Majority-rule (+) consensus trees

The construction of a consensus tree to summarize the information of a given set of phylogenetic trees is now routinely a part of many studies in systematic biology. One popular method is the majority-rule consensus tree. In this paper we introduce and characterize a new consensus method that refines the majority-rule tree by adding certain compatible clusters satisfying a simple criterion.     

Multipolar consensus for phylogenetic trees

Collections of phylogenetic trees are usually summarized using consensus methods. These methods build a single tree, supposed to be representative of the collection. However, in the case of heterogeneous collections of trees, the resulting consensus may be poorly resolved (strict consensus, majority-rule consensus, ...), or may perform arbitrary choices among mutually incompatible clades, or splits (greedy consensus). Here, we propose an alternative method, which we call the multipolar consensus (MPC). Its aim is to display all the splits having a support above a predefined threshold, in a minimum number of consensus trees, or poles. We show that the problem is equivalent to a graph-coloring problem, and propose an implementation of the method. Finally, we apply the MPC to real data sets. Our results indicate that, typically, all the splits down to a weight of 10% can be displayed in no more than 4 trees. In addition, in some cases, biologically relevant secondary signals, which would not have been present in any of the classical consensus trees, are indeed captured by our method, indicating that the MPC provides a convenient exploratory method for phylogenetic analysis. The method was implemented in a package freely available at http://www.lirmm.fr/~cbonnard/MPC.html     

Rooted triple consensus and anomalous gene trees

Background  

Anomalous gene trees (AGTs) are gene trees with a topology different from a species tree that are more probable to observe than congruent gene trees. In this paper we propose a rooted triple approach to finding the correct species tree in the presence of AGTs.     

Weighted bootstrapping: a correction method for assessing the robustness of phylogenetic trees

Background  

Non-parametric bootstrapping is a widely-used statistical procedure for assessing confidence of model parameters based on the empirical distribution of the observed data [1] and, as such, it has become a common method for assessing tree confidence in phylogenetics [2]. Traditional non-parametric bootstrapping does not weigh each tree inferred from resampled (i.e., pseudo-replicated) sequences. Hence, the quality of these trees is not taken into account when computing bootstrap scores associated with the clades of the original phylogeny. As a consequence, traditionally, the trees with different bootstrap support or those providing a different fit to the corresponding pseudo-replicated sequences (the fit quality can be expressed through the LS, ML or parsimony score) contribute in the same way to the computation of the bootstrap support of the original phylogeny.     

Axioms for consensus functions on undirected phylogenetic trees

A version of Arrow's impossibility theorem is established for consensus functions on undirected phylogenetic trees.     

A fully resolved consensus between fully resolved phylogenetic trees

Nowadays, there are many phylogeny reconstruction methods, each with advantages and disadvantages. We explored the advantages of each method, putting together the common parts of trees constructed by several methods, by means of a consensus computation. A number of phylogenetic consensus methods are already known. Unfortunately, there is also a taboo concerning consensus methods, because most biologists see them mainly as comparators and not as phylogenetic tree constructors. We challenged this taboo by defining a consensus method that builds a fully resolved phylogenetic tree based on the most common parts of fully resolved trees in a given collection. We also generated results showing that this consensus is in a way a kind of "median" of the input trees; as such it can be closer to the correct tree in many situations.     

Discordance of species trees with their most likely gene trees

Because of the stochastic way in which lineages sort during speciation, gene trees may differ in topology from each other and from species trees. Surprisingly, assuming that genetic lineages follow a coalescent model of within-species evolution, we find that for any species tree topology with five or more species, there exist branch lengths for which gene tree discordance is so common that the most likely gene tree topology to evolve along the branches of a species tree differs from the species phylogeny. This counterintuitive result implies that in combining data on multiple loci, the straightforward procedure of using the most frequently observed gene tree topology as an estimate of the species tree topology can be asymptotically guaranteed to produce an incorrect estimate. We conclude with suggestions that can aid in overcoming this new obstacle to accurate genomic inference of species phylogenies.     

泽西牛犊对热胁迫的生理应答及其作为动物福利下降指标的潜在应用性

本研究以泽西奶牛(Bostaurus)牛犊为对象,探讨温、热环境(30℃)下短暂暴露是否影响其体温、心跳和呼吸频率以及细胞和内分泌应激反应(皮质醇、甲状腺激素、牛生长激素及热应激蛋白72)。结果表明:热暴露导致呼吸频率和心率加快,体温显著升高,但幅度较小。在所研究的细胞和内分泌应激反应中,血浆甲状腺激素浓度略下降,肌肉热应激蛋白72的浓度稍增加。因此,尽管夏季饲养动物所经历的较高环境温度(但非极端温度)能影响泽西牛犊的生理,但是泽西牛犊能对温和的暂时性环境温度改变做出适应性反应。我们认为,直肠温度和细胞热应激蛋白72浓度是所研究参数中评价热胁迫降低动物福利的最适指标。     

Water use and sodium chloride uptake by apple trees

Summary Apple trees grown with their root systems split into halves were used to study the effects of non-uniform salinity stress within a root system upon salt and water uptake. Water uptake declined rapidly when sodium chloride solution (90 meq l⁻¹) was added to any root zone but uptake increased correspondingly in the non-saline root zone of each tree. This changed pattern of water uptake with partial salinization did not change the total water use by the trees compared with their water use when neither root zone was salt stressed. After a‘steady-state’ condition of water uptake had been reached 80 to 85% of the water was taken up in the non-saline root zone. Irrigation at three soil matric potential intervals of −6.6, −33 and −66 kPa allowed to develop in the non-saline root zone of each tree did not affect water use responses. Leaf concentrations of Ca, Mg and K were unaffected by treatments. Chloride and Na concentrations increased in leaves with exposure to salinity stress in half root zones and with increasing soil matric potential stress. Some evidence was obtained using tritium enriched water that water was transferred from a non-saline root zone into a saline root zone but the volume involved was unmeasurable.     

Historical linguistics in Australia: trees, networks and their implications

This paper presents an overview of the current state of historical linguistics in Australian languages. Australian languages have been important in theoretical debates about the nature of language change and the possibilities for reconstruction and classification in areas of intensive diffusion. Here are summarized the most important outstanding questions for Australian linguistic prehistory; I also present a case study of the Karnic subgroup of Pama-Nyungan, which illustrates the problems for classification in Australian languages and potential approaches using phylogenetic methods.     

Increased growth of young citrus trees under reduced radiation load in a semi-arid climate

This study investigated the effects of radiation heat-load reduction by shading on the growth and development of citrus trees in a warm subtropical region. The experiment was conducted from mid-June until late October when daily maximal air temperature averaged 29.3 degrees C. Two-year-old de-fruited Murcott tangor (Citrus reticulata BlancoxCitrus sinensis (L.) Osb.) trees were grown under 30% or 60% shade tunnels, or 60% flat shade (providing midday shade only), using highly reflective aluminized nets. Non-shaded trees were used as the control. Shading reduced direct more than diffuse radiation. Daily radiation was reduced by 35% for the 30% Tunnel and 60% Flat treatments, and by 55% for the 60% Tunnel. Two days of intensive measurement showed that shading increased average sunlit leaf conductance by 44% and photosynthesis by 29%. Shading did not significantly influence root and stem dry weight growth, but it increased the increment in leaf dry weight during the three month period by an average of 28% relative to the control, while final tree height in the 30% Tunnel treatment exceeded the control by 35%. Shoot to root and shoot mass ratios increased and root mass ratio decreased due to shading because of the increase in leaf dry weight. Shading increased starch concentration in leaves while the shadiest treatment, 60% Tunnel, decreased starch concentration in the roots. Carbon isotope ratio (delta(13)C) of exposed leaves that developed under shading was significantly reduced by 1.9 per thousand in the 60% Tunnel, indicating that shading increased CO(2) concentrations at the chloroplasts (C(c)), as would be expected from increased conductance. Substomatal CO(2) concentrations, C(i), computed from leaf net CO(2) assimilation rate and conductance values, also indicate that shading increases internal CO(2) concentrations. Based on tree dry mass, tree height, and total carbohydrates fractions, the 30% Tunnel and the 60% Flat were the optimal shade treatments.     

Underground water use by Eucalyptus trees in an arid climate

 Expanding the area of tree plantations in the Negev desert of Israel requires prior quantification of the water resources in small watersheds. Combined hydrological and physiological measurements were used to study a “liman” (floodwater irrigated plot) in the Negev highlands, where Eucalyptus and other tree species are grown successfully. The amount of water flowing into the liman, surplus water flowing out of the liman, temporal soil moisture distribution, and water uptake by the trees were determined. Depending on rainfall intensity and distribution during the season, the liman received 2 – 3 times the total seasonal rainfall. Although the study was conducted during a year with a negligible amount of rainfall, the transpiration rate was closely correlated with potential transpiration throughout the year. The amount of water extracted from the soil was less than the time-integrated transpiration rate from the trees, suggesting that a water source other than soil water storage was available to the trees. We suggest that the trees extracted water from the rock fractures and/or utilized the lateral flows over the rock/soil interface.     

Uprooted trees,their distribution and influence in the primeval forest biotope

Summary The paper reports results of a long-term (1964–1974) investigation on permanent study sites in natural forest ecosystems of the Tilio-Carpinetum and the Pino-Quercetum in the Bialowieza Forest. The influence of decaying logs and root craters was investigated. It was found that the main causes of uprooting were the spring and autumn winds. Wind direction and the position of logs lying on the ground are correlated. Picea is most susceptible to uprooting by winds. Almost one half of the trees of this species are alive at the moment of uprooting.By mapping changes in the distribution of uprooted trees on a permanent area in time, a balance of the change over in a 10-year period was determined. It appeared that the decomposition is slower than accumulation. From this, it was concluded that the stand is in a phase of natural thinning. In the study site, compartments were disinguished with various degrees of change in the number of uprooted trees, and the consequences of differentiation and constant transformation of the biotope and biocenosis by the occurrence of uprooted trees and by their decay are described.Nomenclature of species follows Flora Europaea.Contribution to the Symposium of the Working Group for Succession Research on Permanent Plots, held at Yerseke, the Netherlands, October 1975.     

广西南宁市园林树木白蚁发生种类及危害情况

2009年311月对南宁市园林树木白蚁为害情况进行了调查。结果表明,台湾乳白蚁Coptotermes formosanus Shiraki是危害园林树木的优势种;调查的57种树木中,45种树木受到了白蚁的侵害,占总数的78.95%,树木受害株率达13.11%,严重受害株率为1.66%。银桦、侧柏和樟树等树种受白蚁危害最为严重。