows for an application within established ESS software programs, in our case InVEST, using aggregated indices while additionally providing enhanced opportunities for comparable, spatially explicit assessments of the expected impact of the analyzed scenarios on specific species groups.     

Commentary: Do we have a consistent terminology for species diversity? The fallacy of true diversity

There is no single best index that can be used to answer all questions about species diversity. Entropy-based diversity indices, including Hill’s indices, cannot account for geographical and phylogenetic structure. While a single diversity index arises if we impose several constraints—most notably that gamma diversity be completely decomposed into alpha and beta diversity—there are many ecological questions regarding species diversity for which it is counterproductive, requiring decomposability. Non-decomposable components of gamma diversity may quantify important intrinsic ecological properties, such as resilience or nestedness.     

Cover versus biomass as an estimate of species abundance: does it make a difference to the conclusions?

Abstract. Different measures of species abundance, particularly cover and biomass, are often used as if they were interchangeable. We ask to what extent the measure of abundance affects conclusions reached in plant community ecology. The test data comprised 35 plots, each 1 m × 1 m, on serpentine vegetation in Tuscany, Italy, in which both cover and biomass were measured. The measure of abundance used made rather little difference when plots were examined in terms of the rank abundance of the species present, and little difference to the results of a DCA-ordination. Likewise, species showed similar variation across plots in cover as in biomass. In calculating species diversity, agreement between measures of abundance was lower, but still good. For evenness, the correlation between cover and biomass results was lower again, though more so with some indices than with others. For the shape of the RAD (Relative Abundance Distribution), cover and biomass gave quite different results, the Zipf-Mandelbrot RAD model most commonly giving the best fit to the cover data, but the General lognormal model to the biomass data. These tendencies can be related to the intrinsic characteristics of cover and biomass as measures of abundance. The parameters of the model fits also differed between abundance measures. We conclude that the importance of using biomass as the measure of abundance depends on the ecological feature being examined. The difference between the two measures may be greater in other vegetation; very little information is available. In the current state of knowledge it is dangerous to use another measure as a surrogate for biomass.     

Time versus size: which characteristic of a neural response carries more information?

 Considering a variety of quite different candidate neural codes, Cheng and Wasserman [(1996) Biol Cybern 75, 93–103, 105–115] reported data which suggested that amplitude codes transmitted information more faithfully than temporal codes. Reanalyzing their data, the present study measured how well size and time represented information resident within the same neural response feature, namely the response peak. Responses from photoreceptor cells and optic nerve fibers in the peripheral visual system of Limulus polyphemus were therefore re-examined using signal detectability values provided by receiver-operating-characteristic analyses to compare how well the timing and the amplitude of the response peak represent information within a single cell and how well they transmit information between cells. Data were available for several cells in several different light-adaptation states onto which several different test-flash intensities had been superimposed. The present reanalysis of these data replicated the results yielded earlier by the peak candidate code, and compared them with the data produced by two different measurements of the timing of the same response peak. A relative-timing code was derived from measurements of the time that elapsed between the moment when the response exceeded a criterion potential and when it reached its peak. An absolute-timing code was derived from the time that elapsed between test flash onset and the peak. The results clearly indicated that the peak code represented information within cells better than either of the two timing codes. However, both peak and absolute-timing codes clearly transmitted the available information between cells more faithfully than the relative-timing code. These data lead to two conclusions. First, that the same response feature, when measured in different ways, can produce remarkably different information processing outcomes. In this particular case, time represented information resident within a cell less well than did size. Second, that the fidelity of information transmission between nerve cells may be relatively independent of the quantity of information resident within any particular cell. Received: 5 November 2001 / Accepted in revised form: 8 July 2002 Acknowledgements. We are deeply indebted to Huiqi Yin for her technical assistance with all the calculations and the graphics. We also sincerely thank Tony Hosking, who wrote the computer programs that extracted the code data for this project, and Brendan Marr, who assisted with data analysis. Correspondence to: G.S. Wasserman (e-mail: codelab@purdue.edu, Fax: +1-765-4961264)     

The GTP-binding domain of McrB: more than just a variation on a common theme?

The methylation-dependent restriction endonuclease McrBC from Escherichia coli K12 cleaves DNA containing two R(m)C dinucleotides separated by about 40 to 2000 base-pairs. McrBC is unique in that cleavage is totally dependent on GTP hydrolysis. McrB is the GTP binding and hydrolyzing subunit, whereas MrC stimulates its GTP hydrolysis. The C-terminal part of McrB contains the sequences characteristic for GTP-binding proteins, consisting of the GxxxxGK(S/T) motif (position 201-208), followed by the DxxG motif (position 300-303). The third motif (NKxD) is present only in a non-canonical form (NTAD 333-336). Here we report a mutational analysis of the putative GTP-binding domain of McrB. Amino acid substitutions were initially performed in the three proposed GTP-binding motifs. Whereas substitutions in motif 1 (P203V) and 2 (D300N) show the expected, albeit modest effects, mutation in the motif 3 is at variance with the expectations. Unlike the corresponding EF-Tu and ras -p21 variants, the D336N mutation in McrB does not change the nucleotide specificity from GTP to XTP, but results in a lack of GTPase stimulation by McrC. The finding that McrB is not a typical G protein motivated us to perform a search for similar sequences in DNA databases. Eight microbial sequences were found, mainly from unfinished sequencing projects, with highly conserved sequence blocks within a presumptive GTP-binding domain. From the five sequences showing the highest homology, 17 invariant charged or polar residues outside the classical three GTP-binding motifs were identified and subsequently exchanged to alanine. Several mutations specifically affect GTP affinity and/or GTPase activity. Our data allow us to conclude that McrB is not a typical member of the superfamily of GTP-binding proteins, but defines a new subfamily within the superfamily of GTP-binding proteins, together with similar prokaryotic proteins of as yet unidentified function.     

BIODIVERSITY RESEARCH: Parasites of exotic species in invaded areas: does lower diversity mean lower epizootic impact?

Aim Exotic species may serve as vectors for the introduction of parasites from their native range and may also become infected by parasites already present in invaded areas, but the total number of parasites infecting such exotic species in their invaded areas is typically less than that in their native range. We tested whether the diversity of parasites associated with exotic species in the native and invaded areas is related to the epizootic impact these parasites cause. Location Global. Methods We examined the diversity and epizootic impact of 384 parasite taxa associated with 22 exotic freshwater invertebrate species. The epizootic impact of each parasite was rated based on whether it had been documented to cause a major pathological impact on a large proportion of an infected host population (other than the invader under consideration). Results The total number of parasites associated with an exotic host in its native range was about twice that of all parasites associated with it in its entire invaded range. This was mainly because of the loss in the invaded areas of low impact parasites, whereas the average number of high impact parasites per host in these areas did not differ statistically from that in the native range. Main conclusions Our study suggests similar levels of adverse impact of parasites of exotic species in both their native and invaded areas. In addition to the introduction of highly pathogenic exotic parasites, other mechanisms that may be involved include (1) acquisition by the invaders of new high impact parasites in the invaded ranges, (2) high abundance of the invaders in their new ranges and (3) susceptibility of novel hosts to exotic parasites because of the ‘naive host syndrome’.     

The ins and outs of tubulin acetylation: more than just a post-translational modification?

Microtubules are highly dynamic polymers of α/β tubulin heterodimers that play key roles in cell division and in organizing cell cytoplasm. Although they have been discovered more than two decades ago, tubulin post-translational modifications recently gained a new interest as their role was increasingly highlighted in neuron differentiation and neurodegenerative disorders. Here, we specifically focus on tubulin acetylation from its discovery to recent studies that provide new insights into how it is regulated in health and disease and how it impacts microtubule functions. Even though new mechanisms involving tubulin acetylation are regularly being uncovered, the molecular links between its location inside the microtubule lumen and its regulators and effectors is still poorly understood. This review highlights the emerging roles of tubulin acetylation in multiple cellular functions, ranging from cell motility, cell cycle progression or cell differentiation to intracellular trafficking and signalling. It also points out that tubulin acetylation should no longer be seen as a passive marker of microtubule stability, but as a broad regulator of microtubule functions.     

Island area and species diversity in the southwest Pacific Ocean: is the lizard fauna of Vanuatu depauperate?

One island group suggested to be an exception to the species–area Relationship is the Vanuatu Archipelago, a group of 13 large and 80 small islands in the southwest Pacific Ocean. To test the hypothesis that the lizard fauna of the Vanuatu Archipelago does not meet the predictions of the species-area relationship, and thus is depauperate, we compare diversity among several island groups in the southwest Pacific: Fiji, the Loyalty Islands, New Caledonia, Samoa, the Solomon Islands, Tonga, and Vanuatu. We found that the lizard diversity of Vanuatu meets the pattern of diversity predicted by the species-area relationship. The Solomon Islands, the largest and least isolated oceanic archipelago considered, has the greatest species diversity and endemism of the oceanic islands. Inclusion or exclusion of island groups based on factors such as geologic history or faunal source affects the strength of the relationship between diversity, area, and history of emergence, and influences perceptions of diversity within individual archipelagos. In addition to island size, factors such evolutionary time scale, speciation, and archipelago complexity influence species richness on islands.     

Radiation of the Australian flora: what can comparisons of molecular phylogenies across multiple taxa tell us about the evolution of diversity in present-day communities?

The Australian fossil record shows that from ca. 25 Myr ago, the aseasonal-wet biome (rainforest and wet heath) gave way to the unique Australian sclerophyll biomes dominated by eucalypts, acacias and casuarinas. This transition coincided with tectonic isolation of Australia, leading to cooler, drier, more seasonal climates. From 3 Myr ago, aridification caused rapid opening of the central Australian arid zone. Molecular phylogenies with dated nodes have provided new perspectives on how these events could have affected the evolution of the Australian flora. During the Mid-Cenozoic (25-10 Myr ago) period of climatic change, there were rapid radiations in sclerophyll taxa, such as Banksia, eucalypts, pea-flowered legumes and Allocasuarina. At the same time, taxa restricted to the aseasonal-wet biome (Nothofagus, Podocarpaceae and Araucariaceae) did not radiate or were depleted by extinction. During the Pliocene aridification, two Eremean biome taxa (Lepidium and Chenopodiaceae) radiated rapidly after dispersing into Australia from overseas. It is clear that the biomes have different histories. Lineages in the aseasonal-wet biome are species poor, with sister taxa that are species rich, either outside Australia or in the sclerophyll biomes. In conjunction with the fossil record, this indicates depletion of the Australian aseasonal-wet biome from the Mid-Cenozoic. In the sclerophyll biomes, there have been multiple exchanges between the southwest and southeast, rather than single large endemic radiations after a vicariance event. There is need for rigorous molecular phylogenetic studies so that additional questions can be addressed, such as how interactions between biomes may have driven the speciation process during radiations. New studies should include the hitherto neglected monsoonal tropics.     

Photoinactivation of photosystem II: is there more than one way to skin a cat?

We briefly review the main mechanisms proposed for photodamage to photosystem II (PSII), at the donor and acceptor sides, and then discuss the mechanism whereby filamentous cyanobacteria inhabiting biological sand crusts such as Microcoleus sp. are able to avoid serious damage to their photosynthetic machinery. We show that the decline in fluorescence following exposure to excess light does not reflect a reduction in PSII activity but rather the activation of a non-radiative charge recombination in PSII. Furthermore, we show that the difference in the thermoluminescent peak temperature intensities in these organisms, in the presence and absence of inhibitors such as dichlorophenyl-dimethylurea (DCMU), is smaller than observed in model organisms suggesting that the redox gap between Q(A)? and P???+ is smaller. On the basis of these data, we propose that this could enable an alternative, pheophytin-independent recombination, thereby minimizing the damaging 1O? production associated with radiative recombination.     

Mixed messages from multiple information sources on invasive species: a case of too much of a good thing?

Aim The increasing number and availability of online databases of alien species beg a question of their comparability given most do not adopt standard criteria in the definition of species status or taxonomic treatment and vary in their comprehensiveness. In this study, we compare the consistency of two major European databases for the regions they have in common. We assess whether they use consistent terminology to classify species status, provide similar taxonomic classification and coverage, deliver comparable estimates of alien richness per country and identify comparable correlates of alien richness. Location Northern Europe. Methods Data on the total number of alien species as well as the number of established alien species were extracted from the online databases DAISIE and NOBANIS for 13 European countries and classified into comparable taxonomic groups. Analyses across countries examined trends in alien species richness, correlations among taxonomic groups and the explanatory power of population density, country area and per capita GDP on alien species richness. Results Alien species richness, intertaxon correlations and the significance of individual drivers of invasion were all strongly database dependent. Differences were more marked for total numbers of aliens than established aliens. Over all taxonomic groups, DAISIE had lower species richness and fewer significant intertaxon correlations but presented a greater number of significant explanatory models of alien species richness. Trends in species richness were not generally correlated between the two databases with human population density being a more important driver in DAISIE while country area had greater explanatory power in NOBANIS. Main conclusions Considerable caution should be applied when collating data from different databases because often their underlying structure and content may differ markedly. For Europe, the analysis indicates that having two contrasting databases is not an ideal basis for implementing invasive species policy and moves should be made soon to establish a central pan‐European database.     

The prospects for vaccines against HIV-1: more than a field of long-term nonprogression?

More than 20 years have passed since the human immunodeficiency virus (HIV)-1 was identified as the cause of AIDS (acquired immune deficiency syndrome). With rapid early progress, the development of a vaccine was predicted within 2-10 years. However, over two decades later, we have seen only a single vaccine candidate complete Phase III clinical efficacy trials. These trials showed the vaccine was not able to protect the trial volunteers from HIV infection or subsequently modify the early clinical progression. It is now accepted that the initial optimism in the field was misguided, as the complexity of the problem stretched beyond the known horizons of vaccinology, immunology and retrovirology. In the intervening 20 years, unprecedented research efforts have pushed the cutting edge of these fields forward to such a degree that we are better able to put the problem of developing a vaccine for HIV-1 into context. Now it is time to examine the prospects for HIV-1 vaccines and ascertain whether real progress is being made.     

Test of an environmental flow release in a British Columbia river: does more water mean more fish?

1. Water managers must make difficult decisions about the allocation of streamflows between out‐of‐channel human uses and environmental flows for aquatic resources. However, the effects environmental flows on stream ecosystems are infrequently evaluated. 2. We used a 13‐year experiment in the regulated Bridge River, British Columbia, Canada, to determine whether an environmental flow release designed to increase salmonid productivity was successful. A hierarchical Bayesian model was used to compare juvenile Pacific salmon (Oncorhynchus spp.) abundance before and after the flow release. 3. We found that the total number of salmonids did increase after the release, but most of the gains could be attributed to the rewatering of a previously dry channel located immediately below the dam. In reaches that had flowing water during the baseline period, the response of individual salmon species to the increase in flow was variable, and there was little change in total abundance after the flow release. Our results were inconsistent with both habitat modelling, which predicted a decrease in habitat quality with increasing flow, and holistic instream flow approaches, which imply greater benefits with larger flows. 4. We question whether biotic responses to flow changes can be predicted reliably with currently available methods and suggest that adaptive management or the use of decision tools that account for the uncertainty in the biotic response is required for instream flow decisions when the competing demands for water are great.     

Use of space and habitat selection by roe deer Capreolus capreolus in a Mediterranean coastal area: how does woods landscape affect home range?

The home-range dynamics and habitat selection of nine roe deer were studied from March 1994 to August 1994 in the Maremma Natural Park along the Tyrrhenian coast of Italy. The habitat was highly fragmented, with open agricultural fields prevailing in the study area (57%); the climate was Mediterranean. Data on spatial behaviour were collected by radio-tracking techniques. Habitat selection and structure were investigated by compositional and landscape analysis, both within the study area and within the home ranges. Animals of our sample showed spatial-use patterns varying from stationary to roaming. Stationary individuals used small home ranges while roaming ones moved, especially during the reproductive period in July and August. The percentage and structure of woodlands influenced the size of home ranges and the behaviour of males: stationary males used large amounts of woodlands within their home ranges and showed a territorial behaviour whereas males that used a high percentage of fields showed wider home ranges even during the territorial period. Females seemed to be less influenced by the presence and patch-structure of woodland within their home range. Landscape structure and habitat composition seemed to be important factors influencing the spatial behaviour of this roe deer population.