Tree thinking cannot taken for granted: challenges for teaching phylogenetics

Tree thinking is an integral part of modern evolutionary biology, and a necessary precondition for phylogenetics and comparative analyses. Tree thinking has during the 20th century largely replaced group thinking, developmental thinking and anthropocentricism in biology. Unfortunately, however, this does not imply that tree thinking can be taken for granted. The findings reported here indicate that tree thinking is very much an acquired ability which needs extensive training. I tested a sample of undergraduate and graduate students of biology by means of questionnaires. Not a single student was able to correctly interpret a simple tree drawing. Several other findings demonstrate that tree thinking is virtually absent in students unless they are explicitly taught how to read evolutionary trees. Possible causes and implications of this mental bias are discussed. It seems that biological textbooks can be an important source of confusion for students. While group and developmental thinking have disappeared from most textual representations of evolution, they have survived in the evolutionary tree drawings of many textbooks. It is quite common for students to encounter anthropocentric trees and even trees containing stem groups and paraphyla. While these biases originate from the unconscious philosophical assumptions made by authors, the findings suggest that presenting unbiased evolutionary trees in biological publications is not merely a philosophical virtue but has also clear practical implications.

Simulated Evolutionary Optimization and Local Search: Introduction and Application to Tree Search

Tree search and its more complicated variant, tree search and simultaneous multiple DNA sequence alignment, are difficult NP-complete optimization problems, which require the application of advanced computational techniques, if large data sets are to be solved within reasonable computation times. Traditionally tree search has been attacked with a search strategy that is best described as multistart hill-climbing; local search by branch swapping has been performed on several different starting trees. Recently a different tree search strategy was tested in the Parsigal parsimony program, which used a combination of evolutionary optimization and local search. Evolutionary optimization algorithms use principles adopted from biological evolution to solve technical optimization tasks. Evolutionary optimization is a stochastic global search method, which means that the method is able to escape local optima, and is in principle able to produce any solution in the search space (although this may take a long time). Local search techniques, such as branch swapping, employ a completely different search strategy; they exploit local information maximally in order to achieve quick improvement in the value of the objective function. However, local search algorithms lack the ability to escape from local optima, which is a fundamental requirement for any search algorithm that aims to be able to discover the global optimum of a multimodal optimization problem. Hence it seems that an optimization strategy combining the good properties of both evolutionary algorithms and local search would be ideal. In this study, aspects of global optimization and local search are discussed, and the method of simulated evolutionary optimization is reviewed in detail. The application of simulated evolutionary optimization to tree search in Parsigal is then reviewed briefly.     

How and Why to Build a Unified Tree of Life

Phylogenetic trees are a crucial backbone for a wide breadth of biological research spanning systematics, organismal biology, ecology, and medicine. In 2015, the Open Tree of Life project published a first draft of a comprehensive tree of life, summarizing digitally available taxonomic and phylogenetic knowledge. This paper reviews, investigates, and addresses the following questions as a follow‐up to that paper, from the perspective of researchers involved in building this summary of the tree of life: Is there a tree of life and should we reconstruct it? Is available data sufficient to reconstruct the tree of life? Do we have access to phylogenetic inferences in usable form? Can we combine different phylogenetic estimates across the tree of life? And finally, what is the future of understanding the tree of life?

     

进化距离与相对替代率的比较研究

系统树是描述物种、人种甚至基因间亲缘关系和演化的重要工具,必须以进化距离或(相对)替代率作为重要的参数。但以哪一个参数构建的树更能反映真实的系统树呢?事实上迄今并无人对此作过认真的研究。本文以模拟数据并用方差分析法检验两个参数的异同并讨论其包含的生物学意义。研究结果表明,当氨基酸的替代率和核苷酸的替代率分别为0.18和0.13时,它们的进化距离分别为0.199和0.143。经方差分析证实,若检验的氨基酸和核苷酸最大数目均为75只时,不论以替代率或进化距离中那一个作为构树参数,拓扑树事实上几乎只有一个。这就是说,该时拓扑树可靠性很大,而且随着它们替代率的减少,则检验的氨基酸和核苷酸的数目会随之增加。但是一旦氨基酸的替代率和核苷酸的替代率超过上述数字,则两个参数构建的树在拓扑长度上是不等价的。经分析,若进化距离大致上与进化时间成线性关系的话,则应选用进化距离。用进化距离重建的系统树事实上支持中性学说;若进化距离与进化时间显著地不存在线性关系的话,则可选用替代率,该情况表明中性学说不适用,似更倾向于新达尔文主义。     

Integrins during evolution: Evolutionary trees and model organisms

The integrins form a large family of cell adhesion receptors. All multicellular animals express integrins, indicating that the family evolved relatively early in the history of metazoans, and homologous sequences of the component domains of integrin α and β subunits are seen in prokaryotes. Some integrins, however, seem to be much younger. For example, the αI domain containing integrins, including collagen receptors and leukocyte integrins, have been found in chordates only. Here, we will discuss what conclusions can be drawn about integrin function by studying the evolutionary conservation of integrins. We will also look at how studying integrins in organisms such as the fruit fly and mouse has helped our understanding of integrin evolution-function relationships. As an illustration of this, we will summarize the current understanding of integrin involvement in skeletal muscle formation.     

Dimetrodon Is Not a Dinosaur: Using Tree Thinking to Understand the Ancient Relatives of Mammals and their Evolution

The line of descent that includes all living mammals extends back in time over 300 million years. Many of the ancient relatives of mammals that fall along this line are very different in appearance from living mammals and are frequently mistaken for reptiles such as dinosaurs. This misconception is reinforced by the fact that these animals are often referred to as “mammal-like reptiles,” a term reflecting outdated methods for classifying organisms. In reality, these ancient mammal-relatives, known as synapsids, are more closely related to living mammals than they are to any reptiles. Evolutionary trees, which depict patterns of descent from common ancestors among organisms, are very useful for understanding why this is the case and for reconstructing the evolutionary histories of many of the unique characters found in mammals. Here, I provide an introduction to evolutionary trees and their implications for understanding the relationships between mammals, synapsids, and reptiles. This is followed by a review of synapsid diversity and a discussion of how evolutionary trees can be used to investigate when in synapsid history different mammalian characteristics first appeared.     

Evolutionary processes and evolutionary noise at the molecular level

Summary On account, notably, of a competition between different component functions for individual sites in polypeptide chains, each protein molecule represents a functional compromise, with some functions optimized, but the overall state of the molecule –suboptimal–. The proposal is made that the selection coefficient relating to a protein molecule under given conditions can in principle be broken down into partial selection coefficients relevant to the different functions that the molecule carries out. At generalfunction sites, each fixation improves some function, while others deteriorate, at first nonsignificantly, and the overall adaptive state of the molecule fluctuates around its maximum. A selective mechanism is described whereby kaleidoscopic changes in primary structure at variable sites are indefinitely promoted, independently of any environmental changes and with the molecule remaining close to a state of maximal overall adaptation. The paradoxical aspect of this proposal is analyzed. The implication of specific functions in substitutions at general-function sites is noted. Further, it is shown that a certain category of changes in the internal environment of the organism can be integrated into the constantenvironment model for selection. Genetic sufficiency is considered a notion more adequate than genetic optimality for describing biological fitness and for providing a basis for the present model. On this basis selection occurs without genetic load. Multipolymorphism is one of the consequences. Several lines of evidence, in particular observations on polymorphism in deep sea organisms, seem to support the model. It is pointed out that it provides a theoretical foundation for a molecular evolutionary clock. The theoretical constancy of the clock depends on the constancy of functional density. The question of the evolution of functional density is examined. Comparisons of observed substitution frequencies with values expected on a random basis are rejected as a measure of the contribution to evolution of nondetermination. They are considered to reflect a hierarchy in the resistance of the molecules to different amino acid residues as substituents. A limited component of –true– randomness, again accompanied by selection, is on the other hand provided by the model. Most amino acid substitutions are considered evolutionary noise, even though noise compatible with selection. It is proposed that evolutionarily significant substitutions may be identified by monitoring changes in functional density and weighted functional density.Directeur de Recherche at Centre National de la Recherche Scientifique, Paris.     

Correlation Between Ka/Ks and Ks is Related to Substitution Model and Evolutionary Lineage

In 2005, Wyckoff and coworkers described a surprisingly strong correlation between Ka/Ks and Ks in several data sets using the LPB93 algorithm. This finding indicated the possibility of a paradigm shift in the way selection strength can be measured using the Ka/Ks ratio. We carried out a calculation of Ka and Ks using six different algorithms on three cross-species orthologous data sets and found a highly variable correlation among the algorithms and lineages. Algorithms based on the GY-HKY substitution model exhibit a weaker positive correlation or a stronger negative correlation than those based on the K2P and JC69 substitution model. Even if one algorithm shows a positive correlation between Ka/Ks and Ks in a warm-blooded lineage, it may show no correlation in a cold-blooded lineage. This algorithm-related and evolutionary lineage-related correlation indicates the need for great caution in drawing conclusions when using only one Ka and Ks algorithm in a genomewide analysis of selection strength. Our results indicated that currently used algorithms for Ka and Ks calculations are flawed and need improvements.     

Evolutionary stability of egg trading and parceling in simultaneous hermaphrodites: the chalk bass revisited

Several species of simultaneously hermaphroditic seabasses living on coral reefs mate by alternating male and female roles with a partner. This is known as egg trading, one of the classic and most widely cited examples of social reciprocity among animals. Some of the egg-trading seabass species, including the chalk bass, Serranus tortugarum, switch mating roles repeatedly, having subdivided their clutch of eggs into parcels offered to the partner for fertilization. Here we attempt to understand these dynamics as a pair of evolutionary games, modifying some previous approaches to better reflect the biological system. We find that the trading of egg clutches is evolutionarily stable via byproduct mutualism and resistant to invasion by rare individuals that take the male role exclusively. We note why and how parceling may reflect sexual conflict between individuals in the mating pair. We estimate evolutionarily stable parcel numbers and show how they depend on parameter values. Typically, two or more sequential parcel numbers are evolutionarily stable, though the lowest of these yields the highest fitness. Assuming that parcel numbers are adjusted to local conditions, we predict that parcel numbers in nature are inversely related both to mating group density (except at low density) and predation risk.     

Classification of elapid snake neurotoxins and cytotoxins according to chain length: Evolutionary implications

Summary The amino acid sequences of the 139 homologous short neurotoxins, long neurotoxins and cytotoxins so far characterised from elapid snake venoms were compared on the basis of the amino acid deletion/insertion events that have occurred during evolution. Systematic grouping of the toxins according to similarity suggests that the short neurotoxins resemble the cytotoxins more closely than they do the long neurotoxins. The significance of this finding is discussed in relation to the methodology, the conformations of the toxins (as represented by circular dichroism spectra) and the outcome of the study that would have been obtained had more traditional methods been used. It appears probable that the cytotoxins evolved relatively recently from neurotoxic ancestors.     

Slow evolution of transferrin and albumin in birds according to micro-complement fixation analysis

Summary Rabbit antisera were prepared to purified ovotransferrin from chicken (order Galliformes) and red-winged blackbird (order Passeriformes) and to purified serum albumin from chicken and rhea (order Rheiformes). Quantitative microcomplement fixation was used to compare these proteins immunologically with those of representatives of all 27 orders of birds. The average interordinal immunological distances were 123 units for transferrin and 53 units for albumin.Extensive intraordinal comparisons of transferrin among 51 species within the order Galliformes and 33 species within the order Passeriformes were also carried out. Values ranging from 0–75 immunological distance units were found within each order.Rabbit antisera to purified alligator albumin were also prepared and shown to react with representatives of all 27 orders of birds, the average immunological distance being 166 units.When the data presented here are considered in relation to the fossil record of birds, it appears that transferrin and albumin have evolved more slowly in birds than in other vertebrates. If prevailing interpretations of the fossil record are correct, transferrin has evolved 2–4 times as fast in mammals and snakes as in birds, while serum albumin has evolved about 3 times as fast in mammals, iguanids, crocodilians, and frogs as in birds. Published immunological and sequence comparisons of lysozyme and cytochromec are also consistent with a slower rate of evolution in birds than in other vertebrates. The implications of a general slowdown in the evolution of bird proteins are discussed.This research was supported in part by grants from the National Science Foundation and the National Institutes of Health to A. C. Wilson and fellowship awards to A. H. Brush and R. A. Nolan (from NIH) and A. C. Wilson (from the Guggenheim Foundation). A preliminary account of part of this work was presented at the International Congress of Systematic and Evolutionary Biology in Boulder, Colorado, on August 9, 1973.The following abbreviations are used in this work: RWBB = red-winged blackbird; OT = ovotransferrin; EW = egg white; TE = tissue extract; ND = not done; MY = million years.     

牡丹开花相关基因PsAP1的克隆与表达

APETALA1基因对花器官的形成具有重要作用,并且能够调节花期.以牡丹品种赵粉(Paeoniasuffru-ticosaL.cv.Zhaofen)为试材,采用RT-PCR和RACE方法从花瓣中获得了1个牡丹APETALA1基因cDNA全长,命名为PsAP1,GenBank登录号为HM143943.其cDNA全长1103 bp,包含130 bp的5′非编码区、244 bp的3′非编码区和1个长度为729 bp编码242个氨基酸的开放阅读框.序列比对和系统进化分析表明,PsAP1与葡萄的亲缘关系最近,相似性达80%以上,属于MADS家族AP1/SQUA亚家族.相对荧光定量PCR分析表明,PsAP1在花瓣中的表达量最高,在雄蕊中表达量最低.     

Why Science Standards are Important to a Strong Science Curriculum and How States Measure Up

In 2000, Lawrence Lerner and the Thomas B. Fordham Foundation reviewed state science standards in 49 states and the District of Columbia, specifically with respect to the coverage of evolution. We repeat his survey for all current standards publicly available as of May 2009 and discuss the history and role of state science standards in American public education. Our survey indicates that science standards tend to cover evolution more extensively than they did a decade ago, and that the average quality of the treatment has increased. However, certain types of creationist language are also becoming more common in state standards. We also discuss the history and role of state science standards in American public education.     

Evolutionary responses of dispersal distance to landscape structure and habitat loss

It is generally well understood that some ecological factors select for increased and others for decreased dispersal. However, it has remained difficult to assess how the evolutionary dynamics are influenced by the spatio-temporal structure of the environment. We address this question with an individual-based model that enables habitat structure to be controlled through variables such as patch size, patch turnover rate, and patch quality. Increasing patch size at the expense of patch density can select for more or less dispersal, depending on the initial configuration. In landscapes consisting of high-quality and long-lived habitat patches, patch degradation selects for increased dispersal, yet patch loss may select for reduced dispersal. These trends do not depend on the component of life-history that is affected by habitat quality or the component of life-history through which density-dependence operates. Our results are based on a mathematical method that enables derivation of both the evolutionary stable strategy and the stationary genotype distribution that evolves in a polymorphic population. The two approaches generally lead to similar predictions. However, the evolutionary stable strategy assumes that the ecological and evolutionary time scales can be separated, and we find that violation of this assumption can critically alter the evolutionary outcome.     

Exceptions to the one:one relationship between African fig trees and their fig wasp pollinators: possible evolutionary scenarios

Abstract. The mutualistic breeding system involving fig trees (Moraceae, Ficus ) and fig wasps (Hymenoptera, Chalcidoidea, Agaoninae) would appear so specialized that one may wonder at the evolutionary processes that could be responsible for the existence of about 750 species-specific associations. In this paper we present data concerning two cases of species specificity breakdown between African fig trees and fig wasps. We then analyse the possible evolutionary scenarios which could be responsible, as well as the possible evolutionary outcomes of the observed situations. Our analyses range in scale from continental to habitats, and fig crops to individual figs (syconia). Habitat shifts and ecological barriers seem to be the more likely explanations for the evolution of novel fig tree-fig wasp associations, but sympatric and parapatric scenarios cannot be ruled out.     

Markov and Semi‐Markov Switching Linear Mixed Models Used to Identify Forest Tree Growth Components

Summary Tree growth is assumed to be mainly the result of three components: (i) an endogenous component assumed to be structured as a succession of roughly stationary phases separated by marked change points that are asynchronous among individuals, (ii) a time‐varying environmental component assumed to take the form of synchronous fluctuations among individuals, and (iii) an individual component corresponding mainly to the local environment of each tree. To identify and characterize these three components, we propose to use semi‐Markov switching linear mixed models, i.e., models that combine linear mixed models in a semi‐Markovian manner. The underlying semi‐Markov chain represents the succession of growth phases and their lengths (endogenous component) whereas the linear mixed models attached to each state of the underlying semi‐Markov chain represent—in the corresponding growth phase—both the influence of time‐varying climatic covariates (environmental component) as fixed effects, and interindividual heterogeneity (individual component) as random effects. In this article, we address the estimation of Markov and semi‐Markov switching linear mixed models in a general framework. We propose a Monte Carlo expectation–maximization like algorithm whose iterations decompose into three steps: (i) sampling of state sequences given random effects, (ii) prediction of random effects given state sequences, and (iii) maximization. The proposed statistical modeling approach is illustrated by the analysis of successive annual shoots along Corsican pine trunks influenced by climatic covariates.     

Comparing the Performance of Tree Stakes and Seedlings to Restore Abandoned Tropical Pastures

Tree seedlings are commonly planted to restore abandoned agricultural lands, whereas vegetative plantings have received little study. We evaluated the ability of 10 tree species to establish and survive over 3 years by planting 2‐m‐tall vegetative stakes at three sites in southern Costa Rica. We quantified above‐ and belowground stake and seedling biomass for two species (Erythrina poeppigiana and Gliricidia sepium) after 1 year and canopy cover and height of E. poeppigiana stakes and saplings at 3 years. We also compared economic, logistical, and ecological advantages of each methodology. Erythrina poeppigiana and E. berteroana had the highest number of live stakes by the study’s conclusion (>90%) and were among species with largest canopies. Most others ranged between 40 and 70% with highly site‐specific survival and growth rates, whereas three species did poorly. Four species developed fruit by year 3, including Ficus pertusa and Acnistus arborescens, that are consumed by frugivores. Above‐ and belowground biomass was 7–50 times greater in stakes (65–125 g) than seedlings (2–15 g). Stake roots were considerably more extensive and reached lengths more than 6 m. Erythrina poeppigiana stakes had higher canopy cover than saplings after 3 years but not height. Seedlings are 2–10 times more expensive to establish, although transporting stakes is more cumbersome and the suite of species that establish vegetatively is limited. This underused technique should be included in the growing repertoire of tropical forest restoration tools. Given tradeoffs in propagation methods, a combination is likely to be most efficient and successful.     

树木年轮对气候变化的响应研究及其应用

树木年轮的宽度、密度、亮度和同位素含量等都与气候因子光、温和湿度等的变化有复杂的相关关系, 对这种相关生理机理的研究也有较大的进展。综述了这方面的研究进展及这些成果在古气候和环境研究、生理生态学、林学、群落学甚至历史社会学等领域的应用。