Allee effects, invasion pinning, and species' borders

All species' ranges are the result of successful past invasions. Thus, models of species' invasions and their failure can provide insight into the formation of a species' geographic range. Here, we study the properties of invasion models when a species cannot persist below a critical population density known as an "Allee threshold." In both spatially continuous reaction-diffusion models and spatially discrete coupled ordinary-differential-equation models, the Allee effect can cause an invasion to fail. In patchy landscapes (with dynamics described by the spatially discrete model), range limits caused by propagation failure (pinning) are stable over a wide range of parameters, whereas, in an uninterrupted habitat (with dynamics described by a spatially continuous model), the zero velocity solution is structurally unstable and thus unlikely to persist in nature. We derive conditions under which invasion waves are pinned in the discrete space model and discuss their implications for spatially complex dynamics, including critical phenomena, in ecological landscapes. Our results suggest caution when interpreting abrupt range limits as stemming either from competition between species or a hard environmental limit that cannot be crossed: under a wide range of plausible ecological conditions, species' ranges may be limited by an Allee effect. Several example systems appear to fit our general model.     

Comparison of the effect of different infusion rates of sufentanil on surgical stress index during cranial pinning in children under general anaesthesia: a randomized controlled study

Background

Surgical stress index (SSI) is an established indicator for intraoperative nociception. Opioids are used to block stimulus of cranial pinning in neurosurgery. We investigated the effect of different infusion rates of sufentanil on SSI during cranial pinning in children under general anaesthesia.

Methods

Forty-nine children (2–12 years of age) underwent neurosurgery with pinning. The children were randomized into three groups based on the rate of sufentanil infusion: 0.2, 0.5, and 0.8 μg·kg^?1·hr.^?1. Continuous sufentanil infusion began following neuromuscular blockade administration, at a rate determined by each patient’s assigned treatment group. Following preparation for surgery, cranial pinning was performed. Systolic, diastolic, and mean blood pressures, along with heart rate and photoplethysmographic data, were continuously recorded from 1 min prior to cranial pinning through 5 min after cranial pinning, in 1-min intervals. SSI was calculated following the completion of surgery. Differences in measured outcomes over time among the three groups were evaluated using a generalized estimation equation. Differences in pinning outcomes in the same group were evaluated with Freidman test.

Results

We found no statistical differences in long-term SSI that were associated with different infusion rates of sufentanil during cranial pinning. Blood pressures in all groups increased for 2 min after cranial pinning, and then decreased; we found no statistical difference in long-term blood pressure values among the groups. Heart rate increased after pinning in the group that received a low-dose infusion of sufentanil.

Conclusions

Since SSI was intended to measure the blunting effects of sufentanil towards the noxious stimulus of cranial pinning, our results suggest that SSI might not be sufficiently sensitive to monitor the nociceptive response in children.

Trial registration

(KCT0000978, Jan-07, 2014).

     

Wave pinning and spatial patterning in a mathematical model of Antivin/Lefty–Nodal signalling

Nodal signals are key regulators of mesoderm and endoderm development in vertebrate embryos. It has been observed experimentally that in Xenopus embryos the spatial range of Nodal signals is restricted by the signal Antivin (also known as Lefty). Nodal signals can activate both Nodal and Antivin, whereas Antivin is thought to antagonise Nodal by binding either directly to it or to its receptor. In this paper we develop a mathematical model of this signalling network in a line of cells. We consider the heterodimer and receptor-mediated inhibition mechanisms separately and find that, in both cases, the restriction by Antivin to the range of Nodal signals corresponds to wave pinning in the model. Our analysis indicates that, provided Antivin diffuses faster than Nodal, either mechanism can robustly account for the experimental data. We argue that, in the case of Xenopus development, it is wave pinning, rather than Turing-type patterning, that is underlying Nodal–Antivin dynamics. This leads to several experimentally testable predictions, which are discussed. Furthermore, for heterodimer-mediated inhibition to prevent waves of Nodal expression from propagating, the Nodal–Antivin complex must be turned over, and diffusivity of the complex must be negligible. In the absence of molecular mechanisms regulating these, we suggest that Antivin restricts Nodal signals via receptor-mediated, and not heterodimer-mediated, inhibition.     

Traveling and Pinned Fronts in Bistable Reaction-Diffusion Systems on Networks

Traveling fronts and stationary localized patterns in bistable reaction-diffusion systems have been broadly studied for classical continuous media and regular lattices. Analogs of such non-equilibrium patterns are also possible in networks. Here, we consider traveling and stationary patterns in bistable one-component systems on random Erdös-Rényi, scale-free and hierarchical tree networks. As revealed through numerical simulations, traveling fronts exist in network-organized systems. They represent waves of transition from one stable state into another, spreading over the entire network. The fronts can furthermore be pinned, thus forming stationary structures. While pinning of fronts has previously been considered for chains of diffusively coupled bistable elements, the network architecture brings about significant differences. An important role is played by the degree (the number of connections) of a node. For regular trees with a fixed branching factor, the pinning conditions are analytically determined. For large Erdös-Rényi and scale-free networks, the mean-field theory for stationary patterns is constructed.     

Finite-time synchronization of coupled neural networks via discontinuous controllers

This paper investigates finite-time synchronization of an array of coupled neural networks via discontinuous controllers. Based on Lyapunov function method and the discontinuous version of finite-time stability theory, some sufficient criteria for finite-time synchronization are obtained. Furthermore, we propose switched control and adaptive tuning parameter strategies in order to reduce the settling time. In addition, pinning control scheme via a single controller is also studied in this paper. With the hypothesis that the coupling network topology contains a directed spanning tree and each of the strongly connected components is detail-balanced, we prove that finite-time synchronization can be achieved via pinning control. Finally, some illustrative examples are given to show the validity of the theoretical results.     

Transient Pinning and Pulling: A Mechanism for Bending Microtubules

Microtubules have a persistence length of the order of millimeters in vitro, but inside cells they bend over length scales of microns. It has been proposed that polymerization forces bend microtubules in the vicinity of the cell boundary or other obstacles, yet bends develop even when microtubules are polymerizing freely, unaffected by obstacles and cell boundaries. How these bends are formed remains unclear. By tracking the motions of microtubules marked by photobleaching, we found that in LLC-PK1 epithelial cells local bends develop primarily by plus-end directed transport of portions of the microtubule contour towards stationary locations (termed pinning points) along the length of the microtubule. The pinning points were transient in nature, and their eventual release allowed the bends to relax. The directionality of the transport as well as the overall incidence of local bends decreased when dynein was inhibited, while myosin inhibition had no observable effect. This suggests that dynein generates a tangential force that bends microtubules against stationary pinning points. Simulations of microtubule motion and polymerization accounting for filament mechanics and dynein forces predict the development of bends of size and shape similar to those observed in cells. Furthermore, simulations show that dynein-generated bends at a pinning point near the plus end can cause a persistent rotation of the tip consistent with the observation that bend formation near the tip can change the direction of microtubule growth. Collectively, these results suggest a simple physical mechanism for the bending of growing microtubules by dynein forces accumulating at pinning points.     

Semi-strict supertrees

A method to calculate semi‐strict supertrees is proposed. The semi‐strict supertrees are calculated by creating the matrix that represents all the groups in the source trees (as done in already existing techniques), and then finding the trees determined by the ultra‐clique. The ultra‐clique is defined as the set of characters where each possible subset is compatible with each possible subset from the entire matrix. Finding the ultra‐clique is computationally complex (since in most cases many of the characters have missing entries), but a heuristic method yields reliable results. When the trees have no conflict, or when there are only two trees, the method produces the exact result for any ordering of the input trees and any ordering of the groups within them; when there are more than two trees and they have conflict, a single ordering or sequence can create some spurious groups, but doing multiple sequences eliminates the spurious groups. The method uses only state set operations, and is thus easily implemented in computer programs. Unlike any existing type of supertree, semi‐strict supertrees display all the groups, and only those groups, that are implied by at least some combination of the input trees and contradicted by none. The idea that supertrees should take into account the number of occurences of a given group, so as to retain some groups even in the case of conflict, is discussed; it is argued that a conceptual equivalent of the majority rule consensus is not possible when the sets of taxa differ among trees. Also, when pruning taxa from a set of trees, the supertree can display groups that contradict the consensus for the entire trees, suggesting that supertrees for matrices with very dissimilar sets of taxa should be interpreted with caution. If (for any valid reason) the data cannot be combined in a single matrix, it is advisable that the taxon sets in the matrices be as similar as possible.     

Estimating species trees from unrooted gene trees

In this study, we develop a distance method for inferring unrooted species trees from a collection of unrooted gene trees. The species tree is estimated by the neighbor joining (NJ) tree built from a distance matrix in which the distance between two species is defined as the average number of internodes between two species across gene trees, that is, average gene-tree internode distance. The distance method is named NJ(st) to distinguish it from the original NJ method. Under the coalescent model, we show that if gene trees are known or estimated correctly, the NJ(st) method is statistically consistent in estimating unrooted species trees. The simulation results suggest that NJ(st) and STAR (another coalescence-based method for inferring species trees) perform almost equally well in estimating topologies of species trees, whereas the Bayesian coalescence-based method, BEST, outperforms both NJ(st) and STAR. Unlike BEST and STAR, the NJ(st) method can take unrooted gene trees to infer species trees without using an outgroup. In addition, the NJ(st) method can handle missing data and is thus useful in phylogenomic studies in which data sets often contain missing loci for some individuals.     

ESTIMATING CHARACTER WEIGHTS DURING TREE SEARCH

Abstract— A new method for weighting characters according to their homoplasy is proposed; the method is non-iterative and does not require independent estimations of weights. It is based on searching trees with maximum total fit, with character fits defined as a concave function of homoplasy. Then, when comparing trees, differences in steps occurring in characters which show more homoplasy on the trees are less influential. The reliability of the characters is estimated, during the analysis, as a logical implication of the trees being compared. The "fittest" trees imply that the characters are maximally reliable and, given character conflict, have fewer steps for the characters which fit the tree better. If other trees save steps in some characters, it will be at the expense of gaining them in characters with less homoplasy.     

Visualizing conflicting evolutionary hypotheses in large collections of trees: using consensus networks to study the origins of placentals and hexapods

Many phylogenetic methods produce large collections of trees as opposed to a single tree, which allows the exploration of support for various evolutionary hypotheses. However, to be useful, the information contained in large collections of trees should be summarized; frequently this is achieved by constructing a consensus tree. Consensus trees display only those signals that are present in a large proportion of the trees. However, by their very nature consensus trees require that any conflicts between the trees are necessarily disregarded. We present a method that extends the notion of consensus trees to allow the visualization of conflicting hypotheses in a consensus network. We demonstrate the utility of this method in highlighting differences amongst maximum likelihood bootstrap values and Bayesian posterior probabilities in the placental mammal phylogeny, and also in comparing the phylogenetic signal contained in amino acid versus nucleotide characters for hexapod monophyly.     

Superhydrophobic cuticle with a "pinning effect" in the larvae of the iris sawfly, Rhadinoceraea micans (Hymenoptera, Tenthredinidae)

The integument of some sawfly larvae can be easily damaged causing haemolymph bleeding (easy bleeding phenomenon). In the present study, we investigated intact cuticle, cuticle without wax coverage and cuticle replicas of sawfly larvae by using cryo-scanning electron microscopy and contact angle (CA) measurements. The easy bleeder Rhadinoceraea micans was compared to the non-easy bleeder Nematus pavidus (both Tenthredinidae), and the examination showed that the surface structures of R. micans were hierarchically arranged, whereas the cuticle surface of N. pavidus appeared much smoother. The intact cuticle proved to be superhydrophobic in R. micans (CAs: 156° dorsally, 120° ventrally), but not in N. pavidus (CAs: 67° dorsally, 47° ventrally). The wettability of R. micans increased significantly after the waxes had been peeled off. Replicas of the intact cuticle surface were hardly wettable in both species. It is suggested that wax crystals in combination with cuticle microsculptures are the most important features for rendering the integument of the easy bleeder species superhydrophobic. The wax-free tips of the cuticle microsculptures in R. micans are sites where haemolymph droplets can adhere. The integument surface of easy bleeders is assumed to be adapted to their particular defence strategy, simultaneously contributing to the maintenance and "reuse" of released haemolymph droplets on the superhydrophobic surface due to this "pinning effect".     

洞庭湖洲滩速生杨树林变化信息提取方法

洞庭湖是我国第二大淡水湖,其湿地资源具有重要的生态功能和经济价值。近20年来,洞庭湖洲滩速生杨树林发展迅速,其中西洞庭湖杨树林的扩张最为明显,极大改变了湖区湿地植被分布格局,隐含极大的生态风险。以Landsat ETM+和HJ-1A/1B CCD影像为数据源,提出了洞庭湖速生杨树林变化信息提取的两种方法,并对这两种方法进行了比较研究。一种是分类的方法,即采用面向对象分层信息提取的方法先提取出树林滩地信息,再将距离大堤一定范围内的树林滩地归为防护林,速生杨树林变化的面积即为两个时相提取结果的差值。另一种是变化检测的方法,它是基于像元进行变化检测,先确定出总的变化区域,再从中筛选速生杨树林的变化信息。结果表明:(1)两种提取方法都是可行的,不同方法提取的速生林变化信息存在一定差异,但空间分布大体一致;(2)基于分类的方法总体精度和Kappa系数均略高于基于变化检测的方法:其中基于分类的方法总体精度达84.00%,Kappa系数为0.67,基于变化检测的方法总体精度达83.00%,Kappa系数为0.65;(3)基于分类的方法图斑较大、图斑数较少,基于变化检测的方法图斑较小且较破碎、图斑数多;(4)基于分类的方法漏分较少、错分较多,基于变化检测的方法漏分较多、错分较少。为洞庭湖洲滩杨树林的动态监测提供了研究方法,也为杨树林扩张原因及其生态效应分析提供研究基础。     

Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions

The desire to infer the evolutionary history of a group of species should be more viable now that a considerable amount of multilocus molecular data is available. However, the current molecular phylogenetic paradigm still reconstructs gene trees to represent the species tree. Further, commonly used methods of combining data, such as the concatenation method, are known to be inconsistent in some circumstances. In this paper, we propose a Bayesian hierarchical model to estimate the phylogeny of a group of species using multiple estimated gene tree distributions, such as those that arise in a Bayesian analysis of DNA sequence data. Our model employs substitution models used in traditional phylogenetics but also uses coalescent theory to explain genealogical signals from species trees to gene trees and from gene trees to sequence data, thereby forming a complete stochastic model to estimate gene trees, species trees, ancestral population sizes, and species divergence times simultaneously. Our model is founded on the assumption that gene trees, even of unlinked loci, are correlated due to being derived from a single species tree and therefore should be estimated jointly. We apply the method to two multilocus data sets of DNA sequences. The estimates of the species tree topology and divergence times appear to be robust to the prior of the population size, whereas the estimates of effective population sizes are sensitive to the prior used in the analysis. These analyses also suggest that the model is superior to the concatenation method in fitting these data sets and thus provides a more realistic assessment of the variability in the distribution of the species tree that may have produced the molecular information at hand. Future improvements of our model and algorithm should include consideration of other factors that can cause discordance of gene trees and species trees, such as horizontal transfer or gene duplication.     

UPGMA树的不惟一性问题及其解决方法

对于一组给定的DNA或蛋白质序列,UPGMA算法构建的二叉进化树可能是不惟一的,其具体拓扑结构与序列输入顺序相关,这一现象通常被称为"tied trees"。提出了UPGMA的一种改进算法——不加权算术平均组群方法(UMGMA),用以解决UPGMA树的不惟一问题。在UPGMA树惟一时,该方法产生的进化树与UPGMA树相同;而在UPGMA树不惟一时,该方法可以产生一棵惟一的、与序列输入顺序无关的多叉进化树,而且该算法还具有一个可调的容差参数,来控制生成进化树的主要分枝结构,这对于突出大规模进化树的总体脉络具有重要意义。     

长白山红松混交林干扰历史的重构研究

 本文通过对取自300棵林木的年轮盘年轮宽度分析,利用林木年轮中表现出的释压(release)反应,进行红松混交林干扰历史重构研究,结果表明：利用林木的释压反应,分析诸如长白山红松混交林这种以风作为主要干扰类型的林分干扰历史是合理的方法,也是现行林分干扰历史推测方法中最准确、可靠、提供信息量最大的方法;只要满足一定的样本数,是可以通过样树的释压反应分析出林分的干扰历史;对红松混交林而言,臭松、鱼林松和红松是干扰历史分析的理想树种;在天然红松混交林中被压林木比率与干扰密切相关,一次干扰导致林分被压林木一次大幅度下降,而当较长时间不发生干扰时,林分被压林木比率逐渐上升。群落干扰历史的重构为群落和生态系统动态研究提供有利的历史资料。     

Phylogenetic super-networks from partial trees

In practice, one is often faced with incomplete phylogenetic data, such as a collection of partial trees or partial splits. This paper poses the problem of inferring a phylogenetic super-network from such data and provides an efficient algorithm for doing so, called the Z-closure method. Additionally, the questions of assigning lengths to the edges of the network and how to restrict the "dimensionality" of the network are addressed. Applications to a set of five published partial gene trees relating different fungal species and to six published partial gene trees relating different grasses illustrate the usefulness of the method and an experimental study confirms its potential. The method is implemented as a plug-in for the program SplitsTree4     

Construction of linear invariants in phylogenetic inference.

An analytical method is presented for constructing linear invariants. All linear invariants of a k-species tree can be derived from those of (k-1)-species trees using this method. The new method is simpler than that of Cavender, which relies on numerical computations. Moreover, the new method provides a convenient tool to study the relationships between linear invariants of the same tree or of different trees. All linear invariants of trees of up to five species are derived in this study. For four species, there are 16 independent linear invariants for each of the three possible unrooted trees, 14 of which are shared by two unrooted trees and 12 of these are shared by all three unrooted trees; the last types of linear invariants can be used to construct tests on the assumptions about nucleotide substitutions. The number of linear invariants for a tree is found to increase rapidly with the number of species.     

Cambial Growth Season of Brevi-Deciduous Brachystegia spiciformis Trees from South Central Africa Restricted to Less than Four Months

We investigate cambial growth periodicity in Brachystegia spiciformis, a dominant tree species in the seasonally dry miombo woodland of southern Africa. To better understand how the brevi-deciduous (experiencing a short, drought-induced leaf fall period) leaf phenology of this species can be linked to a distinct period of cambial activity, we applied a bi-weekly pinning to six trees in western Zambia over the course of one year. Our results show that the onset and end of cambial growth was synchronous between trees, but was not concurrent with the onset and end of the rainy season. The relatively short (three to four months maximum) cambial growth season corresponded to the core of the rainy season, when 75% of the annual precipitation fell, and to the period when the trees were at full photosynthetic capacity. Tree-ring studies of this species have found a significant relationship between annual tree growth and precipitation, but we did not observe such a correlation at intra-annual resolution in this study. Furthermore, a substantial rainfall event occurring after the end of the cambial growth season did not induce xylem initiation or false ring formation. Low sample replication should be taken into account when interpreting the results of this study, but our findings can be used to refine the carbon allocation component of process-based terrestrial ecosystem models and can thus contribute to a more detailed estimation of the role of the miombo woodland in the terrestrial carbon cycle. Furthermore, we provide a physiological foundation for the use of Brachystegia spiciformis tree-ring records in paleoclimate research.