Reinvestigation of Nystroemia pectiniformis Halle, an enigmatic seed plant from the Upper Permian of China

Reinvestigation of Nystroemia pectiniformis Halle from the Upper Shihhotze Formation of Shanxi Province, China, has led to the identification of new and important features of this enigmatic Late Permian seed plant, permitting its typification and diagnosis. After reassembling several of the previously studied specimens to form a single articulated branching system comprising at least four orders of branching, previously unknown features of its branching pattern and morphology have been characterized. First–order axes are wide and branch to one side only, bearing second–order branches either singly or in pairs and of two kinds: one fertile and bearing characteristic ovulate branching systems and the other presumably vegetative. Ovulate second–order axes are narrow and branch to one side only, producing numerous, closely spaced lateral branches in two alternate to sub–opposite rows. Lateral branches are slender and produce numerous ovulate branching systems to one side of the axis only. Ovulate branching systems divide unequally to produce 3–15 ultimate axes of different lengths that are planated. Each ultimate axis bears a single terminal ovule with 180 degree rotational symmetry and two horn–like integumentary projections distally. The other kind of second–order axes are distinct from those bearing ovules; they are wider and longer and branches occur on both sides of the secondary axis, lacking divisions in close proximity to the first–order axis. These have only been observed incomplete although their distinct morphology indicates they are unlikely to be ovulate branches from which ovules/seeds have been shed. Additional organs of the Nystroemia plant are considered, including pollen organs previously assigned by Halle to the same species (displaying its characteristic branching style), and also leaves of Chiropteris reniformis Halle that were probably borne on the larger kind of second–order branches. Implications of Nystroemia on seed plant evolution and distribution are discussed, and it is concluded that this most likely represents a late stratigraphic occurrence of a plesiomorphic hydrasperman–type seed plant with affinities closely allied to members of the Lyginopteridales.     

Papillomavirus subtypes are natural and old taxa: phylogeny of human papillomavirus types 44 and 55 and 68a and -b

A human papillomavirus (HPV) type is defined as an HPV isolate whose L1 gene sequence is at least 10% different from that of any other type, while a subtype is 2 to 10% different from any HPV type. In order to analyze the phylogeny behind the subtype definition, we compared 49 isolates of HPV type 44 (HPV-44) and its subtype HPV-55, previously misclassified as a separate type, and 41 isolates of the subtype pair HPV-68a and -b, sampled from cohorts in four continents. The subtypes of each pair are separated by deep dichotomic branching, and three of the four subtypes have evolved large phylogenetic clusters of genomic variants forming a "star" phylogeny, with some branches specific for ethnically defined cohorts. We conclude that subtypes of HPV types are natural and old taxa, equivalent to types, which either diverged more recently than types or evolved more slowly.     

Phylogeny and molecular evolution in primates

Statistical methods for estimating the branching order and the branching dates from DNA sequence data, taking into account of the rate variation among lineages, are reviewed. An application of the methods to data from primates suggests that chimpanzee is the closest relative of man, and further suggests that these two species diverged about 4-5 million years ago.     

Evaluating a non-destructive method for calibrating tree biomass equations derived from tree branching architecture

Key message

Functional branch analysis (FBA) is a promising non-destructive method that can produce accurate tree biomass equations when applied to trees which exhibit fractal branching architecture.

Abstract

Functional branch analysis (FBA) is a promising non-destructive alternative to the standard destructive method of tree biomass equation development. In FBA, a theoretical model of tree branching architecture is calibrated with measurements of tree stems and branches to estimate the coefficients of the biomass equation. In this study, species-specific and mixed-species tree biomass equations were derived from destructive sampling of trees in Western Kenya and compared to tree biomass equations derived non-destructively from FBA. The results indicated that the non-destructive FBA method can produce biomass equations that are similar to, but less accurate than, those derived from standard methods. FBA biomass prediction bias was attributed to the fact that real trees diverged from fractal branching architecture due to highly variable length–diameter relationships of stems and branches and inaccurate scaling relationships for the lengths of tree crowns and trunks assumed under the FBA model.     

Pattern of Shoot Growth in Zizyphus mauritiana and Z. oenoplia

Shoot polymorphism and patterns of sylleptic branching and shoottip abscission in two Zizyphus species are reported. Z. mauritiana(ber) produced three types of proleptic shoots: vigorous, normaland spur-type, by reiteration or following pruning;Z. oenopliahad only one type of shoot. Both species revealed up to thirdorder sylleptic branching on the vigorous proleptic shoots witha characteristic pattern and rhythm. Bud dormancy breaking chemicalsgiven as pre-pruning foliar sprays in ber, did not alter thepattern of sylleptic branching. Zizyphus oenoplia produced morefirst and second order sylleptic branches compared to Z. mauritiana.All main axes and 97% of first order sylleptic branches ofZ.mauritiana abscised their apical buds during summer, but inZ. oenoplia all main axes and 54% of first order sylleptic branchesremained active. Shoot tip abscission was almost complete onthe higher order sylleptic branches of both species. Activefirst order branches in Z. oenoplia were confined to the tophalf of the shoot. Both species had a few dormant apical budsduring the summer on their sylleptic branches, emerging mostlyfrom the middle portion of the shoot. Some of the most vigorousfirst order branches of Z. oenoplia, which had dormant apicalbuds during summer, showed a change in the frequency of syllepticbranching when they resumed growth following monsoon showers.These characteristic growth and branching patterns may haveadaptive value for canopy development under arid and semi-aridconditions. Copyright 1999 Annals of Botany Company Ber, branching pattern, shoot polymorphism, shoot tip abscission, sylleptic branching, Zizyphus mauritiana, Zizyphus oenoplia.     

Ramification pattern of intermetacarpal branches of the deep branch (ramus profundus) of the ulnar nerve in the human hand.

The branching pattern of the deep branch (ramus profundus) of the ulnar nerve and its relation with the target were analyzed in the human hand by an improved dissection method. After sending off branches to the hypothenar muscles, the r. profundus branched off an ulnar stem and a radial stem to the fourth, to the third and to the second intermetacarpal spaces, respectively, in this order, and an ulnar stem to the first to become terminal branches. The ulnar stems included an ulnar interosseous branch and a superficial articular branch in addition to a lumbrical branch in the third and fourth intermetacarpal spaces. The radial stems included only a radial interosseous branch. The branching pattern of the ulnar stems as well as its topographical relationship with the radial stems indicated a fundamental spatial arrangement of the branches in the intermetacarpal spaces: the lumbrical, superficial articular, ulnar interosseous and radial interosseous branches were arranged fundamentally in this order from ulnar to radial in each space; the first three branches may form a common trunk. The present observations demonstrate that individual nerves in the extremities may have a regular branching pattern, contrary to most of the previous observations.     

Inter- and intraspecific variation in gorgonian colony morphology: quantifying branching patterns in arborescent animals

Geomorphological methods for quantifying branching networks are used to describe inter- and intra-specific differences in branching patterns among two species of arborescent Caribbean gorgonian, Plexaura homomalla, P. flexuosa, and a third, undescribed plexaurid from the San Blas Islands, Panama. There were significant differences among species for first, second and third order branch lengths, and for tributary to source ratios for first and second order branches. Extrapolations from the branching parameters successfully predicted differences in the branch structure of naturally generated colony fragments. Within P. homomalla, significant differences with depth in the lengths and tributary to source ratios of first, second, and third order branches provide a measure of the greater bushiness of shallow water colonies. These measures can be used to quantify morphological differences in both ecological and systematic analyses. Data on the branching characters of these three gorgonian species demonstrate that gross colony form can be studied as a quantifiable component of phenotype and that gorgonians display both species level and ecophenotypic variation in colony form.     

Crown alterations induced by decline: a study of relationships between growth rate and crown morphology in beech (Fagus sylvatica L.)

One of the first symptoms expressed by declining trees is reduced growth in stem diameter and length increment. The possibility of a relationship between length increment and crown thinning in beech (Fagus sylvatica L.) was investigated by developing a computer model to simulate first order branching patterns of the apical 2 m of monopodially branching beech trees, 70–100 years old, for a range of length increment rates. The model was based on values for branching angle, main axis and branch length increment, number of branches produced per year and branch mortality rates for six healthy and declining trees. Shoot growth rates in the apical 2 m of the sample trees ranged from about 5 cm/year (decline class 3) to 43 cm/ year (healthy). Simulations of branching patterns in the apical 2 m of trees growing at different rates indicated that, when growth rate exceeded about 20 cm/year, total first order branch length and area explored were independent of growth rate. When growth rates fell below this value there was a reduction in total area explored and first order branch length due primarily to the formation of fewer branches. More acute branching angles contributed to a reduction in the area explored. Growth rate-related crown thinning could increase the risk of bark necrosis and secondary pathogen infection during dry and/or hot spells.     

Drosophila Dscam is required for divergent segregation of sister branches and suppresses ectopic bifurcation of axons

Axon bifurcation results in the formation of sister branches, and divergent segregation of the sister branches is essential for efficient innervation of multiple targets. From a genetic mosaic screen, we find that a lethal mutation in the Drosophila Down syndrome cell adhesion molecule (Dscam) specifically perturbs segregation of axonal branches in the mushroom bodies. Single axon analysis further reveals that Dscam mutant axons generate additional branches, which randomly segregate among the available targets. Moreover, when only one target remains, branching is suppressed in wild-type axons while Dscam mutant axons still form multiple branches at the original bifurcation point. Taken together, we conclude that Dscam controls axon branching and guidance such that a neuron can innervate multiple targets with minimal branching.     

Techniques for determining protein sequence evolution applied to primates

Each amino acid in a protein is considered to be an individual, mutable characteristic of the species from which the protein is extracted. For a branching tree representing the evolutionary history of the known sequences in different species, our computer programs use majority logic and parsimony of mutations to determine the most likely ancestral amino acid for each position of the protein at each node of the tree. The number of mutations necessary between the ancestral and present species is summed for each branch and the entire tree. The programs then move branches to make many different configurations, from which we select the one with the minimum number of mutations as the most likely evolutionary history. We used this method to elucidate primate phylogeny from sequences of fibrinopeptides, carbonic anhydrase, and the hemoglobin beta, delta and alpha chains. All available sequences indicate that the early Pongidae had diverged into two lines before the divergence of an ancestor for the human line alone. We have constructed some probable ancestral sequences at major points during primate evolution and have developed tentative trees showing the order of divergences and evolutionary distances among primate groups. Further questions on primate evolution could be answered in the future by the detemination of the appropriate sequences.     

Separated components of root exudate and cytosol stimulate different morphologically identifiable types of branching responses by arbuscular mycorrhizal fungi

Two morphologically distinct hyphal branching responses by the AM fungus, Glomus intraradices, were stimulated by separated components of carrot root exudate. Complex branching up to the sixth order was induced by compounds most soluble in 35 % methanol, whereas the formation of more lateral branches (second order) was stimulated by compounds most soluble in 70 % methanol. This same 70 % alcohol soluble fraction also stimulated a completely different type of branching pattern in another fungus, Gigaspora gigantea. This pattern consisted of a very periodic distribution of dense clusters of hyphal branches that had a very high degree of complexity. In contrast to exudate components, separated cytosolic components of carrot roots did not stimulate any of the observed hyphal branching patterns. Alcohol-soluble fractions actually inhibited hyphal tip growth of G. gigantea and induced the formation of “recovery” branches that were identical to those induced by an inhibitor found in the exudate of Chard (Beta vulgaris ssp. cicla), a non-host plant.     

Maintenance mechanisms of the pipe model relationship and Leonardo da Vinci’s rule in the branching architecture of <Emphasis Type="Italic">Acer rufinerve</Emphasis> trees

The pipe model relationship (constancy of branch cross-sectional area/leaf area) and Leonardo da Vinci’s rule (equality of total cross-sectional area of the daughter branches and cross-sectional area of their mother branch) are empirical rules of tree branching. Effects of branch manipulation on the pipe model relationships were examined using five Acer rufinerve trees. Half the branches in each tree were untreated (control branches, CBs), and, for the others (manipulated branches, MBs), either light intensity or leaf area (both relating to photosynthetic source activity), or shoot elongation (source + sink activities), was reduced, and responses of the pipe model relationships were followed for 2 years. The pipe model relationship in MBs changed by suppression of source activity, but not by simultaneous suppression of source + sink activities. The manipulations also affected CBs in the year of manipulation and both branches in the next year. The branch diameter growth was most affected by light, followed by shoot elongation and leaf area, in that order. Because of the decussate phyllotaxis of A. rufinerve, one branching node can potentially have one main and two lateral branches. Analysis of 295 branching nodes from 13 untreated trees revealed that the da Vinci’s rule held in branching nodes having one shed branch but not in the nodes without branch shedding, indicating the necessity of natural shedding of branches for da Vinci’s rule to hold. These analyses highlight the importance of the source–sink balance and branch shedding in maintenance of these empirical rules. This article was contributed at the invitation of the Editorial Committee.     

Computational modeling of retinotopic map development to define contributions of EphA-ephrinA gradients, axon-axon interactions, and patterned activity

The topographic projection of retinal ganglion cell (RGC) axons to mouse superior colliculus (SC) or chick optic tectum (OT) is formed in three phases: RGC axons overshoot their termination zone (TZ); they exhibit interstitial branching along the axon that is topographically biased for the correct location of their future TZ; and branches arborize preferentially at the TZ and the initial exuberant projection refines through axon and branch elimination to generate a precise retinotopic map. We present a computational model of map development that demonstrates that the countergradients of EphAs and ephrinAs in retina and the OT/SC and bidirectional repellent signaling between RGC axons and OT/SC cells are sufficient to direct an initial topographic bias in RGC axon branching. Our model also suggests that a proposed repellent action of EphAs/ephrinAs present on RGC branches and arbors added to that of EphAs/ephrinAs expressed by OT/SC cells is required to progressively restrict branching and arborization to topographically correct locations and eliminate axon overshoot. Simulations show that this molecular framework alone can develop considerable topographic order and refinement, including axon elimination, a feature not programmed into the model. Generating a refined map with a condensed TZ as in vivo requires an additional parameter that enhances branch formation along an RGC axon near sites that it has a higher branch density, and resembles an assumed role for patterned neural activity. The same computational model generates the phenotypes reported in ephrinA deficient mice and Isl2-EphA3 knockin mice. This modeling suggests that gradients of counter-repellents can establish a substantial degree of topographic order in the OT/SC, and that repellents present on RGC axon branches and arbors make a substantial contribution to map refinement. However, competitive interactions between RGC axons that enhance the probability of continued local branching are required to generate precise retinotopy.     

樟子松人工林分枝结构的分析

基于对6块樟子松(Pinus sylvestris var. mongolica)人工林固定标准地中的30株样木枝解析调查数据,通过分析不同林分、不同大小林木1级枝和2级枝的分枝概率、分枝格局和分枝角度,揭示了樟子松人工林树冠的分枝结构特点。研究结果表明：樟子松人工林1级枝和2级枝的平均分枝数量分别为3.84个和2.80个,两者分枝概率均呈正态分布;1级和2级枝条在光照条件好的几个区间（方位角46°～225°）分布较多,1级枝条的水平分布遵从均匀分布,而2级枝条则不遵从均匀分布;树冠上层枝条的分枝角度略小于树冠中、下层,上层平均分枝角度为45.6°,而中下层平均分枝角度都为49.4°。不同大小林木的1级枝分枝结构规律表明：Ⅰ级木和Ⅴ级木的每轮平均分枝数非常接近,分别为3.89和3.94个,比Ⅲ级木每轮分枝数大0.5个左右;1级枝水平分布在各区间内(45°间隔)相差在0.24%～2.81%之间,方差分析结果表明枝条水平分布与林木大小无关;不同大小林木的分枝角度有所差别,Ⅰ级木、Ⅲ级木和Ⅴ级木的平均分枝角度分别为48.5°、42.2°和50.7°。     

Research Progress and Application of Plant Branching

Plant branching development plays an important role in plant morphogenesis (aboveground plant type), the number and angle of branches are important agronomic characters that determine crop plant type. Effective branches determine the number of panicles or pods of crops and then control the yield of crops. With the rapid development of plant genomics and molecular genetics, great progress has been made in the study of branching development. In recent years, a series of important branching-related genes have been validated from Arabidopsis thaliana, rice, pea, tomato and maize mutants. It is reviewed that plant branching development is controlled by genetic elements and plant hormones, such as auxin, cytokinin and lactones (or lactone derivatives), as well as by environment and genetic elements. Meanwhile, shoot architecture in crop breeding was discussed in order to provide theoretical basis for the study of crop branching regulation.     

Branching is coordinated with mitosis in growing hyphae of Aspergillus nidulans

Filamentous fungi like Aspergillus nidulans can effectively colonize their surroundings by the formation of new branches along the existing hyphae. While growth conditions, chemical perturbations, and mutations affecting branch formation have received great attention during the last decades, the mechanisms that regulates branching is still poorly understood. In this study, a possible relation between cell cycle progression and branching was studied by testing the effect of a nuclei distribution mutation, cell cycle inhibitors, and conditional cell cycle mutations in combination with tip-growth inhibitors and varying substrate concentrations on branch initiation. Formation of branches was blocked after inhibition of nuclear division, which was not caused by a reduced growth rate. In hyphae of a nuclei distribution mutant branching was severely reduced in anucleated hyphae whereas the number of branches per hyphal length was linearly correlated to the concentration of nuclei, in the nucleated hyphae. In wild type cells, branching intensity was increased when the tip extension was reduced, and reduced when growing on poor substrates. In these situations, the hyphal concentration of nuclei was maintained and it is suggested that branching is correlated to cell cycle progression in order to maintain a minimum required cytoplasmic volume per nucleus and to avoid the formation of anucleated hyphae in the absence of nuclear divisions. The presented results further suggest the hyphal diameter as a key point through which the hyphal element regulates its branching intensity in response to the surrounding substrate concentrations.     

不同土壤雷竹盆栽苗地下茎分枝数量特征及其分布格局

为了探究竹子分株系统构建过程及其与人工经营的关系,本文对雷竹(Phyllostachys praecox C. D. Chu et C. S. Chao ‘Prevernalis’)不同年龄母竹、不同覆盖年限竹林进行土壤盆栽实验,比较了各处理竹苗地下茎分枝生长差异。结果显示：在盆栽竹苗分株系统构建过程中,地下茎以竹鞭分枝为主;2年生母竹盆栽苗地下茎分枝数量普遍高于1年生盆栽苗,且地下茎分枝表现出随竹林土壤覆盖年限增加而减少的趋势;盆栽苗地下茎分枝主要分布于第Ⅱ、Ⅲ、Ⅳ分枝的鞭中位置;1年生母竹盆栽苗地下茎分枝以第Ⅱ分枝级别的鞭中、鞭梢部位为多,而2年生母竹盆栽苗则以第Ⅲ分枝级别的鞭中、鞭梢部位为多;随土壤覆盖年限增加,地下茎分枝偏向分布于较为靠前的分枝级别。研究发现,母竹盆栽苗分株系统的构建主要采取了扩大地下分枝的策略,其2年生母竹与竹鞭中部着生侧芽的分枝生长对分株系统拓展贡献率较大;竹林土壤覆盖时间越久越不利于地下茎分枝。由于竹子分株系统具有时空拓展性,其地下茎分枝生长特征尚需持续观察。     

BRANCH GEOMETRY AND EFFECTIVE LEAF AREA: A STUDY OF TERMINAUA-BRANCHING PATTERN. 1. THEORETICAL TREES

Single lateral branches and branch tiers of Terminalia catappa L. are simulated and drawn by computer. Leaf clusters on the branches are approximated by discs, and the effective leaf areas are determined by use of Dirichlet domains. Theoretical optimal branching angles which produce the maximum effective leaf area are obtained from simulations. Symmetrical and asymmetrical branching angles are contrasted; the latter characterize real trees. Varying leaf disc radius and ratio of branch-unit lengths affects optimal branching angles, as does the symmetry of a tier of five branches. Leaf area indices for individual branches and branch tiers are given for all simulations. The number of branches in a tier has a major effect on leaf area index and effective leaf area. The theoretical optimal branching angles of many simulations are very close to the values observed in real trees of T. catappa. We conclude that the observed branching angles and number of branches in a tier of this species optimize light interception within constraints of a fixed pattern of branching, one that is widespread among tropical trees.     

The Development and Behaviour of Mycelial Strands in Merulius lacrymans (Wulf.) Fr.: II. Hyphal Behaviour during Strand Formation

The system of hyphal branching by Merulius lacrymans was observedin mycelium which had grown from a wood food-base on to glassslides during incubation in sterile moist chambers. A hierarchyof branches and sub-branches arose from the region of clampconnexions, or nodes, of relatively wide main hyphae. Therewas evidence that the sequence of branches occurring at nodesin basipetal succession represented the time sequence of branchdevelopment at any one node. Later-formed branches at any nodewere smaller than earlier branches, but such earlier branchesusually became smaller towards the tip as growth continued.Mycelial strands were built up by growth and branching of thigmo-tropicallysensitive ‘tendril’ hyphae in association with thewide main hyphae. Tendril hyphae were characteristically narrow,thin-walled hyphae arising both as later-formed branches fromthe nodes of the main hyphae and as the narrowed tips of earlierbranches. Although this branching behaviour could be seen amongstaerial hyphae growing over agar media, hyphae growing in contactwith or within the agar behaved differently and did not formstrands.     

Gene trees and species trees are not the same

The relationship between species is usually represented as a bifurcating tree with the branching points representing speciation events. The ancestry of genes taken from these species can also be represented as a tree, with the branching points representing ancestral genes. The time back to the branching points, and even the branching order, can be different between the two trees. This possibility is widely recognized, but the discrepancies are often thought to be small. A different picture is emerging from new empirical evidence, particularly that based on multiple loci or on surveys with a wide geographical scope. The discrepancies must be taken into account when estimating the timing of speciation events, especially the more recent branches. On the positive side, the different timings at different loci provide information about the ancestral populations.