Reproductive barriers between two sympatric beetle species specialized on different host plants

Knowledge on interspecific pre‐ and post‐zygotic isolation mechanisms provides insights into speciation patterns. Using crosses (F₁ and backcrosses) of two closely related flea beetles species, Altica fragariae and A. viridicyanea, specialized on different hosts in sympatry, we measured: (a) the type of reproductive isolation and (b) the inheritance mode of preference and host‐specific performance, using a joint‐scaling test. Each species preferred almost exclusively its host plant, creating strong prezygotic isolation between them, and suggesting that speciation may occur at least partly in sympatry. Reproductive isolation was intrinsic between females of A. fragariae and either A. viridicyanea or F₁ males, whereas the other crosses showed ecologically dependent reproductive isolation, suggesting ecological speciation. The genetic basis of preference and performance was at least partially independent, and several loci coded for preference, which limits the possibility of sympatric speciation. Hence, both ecological and intrinsic factors may contribute to speciation between these species.     

Use of Camera-Trapping to Estimate Puma Density and Influencing Factors in Central Brazil

Abstract: We used remotely triggered cameras to collect data on Puma (Puma concolor) abundance and occupancy in an area of tropical forest in Brazil where the species' status is poorly known. To evaluate factors influencing puma occupancy we used data from 5 sampling campaigns in 3 consecutive years (2005 to 2007) and 2 seasons (wet and dry), at a state park and a private forest reserve. We estimated puma numbers and density for the 2007 sampling data by developing a standardized individual identification method. We based individual identification on 1) time-stable parameters (SP; physical features that do not change over time), and 2) time-variable parameters (VP; marks that could change over time such as scars and botfly marks). Following individual identification we established a capture-recapture history and analyzed it using closed population capture-mark-recapture models. Puma capture probability was influenced by camera placement (roads vs. trails), sampling year, and prey richness. Puma occupancy was positively associated with species richness and there was a correlation between relative puma and jaguar (Panthera onca) abundance. Identifications enabled us to generate 8 VP histories for each photographed flank, corresponding to 8 individuals. We estimated the sampled population at 9 pumas (SE = 1.03, 95% CI = 8–10 individuals) translating to a density of 3.40 pumas/100 km². Information collected using camera-traps can effectively be used to assess puma population size in tropical forests. As habitat progressively disappears and South American felines become more vulnerable, our results support the critical importance of private forest reserves for conservation.     

Modification of the glycolytic pathway in Pyrococcus furiosus and the implications for metabolic engineering

Extremophiles - The key difference in the modified Embden–Meyerhof glycolytic pathway in hyperthermophilic Archaea, such as Pyrococcus furiosus, occurs at the conversion from...     

Effects of multi-year droughts on fish assemblages of seasonally drying Mediterranean streams

1. This study analysed changes occurring in Mediterranean stream fish assemblages over a sequence of dry years followed by a generally wet period (1991–98). Variations in assemblage attributes were quantified at the basin and stream reach scales, and related to variables reflecting the occurrence of unusually dry or wet conditions. 2. Assemblage variability increased along with the resolution of analysis, with little changes in species richness, composition and rank abundances, but significant variation in individual species abundances. Fluctuations in relative abundances were significantly affected by variables reflecting the severity of summer droughts and the occurrence of rainy springs. These patterns were evident at the basin scale, while variability at individual stream reaches tended to be higher and less related to rainfall patterns. 3. At least three response guilds to rainfall variation could be identified: two of the four abundant and widespread species (chub and loach) declined following dry years, whereas the two other core species (nase and eel) declined after rainy spring; one scarce native species (stickleback) increased in dry years. 4. Except at the two most upstream reaches, the assemblages tended to recover quickly to previous configuration after the changes occurring during the sequence of dry years. 5. Temporal variability of local assemblages was concordant among reaches but did not follow any consistent spatial pattern. Instead, spatial patterns in assemblage attributes changed over time in response to environmental variability, with a tendency for a disruption of upstream–downstream gradients following dry years. 6. Results supported the view that present‐day droughts cause relatively small and transient changes to Mediterranean stream fish assemblages. However, longer and more severe droughts expected under altered future climates, may result in declines or local extinctions of the most sensitive species and their potential replacement by more resistant species. Changing drought regimes thus need to be duly considered in the development of conservation strategies for Mediterranean stream fish.     

Phylogenetic analysis of Micrathena and Chaetacis spiders (Araneae: Araneidae) reveals multiple origins of extreme sexual size dimorphism and long abdominal spines

The phylogenetic relationships amongst the New World spiny orb‐weaving spiders Micrathena and Chaetacis were assessed through parsimony and Bayesian analyses of morphological characters. A total of 146 characters was scored for ten outgroup taxa and 37 Micrathena and four Chaetacis species. The results indicate that Chaetacis nests within Micrathena and we propose Chaetacis as a junior synonym of Micrathena. Twelve subgeneric species groups of Micrathena are recognized and diagnosed. Species with extremely long spines evolved at least eight times in the genus and we suggest that this may be related to antipredator defences. Micrathena is primitively sexually monomorphic and extreme sexual size dimorphism has arisen at least six times in the genus. Most of these events are because of enlargement of the female in relation to the ancestral size, although in two cases sexual dimorphism was attained through male reduction, adding more data to the ‘giant females’ vs. ‘dwarf males’ controversy. The genus is probably of South American origin and has repeatedly invaded Central and North America. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 166 , 14–53.     

Gradients in stream fish assemblages across a Mediterranean landscape: contributions of environmental factors and spatial structure

1. Despite wide recognition that fish assemblages are influenced by factors operating over a range of spatial scales, little effort has been devoted to quantifying large‐scale variation and the multiscale dependencies of assemblage patterns and processes. This is particularly true for Mediterranean streams, where seasonally predictable drying‐up may lead to a strong association between assemblage attributes and large‐scale factors affecting the distribution of population sources and extinction likelihood. 2. The contribution of large‐scale factors to stream fish assemblage variation was quantified across a Mediterranean landscape, in south‐west Portugal. Fish abundance and species composition were estimated at 166 sites across third‐ to sixth‐order streams, in March–July 1998. Variance partitioning by redundancy analyses was used to analyse assemblage variation against three sets of predictor variables: environmental (catchment position, and geomorphic and hydrological factors), large‐scale spatial trends and neighbourhood effects. 3. Environmental variables and spatial trends accounted for 34.6% of the assemblage variation across the entire region, and for 36.6 and 57.8% within the two largest catchments (Mira and Seixe). Neighbourhood effects were analysed at the catchment scale, increasing the explained variation to 56.1% (Mira) and 70.7% (Seixe). 4. A prevailing environmental gradient was reflected in an increase in the abundance of all species and size‐classes in relation to catchment position, with more fish present in larger streams and in downstream reaches. Variables describing geomorphic and hydrological settings were less important in explaining assemblage variation. 5. Spatial trends always accounted for the smallest fraction of assemblage variation, and they were probably associated with historical barriers to fish dispersal. The strong neighbourhood effects may be related to spatially autocorrelated habitat conditions, but they are also a likely consequence of fish emigration/extinction and colonisation processes. 6. These results emphasise that a substantial proportion of fish assemblage variation in Mediterranean streams may be explained by large‐scale factors, irrespective of microhabitats and local biotic interactions. It is suggested that this pattern results to a large extent from the seasonal drying‐up, with the summer shortage of surface water limiting fish occurrence in headwaters, and consequently the key core areas for fish concentrating in larger streams and tributaries adjacent to large streams because of neighbourhood effects.     

Trends in Global Vegetation Activity and Climatic Drivers Indicate a Decoupled Response to Climate Change

Detailed understanding of a possible decoupling between climatic drivers of plant productivity and the response of ecosystems vegetation is required. We compared trends in six NDVI metrics (1982–2010) derived from the GIMMS3g dataset with modelled biomass productivity and assessed uncertainty in trend estimates. Annual total biomass weight (TBW) was calculated with the LINPAC model. Trends were determined using a simple linear regression, a Thiel-Sen medium slope and a piecewise regression (PWR) with two segments. Values of NDVI metrics were related to Net Primary Production (MODIS-NPP) and TBW per biome and land-use type. The simple linear and Thiel-Sen trends did not differ much whereas PWR increased the fraction of explained variation, depending on the NDVI metric considered. A positive trend in TBW indicating more favorable climatic conditions was found for 24% of pixels on land, and for 5% a negative trend. A decoupled trend, indicating positive TBW trends and monotonic negative or segmented and negative NDVI trends, was observed for 17–36% of all productive areas depending on the NDVI metric used. For only 1–2% of all pixels in productive areas, a diverging and greening trend was found despite a strong negative trend in TBW. The choice of NDVI metric used strongly affected outcomes on regional scales and differences in the fraction of explained variation in MODIS-NPP between biomes were large, and a combination of NDVI metrics is recommended for global studies. We have found an increasing difference between trends in climatic drivers and observed NDVI for large parts of the globe. Our findings suggest that future scenarios must consider impacts of constraints on plant growth such as extremes in weather and nutrient availability to predict changes in NPP and CO₂ sequestration capacity.     

Bioclipse: an open source workbench for chemo- and bioinformatics

Background  

There is a need for software applications that provide users with a complete and extensible toolkit for chemo- and bioinformatics accessible from a single workbench. Commercial packages are expensive and closed source, hence they do not allow end users to modify algorithms and add custom functionality. Existing open source projects are more focused on providing a framework for integrating existing, separately installed bioinformatics packages, rather than providing user-friendly interfaces. No open source chemoinformatics workbench has previously been published, and no sucessful attempts have been made to integrate chemo- and bioinformatics into a single framework.     

The reductive half-reaction of two bifurcating electron-transferring flavoproteins: Evidence for changes in flavin reduction potentials mediated by specific conformational changes

The EtfAB components of two bifurcating flavoprotein systems, the crotonyl-CoA-dependent NADH:ferredoxin oxidoreductase from the bacterium Megasphaera elsdenii and the menaquinone-dependent NADH:ferredoxin oxidoreductase from the archaeon Pyrobaculum aerophilum, have been investigated. With both proteins, we find that removal of the electron-transferring flavin adenine dinucleotide (FAD) moiety from both proteins results in an uncrossing of the reduction potentials of the remaining bifurcating FAD; this significantly stabilizes the otherwise very unstable semiquinone state, which accumulates over the course of reductive titrations with sodium dithionite. Furthermore, reduction of both EtfABs depleted of their electron-transferring FAD by NADH was monophasic with a hyperbolic dependence of reaction rate on the concentration of NADH. On the other hand, NADH reduction of the replete proteins containing the electron-transferring FAD was multiphasic, consisting of a fast phase comparable to that seen with the depleted proteins followed by an intermediate phase that involves significant accumulation of FAD⋅⁻, again reflecting uncrossing of the half-potentials of the bifurcating FAD. This is then followed by a slow phase that represents the slow reduction of the electron-transferring FAD to FADH⁻, with reduction of the now fully reoxidized bifurcating FAD by a second equivalent of NADH. We suggest that the crossing and uncrossing of the reduction half-potentials of the bifurcating FAD is due to specific conformational changes that have been structurally characterized.