Long‐term effects of flow regulation by dams simplify fish functional diversity

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Beyond Surrogacy—A Multi‐taxon Approach to Conservation Biogeography

Biogeographic analysis of species turnover (β diversity) of plants and animals among regions often yields conflicting results, with regions of high β diversity identified for some taxonomic groups but not others. Such discordance calls into question the use of surrogate taxa to forge conservation plans. This discordance begs for a means of comparing multiple taxa across phyla in a manner that is cost‐effective, considers limitations in computer resources in certain global regions, and is understood by policy makers and land managers. As a test case for a method taking into account these considerations, we used species lists for ten organismal groups (spanning plants, vertebrates, and invertebrates) to identify regions of high β diversity using Monmonier's algorithm, a spatially explicit technique that is readily implemented and interpreted. Data were for montane (>1000 m elevation) species across the Eastern Arc of Tanzania and Kenya and surrounding areas. Our results indicate that surrogacy does not make for the most effective expenditure of conservation efforts. We also show that to use a multi‐taxon approach one need not rely on intensive surveys of areas in order to make conservation decisions, including reserve selection. Our approach also eliminates the need for complex modeling and comparisons common to many GIS‐based complementarity techniques. Additionally, a wide variety of socioeconomic, political, demographic, geological, climatological, and evolutionary factors can be incorporated into the technique to help shape conservation biogeography from a local and regional perspective. This technique can bridge the gap between conservation biogeography theory and application in tropical regions and beyond.     

Geometrical principles of homomeric β‐barrels and β‐helices: Application to modeling amyloid protofilaments

Examples of homomeric β‐helices and β‐barrels have recently emerged. Here we generalize the theory for the shear number in β‐barrels to encompass β‐helices and homomeric structures. We introduce the concept of the “β‐strip,” the set of parallel or antiparallel neighboring strands, from which the whole helix can be generated giving it n‐fold rotational symmetry. In this context, the shear number is interpreted as the sum around the helix of the fixed register shift between neighboring identical β‐strips. Using this approach, we have derived relationships between helical width, pitch, angle between strand direction and helical axis, mass per length, register shift, and number of strands. The validity and unifying power of the method is demonstrated with known structures including α‐hemolysin, T4 phage spike, cylindrin, and the HET‐s(218‐289) prion. From reported dimensions measured by X‐ray fiber diffraction on amyloid fibrils, the relationships can be used to predict the register shift and the number of strands within amyloid protofilaments. This was used to construct models of transthyretin and Alzheimer β(40) amyloid protofilaments that comprise a single strip of in‐register β‐strands folded into a “β‐strip helix.” Results suggest both stabilization of an individual β‐strip helix and growth by addition of further β‐strip helices can involve the same pair of sequence segments associating with β‐sheet hydrogen bonding at the same register shift. This process would be aided by a repeat sequence. Hence, understanding how the register shift (as the distance between repeat sequences) relates to helical dimensions will be useful for nanotube design.     

Intra‐ and inter‐specific variation in size and habitus of two sibling spider species (Araneae: Lycosidae): taxonomic and biogeographic insights from sampling across Europe

Discriminating closely related species can become a taxonomical challenge if a clear morphological diagnosis is lacking. Two subspecies have been recognized in Pardosa agrestis (Westring, 1861); however, their validity is still debated. To resolve this dilemma, quantitative and qualitative traits were measured for 30 females and 30 males per site from ten localities throughout Western Europe (11 measurements on each individual) and compared between subspecies. Mean annual temperature and geographical coordinates from all sites were also included in the statistical models in order to test for variations in size over the distribution range of each subspecies. We found significant differences in body size and size of copulatory organs as well as accurate criteria of discrimination between P. a. agrestis and P. a. purbeckensis F.O.P. Cambridge, 1895, suggesting that these taxa are two valid morphological species, occurring sympatrically. We also showed that temperatures did not directly influence the size of individuals, but that one species had smaller individuals at higher latitudes (following the converse Bergmann's rule), and that both species had larger individuals in centrally sampled populations (fitting to the centre hypothesis). © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113, 85–96.     

An approach based on the total‐species accumulation curve and higher taxon richness to estimate realistic upper limits in regional species richness

Most of accumulation curves tend to underestimate species richness, as they do not consider spatial heterogeneity in species distribution, or are structured to provide lower bound estimates and limited extrapolations. The total‐species (T–S) curve allows extrapolations over large areas while taking into account spatial heterogeneity, making this estimator more prone to attempt upper bound estimates of regional species richness. However, the T–S curve may overestimate species richness due to (1) the mismatch among the spatial units used in the accumulation model and the actual units of variation in β‐diversity across the region, (2) small‐scale patchiness, and/or (3) patterns of rarity of species. We propose a new framework allowing the T–S curve to limit overestimation and give an application to a large dataset of marine mollusks spanning over 11 km² of subtidal bottom (W Mediterranean). As accumulation patterns are closely related across the taxonomic hierarchy up to family level, improvements of the T–S curve leading to more realistic estimates of family richness, that is, not exceeding the maximum number of known families potentially present in the area, can be considered as conducive to more realistic estimates of species richness. Results on real data showed that improvements of the T–S curve to accounts for true variations in β‐diversity within the sampled areas, small‐scale patchiness, and rarity of families led to the most plausible richness when all aspects were considered in the model. Data on simulated communities indicated that in the presence of high heterogeneity, and when the proportion of rare species was not excessive (>2/3), the procedure led to almost unbiased estimates. Our findings highlighted the central role of variations in β‐diversity within the region when attempting to estimate species richness, providing a general framework exploiting the properties of the T–S curve and known family richness to estimate plausible upper bounds in γ‐diversity.     

The importance of rare species: a trait‐based assessment of rare species contributions to functional diversity and possible ecosystem function in tall‐grass prairies

The majority of species in ecosystems are rare, but the ecosystem consequences of losing rare species are poorly known. To understand how rare species may influence ecosystem functioning, this study quantifies the contribution of species based on their relative level of rarity to community functional diversity using a trait‐based approach. Given that rarity can be defined in several different ways, we use four different definitions of rarity: abundance (mean and maximum), geographic range, and habitat specificity. We find that rarer species contribute to functional diversity when rarity is defined by maximum abundance, geographic range, and habitat specificity. However, rarer species are functionally redundant when rarity is defined by mean abundance. Furthermore, when using abundance‐weighted analyses, we find that rare species typically contribute significantly less to functional diversity than common species due to their low abundances. These results suggest that rare species have the potential to play an important role in ecosystem functioning, either by offering novel contributions to functional diversity or via functional redundancy depending on how rare species are defined. Yet, these contributions are likely to be greatest if the abundance of rare species increases due to environmental change. We argue that given the paucity of data on rare species, understanding the contribution of rare species to community functional diversity is an important first step to understanding the potential role of rare species in ecosystem functioning.     

The strength of negative plant–soil feedback increases from the intraspecific to the interspecific and the functional group level

One of the processes that may play a key role in plant species coexistence and ecosystem functioning is plant–soil feedback, the effect of plants on associated soil communities and the resulting feedback on plant performance. Plant–soil feedback at the interspecific level (comparing growth on own soil with growth on soil from different species) has been studied extensively, while plant–soil feedback at the intraspecific level (comparing growth on own soil with growth on soil from different accessions within a species) has only recently gained attention. Very few studies have investigated the direction and strength of feedback among different taxonomic levels, and initial results have been inconclusive, discussing phylogeny, and morphology as possible determinants. To test our hypotheses that the strength of negative feedback on plant performance increases with increasing taxonomic level and that this relationship is explained by morphological similarities, we conducted a greenhouse experiment using species assigned to three taxonomic levels (intraspecific, interspecific, and functional group level). We measured certain fitness‐related aboveground traits and used them along literature‐derived traits to determine the influence of morphological similarities on the strength and direction of the feedback. We found that the average strength of negative feedback increased from the intraspecific over the interspecific to the functional group level. However, individual accessions and species differed in the direction and strength of the feedback. None of our results could be explained by morphological dissimilarities or individual traits. Synthesis. Our results indicate that negative plant–soil feedback is stronger if the involved plants belong to more distantly related species. We conclude that the taxonomic level is an important factor in the maintenance of plant coexistence with plant–soil feedback as a potential stabilizing mechanism and should be addressed explicitly in coexistence research, while the traits considered here seem to play a minor role.     

Half a century of succession in a temperate oakwood: from species‐rich community to mesic forest

Aim Lowland woodlands in Europe went through dramatic changes in management in the past century. This article investigates the influence of two key factors, abandonment of coppicing and increased pressure of ungulates, in thermophilous oakwoods. We focused on three interconnected topics: (1) Has the assumed successional trend lead to impoverishment of the vegetation assemblages? (2) Has it resulted in vegetation homogenization? (3) Are the thermophilous oakwoods loosing their original character? Location Czech Republic, Central Europe. Methods The vegetation in 46 semi‐permanent plots was recorded three times: firstly, shortly after the abandonment of coppicing (1953) and then, after four to six decades of secondary succession and strong game impact (1992 and 2006). Overall trends and changes in species spectra were analysed. Results There is a marked successional shift towards species‐poorer communities growing in cooler, moister and nutrient‐richer conditions. The change was significantly different in parts affected and unaffected by high numbers of ungulates yet only for herbs, not the woody species. However, observed change in species composition was not accompanied by significant homogenization process that is the general process reported from elsewhere. A sharp decline in plant species typical for thermophilous woodland communities and in endangered species indicates that the original character of the woodland has been gradually lost. Main conclusions Thermophilous oakwoods have been largely replaced by mesic forests. Lowland oakwoods in continental parts of Europe historically depended on active management, which kept the understorey conditions light and warm. Successional processes in the 20th century caused a critical loss of species diversity at various spatial levels. However, artificially high numbers of ungulates, which otherwise have a negative impact, probably held up succession, so that the changes may still be reversible.     

Hydrodynamic advantages in the free‐living spiriferinide brachiopod Pachycyrtella omanensis: functional insight into adaptation to high‐energy flow environments

Immobile benthic organisms lacking attachment or cementation mechanisms are considered to be best adapted to quiet bottom environments. Since the free‐living Lower Permian spiriferinide brachiopod Pachycyrtella omanensis inhabited a sandy substrate with high‐energy water flow, flume experiments were performed to show the possible hydrodynamic advantages of shell morphology in postural stability and generation of feeding flows. Modelling indicates that a vertical position, with the commissure plane perpendicular to the seabed, was the most unstable, although it is considered to have been its original life position. On the other hand, the passive flow inside the model in vertical position exhibited vortex movement with constant degree of inhalent flow and exhalent flow, conferring advantages on the effective filtration of food particles using a spiral lophophore. The intensity and movement of the passive flow for feeding could have been adjusted through changes in the angle of opening of the valves. As the shoreface habitat was affected by oscillatory flows, a small‐sized animal could have undergone a high risk of burial, while an increase in size would have led to easier removal from the sandy bottom. To avoid both physical risks, Pachycyrtella developed a thick shell with a high rate of growth, specifically increasing the weight of the ventral umbo without altering its morphofunction to generate passive feeding flows. Biomechanics, functional morphology, opportunistic species, Pachycyrtella, Spiriferinida, suspension feeder.     

Demographic costs and benefits of herbicide‐based restoration to enhance habitat for an endangered butterfly and a threatened plant

Restoring habitat degraded by invasive species is often a primary focus of conservation strategies, yet few studies investigate the effects of invasive species control on multiple at‐risk taxa. Selective herbicides are increasingly used because they can selectively reduce aggressive invasive plant species with the aim of minimizing effects on other taxa within the habitat. We conducted a four‐year experiment to test how annual application of grass‐specific herbicide affected the demography on Fender's blue butterfly (Icaricia icarioides fenderi) and Kincaid's lupine (Lupinus oreganus), two federally protected species which persist in highly degraded prairie remnants in western Oregon, USA. Effects of herbicide application were transitory for the butterfly; reduction of invasive grasses increased fecundity and led to higher annual population growth (λ) at one of two conservation areas in the first season. There were no detectable differences in λ in subsequent seasons—suggesting that treatments caused neither extensive harm nor extensive benefit to the butterfly population. For the lupine, there were no detectable differences in leaf and flower abundance between control and herbicide treatments. However, greater seed production in herbicide plots in the first and third seasons suggests that lupines in herbicide‐treated plots have greater potential reproductive success. While treatments do not have a long‐term benefit to annual population growth for the butterfly, increasing reproductive success of the threatened plant may justify integrating this strategy into restoration plans. Considering the impact of restoration practices on the demography of multiple at‐risk taxa within a community is critical to effective recovery strategies.     

An integrative approach to species discovery in odonates: from character‐based DNA barcoding to ecology

Modern taxonomy requires an analytical approach incorporating all lines of evidence into decision‐making. Such an approach can enhance both species identification and species discovery. The character‐based DNA barcode method provides a molecular data set that can be incorporated into classical taxonomic data such that the discovery of new species can be made in an analytical framework that includes multiple sources of data. We here illustrate such a corroborative framework in a dragonfly model system that permits the discovery of two new, but visually cryptic species. In the African dragonfly genus Trithemis three distinct genetic clusters can be detected which could not be identified by using classical taxonomic characters. In order to test the hypothesis of two new species, DNA‐barcodes from different sequence markers (ND1 and COI) were combined with morphological, ecological and biogeographic data sets. Phylogenetic analyses and incorporation of all data sets into a scheme called taxonomic circle highly supports the hypothesis of two new species. Our case study suggests an analytical approach to modern taxonomy that integrates data sets from different disciplines, thereby increasing the ease and reliability of both species discovery and species assignment.     

Sex in the wild: How and why field‐based studies contribute to solving the problem of sex*

Why and how sexual reproduction is maintained in natural populations, the so‐called “queen of problems,” is a key unanswered question in evolutionary biology. Recent efforts to solve the problem of sex have often emphasized results generated from laboratory settings. Here, we use a survey of representative “sex in the wild” literature to review and synthesize the outcomes of empirical studies focused on natural populations. Especially notable results included relatively strong support for mechanisms involving niche differentiation and a near absence of attention to adaptive evolution. Support for a major role of parasites is largely confined to a single study system, and only three systems contribute most of the support for mutation accumulation hypotheses. This evidence for taxon specificity suggests that outcomes of particular studies should not be more broadly extrapolated without extreme caution. We conclude by suggesting steps forward, highlighting tests of niche differentiation mechanisms in both laboratory and nature, and empirical evaluation of adaptive evolution‐focused hypotheses in the wild. We also emphasize the value of leveraging the growing body of genomic resources for nonmodel taxa to address whether the clearance of harmful mutations and spread of beneficial variants in natural populations proceeds as expected under various hypotheses for sex.     

It's a long way to the top: Plant species diversity in the transition from managed to old‐growth forests

Questions

Do vascular plant species richness and beta‐diversity differ between managed and structurally complex unmanaged stands? To what extent do species richness and beta‐diversity relate to forest structural attributes and heterogeneity?

Location

Five national parks in central and southern Italy.

Methods

We sampled vascular plant species composition and forest structural attributes in eight unmanaged temperate mesic forest stands dominated or co‐dominated by beech, and in eight comparison stands managed as high forests with similar environmental features. We compared plant species richness, composition and beta‐diversity across pairs of stands (unmanaged vs managed) using GLMM s. Beta‐diversity was quantified both at the scale of each pair of stands using plot‐to‐plot dissimilarity matrices (species turnover), and across the whole data set, considering the distance in the multivariate species space of individual plots from their centroid within the same stand (compositional heterogeneity). We modelled the relationship between species diversity (richness and beta‐diversity) and forest structural heterogeneity and individual structural variables using GLMM s and multiple regression on distance matrices.

Results

Species composition differed significantly between managed and unmanaged stands, but not richness and beta‐diversity. We found weak evidence that plant species richness increased with increasing levels of structural heterogeneity and canopy diversification. At the scale of individual stands, species turnover was explained by different variables in distinct stands, with variables related to deadwood quantity and quality being selected most often. We did not find support for the hypothesis that compositional heterogeneity varies as a function of forest structural characteristics at the scale of the whole data set.

Conclusions

Structurally complex unmanaged stands have a distinct herb layer species composition from that of mature stands in similar environmental conditions. Nevertheless, we did not find significantly higher levels of vascular plant species richness and beta‐diversity in unmanaged stands. Beta‐diversity was related to patterns of deadwood accumulation, while for species richness the evidence that it increases with increasing levels of canopy diversification was weak. These results suggest that emulating natural disturbance, and favouring deadwood accumulation and canopy diversification may benefit some, but not all, facets of plant species diversity in Apennine beech forests.

     

Building a foundation for structure‐based cellulosome design for cellulosic ethanol: Insight into cohesin‐dockerin complexation from computer simulation

The organization and assembly of the cellulosome, an extracellular multienzyme complex produced by anaerobic bacteria, is mediated by the high‐affinity interaction of cohesin domains from scaffolding proteins with dockerins of cellulosomal enzymes. We have performed molecular dynamics simulations and free energy calculations on both the wild type (WT) and D39N mutant of the C. thermocellum Type I cohesin‐dockerin complex in aqueous solution. The D39N mutation has been experimentally demonstrated to disrupt cohesin‐dockerin binding. The present MD simulations indicate that the substitution triggers significant protein flexibility and causes a major change of the hydrogen‐bonding network in the recognition strips—the conserved loop regions previously proposed to be involved in binding—through electrostatic and salt‐bridge interactions between β‐strands 3 and 5 of the cohesin and α‐helix 3 of the dockerin. The mutation‐induced subtle disturbance in the local hydrogen‐bond network is accompanied by conformational rearrangements of the protein side chains and bound water molecules. Additional free energy perturbation calculations of the D39N mutation provide differences in the cohesin‐dockerin binding energy, thus offering a direct, quantitative comparison with experiments. The underlying molecular mechanism of cohesin‐dockerin complexation is further investigated through the free energy profile, that is, potential of mean force (PMF) calculations of WT cohesin‐dockerin complex. The PMF shows a high‐free energy barrier against the dissociation and reveals a stepwise pattern involving both the central β‐sheet interface and its adjacent solvent‐exposed loop/turn regions clustered at both ends of the β‐barrel structure.     

Influence of soils and topography on Amazonian tree diversity: a landscape‐scale study

Question: How do soils and topography influence Amazonian tree diversity, a region with generally nutrient‐starved soils but some of the biologically richest tree communities on Earth? Location: Central Amazonia, near Manaus, Brazil. Methods: We evaluated the influence of 14 soil and topographic features on species diversity of rain forest trees (≥10 cm diameter at breast height), using data from 63 1‐ha plots scattered over an area of ～400 km². Results: An ordination analysis identified three major edaphic gradients: (1) flatter areas had generally higher nutrient soils (higher clay content, carbon, nitrogen, phosphorus, pH and exchangeable bases, and lower aluminium saturation) than did slopes and gullies; (2) sandier soils had lower water storage (plant available water capacity), phosphorus and nitrogen; and (3) soil pH varied among sites. Gradient 2 was the strongest predictor of tree diversity (species richness and Fisher's α values), with diversity increasing with higher soil fertility and water availability. Gradient 2 was also the best predictor of the number of rare (singleton) species, which accounted on average for over half (56%) of all species in each plot. Conclusions: Although our plots invariably supported diverse tree communities (≥225 species ha^?1), the most species‐rich sites (up to 310 species ha^?1) were least constrained by soil water and phosphorus availability. Intriguingly, the numbers of rare and common species were not significantly correlated in our plots, and they responded differently to major soil and topographic gradients. For unknown reasons rare species were significantly more frequent in plots with many large trees.