Community‐level effects of herbicide‐based restoration treatments: structural benefits but at what cost?

Invasive species alter ecosystem structure, impact biodiversity, and have significant economic costs. In Oregon's Willamette Valley, invasive grasses Arrhenatherum elatius and Schedonorus arundinaceus alter the dynamics of the phenologically paired interaction between an endangered butterfly, Icaricia icarioides fenderi (Fender's blue), and its larval host plant, Lupinus oreganus (Kincaid's lupine). To test methods to restore this interaction, we established a 3‐year experiment where a post‐emergent grass‐specific herbicide, fluazifop‐p‐butyl, was applied to Fender's blue habitat. Plant community data were recorded throughout the growing season at eight paired plots for 1 year prior to treatment and 3 years during treatment. We asked whether annual application of herbicide could reduce the height of invasive grasses to levels at or beneath the height of Kincaid's lupine racemes throughout the Fender's blue flight season. We hypothesized that native forb species, which are critical nectar sources for Fender's blue, would increase in cover and frequency following the release from competitive dominance of invasive grasses. Grass‐specific herbicide reduced grass height during the flight season of Fender's blue, but with several costs. We found no change in nectar and a suppression of lupine growth in plots in response to experimental herbicide treatment. Each study site had multiple secondary invaders; the long‐term impact of these new invaders is unknown. We suggest that herbicide application results in a net negative effect in the context of Fender's blue habitat restoration. That is, the costs to primary resources for Fender's blue and the influx of secondary invaders may be as problematic as the primary invasion by non‐native grasses.     

Sex‐specific foraging behaviour in tropical boobies: does size matter?

Sex differences in the foraging behaviour of adults have been observed in a number of sexually size-dimorphic birds, and the usual inference has been that these sex-specific differences are driven primarily by differences in body size. An alternative explanation is that foraging differences result from sex differences unrelated to size, such as sex-specific nutritional requirements. To examine these alternative hypotheses, the foraging behaviour of parents was compared between two sympatric and congeneric species of seabird, the Brown Booby Sula leucogaster , which is highly sexually size-dimorphic (females 38% larger) and the Red-footed Booby S. sula , in which sex differences in body size are less marked (females 15% larger). Using temperature and depth loggers, we found that there were highly significant differences in the foraging trip durations and diving behaviour of male and female Brown Boobies. These sex differences were less marked in Red-footed Boobies. Thus, our interspecies comparison revealed that the magnitude of the difference between the sexes matched the sexual size dimorphism of the species, providing support for the size hypothesis.     

Natural attenuation: what does the subsurface have in store?

Throughout the world, organic and inorganic substances leach intothe subsurface as a result of human activities and accidents. There, the chemicals pose director indirect threats to the environment and to increasingly scarce drinking water resources.At many contaminated sites the subsurface is able to attenuate pollutants which, potentially,lowers the costs of remediation. Natural attenuation comprises a wide range of processesof which the microbiological component, which is responsible for intrinsic bioremediation,can decrease the mass and toxicity of the contaminants and is, therefore, the mostimportant. Reliance on intrinsic bioremediation requires methods to monitor the process. Thesubject of this review is how knowledge of subsurface geology and hydrology, microbial ecologyand degradation processes is used and can be used to monitor the potential andcapacity for intrinsic bioremediation in the subsurface and to verify degradation in situ.As research on natural attenuation in the subsurface has been rather fragmented and limitedand often allows only conclusions to be drawn of the site under investigation, we providea concept based on Environmental Specimen Banking which will contribute to furtherunderstanding subsurface natural attenuation processes and will help to develop andimplement new monitoring techniques.     

Lack of pattern among phytoplankton assemblages. Or,what does the exception to the rule mean?

In Science we cannot say that `the exception proves the rule'. We have been looking to define patterns in phytoplankton occurrence across trophic spectra where conspicuous covariations between algae and trophic states have been reported. We consider quite different phytoplankton communities observed under similar trophic conditions: we illustrate this point by considering five different phytoplankton communities living in five water bodies in the same wetland, along a TP gradient and over a period of 2 years. This system showed a remarkable dissimilarity of species representation, implying communities of uncorrelated species vary considerably over time. Despite the presence of some characteristic species, communities were not related to a given trophic state. However, coarser community attributes, such as clusters of taxonomic classes, appeared to be more useful in identifying patterns and assembly rules related to trophic spectra. Some ecological concepts can be related to this lack of pattern, e.g., nonconvergence, trajectories far from equilibrium and assembly rules of communities.     

Controlling X-inactivation in mammals: what does the centre hold?

Controlling gene expression is one of the most fundamental task of living organisms, from prokaryotes to higher eukaryotes, in order to develop, grow, and reproduce in an ever changing environment. In many cases, the expression status of a given gene is controlled independently of that of its neighbours through localised cis DNA elements responsible for the recruitment of specific factors and enzymatic activities. However, in a growing number of cases, genomic regions including several genes have been shown to be regulated in a coordinated manner. X-chromosome inactivation, the dosage compensation mechanism encountered in mammals, is one of the most Striking example of such coordinated gene regulation. This process, which occurs at the chromosome-wide level, affecting many hundreds of genes, is under the control of a unique, cis acting region, termed the X-inactivation centre, whose complexity is just beginning to be unravelled.     

Does the seed bank contribute to the restoration of species‐rich vegetation in wet dune slacks?

Questions: What is the contribution of the seed bank to restoration of species‐rich vegetation in oligotrophic wet dune slacks? Does the restoration management affect the seed bank? Location: Calcareous coastal dune slacks at the west coast of The Netherlands. Methods: Species composition of the seed bank and the above‐ground vegetation was sampled in dune slacks that had a variable extent of groundwater level rise in combination with either topsoil removal or mowing. Results: The seed bank had a high potential for restoration of species‐rich vegetation: 60 species were found in the seed bank of which 14 were characteristic of oligotrophic, wet dune vegetation. While topsoil removal almost completely removed the seed bank, groundwater level rise did not permanently submerge the seed bank of species of oligotrophic, wet conditions. Changes in abundance in the established vegetation were unrelated to species abundance in the seed bank. Of all new species establishments in the vegetation relevés, 76% occurred where the species was not found in the seed bank. The chance that presence of a species in the seed bank led to establishment the following year was only 11%. Conclusion: The seed bank was not the dominant source for newly establishing species following the large disturbance that was induced by restoration management. Changes in species abundance after the restoration impact were not related to species abundance in the seed bank, but to ongoing succession and current year dispersal. To attain a high number of new establishments, restoration projects should preferably be planned in the proximity of refuge populations, rather than relying on the seed bank alone.     

Smith‐Lemli‐Opitz syndrome in trisomy 13: How does the mix work?

BACKGROUND: Trisomy 13 and Smith-Lemli-Opitz syndrome (SLOS) are both well-recognized multiple congenital anomaly/mental retardation syndromes. CASE: In this report we describe a male newborn with trisomy 13 who also has features of SLOS, such as 2/3 toe syndactyly and a shawl-like scrotum. Biochemical analysis was consistent with SLOS, and limited molecular analysis revealed 1 mutation in the DHCR7 gene. CONCLUSIONS: The challenges in establishing the diagnosis of SLOS in this patient are presented and the unique coexistence of the 2 major malformation syndromes is discussed. Given the overlapping phenotype of the 2 syndromes, our report should encourage further research on cholesterol biosynthesis in patients with trisomy 13.     

What does it mean to identify a protein in proteomics?

The annotation of the human genome indicates the surprisingly low number of approximately 40,000 genes. However, the estimated number of proteins encoded by these genes is two to three orders of magnitude higher. The ability to unambiguously identify the proteins is a prerequisite for their functional investigation. As proteins derived from the same gene can be largely identical, and might differ only in small but functionally relevant details, protein identification tools must not only identify a large number of proteins but also be able to differentiate between close relatives. This information can be generated by mass spectrometry, an approach that identifies proteins by partial analysis of their digestion-derived peptides. Information gleaned from databases fills in the missing sequence information. Because both sequence databases and experimental data are limited, a certain ambiguity often remains concerning which sequence variant(s) and modification(s) are present. As the common denominator of all the isoforms is a gene, in our opinion, it would be more accurate to state that a product of this particular gene rather than a certain protein has been identified by mass spectrometry.     

From cells to colonies: at what levels of body organization does the ‘temperature‐size rule’ apply?

SUMMARY An inverse relationship between temperature during ontogeny and final body size is widespread in ectotherms, but poorly understood. Evidence suggests that within organs, this “temperature‐size rule” (TSR) may also apply to cell size with no change in numbers. So how closely do reductions in size and number of cells and other repeated structures correlate with size reduction at higher levels of organization? We examine this in the context of a proposal that size and/or number changes at various organizational levels are adaptive responses to temperature‐ and size‐dependent oxygen supply. We subjected two clones of the modular colonial bryozoan, Celleporella hyalina, to orthogonal combinations of two temperatures and two oxygen concentrations during ontogeny, observing effects on sizes of colonies and larvae, and sizes and numbers of cells, tentacles, and modules (autozooids). We found that the size:number responses varied among cell types and among structures at different levels of organization, with the inverse temperature‐size relationship applying only to larval parenchymal cells and colony modules. Using our findings and other evidence we propose a unifying adaptive hypothesis that predicts how temperature affects the sizes of mitochondria, cells, organs, modules and organisms, and their relationships with processes that determine the functional capacity of aerobic metabolism.     

The politics of fear: what does it mean to those who are otherized and feared?

Islamophobia has, of late, created a tendency to conflate all Muslims as belonging to a single nation of Islam that does not recognize and respect boundaries imposed by western geopolitics. This has been done by some to create and by others to generate a sense of exclusive unity that would separate all Muslims and make them into ‘others’ within western societies. It is the contention of this paper that such calls both embody and ignore the diversities of Islam as understood and practised by its adherents. Furthermore by ‘otherizing’ the entire community of Muslims in the West, the singular label of ‘Islamism’ marginalizes and may even silence the vibrant contestations among Muslims about their faith and its teachings; these include questions posed by women who may be described as feminists. The attributes of Islamism, ascribed to the faith by public, the media and politicians in the West and adopted by some Muslims primarily as a politically unifying force, are very different from the fluidity and flexibility that has been a historic part of lived Islam. Many Muslims may well aspire to belong to the umma: people of Islam conceptualized as crossing ethnic, racial, geographical and political boundaries. But Muslims in general and Muslim women in particular do not wish to do so at the expense of being otherized and conforming to the negative stereotypes ascribed to them that mask their fluid identities and, in the case of ‘white’ women, their close ties with their kinship networks. The multiplicity of Muslim's identities sits more easily within the permeable unbounded umma applicable to the global as well as the local without necessarily always privileging one or other identity.     

Punctuated equilibrium and species selection: what does it mean for one theory to suggest another?

McMullin (In: Cohen et al. (eds.) Essays in memory of Imre Lakatos, 1976, In: Leplin (ed.) Scientific realism, 1984) argues that fertility is a theoretical virtue. He thinks of a fertile theory as one whose central metaphors suggest new directions for theoretical development, where those new developments help solve previous problems and anomalies. Nolan (Br J Philos Sci 50:265–282, 1999) argues that fertility in this sense is not a distinctive theoretical virtue in its own right. Rather, Nolan thinks that fertility is reducible to predictive novelty. This article explores the relationship between punctuated equilibrium (PE) and species selection in the light of this philosophical debate about the nature of theoretical fertility, or suggestiveness. I argue that (1) PE suggests, but does not imply, that species selection is a mechanism of evolution; (2) the suggestiveness in this case is not reducible to predictive novelty; (3) species selection is not a metaphorical extension of PE; and (4) getting clear about the way in which PE suggests species selection can help solve a puzzle about punctuated equilibrium. The puzzle is that Eldredge and Gould’s initial presentation of PE seems to presuppose a minimalist or extrapolationist view of macroevolution, even though many scientists take PE to challenge that minimalist view.     

Vegetation dynamics in side-channels reconnected to the Rhine River: what are the main factors controlling communities trajectories after restoration?

The hydraulic management of large rivers led to a disconnection of side-channels. Restoration works were to reconnect these side-channels to the main course in order to recover hydrological and ecological functions. The aim of the study was to analyze the vegetation dynamics after restoration and to link it to the change in chemical and hydro-geomorphological characteristics. Changes in species richness, cover and composition of the macrophytes communities were studied in nine side-channels of the Rhine river (France) after reconnection which occurred between 1998 and 2006. Vegetation dynamics was surveyed between 2007 and 2011 and compared to the ones of three target side-channels (never disconnected). Three vegetation communities were identified: one characterized by rheophilic species, a second one by mesotrophic species, and a third one by eutrophic species. Distribution of communities depended mainly on the flow velocity and the sediment texture of the side-channels. The floristic composition of communities evolved rapidly and remained stable a few years after restoration. Changes in species richness and cover remained relatively low in all side-channels over the study period. Time after restoration did not affect the dynamics of colonization. Reconnection allowed the restored side-channels to exhibit vegetation dynamics similar to those of the target side-channels.     

Structure of fish assemblages in seven tropical reservoirs in southeastern Brazil during the rainy season; what matters: physico‐chemical or hydrological connectivity influences?

Closely connected reservoirs were hypothesized to have more similar fish compositions than do spatially isolated reservoirs, and that environmental variables play an important role in shaping assemblage structure on a local scale. Fish assemblages and environmental variables were sampled in seven reservoirs constructed to generate hydroelectricity, with most inflowing water coming directly or via transposition of the Paraiba do Sul River, in Southeastern Brazil. Using gill nets and environmental measurement variables, fish collections were carried out between January and February 2008 (wet season), when increases in temperature and rainfall increase hydrological connectivity, facilitating fish movements throughout the river‐reservoir system. Mean fish density, biomass and the number of species did not differ significantly among the seven reservoirs. On the other hand, the assemblage structure differed among almost all pairs of reservoirs. Of the reservoirs connected in series, only two (Santana and Vigário) showed a similar assemblage structure, suggesting that hydrological connectivity plays a minor role. Physico‐chemical variables changed among reservoirs and seemed to play an important role in determining the assemblage structure, with higher conductivity (average = 108 μS cm^?1) and TDS – total dissolved solid (0.07 g L^?1), and low pH (5.8) in the Pereira Passos Reservoir associated with a high number of the Siluriformes Loricariichthys castaneus, and with the opposite conditions in Tocos (conductivity = 27 μS cm^?1; TDS = 0.02 g L^?1; pH = 7) that were associated with a high number of the carnivorous Characiformes Oligosarcus hepsetus and Hoplias malabaricus. A direct relationship was found between abundance of the catfishes Pimelodus fur and Glanidium albescens and high turbidity (90.4 NTU) and low temperature (25.3°C) and transparency (0.1 m) in the Ilha dos Pombos Reservoir. Moreover, a close relationship was found between high abundance of the cichlid Cichla kelberi and the high temperature and transparency of Lajes (28.3°C; 2.2 m) and Santa Branca (27.1°C; 2.6 m) reservoirs. These findings support the hypothesis that physico‐chemical variables structure fish assemblages in reservoirs, but that hydrological connectivity seems to play a minor role in shaping assemblage structure. However, other unmeasured variables (e.g. physical habitat characteristics and biotic interactions) and other seasons need to be evaluated in further studies.     

From spatial form to system and process through pattern making in the landscape: can landscape design contribute to nature restoration?

This study presents a scenario in which recent development of landscape design based on modernism and modernists works is depicted in conjunction with its possible contribution toward nature restoration. Spatial pattern found in modernists works enhanced the designers understanding of landscape pattern underlying the land and environment at an extensive scale. In search of solid ground for pattern making, landscape designers further investigated the environmental system and its structure. A morphological approach employed in the discourse of landscape ecology gives a theoretical foundation to those endeavors. Also, the process through which the environmental system functions and is maintained becomes another potential field of design expression in landscape. Detailed studies of several works and p landscape design projects, which have already indicated a direction of development, will promote a productive and creative co-relationship between landscape design and nature restoration.This revised version was published online in April 2005 with corrections to keywords.