Are post-fire residual forest patches refugia for boreal bryophyte species? Implications for ecosystem based management and conservation

Residual patches of forest remaining after natural or anthropogenic disturbance may facilitate regeneration of fragmented forest. However, residual patch function remains unclear, especially after natural wildfire. We investigate the role of residual boreal forest patches as refugia for bryophytes and ask the question, do they house bryophyte communities similar to those encountered in undisturbed forests? Bryophytes were sampled in three habitat types in black spruce boreal forests illustrating a gradient of disturbance severity: undisturbed forests, residual patches and burned matrices. Temporal, disturbance severity, spatial and structural variables of habitats were also recorded. Bryophyte community composition differed among habitat types with residual patches characterized by higher species richness, the loss of forest specialists and the addition of disturbance-prone species. The bryophyte community found in residual patches is at the interface between the communities of undisturbed forests and burned matrices. As residual patches did not conserve all species, particularly forest specialists, they were not refugia. However, we identify temporal, spatial and structural characteristics that can maintain bryophyte communities most similar to undisturbed forests and enhance residual patch “refugia potential”. Residual patches enhance bryophyte diversity of the landscape housing species that cannot survive in the burned matrix. As conclusion we discuss the use of retention patches in harvested stands, together with the preservation of undisturbed stands that house singular bryophyte communities and especially sensitive forest specialists.     

Are seed set and speciation rates always low among species that resprout after fire, and why?

A general dichotomy in response to catching alight during fire is for perennial plants to die (nonsprouters, N) or to regrow via dormant buds (resprouters, R). Contrasting effects on other life-history traits, especially those relating to sexual reproduction, can be expected. We hypothesized that fecundity should be lower in R. Our meta-analysis of 33 case studies of co-occurring generic pairs of N and R showed that viable seed and fruit set relative to inflorescence, flower and ovule production were lower for R than N in 30 cases. Three mechanisms have been invoked to explain these trends: resource competition between vegetative and reproductive growth, an outbreeding (R)/inbreeding (N) dichotomy, and higher genetic load among R due to their accumulation of deleterious somatic mutations over many fire cycles. Though poorly researched, we conclude that the high genetic load of R in association with strong self-incompatibility (xenogamy) can best explain the dichotomy in lifeform-fecundity as well as the exceptions. Over the long-term, we suggest that marked xenogamy-longevity in association with frequent axillary branching (induced by recurrent fire, herbivory and drought) via copious stored buds within R might favour expression among their genets and ramets of beneficial somatic mutations present in their meristematic tissues. These conditions would favour ecotypic differentiation and speciation among R that has contributed, along with N, to the exceptional species richness of several fire-prone mediterranean regions.     

Are presenilins intramembrane-cleaving proteases? Implications for the molecular mechanism of Alzheimer's disease.

The amyloid-beta protein (Abeta) is strongly implicated in the pathogenesis of Alzheimer's disease. The final step in the production of Abeta from the amyloid precursor protein (APP) is proteolysis by the unidentified gamma-secretases. This cleavage event is unusual in that it apparently occurs within the transmembrane region of the substrate. Studies with substrate-based inhibitors together with molecular modeling and mutagenesis of the gamma-secretase cleavage site of APP suggest that gamma-secretases are aspartyl proteases that catalyze a novel intramembranous proteolysis. This proteolysis requires the presenilins, proteins with eight transmembrane domains that are mutated in most cases of autosomal dominant familial Alzheimer's disease. Two conserved transmembrane aspartates in presenilins are essential for gamma-secretase activity, suggesting that presenilins themselves are gamma-secretases. Moreover, presenilins also mediate the apparently intramembranous cleavage of the Notch receptor, an event critical for Notch signaling and embryonic development. Thus, if presenilins are gamma-secretases, then they are also likely the proteases that cleave Notch within its transmembrane domain. Another protease, S2P, involved in the processing of the sterol regulatory element binding protein, is also a multipass integral membrane protein which cleaves within or very close to the transmembrane region of its substrate. Thus, presenilins and S2P appear to be members of a new type of polytopic protease with an intramembranous active site.     

Review: Are there indigenous Saccharomyces in the digestive tract of livestock animal species? Implications for health,nutrition and productivity traits

All livestock animal species harbour complex microbial communities throughout their digestive tract that support vital biochemical processes, thus sustaining health and productivity. In part as a consequence of the strong and ancient alliance between the host and its associated microbes, the gut microbiota is also closely related to productivity traits such as feed efficiency. This phenomenon can help researchers and producers develop new and more effective microbiome-based interventions using probiotics, also known as direct-fed microbials (DFMs), in Animal Science. Here, we focus on one type of such beneficial microorganisms, the yeast Saccharomyces. Saccharomyces is one of the most widely used microorganisms as a DFM in livestock operations. Numerous studies have investigated the effects of dietary supplementation with different species, strains and doses of Saccharomyces (mostly Saccharomyces cerevisiae) on gut microbial ecology, health, nutrition and productivity traits of several livestock species. However, the possible existence of Saccharomyces which are indigenous to the animals’ digestive tract has received little attention and has never been the subject of a review. We for the first time provide a comprehensive review, with the objective of shedding light into the possible existence of indigenous Saccharomyces of the digestive tract of livestock. Saccharomyces cerevisiae is a nomadic yeast able to survive in a broad range of environments including soil, grass and silages. Therefore, it is very likely that cattle and other animals have been in direct contact with this and other types of Saccharomyces throughout their entire existence. However, to date, the majority of animal scientists seem to agree that the presence of Saccharomyces in any section of the gut only reflects dietary contamination; in other words, these are foreign organisms that are only transiently present in the gut. Importantly, this belief (i.e. that Saccharomyces come solely from the diet) is often not well grounded and does not necessarily hold for all the many other groups of microbes in the gut. In addition to summarizing the current body of literature involving Saccharomyces in the digestive tract, we discuss whether the beneficial effects associated with the consumption of Saccharomyces may be related to its foreign origin, though this concept may not necessarily satisfy the theories that have been proposed to explain probiotic efficacy in vivo. This novel review may prove useful for biomedical scientists and others wishing to improve health and productivity using Saccharomyces and other beneficial microorganisms.     

Are cattle,sheep, and goats endangered species?

For about 10 000 years, farmers have been managing cattle, sheep, and goats in a sustainable way, leading to animals that are well adapted to the local conditions. About 200 years ago, the situation started to change dramatically, with the rise of the concept of breed. All animals from the same breed began to be selected for the same phenotypic characteristics, and reproduction among breeds was seriously reduced. This corresponded to a strong fragmentation of the initial populations. A few decades ago, the selection pressures were increased again in order to further improve productivity, without enough emphasis on the preservation of the overall genetic diversity. The efficiency of modern selection methods successfully increased the production, but with a dramatic loss of genetic variability. Many industrial breeds now suffer from inbreeding, with effective population sizes falling below 50. With the development of these industrial breeds came economic pressure on farmers to abandon their traditional breeds, and many of these have recently become extinct as a result. This means that genetic resources in cattle, sheep, and goats are highly endangered, particularly in developed countries. It is therefore important to take measures that promote a sustainable management of these genetic resources; first, by in situ preservation of endangered breeds; second, by using selection programmes to restore the genetic diversity of industrial breeds; and finally, by protecting the wild relatives that might provide useful genetic resources.     

EST contig-based SSR linkage maps for Malus?×?domestica cv Royal Gala and an apple scab resistant accession of M. sieversii, the progenitor species of domestic apple

Malus sieversii is a progenitor species of domestic apple M. × domestica. Using population “GMAL 4595” of 188 individuals derived from a cross of Royal Gala × PI 613988 (apple scab resistant, M. sieversii), 287 SSR (simple sequence repeats) loci were mapped. Of these SSRs, 80 are published anchors and 207 are newly developed EST (expressed sequence tag) contig-based SSRs, representing 1,630 Malus EST accessions in GenBank. Putative gene functions of these EST contigs are diverse, including regulating plant growth, development and response to environmental stresses. Among the 80 published SSRs, 18 are PI 613988 specific, 38 are common and 24 are Royal Gala specific. Out of the 207 newly developed EST contig-based SSRs, 79 are PI 613988 specific, 45 are common and 83 are Royal Gala specific. These results led to the construction of a M. sieversii map (1,387.0 cM) of 180 SSR markers and a Royal Gala map (1,283.4 cM) of 190 SSR markers. Mapping of scab resistance was independently conducted in two subsets of population “GMAL 4595” that were inoculated with Ventura inaequalis races (1) and (2), respectively. In combination with the two major resistance reactions Chl (chlorotic lesions) and SN (stellate necrosis) to each race, four subsets of resistance data, i.e., Chl/race (1), SN/race (1), Chl/race (2) and SN/race (2), were constituted and analyzed, leading to four resistance loci mapped to the linkage group 2 of PI 613988; SNR1 (stellate necrosis resistance to race (1)) and SNR2 are tightly linked in a region of known scab resistance genes, and ChlR1 (Chlorotic lesion resistance to race (1)) and ChlR2 are also linked tightly but in a region without known scab resistance genes. The utility of the two linkage maps, the new EST contig-based markers and M. sieversii as sources of apple scab resistance are discussed.     

Biofilms and Biocides: Are there Implications for Antibiotic Resistance?

Considerable controversy surrounds the use of biocides in an ever increasing range of consumer products and the possibility that their indiscriminate use might reduce biocide effectiveness and alter susceptibilities towards antibiotics. These concerns have been based largely on the isolation of resistant mutants from in vitro monoculture experiments. To date, however the emergence of biocide-resistant strains in-vivo has not been reported and a number of environmental survey studies have failed to associate biocide use with antibiotic resistance. This article gives an overview of the issues as they currently stand and reviews data generated in our laboratory over the last five years where we have used laboratory microcosms of the environment and oral cavity to better understand the possible effects of real-life biocide exposure of these high risk ecosystems. In general, whilst biocide susceptibility changes can be demonstrated in pure culture, especially for E. coli towards triclosan, it has not been possible to reproduce these effects during chronic, sublethal dosing of complex communities. We conclude from this review that whilst the incorporation of antibacterial agents into a widening sphere of personal products may not overtly impact on the patterns of microbial susceptibility observed in the environment, the precautionary principle suggests that the use of biocides should be limited to applications where clear hygienic benefits can be demonstrated.     

Differences in larval emergence chronotypes for sympatric Rhagoletis brncici Frías and Rhagoletis conversa (Bréthes) (Diptera,Tephritidae)

In central Chile, Rhagoletis brncici and R. conversa, can be found in sympatry, associated with the fruit of their native host plants: Solanum tomatillo and S. nigrum (Solanaceae), respectively. Third-stage larvae must emerge from its host in search of pupation sites, and during this period larvae must find an appropriate pupation microhabitat while avoiding predation and adverse abiotic factors. In this study, we explored whether these sympatric species differ in terms of the timing of their larval exit from the host fruit in search of pupation sites. Field-collected fruits from host plants were checked daily for larval emergence, within 24 h, under laboratory conditions, in order to determine the time of the event. We found that these species differed significantly in their diel larval emergence. For R. brncici, most larvae left the host fruit between late evening and past midnight, meanwhile larvae from R. conversa concentrated their peak of emergence near midnight and early morning. We discuss these findings in terms of the ecological and evolutionary implications of the temporal separation of larval emergence regarding the use of pupation sites, abiotic stress and risk of predation for these sympatric species.     

Are Mojave Desert annual species equal? Resource acquisition and allocation for the invasive grass Bromus madritensis subsp. rubens (Poaceae) and two native species

Abundance of invasive plants is often attributed to their ability ot outcompete native species. We compared resource acquisition and allocation of the invasive annual grass Bromus madritensis subsp. rubens with that of two native Mojave Desert annuals, Vulpia octoflora and Descurainia pinnata, in a glasshouse experiment. Each species was grown in monoculture at two densities and two levels of N availability to compare how these annuals capture resources and to understand their relative sensitivities to environmental change. During >4 mo of growth, Bromus used water more rapidly and had greater biomass and N content than the natives, partly because of its greater root-surface area and its exploitation of deep soils. Bromus also had greater N uptake, net assimilation and transpiration rates, and canopy area than Vulpia. Resource use by Bromus was less sensitive to changes in N availability or density than were the natives. The two native species in this study produced numerous small seeds that tended to remain dormant, thus ensuring escape of offspring from unfavorable germination conditions; Bromus produced fewer but larger seeds that readily germinated. Collectively, these traits give Bromus the potential to rapidly establish in diverse habitats of the Mojave Desert, thereby gaining an advantage over coexisting native species.     

When is sympatric speciation truly adaptive? An analysis of the joint evolution of resource utilization and assortative mating

The plausibility of sympatric speciation has long been debated among evolutionary ecologists. The process necessarily involves two key elements: the stable coexistence of at least two ecologically distinct types and the emergence of reproductive isolation. Recent theoretical studies within the theoretical framework of adaptive dynamics have shown how both these processes can be driven by natural selection. In the standard scenario, a population first evolves to an evolutionary branching point, next, disruptive selection promotes ecological diversification within the population, and, finally, the fitness disadvantage of intermediate types induces a selection pressure for assortative mating behaviour, which leads to reproductive isolation and full speciation. However, the full speciation process has been mostly studied through computer simulations and only analysed in part. Here I present a complete analysis of the whole speciation process by allowing for the simultaneous evolution of the branching ecological trait as well as a continuous trait controlling mating behaviour. I show how the joint evolution can be understood in terms of a gradient landscape, where the plausibility of different evolutionary paths can be evaluated graphically. I find sympatric speciation unlikely for scenarios with a continuous, unimodal, distribution of resources. Rather, ecological settings where the fitness inferiority of intermediate types is preserved during the ecological branching are more likely to provide opportunity for adaptive, sympatric speciation. Such scenarios include speciation due to predator avoidance or specialization on discrete resources. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Fish fauna of the Severn Estuary. Are there long-term changes in abundance and species composition and are the recruitment patterns of the main marine species correlated?

Fish were collected from the intake screens of the Oldbury Power Station in the Severn Estuary in each week between early July 1972 and late June 1977 and at least twice monthly between early January 1996 and late June 1999. The annual catches, after adjustment to a common sampling effort, demonstrate that the abundance of fish at Oldbury was far greater in the 1990s than 1970s, mainly due to marked increases in the numbers of certain marine species, such as sand goby, whiting, bass, thin-lipped grey mullet, herring, sprat and Norway pout. These increases may reflect the great improvement that occurred in the water quality of the Severn Estuary between these decades. The only species that declined markedly in abundance was poor cod. Modest declines in flounder and River lamprey paralleled those occurring elsewhere in the UK. The species composition in the two decades also differed, reflecting changes not only in the relative abundances of the various marine estuarine-opportunistic species, which dominated the ichthyofauna, but also in those of the suite of less abundant species in the estuary. The cyclical changes undergone each year by the species composition of the fish fauna of the Severn Estuary reflect sequential intra-annual changes in the relative abundances of species representing each of the marine, diadromous and freshwater categories. New approaches have been developed to test whether or not large sets of correlations between patterns of recruitment amongst abundant marine species (internal correlations), and between those patterns and salinity and water temperature within the estuary (cross-correlations), were significant. The correlation profile analyses found no evidence that the annual recruitment strengths of these species were either intercorrelated, or correlated with either one or a combination of both of the above environmental variables. Yet, the timings of the recruitment of these species into the estuary were intercorrelated, i.e. a slightly earlier or later than normal immigration by one species in a given year was paralleled by the same trend in other species. However, this association in recruitment times could be linked neither to salinity nor water temperature within the estuary, nor to a combination of these two variables. These results indicate that, while the factors that influence the annual recruitment strengths of the juveniles of different marine species vary, inter-annual differences in the phasing of events that regulate spawning times and/or larval dispersal influence, in the same direction, the times when marine species are recruited into the estuary.     

Are Hong Kong and Taiwan stepping‐stones for invasive species to the mainland of China?

Understanding the origins and introduction pathways of invasive species is a fundamental issue for invasion biology, which is necessary for predicting and preventing future invasion. Once an invasive species is established in a new location, this location could serve as a stepping‐stone for further invasions. However, such “stepping‐stone” effect has not been widely investigated. Using the published literature and records, we compiled the first found locations of 127 top invasive species in China. Our study showed that the most common landing spots of these invasive species were Hong Kong (22 species) and Taiwan (20 species), which accounted for one‐third of the invasive species in China. Our analysis revealed that the invasive species in mainland China were more likely to transport from Hong Kong than Macau, a neighboring region with a similar area and colonial history. Similarly, more invasive species were also first landed on Taiwan than Hainan, a nearby island sharing similar climate conditions. Together, our findings indicate that Hong Kong and Taiwan are the most important stepping‐stones for invasive species to the mainland of China and suggesting that the increasing trade exchange of China's coastal ports constitutes a potential risk for the spread of more invasive species. We suppose that they would be the future stepping‐stones for invasive species to the mainland of China and these coastal ports regions where improved biosecurity is needed now.     

Are citrus species favorable hosts for the Mediterranean fruit fly? A demographic perspective

We studied, under laboratory conditions, demographic parameters of adult Mediterranean fruit flies, Ceratitis capitata (Wiedemann) (Diptera: Tephritidae) (medfly), obtained from three sweet orange varieties, lemon, and bitter oranges. These data were combined with immature developmental rates and survival on the same hosts to estimate host‐specific population parameters. Pairs of newly emerged adults from each citrus variety were held individually in transparent plastic cages, and females were allowed to oviposit in either red domes (artificial, pre‐punctured plastic oviposition devices), or intact, whole citrus fruits. We found strong effects of larval host (citrus fruits) on adult longevity and fecundity. In all five citrus varieties, females did not manage to deposit eggs into fruit pulp. The proportion of eggs laid in either the flavedo or albedo area of the fruit peel differed depending on the citrus variety. In all cases except bitter oranges, females oviposited fewer eggs in citrus fruits than in the artificial oviposition substrates, suggesting that most citrus fruits cause a significant reduction in the reproductive potential of medflies. Negative correlations were found between fecundity and (a) the density of oil glands, and (b) the amount of essential oils in the flavedo area of citrus fruits. There was no correlation between fecundity and other fruit physical characteristics, such as resistance of fruit peel to pressure and thickness of the flavedo. Apparently, resistance of citrus fruits to medfly infestation is directly related to citrus essential oils. The intrinsic rate of increase (r) was higher in bitter oranges than in the three sweet orange varieties tested. A negative r was estimated for flies that developed and oviposited in lemons, indicating a tendency for population decrease in this host. The suitability of citrus fruits for medfly development and the practical implications of our findings for management of medflies in citrus orchards are discussed.     

Are spatially correlated or uncorrelated disturbance regimes better for the survival of species?

The survival of species in dynamic landscapes (characterised by patch destruction and subsequent regeneration) depends on both the species' attributes and the disturbance pattern. Using a spatially explicit model we explored how the mean time to extinction of a metapopulation depends on the spatial correlation of patch destruction in relation to the population growth and dispersal abilities of species. Two contrasting answers are possible. On the one hand, increasing spatial correlation of patch destruction increases the spatial correlation of population growth and this is known to decrease metapopulation persistence. On the other hand, spatially correlated patch destruction and regeneration can lead to clustered habitat patches and this is known to increase metapopulation persistence. Therefore, we hypothesised that some species are better off under spatially correlated and alternatively uncorrelated disturbance regimes. However, contrary to this hypothesis, in all kinds of cases spatial correlation reduced metapopulation persistence. We found this to be due to the fact that the spatial correlation of patch destruction causes increasing temporal fluctuations in the regional carrying capacity of the metapopulation and is hence generally disadvantageous for long-term persistence. The main consequence for conservation biology is that reducing spatial correlation in disturbances is likely to be a reliable strategy in a dynamic landscape that will benefit practically all species with a low risk of adverse side effects .     

Is the pollination biology of Bathysa and Schizocalyx consistent with their segregation? A first approach for two sympatric species in southeastern Brazil

Tribe Condamineeae appears to be well supported in recent phylogenetic studies. However, the species of Bathysa were divided into two clades, leading to restoration of Schizocalyx. We studied the reproductive biology of one species from each clade, which occur sympatrically in the montane Brazilian Atlantic forest. Flowering overlap was short (from December to March in B. australis and from February to June in S. cuspidatus). The flowers of both species are protogynous and homostylous and last for about 3 days. The unit of pollination in B. australis is the inflorescence. Its flowers have a greenish hypocrateriform corolla (tube about 5 mm long) and were mainly pollinated by bees and wasps in search of nectar. Schizocalyx cuspidatus has white flowers with an infundibuliform corolla (tube about 8 mm long), and its main pollinators were stingless bees in search of pollen. The pollination systems of the two species did not correspond to their pollination syndromes. Morphological differences between Bathysa and Schizocalyx were reflected in their pollination systems, with greater phenotypic specialization in S. cuspidatus, the flowers of which offer pollen as the main resource, an unusual feature within Rubiaceae. Schizocalyx cuspidatus showed higher reproductive capacity by having more inflorescences per plant, more ovules per flower, and twice the proportion of flowering individuals. However, the reproductive efficiency (fruit set, seed/ovule ratio) did not differ between the species, despite the higher frequency of visits by pollinators to S. cuspidatus. Self-compatibility in B. australis and self-incompatibility in S. cuspidatus seem to explain these results.     

Are mesophotic coral ecosystems distinct communities and can they serve as refugia for shallow reefs?

We analyzed an extensive dataset of over 9000 benthic and suprabenthic species found throughout the Gulf of Mexico (GoMx) to assess whether mesophotic coral ecosystems represent distinct assemblages and evaluate their potential to serve as refugia for shallow reef communities. We assessed community structure of the overall benthic community from 0 to 300 m via non-metric multidimensional scaling (NMDS) of species presence across depth bands. We used the Jaccard index of similarity to calculate the proportion of shared species between adjacent depth bands, measure species turnover with depth, and assess taxonomic overlap between shallow reefs versus progressively deeper depth bands. NMDS ordinations showed that the traditionally defined mesophotic range (30–150 m) as a whole is not a distinct community. In contrast, taxonomically distinct communities, determined by hierarchical clustering, were found at 0–70, 60–120, 110–200, and 190–300 m. Clustering highlighted an important separation in the benthic community at ~60 m, which was especially important for actinopterygian fishes. Species turnover between adjacent depths decreased with depth for all taxa combined and individual taxa, with peaks at ~60, 90–120, and 190–200 m. Fishes showed lower turnover from shallow to upper mesophotic depths (0–50 m) than all taxa combined, a substantial peak at 60 m, followed by a precipitous and continued decline in turnover thereafter. Taxonomic overlap between shallow (0–20 m) and progressively deeper zones declined steadily with depth in all taxa and individual taxa, suggesting that mid- and lower mesophotic habitats have less (but not inconsequential) potential to serve as refugia (60–150 m, 15–25% overlap with shallow habitats) than upper mesophotic zones (30–60 m, 30–45% overlap with shallow habitats) for all taxa combined. We conclude that the traditional mesophotic zone is home to three ecological communities in the GoMx, one that is confluent with shallow reefs, a distinct mesophotic assemblage spanning 60–120 m, and a third that extends onto the outer continental shelf.