PoInTree： A Polar and Interactive Phylogenetic Tree

PoInTree （Polar and Interactive Tree） is an application that allows to build, visualize, and customize phylogenetic trees in a polar, interactive, and highly flexible view. It takes as input a FASTA file or multiple alignment formats. Phylogenetic tree calculation is based on a sequence distance method and utilizes the Neighbor Joining （N J） algorithm. It also allows displaying precalculated trees of the major protein families based on Pfam classification. In PoInTree, nodes can be dynamically opened and closed and distances between genes are graphically represented. Tree root can be centered on a selected leaf. Text search mechanism, color-coding and labeling display are integrated. The visualizer can be connected to an Oracle database containing information on sequences and other biological data, helping to guide their interpretation within a given protein family across multiple species. The application is written in Borland Delphi and based on VCL Teechart Pro 6 graphical component （Steema software）.     

Tree Reconciliation: Reconstruction of Species Phylogeny by Phylogenetic Gene Trees

It is well known that phylogenetic trees derived from different protein families are often incongruent. This is explained by mapping errors and by the essential processes of gene duplication, loss, and horizontal transfer. Therefore, the problem is to derive a consensus tree best fitting the given set of gene trees. This work presents a new method of deriving this tree. The method is different from the existing ones, since it considers not only the topology of the initial gene trees, but also the reliability of their branches. Thereby one can explicitly take into account the possible errors in the gene trees caused by the absence of reliable models of sequence evolution, by uneven evolution of different gene families and taxonomic groups, etc.     

杭州市不同土地利用类型的树木生长和碳固存

随着全球城市化的加剧,城市作为一个受强人类活动支配的生态系统,在显著改变土地利用的同时,也改变了城市内植被的碳吸收和碳储存能力.本文选取杭州具有代表性的2个树种香樟(Cinnamomum camphora)和悬铃木(Platanus acerifolia)为研究对象,调查并测量了720株树木的胸径、株高、株距和冠幅,测量了230株样木近10年的平均轮面积增量,对城市不同土地利用类型上不同树种的碳储存和碳吸收速率进行了估算和比较.结果表明,香樟碳储存为45 kg C·m-2,悬铃木104 kg C·m-2.香樟碳吸收速率在政府机关用地上最大,住宅区最小;而悬铃木在住宅区碳吸收速率远远大干商业区和政府机构用地.冠幅是影响香樟碳吸收速率的主要影响因子,而悬铃木的碳吸收速率与冠幅相关外还受到年龄的影响.在城市土地利用类型中乔木碳吸收是野外相同年龄乔木的5倍甚至更多.     

Relationships between branch spacing, growth rate and light in tropical forest saplings

1. The spacing of branches along central stems was related to growth rate and light level in forest saplings and trees in tropical moist forest on Barro Colorado Island (BCI), Panama. The study included 14 species with tiers of plagiotropic branches (having planar leaf arrangements) and four species with continuous distributions of plagiotropic branches.
2. All species showed increases in branch spacing with increasing light and growth rate of diameter, similar to the patterns in leaf spacing noted previously in species which initially bear large leaves on unbranched stems.
3. Non-tiered species had shorter internodes than tiered species but because the latter bear more branches per node, both groups had similar numbers of branches per unit stem length, when compared at similar growth rates.
4. Differences in the relationship between internode length and growth rate among tiered species were related to demographic characteristics, suggesting that tree architecture may influence forest composition.
5. The strong correlation observed between branch spacing and growth rate suggests that branch spacing may be used to estimate past growth histories of forest tree species with plagiotropic branches.     

Coalescent histories for discordant gene trees and species trees

Given a gene tree and a species tree, a coalescent history is a list of the branches of the species tree on which coalescences in the gene tree take place. Each pair consisting of a gene tree topology and a species tree topology has some number of possible coalescent histories. Here we show that, for each n≥7, there exist a species tree topology S and a gene tree topology G≠S, both with n leaves, for which the number of coalescent histories exceeds the corresponding number of coalescent histories when the species tree topology is S and the gene tree topology is also S. This result has the interpretation that the gene tree topology G discordant with the species tree topology S can be produced by the evolutionary process in more ways than can the gene tree topology that matches the species tree topology, providing further insight into the surprising combinatorial properties of gene trees that arise from their joint consideration with species trees.     

Contribution of paddock trees to the conservation of terrestrial invertebrate biodiversity within grazed native pastures

Abstract: Paddock trees are a common feature in the agricultural landscapes of Australia. Recent studies have demonstrated the value of scattered paddock trees for soil fertility, native pasture plants and arboreal faunas; however, the degree to which scattered paddock trees contribute to the conservation of terrestrial invertebrate biodiversity within grazed landscapes remains unknown. We ask three questions: (i) Is there a difference between the terrestrial invertebrate assemblages found under paddock trees compared with surrounding grazed native pastures? (ii) Can gradients in soil and litter variables from the base of trees explain patterns in invertebrate assemblages? and (iii) Does the presence of scattered paddock trees have implications for the conservation of terrestrial invertebrate biodiversity within grazed native pastures? We used pitfall trapping and extraction from soil cores to sample the invertebrate assemblages under six New England Peppermint trees (Eucalyptus nova‐anglica Deane and Maiden) and compared them with assemblages sampled from the open paddock. Formicidae and Collembola univariate and multivariate data were analysed along with a range of soil and litter variables. We found (i) significant differences in the assemblages of invertebrates under trees compared with surrounding grazed pastures; (ii) that most soil and litter variables revealed gradients away from tree bases and these variables explained significant variation in invertebrate assemblages; and (iii) more native invertebrates and more species of invertebrates were found under trees compared with the surrounding pastures. We discuss the relationships between paddock trees, the ground and soil environments and the invertebrate communities that inhabit these environments, and conclude with a discussion of the future for paddock trees and the biota supported by them.     

mtDNA基因树拓扑距离比较和基因分群

基因树间拓扑距离数据的比较进一步证明：与分割拓扑距离相比,能经拓扑距离是一种更为精确的测度,利用相对通经拓扑距离构建了8个基因的拓扑距离树。基因的拓扑距离树能直观地反映不同基因树的拓扑结构差异大小,可用来对基因进行分群。此外,发现不同DNA序列用于构建多基因树中其系统发生信息存在“累加”,“合取”,“含盖”,“相斥”等数学关系。这可解释在mtDNA基因组中一些基因比另一些基因更适合用来的构建树的结果。结果提示从GenBank中应选择具有累加基因的DNA序列或蛋白质氨基酸序列合并来构建物种。在讨论中还提出了一种获得真树的新建树策略。     

SEARCHING FOR EVOLUTIONARY PATTERNS IN THE SHAPE OF A PHYLOGENETIC TREE

If all species in a clade are equally likely to speciate or become extinct, then highly symmetric and highly asymmetric phylogenetic trees are unlikely to result. Variation between species in speciation and extinction rates can cause excessive asymmetry. We developed six non-parametric statistical tests that test for nonrandom patterns of branching in any bifurcating tree. The tests are demonstrated by applying them to two published phylogenies for genera of beetles. Comparison of the power of the six statistics under a simple model of biased speciation suggests which of them may be most useful for detecting nonrandom tree shapes.     

云南茶树上的附生地衣

对云南茶叶农场中的附生地衣进行调查发现: 附生在茶树上的地衣有25 属, 51 种; 其中, 45 种是首次报道附生在茶树上, 包括2 个中国新记录种: 癞屑衣( Lepraria lobificans) 和阿曼原胚衣( Protoblastenia amagiensis) , 以及20 个云南新分布种。壳状地衣的共生菌丝侵入茶叶树干外皮层组织, 在生长过程中产生地衣酸, 一定程度的加速了农场中茶树的老化; 靠近茶树发芽点生长的壳状地衣和叶状地衣, 造成芽体发育不良, 对茶叶的产量和品质有一定影响。     

分子分类的若干问题

本文简要介绍了分子分类学中的几个重要问题：即,（１）分子分类法的优点及其局限性;（２）分子树和物种树的关系;（３）分子种与分子分类法的关系;（４）核酸序列数据与蛋白质序列数据之比较;（５）ＭＰ、ＮＪ和ＭＬ法之比较;（６）分子树的可靠性。另外还简要介绍了两个分子分类软件,ＰＨＹＬＩＰ和ＣＬＵＳＴＡＬＶ。     

基于随机森林的不同径级树木死亡影响因子研究

树木死亡是多种因素共同作用的结果,然而不同径级的林木,导致其死亡的原因是否相同尚不明确。以坝上地区小叶杨为对象,于2016-2017年调查了100块20m×20m样地。以林木胸径、林木相对断面积、林龄、林分密度、不同土层土壤含水量和土壤容重等11个因子为输入变量,运用随机森林算法分别不同径级建立树木死亡模型,分析各因子对不同径级树木死亡的影响大小,并得到关键影响因子的阈值。结果表明：依据不同径级树木死亡与影响因子的相关性不同,可将林木径级划分为 < 10cm、10-25cm、 > 25cm;胸径 < 10cm时,林木相对断面积对树木死亡的影响最大,当0.23 < 林木相对断面积 < 0.43时,树木死亡率最低;胸径为10-25cm时,密度对树木死亡的影响最大,当密度 > 600株/hm²时,树木死亡率随着密度的增加明显上升;胸径 > 25cm时,20-60cm土壤水分和林分断面积对树木死亡的影响最大且相近,当20-60cm土壤质量含水量 > 5%时,树木死亡率明显下降;基于随机森林算法建立的树木死亡模型可以解释树木死亡70%-90%的变异,具有一定的预测优势和应用价值,可为坝上地区树木死亡预测和防护林的经营管护提供参考。     

Comparative Observations of Resin Canals in Secondary Xylem of Three Species of Normal and Dwarf Pines

The number size and morphology of resin canals in secondary xylem of three species of normal and dwarf pines, i. e. Pinus thunbergii, P. tabulaeformis and P. densiflora, were comparatively studied. It was found that the number of resin canals in dwarf pines was significantly greater than in normal pines, while the size of resin canals in dwarf pines was invariably smaller than in normal pines. In addition, the epithelial cells around the canals of dwarf pines extended laterally, which made the outline of resin canals aliform-like. These findings might indicate that the raviations of resin canals representing a special adaptation to the unfavourable growth conditions were also correlated with the trend of shortening and narrowing of dwarf pines.     

树种及多样性组配对南亚热带人工林早期树木生长的影响

为科学筛选提升南亚热带人工林生产力的树种配置模式,选择南亚热带8个乡土树种,采用随机区组的试验设计,建立了树种多样性梯度(1、2、4、6个树种)人工新造林试验平台,研究树种多样性及不同功能特性树种混交对人工林早期树木生长的影响。结果表明: 在树木生长第5年,树木生长并没有随树种多样性增加而增加;速生树种马尾松和米老排纯林生长量是珍贵树种红椎和格木纯林的2.5～4.5倍;2个树种混交和4个树种混交情况下,针阔树种混交、速生树种与固氮树种混交显著提高树木生长量51.5%～132.8%,而当6个树种混交时,不同树种组配对生长量没有显著影响。不同树种配置模式下土壤氮、磷养分是影响树木早期生长的主要因素。针阔树种混交、速生和固氮树种混交能显著提高南亚热带人工林树木的早期生长。     

昆虫防御素基因( defensin) 的起源与分子进化

果蝇防御素基因位于它的第二条染色体右臂上,其编码产物具有抗菌肽活性,主要时革兰氏阳性菌有抗性。由于其有牢固的分子骨架、广泛的分布以及生物活性,对它的研究已成为当前国际研究热点。本文主要使用NCBI的资源分析黑腹果蝇防御素及其同源序列,并讨论了昆虫防御素的起源和分子进化。     

基于树木年轮学的古树树龄估算——以敦煌市香水梨为例

树龄是古树鉴定的唯一标准。本研究采用树轮年代学方法调查敦煌市莫高镇窦家墩村四组(原杨家园子)梨园中最老的香水梨树的树龄。因老梨树均腐朽中空,调查同时采集不同树龄的香水梨树样芯,建立树木径向生长生理年龄曲线,据此估算缺失段的树轮数。结合准确树轮计数,复原香水梨树树龄。结果表明: 梨园13棵老香水梨树的平均树龄为(280±35)年。由此证明,《敦煌志》中记载的古梨树是真实存在的。按树龄来说,该批梨树至少为三级古树,应妥善保护。本研究为解决敦煌市古梨园存留争议提供了详实的科学依据。     

油松优树选择方法的研究

论述了优树选择应遵循优良种源区选择优良林分,优良林分中的选择优良单株的系统选择原则。提出了标准差法选择方法和标准,要求优树胸径大于林分平均胸径加２倍标准差,且优树年平均出长量：胸径大于０．９ｃｍ、树高大于０．５ｍ。根据１９株人工林优树周转的标准地每木实测数据,对小标准地法和大树选优法作了比较;根据３２株优树的选优结果,比较了１－５株大树法选优法之间的相关关系,大树法间相关都显著,但以３株法为最好;     

Effects of Tree Guards and Weed Mats on the Establishment of Native Tree Seedlings: Implications for Forest Restoration in Hong Kong, China

The effects of tree guards and weed mats on establishment and growth of native tree seedlings, Thick‐leaved oak (Cyclobalanopsis edithiae (Skan) Schott., Fagaceae), planted in an exposed hillside grassland in Hong Kong, were investigated. The natural regeneration of C. edithiae is poor due to a lack of seed dispersal agents and high seed predation, and therefore, this species is often targeted for forest restoration. The experiment lasted for 3.5 years during which the height, basal diameter, and crown diameter of individual seedlings were measured and survivorship recorded. The use of weed mats alone did not have a significant effect, but a combination of tree guards and weed mats led to a significant improvement in establishment, survivorship, and growth of the seedlings during the experimental period. Initially, the guards promoted rapid height growth of the seedlings, although lateral growth and secondary stem thickening were compromised. After the seedlings grew over the tree guards, the basal diameter and crown diameter increased at a notably faster rate. The combined effect of the tree guard and weed mat on the seedling growth pattern was found to be beneficial and contributed to the high survivorship of the seedlings. Comparing the survivorship data and the costs of various treatments, the use of tree guards in combination with the weed mats was demonstrated to be more cost‐effective than planting the seedlings without tree guards or weed mats. The potential for applying the technique in afforestation programs with native tree species for forest restoration in Hong Kong and other tropical regions is discussed.     

NULL MODELS FOR THE NUMBER OF EVOLUTIONARY STEPS IN A CHARACTER ON A PHYLOGENETIC TREE

Random trees and random characters can be used in null models for testing phylogenetic hypothesis. We consider three interpretations of random trees: first, that trees are selected from the set of all possible trees with equal probability; second, that trees are formed by random speciation or coalescence (equivalent); and third, that trees are formed by a series of random partitions of the taxa. We consider two interpretations of random characters: first, that the number of taxa with each state is held constant, but the states are randomly reshuffled among the taxa; and second, that the probability each taxon is assigned a particular state is constant from one taxon to the next. Under null models representing various combinations of randomizations of trees and characters, exact recursion equations are given to calculate the probability distribution of the number of character state changes required by a phylogenetic tree. Possible applications of these probability distributions are discussed. They can be used, for example, to test for a panmictic population structure within a species or to test phylogenetic inertia in a character's evolution. Whether and how a null model incorporates tree randomness makes little difference to the probability distribution in many but not all circumstances. The null model's sense of character randomness appears more critical. The difficult issue of choosing a null model is discussed.     

MrEnt: an editor for publication‐quality phylogenetic tree illustrations

We developed MrEnt, a Windows‐based, user‐friendly software that allows the production of complex, high‐resolution, publication‐quality phylogenetic trees in few steps, directly from the analysis output. The program recognizes the standard Nexus tree format and the annotated tree files produced by BEAST and MrBayes. MrEnt combines in a single software a large suite of tree manipulation functions (e.g. handling of multiple trees, tree rotation, character mapping, node collapsing, compression of large clades, handling of time scale and error bars for chronograms) with drawing tools typical of standard graphic editors, including handling of graphic elements and images. The tree illustration can be printed or exported in several standard formats suitable for journal publication, PowerPoint presentation or Web publication.     

DO PHYLOGENETIC METHODS PRODUCE TREES WITH BIASED SHAPES?

We examine whether phylogenetic methods provide biased estimates of tree shape with respect to the random branching model. We investigate the performance of five commonly used phylogenetic methods using computer simulation: (1) maximum parsimony; (2) neighbor joining; (3) UPGMA with an outgroup taxon; (4) UPGMA without an outgroup taxon; and (5) maximum likelihood. All methods provide estimates of tree shape that are, on average, more asymmetrical than the true tree, especially when rates of evolution are high. We suggest a simple explanation for the bias and propose a modified test of tree shape that corrects for it.