生物演化集合论中的最近共同祖先与分支分类问题的解

本文是“生物演化的数学模型”一文的续篇文章,概要如下：1）讨论最近共同祖先运算的性质;2）引进基本演化集的概念和基本演化集存在性公理;3）给出假设分类单位和导出演化集的严格定义;4）引入保持演化关系概念并讨论分支分类问题的解;5）证明分支分类问题解的存在性和唯一性。上述结果有助于为分支分类问题奠定数学理论基础。     

中国毛茛科植物小志(廿二)

(1)揭示了铁线莲属以下演化趋势:萼片由开展到直立;雄蕊由无毛到有毛;雄蕊花丝由条形演 化到披针状条形或倒披针状条形;花药由长圆形演化到条形或狭条形;药隔不突出到在顶端突出;在雄 蕊被毛时,毛由少而短到多而长;此外花序由具花序梗和苞片到花序梗和苞片消失,以及由自当年生枝 叶腋生出转变到自老枝腋芽中生出。主要根据上述演化趋势,本文将我国铁线莲属各组及组下分类群做出新的排列。(2)描述了6新亚组,6新系,2新种,4新变种,给出了5新组合,4新等级和2新名。     

中国毛茛科植物小志(廿二)

(1)揭示了铁线莲属以下演化趋势:萼片由开展到直立;雄蕊由无毛到有毛;雄蕊花丝由条形演 化到披针状条形或倒披针状条形;花药由长圆形演化到条形或狭条形;药隔不突出到在顶端突出;在雄 蕊被毛时,毛由少而短到多而长;此外花序由具花序梗和苞片到花序梗和苞片消失,以及由自当年生枝 叶腋生出转变到自老枝腋芽中生出。主要根据上述演化趋势,本文将我国铁线莲属各组及组下分类群做出新的排列。(2)描述了6新亚组,6新系,2新种,4新变种,给出了5新组合,4新等级和2新名。     

重建系统演化树的一种新方法--试错法

重建系统演化树是进化研究的一个极为重要的方面。系统树的构建依赖于一定的方法和数据。在分子系统演化研究中,所使用的数据大多是ＤＮＡ序列、氨基酸序列和分子标记。而就构树方法来说,ＮＪ法、ＭＬ法和ＭＰ法是三种最为普遍使用的方法。本文给出了一种新的建树方法,即试错法。该方法不但具有与ＮＪ法一样好的建树效果,而且不存在难以解释的负枝长问题。     

鹿科麂属动物基因组演化研究进展

鹿科麂属(Muntiacus, Cervidae)在近两三百万年内经历了快速物种辐射, 但其物种间核型差异巨大. 5个现生种核型数据显示, 该类群染色体数目范围从小麂(Muntiacus reevesi)的46条到赤麂(M. muntjak vaginalis)的6条. 该类群的基因组在较短时间内发生了快速演化, 使其成为进化生物学研究的理想材料. 40多年来, 技术的革新使该领域的研究不断深入, 染色体重排的类型、推动重排的分子机制及物种间的核型演化历程逐渐被阐释. 而且, 研究中发现, 雄性黑麂(M. crinifrons)1p+4染色体的演化途径与哺乳动物Y染色体的演化历程相似, 可成为哺乳动物性染色体演化研究的珍贵模型. 有关麂属动物基因组演化依然有许多问题等待更加全面、深入的探讨. 本文总结了该领域研究进展, 并对未来研究热点进行了展望.     

铁线莲属一新分类系统

提出毛茛科Ranunculaceae铁线莲属Clematis一新分类系统。首先,简要回顾了此属的分类学研究历史,继对此属的营养器官和生殖器官的重要形态特征和花粉特征进行了分析,揭示出一系列演化趋势。这些趋势,尤其是萼片和雄蕊的演化趋势说明在现存的铁线莲属植物中,绣球藤Clematis montana与其少数近缘种的花构造最接近比铁线莲属原始的银莲花属Anemone,因此,包括绣球藤等植物的绣球藤组sect. Cheirpsis被认为是铁线莲属的原始群。主要根据花构造对铁线莲属现存的15组的亲缘关系进行了分析,发现它们是在4条演化干(绣球藤干、欧洲铁线莲干、尾叶铁线莲干、长瓣铁线莲干)的演化过程中先后形成的。本文将此4条演化干处理为亚属。最后做出属下各级分类群的系统排列,并给出简要的形态特征。     

从电脑的发展管窥人类的起源与未来

从电脑的发展类比人类的起源 19世纪末在印尼爪畦发现了爪哇猿人化石,这些标本具有与现代人相似的颌骨但与猿相似的头骨。爪哇猿人的归属及其在人类起源与演化关系中的位置等问题引发了极大的争议。1929年裴中先生在周口店发现了北京猿人头盖骨,证实了爪哇猿人是处于猿与人之间这一演化阶段的猿人。北京猿人头盖骨之所以能证明人类演化上的猿人阶段,是因为北京猿人头盖骨的平均脑容量为1059毫升,接近现代人的1350毫升平均脑容量,此外还有大量一同出土的石器及用火痕迹等化遗物。     

皖南、赣北早特马道克期Staurograptus的再研究

对皖南和赣北早奥陶世早特马道克期的Staurograptus重新研究表明,该属具有原始枝末端正分推迟、分支级数缩减和笔石枝密度降低的演化趋势,而代表不同演化阶段的三个种类,即Staurograptus dichotomus Emmons,S．apertus Ruedemann和S．hyperboreus Obut et Sobolevskaya,构成了该属基本的系统发育谱系。种群分析进一步显示,其主要性状变异范围尽管较宽但趋于正态分布的S．dichotomus,可能包含了除S．apertus和S．hyperboreus之外的所有已知Staurograptus的异名种类。     

生物复苏——大绝灭后生物演化历史的第一幕

生命史是一部生物界短期,快速剧变与长期,慢速稳定相互交替的历史。大绝灭（即集群绝灭）事件反映了全球环境的大突变,点断了地质历史中的生命记录及其发展历程,预示着生物界的演化出现了最有意义的飞跃,近年来尝试研究大绝灭后全球生物界的残存－复苏及其基本型式,并探索复苏的控制因素,标志着地质科学中一个重心的转移（即从大绝灭转向其后的生物残存与复苏的研究）。生物复苏揭示了大绝灭后生物演化历史的第一幕,其研究的     

本姜子属及山胡椒属的平行演化

本文阐述樟科木姜子属及山胡椒属两者在形态、分布、起源及演化等方面有许多共同之处,不仅在属内具有平行演化的情况,而且各自平行演化成单花木姜子属 Dodecade－nia和单花山胡椒属Iteadaphne。同时两者又分别自4药室的拟擦术属Parasassafras和2药室的黄脉擦术属 sinosassafras演化而来。本文将单花木姜子亚属 Litsea subg．Uniflos Yang et P．H．Huang归人单花木姜子属,并把 Litsea monantha Yang et P．H．Hu－ang一种作为单花木姜子（原变种）Dodecadenia grandiflora Nees var．grandiflora的新异名,恢复了单花山胡椒属Iteadaphne Bl.,并将香面叶Lindera caudata（Nees）Hook·f．重新组合归入该属为Ⅰ．caudata（Nees）H．W．Li,comb．nov。此外,本文还发表了一个新属即黄脉擦木屑 Sinosassafras H．W．Li,gen．nov.,它具有2药室花药而不同于其平行演化的拟擦本属。     

Eco-evolutionary feedbacks,adaptive dynamics and evolutionary rescue theory

Adaptive dynamics theory has been devised to account for feedbacks between ecological and evolutionary processes. Doing so opens new dimensions to and raises new challenges about evolutionary rescue. Adaptive dynamics theory predicts that successive trait substitutions driven by eco-evolutionary feedbacks can gradually erode population size or growth rate, thus potentially raising the extinction risk. Even a single trait substitution can suffice to degrade population viability drastically at once and cause ‘evolutionary suicide’. In a changing environment, a population may track a viable evolutionary attractor that leads to evolutionary suicide, a phenomenon called ‘evolutionary trapping’. Evolutionary trapping and suicide are commonly observed in adaptive dynamics models in which the smooth variation of traits causes catastrophic changes in ecological state. In the face of trapping and suicide, evolutionary rescue requires that the population overcome evolutionary threats generated by the adaptive process itself. Evolutionary repellors play an important role in determining how variation in environmental conditions correlates with the occurrence of evolutionary trapping and suicide, and what evolutionary pathways rescue may follow. In contrast with standard predictions of evolutionary rescue theory, low genetic variation may attenuate the threat of evolutionary suicide and small population sizes may facilitate escape from evolutionary traps.     

Inferring functional linkages between proteins from evolutionary scenarios

Identifying potential protein interactions is of great importance in understanding the topologies of cellular networks, which is much needed and valued in current systematic biological studies. The development of our computational methods to predict protein-protein interactions have been spurred on by the massive sequencing efforts of the genomic revolution. Among these methods is phylogenetic profiling, which assumes that proteins under similar evolutionary pressures with similar phylogenetic profiles might be functionally related. Here, we introduce a method for inferring functional linkages between proteins from their evolutionary scenarios. The term evolutionary scenario refers to a series of events that occurred in speciation over time, which can be reconstructed given a phylogenetic profile and a species tree. Common evolutionary pressures on two proteins can then be inferred by comparing their evolutionary scenarios, which is a direct indication of their functional linkage. This scenario method has proven to have better performance compared with the classical phylogenetic profile method, when applied to the same test set. In addition, predicted results of the two methods are found to be fairly different, suggesting the possibility of merging them in order to achieve a better performance. We analyzed the influence of the topology of the phylogenetic tree on the performance of this method, and found it to be robust to perturbations in the topology of the tree. However, if a completely random tree is incorporated, performance will decline significantly. The evolutionary scenario method was used for inferring functional linkages in 67 species, and 40,006 linkages were predicted. We examine our prediction for budding yeast and find that almost all predicted linkages are supported by further evidence.     

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.     

MOLECULAR PALAEOBIOLOGY

Abstract:  For more than a generation, molecular biology has been used to approach palaeontological problems, and yet only recently have attempts been made to integrate research utilizing the geological and genomic records in uncovering evolutionary history. We codify this approach as Molecular Palaeobiology for which we provide a synthetic framework for studying the interplay among genotype, phenotype and the environment, within the context of deep time. We provide examples of existing studies where molecular and morphological data have been integrated to provide novel insights within each of these variables, and an account of a case study where each variable has been tackled to understand better a single macroevolutionary event: the diversification of metazoan phyla. We show that the promise of this approach extends well beyond research into the evolutionary history of animals and, in particular, we single out plant evolution as the single greatest opportunity waiting to be exploited by molecular palaeobiology. Although most of our examples consider how novel molecular data and techniques have breathed new life into long-standing palaeontological controversies, we argue that this asymmetry in the balance of molecular and morphological evidence is an artefact of the relative 'newness' of molecular data. In particular, palaeontological data provide unique and crucial roles in unravelling evolutionary history given that extinct taxa reveal patterns of character evolution invisible to molecular biology. Finally, we argue that palaeobiologists, rather than molecular biologists, are best placed to exploit the opportunity afforded by molecular palaeobiology, though this will require incorporating the techniques and approaches of molecular biology into their skill-set.     

Evolutionary ethics,Darwinian ethics and ethical naturalism

The relevance of evolutionary theory to ethics goes back to Darwin but until recently discussion employed evolutionary theory to justify ethical, social and political positions. Recently, evolutionary theory has been used to explain the existence of moral systems and moral propensities and, thereby, to provide a naturalistic basis for ethics. I argue that this approach has advanced our understanding of the basis of moral systems and moral propensities but does not as yet adequately incorporate the role of cognition in its account. Cognition has the effect of decoupling to some extent — though, of course, far from fully — human moral systems from their evolutionary origins. In an adequate account, evolutionary theory will play a crucial role but so also will our evolved cognitive abilities.     

Beyond simple adaptation: Incorporating other evolutionary processes and concepts into eco-evolutionary dynamics

Studies of eco-evolutionary dynamics have integrated evolution with ecological processes at multiple scales (populations, communities and ecosystems) and with multiple interspecific interactions (antagonistic, mutualistic and competitive). However, evolution has often been conceptualised as a simple process: short-term directional adaptation that increases population growth. Here we argue that diverse other evolutionary processes, well studied in population genetics and evolutionary ecology, should also be considered to explore the full spectrum of feedback between ecological and evolutionary processes. Relevant but underappreciated processes include (1) drift and mutation, (2) disruptive selection causing lineage diversification or speciation reversal and (3) evolution driven by relative fitness differences that may decrease population growth. Because eco-evolutionary dynamics have often been studied by population and community ecologists, it will be important to incorporate a variety of concepts in population genetics and evolutionary ecology to better understand and predict eco-evolutionary dynamics in nature.     

Digging their own macroevolutionary grave: fossoriality as an evolutionary dead end in snakes

The tree of life is highly asymmetrical in its clade wise species richness, and this has often been attributed to variation in diversification rates either across time or lineages. Variations across lineages are usually associated with traits that increase lineage diversification. Certain traits can also hinder diversification by increasing extinction, and such traits are called evolutionary dead ends. Ecological specialization has usually been considered as an evolutionary dead end. However, recent analyses of specializations along single axes have provided mixed support for this model. Here, we test if fossoriality, a trait that forces specialization at multiple axes, acts as an evolutionary dead end in squamates (lizards and snakes) using recently developed phylogenetic comparative methods. We show that fossoriality is an evolutionary dead end in snakes but not in lizards. Fossorial snakes exhibit reduced speciation and increased extinction compared to nonfossorial snakes. Our analysis also indicates that transition rates from fossoriality to nonfossoriality in snakes are significantly lower than transition rates from nonfossoriality to fossoriality. Overall our results suggest that broad‐scale ecological interactions that lead to specialization at multiple axes limit diversification.     

Species concepts and the ontology of evolution

Biologists and philosophers have long recognized the importance of species, yet species concepts serve two masters, evolutionary theory on the one hand and taxonomy on the other. Much of present-day evolutionary and systematic biology has confounded these two roles primarily through use of the biological species concept. Theories require entities that are real, discrete, irreducible, and comparable. Within the neo-Darwinian synthesis, however, biological species have been treated as real or subjectively delimited entities, discrete or nondiscrete, and they are often capable of being decomposed into other, smaller units. Because of this, biological species are generally not comparable across different groups of organisms, which implies that the ontological structure of evolutionary theory requires modification. Some biologists, including proponents of the biological species concept, have argued that no species concept is universally applicable across all organisms. Such a view means, however, that the history of life cannot be embraced by a common theory of ancestry and descent if that theory uses species as its entities.These ontological and biological difficulties can be alleviated if species are defined in terms of evolutionary units. The latter are irreducible clusters of reproductively cohesive organisms that are diagnosably distinct from other such clusters. Unlike biological species, which can include two or more evolutionary units, these phylogenetic species are discrete entities in space and time and capable of being compared from one group to the next.     

Digging through model complexity: using hierarchical models to uncover evolutionary processes in the wild

The growing interest for studying questions in the wild requires acknowledging that eco-evolutionary processes are complex, hierarchically structured and often partially observed or with measurement error. These issues have long been ignored in evolutionary biology, which might have led to flawed inference when addressing evolutionary questions. Hierarchical modelling (HM) has been proposed as a generic statistical framework to deal with complexity in ecological data and account for uncertainty. However, to date, HM has seldom been used to investigate evolutionary mechanisms possibly underlying observed patterns. Here, we contend the HM approach offers a relevant approach for the study of eco-evolutionary processes in the wild by confronting formal theories to empirical data through proper statistical inference. Studying eco-evolutionary processes requires considering the complete and often complex life histories of organisms. We show how this can be achieved by combining sequentially all life-history components and all available sources of information through HM. We demonstrate how eco-evolutionary processes may be poorly inferred or even missed without using the full potential of HM. As a case study, we use the Atlantic salmon and data on wild marked juveniles. We assess a reaction norm for migration and two potential trade-offs for survival. Overall, HM has a great potential to address evolutionary questions and investigate important processes that could not previously be assessed in laboratory or short time-scale studies.