Sampling-through-time in birth-death trees

I consider the constant rate birth-death process with incomplete sampling. I calculate the density of a given tree with sampled extant and extinct individuals.This density is essential for analyzing datasets which are sampled through time. Such datasets are common in virus epidemiology as viruses in infected individuals are sampled through time. Further, such datasets appear in phylogenetics when extant and extinct species data is available.I show how the derived tree density can be used (i) as a tree prior in a Bayesian method to reconstruct the evolutionary past of the sequence data on a calender-timescale, (ii) to infer the birth- and death-rates for a reconstructed evolutionary tree, and (iii) for simulating trees with a given number of sampled extant and extinct individuals which is essential for testing evolutionary hypotheses for the considered datasets.     

Efficacy of intervention to relieve nest box competition for Orange‐bellied Parrot Neophema chrysogaster

We use an experimental approach to evaluate the effectiveness of removing nests of a dominant competitor to create vacant nest boxes for a critically endangered parrot. We compared the number of times that Tree Martin (Petrochelidon nigricans – the dominant competitor at nest boxes) perched at or entered nest boxes intended for Orange‐bellied Parrot (Neophema chrysogaster – the subordinate nest competitor) over three time periods (before, immediately after and one week after experimental nest destruction). In the before period, rates of nest attendance by martins in treatment and control nests were not explained by treatment group. After experimental nest destruction, total attendance at boxes by martins rose to a mean of 6.1 visits over three five‐minute surveys in the treatment group, compared with 3.3 visits at control boxes. Within individual surveys, martins visited treatment boxes 4.4 times per survey one week after nest destruction, compared with only 1.6 visits in the control group. Martins in the treatment group rapidly rebuilt their nests and laid replacement clutches, and within a week, all boxes were reoccupied. Nest destruction did not increase nesting opportunities for the parrot, and increased vigilance of the dominant competitor may in fact reduce nesting opportunities in nearby boxes. Our study suggests that removing martin nests is an ineffective management action for alleviating nest competition for this parrot.     

The environmental and genetic determinants of chick telomere length in Tree Swallows (Tachycineta bicolor)

Conditions during early life can have dramatic effects on adult characteristics and fitness. However, we still know little about the mechanisms that mediate these relationships. Telomere shortening is one possibility. Telomeres are long sequences of DNA that protect the ends of chromosomes. They shorten naturally throughout an individual's life, and individuals with short telomeres tend to have poorer health and reduced survival. Given this connection between telomere length (TL) and fitness, natural selection should favor individuals that are able to retain longer telomeres for a greater portion of their lives. However, the ability of natural selection to act on TL depends on the extent to which genetic and environmental factors influence TL. In this study, we experimentally enlarged broods of Tree Swallows (Tachycineta bicolor) to test the effects of demanding early‐life conditions on TL, while simultaneously cross‐fostering chicks to estimate heritable genetic influences on TL. In addition, we estimated the effects of parental age and chick sex on chick TL. We found that TL is highly heritable in Tree Swallow chicks, and that the maternal genetic basis for TL is stronger than is the paternal genetic basis. In contrast, the experimental manipulation of brood size had only a weak effect on chick TL, suggesting that the role of environmental factors in influencing TL early in life is limited. There was no effect of chick sex or parental age on chick TL. While these results are consistent with those reported in some studies, they are in conflict with others. These disparate conclusions might be attributable to the inherent complexity of telomere dynamics playing out differently in different populations or to study‐specific variation in the age at which subjects were measured.     

手术室工作流程现状分析

目的 通过具体的手术室流程分析，探索医院手术室流程科学合理的管理方法。方法 运用现场调研法对手术室的流程进行考察分析，并应用流程图的方法显化现有手术室的流程，对现有流程采用德尔菲法和FTA的方法进行分析。结果 得到手术室工作流程的问题报告。结论 手术室的流程问题主要有：等待浪费，沟通失效，操作行为不当，管理技术不当，设施布局不合理。     

A portable,remote‐controlled nest‐box trap

Many researchers catch adult birds at nest boxes using a vertical prop that supports a horizontal flap that drops down when an adult enters to feed nestlings. Because the prop is visible, some birds may be too wary to enter nest boxes, or they may dislodge the prop when they lean in; either way, they are not captured. We describe a remote‐controlled nest‐box trap that has the advantages of portability and being invisible to adults delivering food to nestlings. A receiver is installed on the ceiling of a nest box, the receiver is connected to a spring‐loaded flap that is triggered remotely with a transmitter from > 30 m away, and the flap drops down to cover the box entrance. In 2017 and 2018, our remote‐controlled traps did not increase the likelihood of capturing female Tree Swallows (Tachycineta bicolor), but did improve the likelihood of capturing males. We captured 16 male Tree Swallows in 30 attempts (53.3%) using our remote‐controlled trap compared to only 41 captures of males in 139 attempts (29.5%) with prop traps. In addition, whereas prop traps required an average of ~ 50 min to capture adults in successful attempts, our trap required only ~ 25 min. These results suggest that the savings in time for field researchers using our remote‐controlled trap can be substantial, with the added ethical benefit of reducing the amount of time that nestlings are not being fed. Our remote‐controlled trap is also economical to construct, requiring ~ $60 USD for parts and < 3 h to build.     

Description of Tree Distribution Patterns and Their Development Through Marked Gibbs Processes

Tree distribution patterns in forest stands can be considered as marked point processes in the plane. Gibbs processes are a natural tool for modelling such point processes because the interaction between trees can be taken into account and described by pair potential functions. Consequently, tree distribution patterns can be characterized with few parameters and be compared quantitatively. By means of forest stand examples it is shown how these parametric models can be used for the analysis of tree distribution patterns at different time points.     

Antifungal effects of dimethyl trisulfide against Colletotrichum gloeosporioides infection on mango

Colletotrichum gloeosporioides, one of the main agents of mango anthracnose, causes latent infections in unripe mango and can lead to huge losses during fruit storage and transport. Dimethyl trisulfide (DMTS) is an antifungal agent produced by several microorganisms or plants, but its effects on the infection process of C. gloeosporioides have not been well characterized. A histological investigation demonstrated that DMTS exhibits strong inhibitory effects on the infection process of C. gloeosporioides in planta by inhibiting the germination of conidia and formation of appressoria, damaging cytoplasm to cause cells to vacuolate and contributing to deformation of appressoria prior to penetration. This is the first study to demonstrate antifungal activity of DMTS against C. gloeosporioides on mango by suppression of the infection process, thus providing a novel postharvest biorational control for mango anthracnose.     

An organismal view of dendrochronology

An organism is the most basic unit of independent life. The tree-ring record is defined by organismal processes. Dendrochronology contributes to investigations far removed from organismal biology, e.g., archeology, climatology, disturbance ecology, etc. The increasing integration of dendrochronology into a diverse research community suggests an opportunity for a brief review of the organismal basis of tree rings.Trees are dynamic, competitive, and opportunistic organisms with diverse strategies for survival. As with all green plants, trees capture the energy in sunlight to make and break chemical bonds with the elements essential for life. These essential elements are taken from the atmosphere, water, and soil. The long tree-ring series of special interest to dendrochronology result from long-lived trees containing relatively little decayed wood. Both of those features result from organismal biology. While the tree-ring record tells us many things about local, regional, and even global environmental history, tree rings are first a record of tree survival.     

Long-lived light-demanding emergents in southern temperate forests: the case of Weinmannia trichosperma (Cunoniaceae) in Chile

The prevailing paradigm of tree life histories emphasises strong interrelationships between growth, longevity and reproductive traits, attributing contrasting suites of correlated traits to pioneer and climax or non-pioneer species. In tropical and southern temperate rainforests, although many of the species that require large gaps for regeneration conform to the expectations of small size and short lifespan, a number of others are long-lived canopy or emergent trees. Age data reported here for Weinmannia trichosperma, a shade-intolerant emergent tree in the temperate rainforests of southern Chile, indicate a maximum lifespan (>730 yr) exceeding those previously reported for any other angiosperm of the region. The long lifespan of W. trichosperma is associated with relatively slow growth, reflecting investment of resources in dense wood and possibly other defensive traits. Growth rates of W. trichosperma are much slower than those of associated short-lived pioneer trees, and apparently also slower than some of its more shade-tolerant associates. The light-demanding nature of many of the longest-lived trees in southern temperate forests highlights an important limitation of the classical pioneer-climax paradigm as a framework for understanding tree life history variation and modelling forest dynamics in this biome.A longevity advantage over Nothofagus spp. may help explain the relative abundance of W. trichosperma in the lower to mid-elevation coast range forests in the Chilean lakes district, where the scarcity or absence of Nothofagus in many stands has been attributed to a low frequency of coarse-scale disturbance.p>     

Molecular classification of living organisms

Recent studies in molecular evolution have generated strong conflicts in opinion as to how world living organisms should be classified. The traditional classification of life into five kingdoms has been challenged by the molecular analysis carried out mostly on rRNA sequences, which supported the division of the extant living organisms into three major groups: Archaebacteria, Eubacteria, and Eukaryota. As to the problem of placing the root of the tree of life, the analysis carried out on a few genes has provided discrepant results. In order to measure the genetic distances between species, we have carried out an evolutionary analysis of the glutamine synthetase genes, which previously have been revealed to be good molecular clocks, and of the small and large rRNA genes. All data demonstrate that archaebacteria are more closely related to eubacteria than to eukaryota, thus supporting the classical division of living organisms into two main superkingdoms, Prokaryota and Eukaryota.Abbreviations Mya million years ago - GS glutamine synthetase - Isu large subunit - ssu small subunit - SMC Stationary Markov clock Correspondence to: G. Pesole     

Radial growth response of Pinus sylvestris L. and Fagus sylvatica L. to technological solutions applied in rope climbing parks

Vitality is a genetic preservation factor that keeps a tree in the right condition. Changes in tree vitality are a measure of the impact exerted on trees by environmental factors, such as injuries to trunks and branches, and are among the basic parameters of the state of their preservation. The dynamics of changes in the width of annual increments of trees is one of several parameters characterizing the level of their vitality. The aim of the study is to determine changes in radial increment and linking them to the level of the vitality of Scots pines (Pinus sylvestris L.) and European beeches (Fagus sylvatica L.), on which the standard (old system) and specially designed (new system) systems of fastening of wooden platforms were installed as part of adventure park infrastructure. In the old system, the platforms were installed on square wooden beams placed in milled tree trunks, while in the new system on semi-circular metal brackets matching the curvature of the trunks. The present research is aimed to determine the dynamics of incremental trends in trees with different platform systems in relation to the reference group, and to determine the impact of the tested support systems on trees with different levels of vitality. Most of the studied trees were in the optimum stage of increment. The initial tree vitality level recorded at the beginning of the experiment was clearly better for the beech stands. In the case of Scots pine, the average vitality was close to stable. Pines that were initially in better condition responded much worse to the installation of old system platforms compared to those with the specially new platform system. A similar trend was also visible in the case of beeches, but the differences were not that clear and the annual increments of the trees with platforms installed were slightly higher compared to the reference trees. The trees that were initially in worse condition, both pines and beeches on which the old system of platforms had been installed, responded by increasing the width of annual increments during the measurement period. The described response of trees most probably does not result from the lower harmfulness of the old support system, but from the defensive responses of trees subjected to stronger stress.