ESTimating plant phylogeny: lessons from partitioning

Background  

While Expressed Sequence Tags (ESTs) have proven a viable and efficient way to sample genomes, particularly those for which whole-genome sequencing is impractical, phylogenetic analysis using ESTs remains difficult. Sequencing errors and orthology determination are the major problems when using ESTs as a source of characters for systematics. Here we develop methods to incorporate EST sequence information in a simultaneous analysis framework to address controversial phylogenetic questions regarding the relationships among the major groups of seed plants. We use an automated, phylogenetically derived approach to orthology determination called OrthologID generate a phylogeny based on 43 process partitions, many of which are derived from ESTs, and examine several measures of support to assess the utility of EST data for phylogenies.     

Conservation prospects for threatened Vietnamese tree species: results from a demographic study

Given that changes in population size are slow, information on future prospects of long-lived tree species is necessarily obtained from demographic models. We studied six threatened tree species in four Vietnamese protected areas: the broad-leaved Annamocarya sinensis, Manglietia fordiana and Parashorea chinensis, and the coniferous Calocedrus macrolepis, Dacrydium elatum and Pinus kwangtungensis. With data from a 2-year field study on recruitment, growth and survival, we constructed matrix models for each species. All species showed continuous regeneration, as indicated by annual seedling recruitment and inverse J-shaped population structures. To evaluate the future prospects of our study species, we calculated three parameters: (1) asymptotic growth rates (λ) from matrix models indicated significant population declines of 2–3%/year for two species; (2) population trajectories for 50–100 years showed slight population declines (0–3%/year) for five species; and (3) the reproductive period required for an adult tree to replace itself was excessive for three of the six species, suggesting that these species presently have insufficient recruitment. Overall agreement of the three parameters was low, showing that reliance on just one parameter is risky. Combining the three parameters we concluded that prospects are good for Dacrydium and Parashorea, worrisome for Annamocarya, Manglietia and Pinus, and intermediate for Calocedrus. We argue that conservation should involve strict protection of (pre-)adult trees, as their survival is crucial for population maintenance in all species (high elasticity). For species with poor demographic prospects, active intervention is required to improve seedling and tree growth, enrich populations with seedlings from controlled germination, and restore habitat. Finally, our study suggests that these conservation measures apply to long-lived trees in general, given that their demography is highly similar. Such measures should be taken before populations decline below critical levels, as long-lived species will respond slowly to management. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Conservation of rare and endangered plants using in vitro methods

Summary Many botanic gardens now have tissue culture laboratories for the micropropagation of plants that are difficult to propagate by conventional horticultural techniques. In many cases the work centers on rare and endangered species. Examples of the use of different techniques including micropropagation, in vitro seed germination, dual culture with symbiotic fungi, and regeneration from callus are discussed with reference to their application to plant germplasm conservation. Presented in the Session-in-Depth Cell Culture of Endangered Species at the 1991 World Congress on Cell and Tissue Culture, Anaheim, California, June 16–20, 1991.     

Conservation priority of Italian Alpine habitats: a floristic approach based on potential distribution of vascular plant species

In the European Union, the Directive 92/43/EEC defines a number of species and habitats of community interest that are worthy to be preserved because in danger to disappear or because they are representative of the different European bio-geographical regions. In the light of the limited economic resources generally allocated to conservation efforts, there is the necessity to prioritise conservation actions in order to avoid deterioration of protected areas. To this aim, in the present study the most representative habitats of the Italian Alps are compared on the basis of vascular plant biodiversity and a conservation priority index is proposed for each habitat taking into account the potential distribution of 252 threatened vascular plant species. Rocky slopes, screes and alpine grasslands resulted to have the greatest percentage of endemic plant species so reflecting the general distributional pattern of endemic plant species at high altitudes in Eurasian mountains. The relationship between the conservation priority index and the corresponding habitat extent within the Natura 2000 network suggests that peatlands, arid grasslands, wet meadows and freshwater habitats deserve a higher priority in conservation actions. Although vascular plant biodiversity is not necessarily a surrogate of overall biodiversity of Alpine habitats, the results here reported can be used as an initial reference framework for prioritising conservation actions, so as to accomplish the provisions of Article 6 of Habitats Directive.     

PARsylation-mediated ubiquitylation: lessons from rare hereditary disease Cherubism

Modification of proteins by ADP-ribose (PARsylation) is catalyzed by the poly(ADP-ribose) polymerase (PARP) family of enzymes exemplified by PARP1, which controls chromatin organization and DNA repair. Additionally, PARsylation induces ubiquitylation and proteasomal degradation of its substrates because PARsylation creates a recognition site for E3-ubiquitin ligase. The steady-state levels of the adaptor protein SH3-domain binding protein 2 (3BP2) is negatively regulated by tankyrase (PARP5), which coordinates ubiquitylation of 3BP2 by the E3-ligase ring finger protein 146 (RNF146). 3BP2 missense mutations uncouple 3BP2 from tankyrase-mediated negative regulation and cause Cherubism, an autosomal dominant autoinflammatory disorder associated with craniofacial dysmorphia. In this review, we summarize the diverse biological processes, including bone dynamics, metabolism, and Toll-like receptor (TLR) signaling controlled by tankyrase-mediated PARsylation of 3BP2, and highlight the therapeutic potential of this pathway.     

Conservation biology of a rare plant species,Eriocaulon kornickianum (Eriocaulaceae)

Historical and current ecological and genetic factors were examined in western popultions of Eriocaulon kornickianum to determine the cause and consequence of rarity in this disjunct species and to assess its extinction vulnerability. Reproductive biology was examined, which included an examination of breeding systems, seed set, and pollen viability. Recruitment into and maintenance of the populations was evaluated using seed bank estimates. A disturbance study was conducted that examined the effects of competing vegetation and associated species, and included clipping, burning, and artificial seeding. Enzyme electrophoresis was used to measure genetic variation in an effort to examine gene flow within and among populations. Many factors are contributing to the decline of the western populations of this species and include an annual or weak perennial life history, no vegetative reproduction, low seed set, little seed bank contribution to population growth and maintenance, genetic homogeneity, a restricted habitat, and poor competitive abilities. Continuing studies of genetic variation are being used to examine historical factors that may have resulted in a genetic bottleneck observed in the western populations.     

Fire as a control agent of demographic structure and plant performance of a rare Mediterranean endemic geophyte

We examine the effects of fire and/or surrounding vegetation cover on demographic stage densities and plant performance for a rare endemic geophyte, Acis nicaeensis (Alliaceae), in Mediterranean xerophytic grasslands of the 'Alpes-Maritimes' French 'département', through sampling plots in unburned and burned treatments. Fire increases density of flowering individuals and seedling emergence, as well as clump densities and number of individuals per clump, per limiting vegetation height and cover, and increasing bare soil cover. In contrast, fire has no effect on reproductive success. Nevertheless, two growing seasons after fire, all parameters of demographic stages and plant performance do not significantly differ between the two treatments. Small-scale fire is beneficial for the regeneration of this threatened geophyte at a short-time scale. In this context, a conservation planning with small and controlled fires could maintain the regeneration window for populations of rare Mediterranean geophytes.     

Ecophysiology of cuticular transpiration: comparative investigation of cuticular water permeability of plant species from different habitats

Water permeabilities of astomatous, isolated cuticular membranes (CM) of 24 different plants species were measured. Permeances varied from 1.7×10^–11 m·s^–1 (Vanilla planifolia leaf) up to 2.1×10^–9 m·s^–1 (Malus cf. domestica fruit) among different plant species, thus covering a range of over 2 orders of magnitude. Ranking of species according to permeances resulted in four distinct groups. The first group, of species with the lowest cuticular transpiration rates, included evergreen species growing in warm dry tropical climates (e.g. Vanilla planifolia and Monstera deliciosa leaves). The second class, with slightly higher water permeabilities, included evergreen species with typical scleromorphic leaf properties, adapted to a typical mediterranean type of climate with a dry period during the year (e.g. Citrus limon and Olea europaea leaves). The third group of species, where the highest leaf cuticular transpiration rates were observed, included deciduous species normally growing in a tempeate climate (e.g. Juglans regia and Forsythia suspensa leaves). Fruit cuticular membranes (CM) made up the fourth group (e.g. Capsicum annuum and Malus cf. domestica fruits), with even higher permeances than leaves of species from group 3. Thus, it appears that the plant species investigated show ecophysiological adaptations to the climatic demands of their natural habitats in cuticular water permeability.     

Integrating demographic data and a mechanistic dispersal model to predict invasion spread of Rhododendron ponticum in different habitats

Understanding the invasion potential of a species in different habitat types within the non-native range is crucial in prioritising management and control efforts, and in the protection of vulnerable habitats through monitoring. Here, using the invasive shrub Rhododendron ponticum as a case study, we integrate information on both the demographics and spatial dynamics within an individual-based, spatially-explicit model to investigate invasion potential in different habitats. Firstly, empirical demographic data were used to establish relationships between demographic traits, such as height and fecundity, and habitat variables. The outputs from models fitted using a Generalised Linear Model approach were then incorporated into an individual-based simulation model of plant spread to investigate the invasion potential in different habitats using a factorial design of treatments. Plant height, and thus seed release height, was the main driver of invasion speed through an increase in dispersal potential, which resulted in the highest invasion speeds predicted for evergreen woodlands, and relatively low speeds for open habitats. Conversely, invasion density was driven by plant fecundity and seedling survival and not dispersal potential; the highest invasion densities were predicted for open habitats, with relatively low densities for evergreen habitats. Deciduous woodland had features resulting in intermediate invasion potential, both in terms of speed and density and may, therefore be the habitat that is most vulnerable to relatively rapid and dense invasion.     

Neutrophil proteome: lessons from different standpoints

The present review brings a timeline of some of the major steps given throughout the years towards the development of our knowledge regarding the biology of the neutrophil. The contribution of early articles and their elementary biochemical approach is highlighted. The importance of the development of proteomic techniques is paralleled to the shift in neutrophil research towards high throughput molecular methods. As a last change of standpoint, the study of the neutrophil is presented integrated with other life- sciences technologies such as lipidomics, genomics and systems biology. The paper also brings a perspective/tendency overview at the same time that it discusses some of the difficulties encountered in the research of the neutrophil.     

Conservation of protein-protein interactions - lessons from ascomycota

Interacting proteins from Saccharomyces cerevisiae are evolutionarily conserved and their likelihood of having an ortholog in other ascomycota species correlates with the number of interaction partners. Moreover, interacting proteins show a clear preference to be conserved as a pair, indicating that nature maintains selection pressure on the interaction links between proteins. The conservation of interacting protein pairs between different organisms does not exhibit any bias with respect to protein functional roles.     

Investigating detection success: lessons from trials using decoy rare plants

Imperfect detection leads to underestimates of species presence and decreases the reliability of survey data. Imperfect detection has not been examined in detail for boreal forest understory plants, despite widespread use of surveys for rare plants prior to development. We addressed this issue using detectability trials conducted in Alberta, Canada with decoy vascular plants. Volunteer observers searched in survey plots for species while unaware of their true presence or abundance. Our findings indicate that the detection of cryptic species is very low when abundance is low (0–35%) and plot size is large (<?50% in?≥?100 m²). Plant density (individuals per unit area) was the most important determinant of detection probability, where more abundant species were detected more often and with less survey effort. When abundance was held constant, diffusely arranged species were twice as likely to be detected compared to those in clumps. Detection of cryptic species can be low even when individuals are flowering, and even morphologically distinct species can go unnoticed in small plots. We suggest that future decoy trials investigate search strategies that could improve detection and that field surveys for vascular plants address imperfect detection through careful consideration of plot size, characteristics of the target species, and survey effort, both in terms of time expenditure within an area and the number of observers employed.     

植物生长季节不同栖息地高原鼠兔的食物选择

本文采用胃内容物镜检分析法,对栖息于青藏高原矮嵩草草甸、垂穗披碱草草甸和杂类草草甸中的高原鼠兔的主要食物组成进行了比较分析,旨在探讨栖息地变化对高原鼠兔食物组成的影响,揭示高原鼠兔对栖息地变化的生存对策和适应性.研究结果表明:在矮嵩草草甸,高原鼠兔主要取食垂穗披碱草、早熟禾、蓝花棘豆和甘肃棘豆;在垂穗披碱草草甸,主要选择垂穗披碱草、甘肃棘豆、蓝花棘豆、矮嵩草和二柱头蔗草;在杂类草草甸,喜食植物种类为垂穗披碱草、蓝花棘豆、甘肃棘豆、早熟禾、弱小火绒草、长茎藁本、兰石草和红花岩生忍冬.在整个植物生长季节,高原鼠兔在3种栖息地共取食27种植物,其中垂穗披碱草、甘肃棘豆和蓝花棘豆在不同栖息地中选择指数较高,为高原鼠兔优先选择的食物;在不同栖息地,高原鼠兔取食植物有差别,垂穗披碱草草甸为16种、矮嵩草草甸为22种,杂类草草甸为24种;喜食食物比例也存在着明显差别,在垂穗披碱草草甸,垂穗披碱草比例高达40.5%,在矮嵩草草甸,甘肃棘豆比例也达到23.7%,而在杂类草草甸,选食比例最高的兰石草仅为14.6%,说明在该草甸高原鼠兔食物选择呈现泛化趋势.相似性指数分析结果也表明,杂类草草甸中高原鼠兔主要食物组成与其它两种栖息地有较大的区别.从而说明当栖息地植物群落种类组成发生变化后,高原鼠兔可以通过改变其食物组成而适应新的栖息地.