Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores

Darwin's paradigm holds that the diversity of present-day organisms has arisen via a process of genetic descent with modification, as on a bifurcating tree. Evidence is accumulating that genes are sometimes transferred not along lineages but rather across lineages. To the extent that this is so, Darwin's paradigm can apply only imperfectly to genomes, potentially complicating or perhaps undermining attempts to reconstruct historical relationships among genomes (i.e., a genome tree). Whether most genes in a genome have arisen via treelike (vertical) descent or by lateral transfer across lineages can be tested if enough complete genome sequences are used. We define a phylogenetically discordant sequence (PDS) as an open reading frame (ORF) that exhibits patterns of similarity relationships statistically distinguishable from those of most other ORFs in the same genome. PDSs represent between 6.0 and 16.8% (mean, 10.8%) of the analyzable ORFs in the genomes of 28 bacteria, eight archaea, and one eukaryote (Saccharomyces cerevisiae). In this study we developed and assessed a distance-based approach, based on mean pairwise sequence similarity, for generating genome trees. Exclusion of PDSs improved bootstrap support for basal nodes but altered few topological features, indicating that there is little systematic bias among PDSs. Many but not all features of the genome tree from which PDSs were excluded are consistent with the 16S rRNA tree.     

Darwin and the Galápagos

Charles Darwin's historic visit to the Galápagos Islands in 1835 represents a landmark in the annals of science. But contrary to the legend long surrounding Darwin's famous Galápagos visit, he continued to believe that species were immutable for nearly a year and a half after leaving these islands. This delay in Darwin's evolutionary appreciation of the Galápagos evidence is largely owing to numerous misconceptions that he entertained about the islands, and their unique organic inhabitants, during the Beagle voyage. For example, Darwin mistakenly thought that the Galápagos tortoise–adult specimens of which he did not collect for scientific purposes–was not native to these islands. Hence he apparently interpreted reports of island-to-island differences among the tortoises as analogous to changes that are commonly undergone by species removed from their natural habitats. As for Darwin's finches, Darwin initially failed to recognize the closely related nature of the group, mistaking certain species for the forms that they appear, through adaptive radiation, to mimic. Moreover, what locality information he later published for his Galápagos finch specimens was derived almost entirely from the collections of three other Beagle shipmates, following his return to England. Even after he became an evolutionist, in March of 1837 (when he discussed his Galápagos birds with the eminent ornithologist John Gould), Darwin's theoretical understanding of evolution in the Galápagos continued to undergo significant developments for almost as many years as it took him to publish the Origin of Species (1859). The Darwin-Galápagos legend, with its romantic portrait of Darwin's 'eureka-like' insight into the Galápagos as a microcosmic 'laboratory of evolution', masks the complex nature of scientific discovery, and, thereby, the real nature of Darwin's genius.     

Darwinian gradualism and its limits: The development of Darwin's views on the rate and pattern of evolutionary change

Conclusion The major tenets of the recent hypothesis of punctuated equilibrium are explicit in Darwin's writing. His notes from 1837–1838 contain references to stasis and rapid change. In the first edition of the Origin (1859), Darwin described the importance of isolation of local varieties in the process of speciation. His views on the tempo of speciation were influenced by Hugh Falconer and also, perhaps, by Edward Suess (1831–1914). It is paradoxical that, although both topics were recorded in his unpublished notes of 1837–1838, the second was not explicitly and fully discussed until the fourth edition of the Origin (1866). While no wholly satisfactory explanation of this paradox suggests itself, it seems probable that Falconer's work on the persistence of fossil species of elephant helped Darwin to see the wider significance of the tempo of evolution for his general theory.     

PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships

Background  

Phylogenies, i.e., the evolutionary histories of groups of taxa, play a major role in representing the interrelationships among biological entities. Many software tools for reconstructing and evaluating such phylogenies have been proposed, almost all of which assume the underlying evolutionary history to be a tree. While trees give a satisfactory first-order approximation for many families of organisms, other families exhibit evolutionary mechanisms that cannot be represented by trees. Processes such as horizontal gene transfer (HGT), hybrid speciation, and interspecific recombination, collectively referred to as reticulate evolutionary events, result in networks, rather than trees, of relationships. Various software tools have been recently developed to analyze reticulate evolutionary relationships, which include SplitsTree4, LatTrans, EEEP, HorizStory, and T-REX.     

生命之树及其应用

生命之树的概念由达尔文在1859年提出, 用以反映分类群的亲缘关系和进化历史。近30年来, 随着建树性状种类的多样化、数据量的快速增长以及建树方法的不断发展和完善, 生命之树的规模越来越大, 可信度也越来越高。分子生物学、生态学、基因组学、生物信息学及计算机科学等的快速发展, 使得生命之树成为开展学科间交叉研究的桥梁, 其用途日益广泛。本文综述了生命之树研究的历史和现状, 介绍了生命之树在以下几个方面的应用: (1)通过构建不同尺度的生命之树, 理解生物类群间的系统发育关系; (2)通过时间估算和地理分布区重建, 推测现存生物的起源和地理分布格局及其成因; (3)基于时间树, 结合生态、环境因子及关键创新性状, 探讨生物的多样化进程和成因; (4)揭示生物多样性的来源和格局, 预测生物多样性动态变化, 并提出相应的保护策略。最后, 本文评估了生命之树在目前海量数据情况下遇到的序列比对困难、基因树冲突、“流浪类群”干扰等建树难题, 并指出了构建“超大树”的发展趋势。     

Taxon ordering in phylogenetic trees: a workbench test

Background  

Phylogenetic trees are an important tool for representing evolutionary relationships among organisms. In a phylogram or chronogram, the ordering of taxa is not considered meaningful, since complete topological information is given by the branching order and length of the branches, which are represented in the root-to-node direction. We apply a novel method based on a (λ + μ)-Evolutionary Algorithm to give meaning to the order of taxa in a phylogeny. This method applies random swaps between two taxa connected to the same node, without changing the topology of the tree. The evaluation of a new tree is based on different distance matrices, representing non-phylogenetic information such as other types of genetic distance, geographic distance, or combinations of these. To test our method we use published trees of Vesicular stomatitis virus, West Nile virus and Rice yellow mottle virus.     

Pyric tree spatial patterning interactions in historical and contemporary mixed conifer forests,California, USA

Tree spatial patterns in dry coniferous forests of the western United States, and analogous ecosystems globally, were historically aggregated, comprising a mixture of single trees and groups of trees. Modern forests, in contrast, are generally more homogeneous and overstocked than their historical counterparts. As these modern forests lack regular fire, pattern formation and maintenance is generally attributed to fire. Accordingly, fires in modern forests may not yield historically analogous patterns. However, direct observations on how selective tree mortality among pre‐existing forest structure shapes tree spatial patterns is limited. In this study, we (a) simulated fires in historical and contemporary counterpart plots in a Sierra Nevadan mixed‐conifer forest, (b) estimated tree mortality, and (c) examined tree spatial patterns of live trees before and after fire, and of fire‐killed trees. Tree mortality in the historical period was clustered and density‐dependent, because trees were aggregated and segregated by tree size before fire. Thus, fires maintained an aggregated distribution of tree groups. Tree mortality in the contemporary period was widespread, except for dispersed large trees, because most trees were a part of large, interconnected tree groups. Thus, postfire tree patterns were more uniform and devoid of moderately sized tree groups. Postfire tree patterns in the historical period, unlike the contemporary period, were within the historical range of variability identified for the western United States. This divergence suggests that decades of forest dynamics without significant disturbances have altered the historical means of pyric pattern formation. Our results suggest that ecological silvicultural treatments, such as forest restoration thinnings, which emulate qualities of historical forests may facilitate the reintroduction of fire as a means to reinforce forest structural heterogeneity.     

Understanding Evolutionary Trees

Charles Darwin sketched his first evolutionary tree in 1837, and trees have remained a central metaphor in evolutionary biology up to the present. Today, phylogenetics—the science of constructing and evaluating hypotheses about historical patterns of descent in the form of evolutionary trees—has become pervasive within and increasingly outside evolutionary biology. Fostering skills in “tree thinking” is therefore a critical component of biological education. Conversely, misconceptions about evolutionary trees can be very detrimental to one’s understanding of the patterns and processes that have occurred in the history of life. This paper provides a basic introduction to evolutionary trees, including some guidelines for how and how not to read them. Ten of the most common misconceptions about evolutionary trees and their implications for understanding evolution are addressed.

Do orthologous gene phylogenies really support tree-thinking?

Background  

Since Darwin's Origin of Species, reconstructing the Tree of Life has been a goal of evolutionists, and tree-thinking has become a major concept of evolutionary biology. Practically, building the Tree of Life has proven to be tedious. Too few morphological characters are useful for conducting conclusive phylogenetic analyses at the highest taxonomic level. Consequently, molecular sequences (genes, proteins, and genomes) likely constitute the only useful characters for constructing a phylogeny of all life. For this reason, tree-makers expect a lot from gene comparisons. The simultaneous study of the largest number of molecular markers possible is sometimes considered to be one of the best solutions in reconstructing the genealogy of organisms. This conclusion is a direct consequence of tree-thinking: if gene inheritance conforms to a tree-like model of evolution, sampling more of these molecules will provide enough phylogenetic signal to build the Tree of Life. The selection of congruent markers is thus a fundamental step in simultaneous analysis of many genes.     

天目山柳杉树轮δ13C年序列差异

对天目山3株柳杉树轮δ¹³C年序列分别进行了测定,分析了柳杉树轮δ¹³C年序列变化的异同及其原因.结果表明,在1837～1982年的共同时段,3个树轮δ¹³C年序列彼此间相关系数为：r₁₂=0.47,r₁₃=0.65,r₂₃=0.52 (n=146),都通过了显著性水平α=0.001的信度检验.用多项式拟合法去除原δ¹³C年序列中的高频变化后,所得3个低频序列间高度正相关;原δ¹³C年序列与拟合序列的差值序列即高频序列间也显著正相关,相关系数均达到0.79～0.99,说明气候因素引起树轮δ¹³C年序列的高频变化及大气CO₂浓度引起的低频变化对不同的柳杉个体是共同的.3株树轮δ¹³C年序列间的差异主要是树木立地处局部环境条件的不同所造成的,但是局部环境条件所引起的树轮δ¹³C年序列间的个性差异对其共性变化影响较小.所以,3个树轮δ¹³C年序列间的个性差异,并不影响树轮δ¹³C年作为气候变化研究代用资料的适宜性及重建历史气候结果的可靠性与一致性.     

单细胞生物进化研究的进步

20世纪60年代,生物大致分为5界的谱系图,　经历了几次翻新,开始提出了线粒体和叶绿体的内共生学说。 由于分子生物学的发展,首先将各种生物的蛋白质的分子进行比较,构建成蛋白质的分子系统树。再转向核糖核酸,将核糖体的小亚单位,作为区别生命类型之间亲缘关系的指标。发现有些嗜极端条件的细菌,它们不同于原核生物也不同于真核生物,是第三种类型的生命形式。因此,在 80年代为生命建立了细菌、古细菌和真核生物三界的系统树。对许许多多单个基因的系统树的分析,又使人们认识到,古细菌与细菌和真核微生物之间以及各个物种之间,显然皆发生过大量的基因交换。对单细胞进化来说,基因除垂直传递外,横向的或叫侧向的基因转移也十分繁多。在一张完全的系统图中,要同时表现几千个不同的基因家族的超联结的种系型式才符合实际。因而,最新版本的系统树是分枝交缠、无主干的。 Abstract:In 1960s,kimgdoms of organisms were charted generally in a five branching form.Later,the endosymbiont hypothesis for the mitochondria and the chloroplast was proposed.The life-form is divided into two forms,the prokaryotes (bacteria) and the eukaryotes.The study of the molecular biology made the progress faster.In 1980s,Woese,CR.asserted that two-domain view of life was no longer true,a three-domain construct,the Bacteria,the Archaea,and the Eukaryotes had to take its place.At first,phylogeny trees based on differences in the amino acid sequences,then among ribosomal RNAs and also nuclear gene from hundreds of microbial species were depicted and many mini phylogenetic trees grouped the species according to their differences in the sequences.It was found that they shared genes between their contemporaries and across the species barriers.At the root of the phylogeny tree,there was not a single common cell,it was replaced by a common ancestral community of primitive cells.Genes transfered rather freely as the transposons swapping between those cells.There was no last universal common ancestor of single cell that could be found in the revised Tree of Life,It was not easy to represent the genealogical patterns of thousands of different families of genes,in one systematic map,therefor there was no trunk at all.     

<Emphasis Type="Italic">Maggengo</Emphasis> meadow patches enclosed by forests in the Italian Alps: evidence of landscape legacy on plant diversity

The maggenghi are mid slope meadows typical of all the southern and of great parts of the northern European Alps, for centuries managed with traditional and low intensity techniques. Usually, they are scattered patches in surrounding forests. The spontaneous expansion of trees and shrubs, favored by the recent decline of mountain agriculture, lead the maggengo patches patterns and shapes to change. Our objective was to analyze the effect of this change on current plant diversity of the remnant patches, as the adaptive response could be slow and possibly related more to historical than to current landscape patterns. We analyzed the trend of the size, shape, elongation, fractal dimension and connectivity of maggengo patches of a Central-Eastern Italian Alpine district, in four time steps, from 1973 to 2006, and in 1859, when mountain agriculture was still widespread. Then, we studied the relationships between those landscape metrics and two current patch-level plant diversity measures: interior species richness and species density. Aerial photographs were used to investigate that trend, while a historical cadastral map was used to assess the landscape metrics in 1859. As expected, in the last 30 years, the total size of maggenghi has been reduced by 57% while their shapes have been progressively simplified. Interior species richness was positively related to size, both in 2006 and over the past 30 years, but not to any 1859 measures. Conversely, species density was positively correlated only with 1859 size, shape index and connectivity. We conclude that the historical shape, size and connectivity are some of the key variables affecting the plant species density of maggengo patches, but not of their interior plant species richness.     

Phylogenetic identification of lateral genetic transfer events

Background  

Lateral genetic transfer can lead to disagreements among phylogenetic trees comprising sequences from the same set of taxa. Where topological discordance is thought to have arisen through genetic transfer events, tree comparisons can be used to identify the lineages that may have shared genetic information. An 'edit path' of one or more transfer events can be represented with a series of subtree prune and regraft (SPR) operations, but finding the optimal such set of operations is NP-hard for comparisons between rooted trees, and may be so for unrooted trees as well.     

Effects of lightning on trees: A predictive model based on in situ electrical resistivity

The effects of lightning on trees range from catastrophic death to the absence of observable damage. Such differences may be predictable among tree species, and more generally among plant life history strategies and growth forms. We used field‐collected electrical resistivity data in temperate and tropical forests to model how the distribution of power from a lightning discharge varies with tree size and identity, and with the presence of lianas. Estimated heating density (heat generated per volume of tree tissue) and maximum power (maximum rate of heating) from a standardized lightning discharge differed 300% among tree species. Tree size and morphology also were important; the heating density of a hypothetical 10 m tall Alseis blackiana was 49 times greater than for a 30 m tall conspecific, and 127 times greater than for a 30 m tall Dipteryx panamensis. Lianas may protect trees from lightning by conducting electric current; estimated heating and maximum power were reduced by 60% (±7.1%) for trees with one liana and by 87% (±4.0%) for trees with three lianas. This study provides the first quantitative mechanism describing how differences among trees can influence lightning–tree interactions, and how lianas can serve as natural lightning rods for trees.     

Biological invasion into the nested assemblage of tree–beetle associations on the oceanic Ogasawara Islands

Invasion by alien organisms is a common worldwide phenomenon, and many alien species invade native communities. Invasion by alien species is especially likely to occur on oceanic islands. To determine how alien species become integrated into island plant–insect associations, we analyzed the structure of tree–beetle associations using host plant records for larval feeding by wood-feeding beetles (Coleoptera: Cerambycidae) on the oceanic Ogasawara Islands in the northwestern Pacific Ocean. The host plant records comprised 109 associations among 28 tree (including 8 alien) and 26 cerambycid (including 5 alien) species. Of these associations, 41.3% involved at least one alien species. Most native cerambycid species feed on host trees that have recently died. Alien trees were used by as many native cerambycid species (but by significantly more alien cerambycid species) as were native trees. Native cerambycid species used as many alien tree species (but significantly more native tree species) as did alien cerambycids. Thus, we observed many types of interactions among native and alien species. A network analysis revealed a significant nested structure in tree–cerambycid associations regardless of whether alien species were excluded from the analysis. The original nested associations on the Ogasawara Islands may thus have accepted alien species.     

Tree growth traits and social status affect the wood density of pioneer species in secondary subtropical forest

Wood density (WD) is not only an important parameter to estimate aboveground biomass but also an indicator of timber quality and plant adaptation strategies to stressful conditions (i.e., windthrow, pests, and pathogens). This study had three objectives: (1) to compare WD among seven subtropical tree species; (2) to determine how tree growth traits may influence possible differences in WD between the pioneer and shade‐tolerant species; and (3) to examine whether or not WD differs by tree social status (dominant vs. suppressed trees) within species. To do this, 70 trees were destructively harvested. From each tree, disks at different stem heights were obtained and subjected to a method of stem analysis to measure whole tree level WD. The results showed that WD differed significantly among the seven species (p < .001). Their average WD was 0.537 g/cm³, ranging from 0.409 g/cm³ for Choerospondias axillaris to 0.691 g/cm³ for Cyclobalanopsis glauca. The average WD of the four pioneer species (0.497 ± 0.13 g/cm³) was significantly lower (p < .01) than that of the three shade‐tolerant species (0.589 ± 0.12 g/cm³). The WD of the pioneers had a significant positive correlation with their stem diameter at breast height (DBH), tree height (H), and tree age, but WD had a significant negative correlation with relative growth rate (RGR). In contrast, the WD of the shade‐tolerant tree species had no significant relationships with DBH, H, tree age, or RGR. The dominant trees of the pioneer species had a higher WD than the suppressed trees, whereas the shade‐tolerant species had a lower WD for dominant trees than the suppressed trees. However, the differences in WD between dominant and suppressed trees were not significant. Taken together, the results suggest that classifying species into pioneer and shade‐tolerant groups to examine the effects of tree growth traits and social status could improve our understanding of intra‐ and interspecific variation in WD among subtropical tree species.     

God and natural selection: The Darwinian idea of design

Conclusion If we arrange in chronological order the various statements Darwin made about God, creation, design, plan, law, and so forth, that I have discussed, there emerges a picture of a consistent development in Darwin's religious views from the orthodoxy of his youth to the agnosticism of his later years. Numerous sources attest that at the beginning of the Beagle voyage Darwin was more or less orthodox in religion and science alike.⁷⁸ After he became a transmutationist early in 1837, he concluded that the doctrine of secondary causes must be extented even to the history of life and that after the first forms of life were created, there was no further need for divine intervention, except where man was concerned. Man's body, he thought, was produced by the process of transmutation, but he believed for a time that man's soul was superadded. By mid-1838 he had become convinced that nothing, after the creation of life, was due to miracles. God works only through laws, which are capable of producing every effect of evey kind which surrounds us. The existence of man, the idea of God in man's mind, and the harmony of the whole system were in his eyes prearranged goals of deterministic laws imposed by God. Such a conception excludes the miracles on which Christianity depends; but it is not possible to say whether Darwin's loss of Christian faith, which occurred at about this same time, preceded and made possible his materialism or was rather caused or hastened by it.⁷⁹ In the weeks after his reading of Malthus, Darwin's belief in a plan of creation gave way to the belief that God created matter and life and designed their laws, leaving the details, however, to the workings of chance. This remained his view until the 1860s.There is no exact parallel between this development of Darwin's religious views and the development of his ideas on evolution, but there is a general correspondence. When he believed in a plan of creation, Darwin's theory of transmutation did not depend on struggle or the selection of chance variations. Adaptation was, for him, an automatic response to environmental chance. From late 1838 to 1859 he believed in designed laws and chance, and this belief, too, has its parallel in his theory. The element of chance in natural selection meant that there could be no detailed plan,in which even man's idea of God would be a necessary outcome of nature's laws (man himself is not a necessary outcome of the working of natural selection).⁸⁰ But Darwin still believed nature was programmed to achieve certain general ends. We might say that he believed in a general, though not a special, teleology. Natural selection was for him a law to maximize utility, creating useful organs, retaining vestiges for future use. For many years it was a law designed to produce organisms perfectly adapted to their environments. Only later did Darwin come to doubt even this sort of design in nature.⁸¹ One way of describing the development of Darwin's evolutionary thought is to say that it shows a gradual abandoning of his theistic assumptions, so that by the late 1860s his theory was informed to a slighter extent by notions of purpose and design than it was in 1838 or 1844 or 1859.     

Elastic,not plastic species: Frozen plasticity theory and the origin of adaptive evolution in sexually reproducing organisms

Background  

Darwin's evolutionary theory could easily explain the evolution of adaptive traits (organs and behavioral patterns) in asexual but not in sexual organisms. Two models, the selfish gene theory and frozen plasticity theory were suggested to explain evolution of adaptive traits in sexual organisms in past 30 years.     

Leaf-consumption levels in subtropical mangroves of Paranaguá Bay (SE Brazil)

The objective of this study was to measure leaf consumption levels, mainly by insect herbivores and the tree-dwelling crab Aratus pisonii (H. Milne Edwards, 1837), in mangrove forests of a large subtropical estuarine system in the South Atlantic Ocean, to determine if patterns of herbivory varied with forest structure, tree species and marked seasonal differences in rainfall and temperature. We analyzed three structurally different mangroves located in the euhaline high-energy sector of Paranaguá Bay, all of them with known values of annual litter fall. Consumption levels varied from 2.2–5.4% of total leaf area considering each site as a whole, and from 2.0–6.0% considering each tree species separately. No significant differences in consumption levels were found between summer and winter samples, but significant differences were found among sites and among tree species. Leaves from Laguncularia racemosa were most consumed. The site with lower consumption levels was the one covered with dwarf trees, a condition usually caused by low nutrient availability in the soil. Analysis of nitrogen and phosphorus levels revealed lower amounts of both nutrients in soils and of phosphorus in leaves from this site when compared to the ones containing more developed trees. This result suggests a relationship between herbivory and nutrient availability in the plants.