Reconstructing the evolutionary history of polyploids from multilabeled trees

In recent studies, phylogenetic networks have been derived from so-called multilabeled trees in order to understand the origins of certain polyploids. Although the trees used in these studies were constructed using sophisticated techniques in phylogenetic analysis, the presented networks were inferred using ad hoc arguments that cannot be easily extended to larger, more complicated examples. In this paper, we present a general method for constructing such networks, which takes as input a multilabeled phylogenetic tree and outputs a phylogenetic network with certain desirable properties. To illustrate the applicability of our method, we discuss its use in reconstructing the evolutionary history of plant allopolyploids. We conclude with a discussion concerning possible future directions. The network construction method has been implemented and is freely available for use from http://www.uea.ac.uk/ approximately a043878/padre.html.     

Upper bounds on maximum likelihood for phylogenetic trees

We introduce a mechanism for analytically deriving upper bounds on the maximum likelihood for genetic sequence data on sets of phylogenies. A simple 'partition' bound is introduced for general models. Tighter bounds are developed for the simplest model of evolution, the two state symmetric model of nucleotide substitution under the molecular clock. This follows earlier theoretical work which has been restricted to this model by analytic complexity. A weakness of current numerical computation is that reported 'maximum likelihood' results cannot be guaranteed, both for a specified tree (because of the possibility of multiple maxima) or over the full tree space (as the computation is intractable for large sets of trees). The bounds we develop here can be used to conclusively eliminate large proportions of tree space in the search for the maximum likelihood tree. This is vital in the development of a branch and bound search strategy for identifying the maximum likelihood tree. We report the results from a simulation study of approximately 10(6) data sets generated on clock-like trees of five leaves. In each trial a likelihood value of one specific instance of a parameterised tree is compared to the bound determined for each of the 105 possible rooted binary trees. The proportion of trees that are eliminated from the search for the maximum likelihood tree ranged from 92% to almost 98%, indicating a computational speed-up factor of between 12 and 44.     

Stem diameter variations and cold hardiness in walnut trees

The effect of freezing temperatures on stem diameter was measured in the field and in climatic chambers using linear variable differential transformers (LVDT sensors). In acclimated stems, there was reversible stem shrinkage associated with freeze-thaw cycles. The maximum shrinkage correlated with stem diameter (thickness of the bark). The wood was responsible for only 15% of the shrinkage associated with a freeze event, and experiments with isolated bark showed that connection with the wood was not necessary for most of the freeze-induced shrinkage to occur. Considering the amount of stem shrinkage associated with summer drought in walnut, the amount of contraction of the bark with freezing was actually much less than might be predicted by water relations theory. Reversible stem shrinkage occurred in living tissues, but not in autoclaved tissues. For the latter, swelling was observed with freezing and this swelling could be explained by the bark alone. Similar swelling was observed during September and October for non-acclimated plants. Water was lost with each freeze-thaw cycle starting with the first, and freezing injury of the bark, with discoloration of tissues, was also observed in non-acclimated plants. Given that the diameter fluctuation patterns were dramatically different for acclimated versus non-acclimated plants, and for living versus autoclaved tissues, LVDT sensors could represent a novel, non-invasive approach to testing cold hardiness.     

Metrics for Phylogenetic Networks II: Nodal and Triplets Metrics

The assessment of phylogenetic network reconstruction methods requires the ability to compare phylogenetic networks. This is the second in a series of papers devoted to the analysis and comparison of metrics for tree-child time consistent phylogenetic networks on the same set of taxa. In this paper, we generalize to phylogenetic networks two metrics that have already been introduced in the literature for phylogenetic trees: the nodal distance and the triplets distance. We prove that they are metrics on any class of tree-child time consistent phylogenetic networks on the same set of taxa, as well as some basic properties for them. To prove these results, we introduce a reduction/expansion procedure that can be used not only to establish properties of tree-child time consistent phylogenetic networks by induction, but also to generate all tree-child time consistent phylogenetic networks with a given number of leaves.     

基于茎干直径微变化制定苹果灌溉制度

茎干直径的动态微变化是研究植物体水分和生长状况的重要指标。利用测树器监测西北旱区盛果期苹果树茎干直径微变化规律,根据监测记录获得茎干直径日最大值(MXTD)、茎干直径日最大收缩量(MDS)数据,并探讨茎干直径微变化规律及其对环境因素的响应,为茎干直径微变化用于指导精确灌溉提供科学依据。实验结果表明,晴天或多云天气下,苹果树茎干直径在每天的7:00或8:00时刻达到一天最大值,在16:00左右达到一天的最小值,茎干直径年增长量与果实产量成反比例关系。整个生育期MXTD呈先快速增加后平稳的变化特征。2010年MDS与茎干水势(φstem)呈显著负相关关系(r2=0.76***,n=14),这表明MDS可以反映苹果树的水势状况。生育后期的MDS对环境因素响应比生育前期敏感,全生育期MDS与气象因素的决定系数大小顺序为日最大水汽压差(VPDmax)日最高温度(Tmax)净辐射(Rn)。茎干直径微变化规律可以反映西北旱区盛果期果树的水分状况,可以为果园灌溉制度的确定提供科学依据。     

Growth allocation between height and stem diameter in nonsuppressed reproducing Abies mariesii trees

To understand the growth patterns with respect to competition and leaf‐mass increase in reproducing trees, growth allocation between height and stem diameter was examined for nonsuppressed reproducing Abies mariesii trees in a subalpine forest in northern Honshu, Japan. The growth allocation was analyzed by dividing the relative growth rate of the stem volume into the relative contributions of height and stem‐diameter growth. During a 9‐yr period, height growth and seed‐cone production showed obvious annual variation, while stem‐diameter growth recorded moderate variation. For two of three years of seed‐cone production during the 9‐yr period, trees with larger seed‐cone production were associated with less height growth in the following year of seed‐cone production; however, there was no trend of height growth in the year of seed‐cone production. In the following year of mast seeding, trees with larger stem‐volume growth were associated with less height growth. This trend was also shown for the relationship between the cumulative stem‐volume growth during the 9‐yr period and growth allocation to height, suggesting that trees with a larger biomass increase depress the allocation of photosynthate to competition with a large expenditure for reproduction. In contrast to this, trees with a smaller biomass increase might allocate photosynthate to competition with surrounding trees. The results of this study suggest that an increase in reproductive organs during life history and annual variation in reproduction are closely associated with the growth patterns of the stem in A. mariesii trees.     

Mass Customization: Metrics and Modularity

Mass customization as a competitive strategy is getting progressively increasing attention in business and academic arenas due to its high potential to provide sustained strategic advantage in a unique fashion. It is well documented that a manufacturing company competes with others in its industry on five dimensions: Price, quality, flexibility, delivery, and service. According to the existing literature, mass customization provides significant strategic advantage in two of these dimensions—price and customization. We, however, argue that when properly implemented, the cellular manufacturing structure associated with the appropriate implementation of mass customization strategy, provides additional competitive value in quality and delivery. Furthermore by virtue of the customer co-design as an integral aspect of mass customization, customer satisfaction also improves under this strategy. Mass customization strategy, therefore, provides competitive advantage in all five competitive dimensions simultaneously—a truly unique strategic accomplishment. We also propose, in this paper, new metrics for mass customization strategy that measure the “mass” as well as the “customization” aspects of this strategy. Finally, we describe in the clearest terms the modus operandi of modularity in product design and the role it plays in bringing about high levels of customization on one hand and economies of scale at component level, on the other. We conclude with remarks that underscore the need for conducting research in the areas at the interface of mass customization and supply chain management.     

A dendroclimatological approach to diameter growth in adult cork-oak trees under production

The diameter growth of mature cork oaks under cork production in southwestern Portugal was studied during a 9-year cork-production cycle in relation to fluctuations in precipitation and temperature, and to drought indices combining the two variables. A dendroclimatological approach was applied to the series of 8 complete years contained in the cork-production cycle and growth effects were removed by standardization and calculation of annual growth indices. The most important factor positively influencing diameter growth was cumulative precipitation in the growing season (January-June) and in the previous autumn and winter (October/November of the previous year-June). The monthly temperature is a less influential factor, negatively correlated with diameter growth in high summer drought (August) and positively correlated at the beginning of physiological activity (March).     

MRI links stem water content to stem diameter variations in transpiring trees

In trees, stem diameter variations are related to changes in stem water content, because internally stored water is depleted and replenished over a day. To confirm this relationship, non-invasive magnetic resonance imaging (MRI) was combined with point dendrometer measurements in three actively transpiring oak (Quercus robur L.) trees. Two of these oak trees were girdled to study the stem increment above the girdling zone. MRI images and micrographs of stem cross-sections revealed a close link between the water distribution and the anatomical features of the stem. Stem tissues with the highest amount of water were physiologically the most active ones, being the youngest differentiating xylem cells, the cambium and the youngest differentiating and conductive phloem cells. Daily changes in stem diameter corresponded well with the simultaneously MRI-measured amount of water, confirming their strong interdependence. MRI images also revealed that the amount of water in the elastic bark tissues, excluding cambium and the youngest phloem, contributed most to the daily stem diameter changes. After bark removal, an additional increase in stem diameter was measured above the girdle. This increase was attributed not only to the cambial production of new cells, but also to swelling of existing bark cells. In conclusion, the comparison of MRI and dendrometer measurements confirmed previous interpretations and applications of dendrometers and illustrates the additional and complementary information MRI can reveal regarding water relations in plants.     

Succession and interrelationships of microorganisms on painted surfaces

This paper relates a series of experiments designed to elucidate the interrelationships of microorganisms on painted surfaces. Evidence is given to support the conclusion that bacteria are the earliest colonizers on painted surfaces. Bacterial capsules appear to enhance the later settlement of fungi and their continued growth. Evidence is given to support the hypothesis that bacteria condition painted surfaces and through extracellular enzymes convert paint components to fungal metabolites. Observations were made relative to the influence of proprietary mildewcides on microbial succession on painted surfaces.     

西天目山针叶树直径生长与气候变化的关系

利用树木年轮分析方法研究了西天目山的三种主要针叶树：柳杉、金钱松和黄山松在林分范围内的直径生长与气候因子的关系。用逐步回归分析建立生长指数与１３个气候因子的回归方程,然后将生长曲线加入回归方程获得估计胸高处直径生长量的模型。结果表明,显著影响柳杉直径生长指数的因素为前期生长和夏季气温;影响金钱松生长指数达显著水平的有前期生长和夏、秋两季降水量;显著影响黄山松生长指数的因素有前期生长、夏季气温和秋季降水量。如果未来气温比目前分别升高１℃、２℃和３℃,柳杉的直径生长量将增加３．２％、６．３％和１１．１％;金钱松的将增加３．７％、５．６％和７．４％;黄山松的将增加３．５％、７．１％和１１．８％。文中对影响直径生长的其他因素也进行了讨论。     

Using trunk diameter sensors for regulated deficit irrigation scheduling in early maturing peach trees

The aim of this paper was to test the possibility of scheduling regulated deficit irrigation (RDI) using exclusively maximum daily trunk shrinkage (MDS) measurements, and that RDI strategies can be applied in early maturing peach trees reducing significantly the seasonal water use. During three growing seasons, 6-year-old peach trees (Prunus persica (L.) Batsch cv. Flordastar) grafted on P. persica × P. amygdalus GF-677 peach rootstock were submitted to different drip irrigation treatments. Control (T0) plants were irrigated above the estimated crop evapotranspiration level (≈130% ET_C) and T1 plants were submitted to RDI, which were irrigated in order to maintain MDS signal intensity (SI) values close to unity (no irrigation-related stress) from the fruit thinning stage to 2 weeks after harvest, at MDS SI values close to 1.3 during the early postharvest period, and at MDS SI values of 1.6 during the late postharvest period. The RDI strategy assayed reduced the seasonal water applied by 35-42% with respect to estimated ET_C without affecting yield efficiency components or the distribution of different peach fruit categories, while improving water productivity. The only vegetative growth component affected by RDI was pruning weight, indicating that vigor regulation as a result of RDI may decrease the competition for assimilates between vegetative apexes and reserve tissues. Also, the absence of any significant effect of RDI on the ratio between yield and the increase in trunk cross sectional area suggested similar carbon partitioning schemes during fruit growth. To improve the precision of MDS SI-driven schedule in RDI strategies changes in the irrigation protocol should be considered so that the scheduled water deficit levels are attained more rapidly. For this, when it is necessary to change from a MDS SI threshold value to a higher one, the daily irrigation rate should be decreased by more than 3%.     

Extracting species trees from complex gene trees: reconciled trees and vertebrate phylogeny

Paralogy is a pervasive problem in trying to use nuclear gene sequences to infer species phylogenies. One strategy for dealing with this problem is to infer species phylogenies from gene trees using reconciled trees, rather than directly from the sequences themselves. In this approach, the optimal species tree is the tree that requires the fewest gene duplications to be invoked. Because reconciled trees can identify orthologous from paralogous sequences, there is no need to do this prior to the analysis. Multiple gene trees can be analyzed simultaneously; however, the problem of nonuniform gene sampling raises practical problems which are discussed. In this paper the technique is applied to phylogenies for nine vertebrate genes (aldolase, alpha-fetoprotein, lactate dehydrogenase, prolactin, rhodopsin, trypsinogen, tyrosinase, vassopressin, and Wnt-7). The resulting species tree shows much similarity with currently accepted vertebrate relationships.     

Fire survival of lowland tropical rain forest trees in relation to stem diameter and topographic position

The objective of this study was to relate patterns in forest structure, tree species diversity, and tree species composition to stem diameters and topography in unburned, once burned and twice burned lowland dipterocarp rain forests in East Kalimantan, Indonesia. To do this four unburned old growth forests were compared with three forests that burned once (1997/1998) and three forests that burned twice (1982/1983 and 1997/1998). Fire resulted in a strong reduction of climax tree density which was negatively related to tree diameter. However, a disproportionate reduction in small diameter understorey climax tree species occurred only after repeated fires. Climax tree species in both burned forest types were most common in swamps, river valleys and on lower slopes, while their density was much lower on places higher along hillsides. In unburned forest the opposite was observed, with climax tree density increasing steadily from swamp and river valleys to upper slopes and ridges. In contrast to climax trees, pioneer trees were abundant throughout the burned forest, with highest numbers on hill sides and ridges. Our results indicate that both diameter and topographic position of trees strongly affect their fire survival chances in tropical lowland forests.     

In vivo insulin secretion: Prostaglandin and adrenergic interrelationships

Infusion of prostaglandin (PG) E₁ in anesthetized dogs significantly lowered circulating insulin levels and inhibited insulin responses following intravenous glucose. A similar trend was observed with PGE₂. Alpha adrenergic blockade did not reverse the PGE₁ effect. Epinephrine infusion also inhibited glucose-stimulated insulin secretion, an effect that was not reversed by indomethacin. Therefore, in this investigative model, PGE₁ inhibited insulin secretion but no interdependency of PGE₁ and alpha adrenergic effects were found.     

开敞度调控对次生林林冠下红松径高生长量和地上生物量的影响

以同处于演替层15年生(龄级Ⅰ)和22年生(龄级Ⅱ)的人工红松-天然阔叶混交林为对象,对林下栽植红松个体的开敞度(K)进行调整(K=1.0,1.5,2.0),研究调整后4年间林下红松直径和树高生长量及第4年的红松生物量状况.结果表明:2个龄级红松地径/胸径和树高定期生长量和地上部生物量均以K=1.0处理最大;随时间的延伸,K=1.5和K=2.0处理对年生长量的促进效果不断增强,接近或超过K=1.0处理.龄级Ⅰ的K=1.0处理的树干生物量比例显著高于其他处理和对照,而龄级Ⅱ各处理的差异不明显;龄级Ⅰ各处理的枝叶生物量比值均显著高于对照,而龄级Ⅱ则差异不显著;两个龄级不同年龄针叶的比例及分布状态不同.开敞度为1.0 ～2.0时有利于次生林林冠下栽植的15 ～22年生红松的生长发育.     

Metrics on RNA secondary structures.

Many different programs have been developed for the prediction of the secondary structure of an RNA sequence. Some of these programs generate an ensemble of structures, all of which have free energy close to that of the optimal structure, making it important to be able to quantify how similar these different structures are. To deal with this problem, we define a new class of metrics, the mountain metrics, on the set of RNA secondary structures of a fixed length. We compare properties of these metrics with other well known metrics on RNA secondary structures. We also study some global and local properties of these metrics.