中生代银杏类植物系统发育、分类和演化趋向

长期以来银杏类植物化石分类都依据营养叶形态为基础。由于叶形态的多型性和异源性,导致分类和系统发育解释的紊乱。根据对保存完好的繁殖器官(胚珠器官)系统发育分析结果所作的银杏目分类表明中生代除了银杏和银杏科以外,至少还存在着3．5个已灭绝的科级单元。此方案把已知其繁殖器官的成员和仅仅根据营养器官建立起来的分类位置不明的属严格地区分开来,并注明各科的限定性特征和已知成员的地质地理分布。银杏目植物自古生代起源,至早中生代以后朝着不同的方向辐射,呈现出丰富的多样性并经历了错综复杂的演化过程,其总的演化趋向是退缩：叶片扁化、蹊化和融合;胚珠器官简化,胚珠增大、数目减少,珠柄趋于消失。     

The road less traveled: Phylogenetic perspectives in primatology

Interest in phylogeny is increasing in many areas of evolutionary biology. One area of evolutionary anthropology that has not yet fully embraced this growth in phylogenetic thinking, however, is the study of primate behavior and ecology.¹ The predominant framework for behavioral studies of primates over the last three decades has been socioecological. The goals have been to identify broad correlations between species' behaviors and current environmental conditions. As such, the socioecological approach has been largely nonhistorical, taking little account of phylogeny. In contrast, phylogenetic approaches view the behavior of contemporary taxa within an explicitly historical framework. Although socioecology has proven extremely productive, there are many reasons to think that research in primatology could be profitably supplemented by a phylogenetic perspective.^2,3     

Functional morphology and evolutionary ecology

Functional morphology studies physico-chemical properties and biological roles of organs. If applied to fossils this approach is connected with specific methodological problems. The fields of application of functional morphology in paleontology are illustrated with examples. In a working concept it is shown how the results of functional morphology can be integrated into an account of the evolutionary ecology of fossil taxa.     

Identifying and reconstructing lateral transfers from distance matrices by combining the minimum contradiction method and neighbor-net

Identifying lateral gene transfers is an important problem in evolutionary biology. Under a simple model of evolution, the expected values of an evolutionary distance matrix describing a phylogenetic tree fulfill the so-called Kalmanson inequalities. The Minimum Contradiction method for identifying lateral gene transfers exploits the fact that lateral transfers may generate large deviations from the Kalmanson inequalities. Here a new approach is presented to deal with such cases that combines the Neighbor-Net algorithm for computing phylogenetic networks with the Minimum Contradiction method. A subset of taxa, prescribed using Neighbor-Net, is obtained by measuring how closely the Kalmanson inequalities are fulfilled by each taxon. A criterion is then used to identify the taxa, possibly involved in a lateral transfer between nonconsecutive taxa. We illustrate the utility of the new approach by applying it to a distance matrix for Archaea, Bacteria, and Eukaryota.     

PERSPECTIVE: EVOLUTIONARY PATTERNS IN THE FOSSIL RECORD

The study of large-scale evolutionary patterns in the fossil record has benefited from a diversity of approaches, including analysis of taxonomic data, ecology, geography, and morphology. Although genealogy is an important component of macroevolution, recent visions of phylogenetic analysis as replacing rather than supplementing other approaches are short-sighted. The ability of traditional Linnaean taxa to document evolutionary patterns is mainly an empirical rather than a theoretical issue, yet the use of these taxa has been dismissed without thorough evaluation of their empirical properties. Phylogenetic analysis can help compensate for some of the fossil record's imperfections. However, the shortcomings of the phylogenetic approach have not been adequately acknowledged, and we still lack a rigorous comparison between the phylogenetic approach and probabilistic approaches based on sampling theory. Important inferences about the history of life based on nongenealogical data have later been corroborated with genealogical and other analyses, suggesting that we risk an enormous loss of knowledge and understanding if we categorically dismiss nonphylogenetic data.     

The Use of Functional and Adaptive Criteria in Phylogenetic Systematics

SYNOPSIS. The controversy over whether functional data can contributeto phylogenetic inference has grown in recent years. Steps canbe taken toward its resolution if the relevance of functionaldata is judged for each component of phylogenetic analysis.These components are (1)recognizing of basic taxa (species orsupraspecific taxa), (2) formulating hypotheses of homologyfollowed by character analysis, (3) evaluating character phylogeny,(4) formulating phylogenetic hypotheses, and (5) evaluatingalternative phylogenetic hypotheses. It can be shown that functionaldata do not play a necessary or unique role in any of thesecomponents of phylogenetic analysis. Arguments to the contraryhave failed to provide a rigorous, repeatable methodto incorporatefunctional data; proponents of a functional approach to phylogeneticreconstruction rely too often on subjective, authoritarian argumentation. Students of functional evolutionary morphology frequently havefailed to understand the kinds of information necessary to studyor apply the causal process of adaptation via natural selection.This information, required by the very nature of the theoryitself, includes knowing the pattern of heredity of the phenotypiccharacters being studied, relating intrapopulational phenotypicvariability to variation in fitness, and knowing a sufficientamount about population structure to specify the componentsof natural selection. Studies within functional evolutionarymorphology are not designed to satisfy these requirements. Functionalevolutionary morphology uses the concepts of adaptation andnatural selection axiomatically, and thus such studies contributenothing to our understanding of the evolutionary process becausehypotheses about that process are not being evaluated. Thisalso suggests that, if functional evolutionary morphology wishesto engage in analyses of the evolutionary dynamics of the phenotype,a reorientation of its research strategy and goals will be necessary.     

Molecular systematics,GISH and the origin of hybrid taxa in Nicotiana (Solanaceae)

Phylogenetic relationships in the genus Nicotiana were investigated using parsimony analyses of the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA (nrDNA). In addition, origins of some amphidiploid taxa in Nicotiana were investigated using the techniques of genomic in situ hybridization (GISH), and the results of both sets of analyses were used to evaluate previous hypotheses about the origins of these taxa. Phylogenetic analyses of the ITS nrDNA data were performed on the entire genus (66 of 77 naturally occurring species, plus three artificial hybrids), comprising both diploid and polyploid taxa, and on the diploid taxa only (35 species) to examine the effects of amphidiploids on estimates of relationships. All taxa, regardless of ploidy, produced clean, single copies of the ITS region, even though some taxa are hybrids. Results are compared with a published plastid (matK) phylogeny using fewer, but many of the same, taxa. The patterns of relationships in Nicotiana, as seen in both analyses, are largely congruent with each other and previous evolutionary ideas based on morphology and cytology, but some important differences are apparent. None of the currently recognized subgenera of Nicotiana is monophyletic and, although most of the currently recognized sections are coherent, others are clearly polyphyletic. Relying solely upon ITS nrDNA analysis to reveal phylogenetic patterns in a complex genus such as Nicotiana is insufficient, and it is clear that conventional analysis of single data sets, such as ITS, is likely to be misleading in at least some respects about evolutionary history. ITS sequences of natural and well-documented amphidiploids are similar or identical to one of their two parents-usually, but not always, the maternal parent-and are not in any sense themselves 'hybrid'. Knowing how ITS evolves in artificial amphidiploids gives insight into what ITS analysis might reveal about naturally occurring amphidiploids of unknown origin, and it is in this perspective that analysis of ITS sequences is highly informative.     

Phylogenetic, functional, and structural components of variation in bone growth rate of amniotes

SUMMARY The biological features observed in every living organism are the outcome of three sets of factors: historical (inherited by homology), functional (biological adaptation), and structural (properties inherent to the materials with which organs are constructed, and the morphogenetic rules by which they grow). Integrating them should bring satisfactory causal explanations of empirical data. However, little progress has been accomplished in practice toward this goal, because a methodologically efficient tool was lacking. Here we use a new statistical method of variation partitioning to analyze bone growth in amniotes. (1) Historical component . The variation of bone growth rates contains a significant phylogenetic signal, suggesting that the observed patterns are partly the outcome of shared ancestry. (2) Functional causation . High growth rates, although energy costly, may be adaptive (i.e., they may increase survival rates) in taxa showing short growth periods (e.g., birds). In ectothermic amniotes, low resting metabolic rates may limit the maximum possible growth rates. (3) Structural constraint . Whereas soft tissues grow through a multiplicative process, growth of mineralized tissues is accretionary (additive, i.e., mineralization fronts occur only at free surfaces). Bone growth of many amniotes partially circumvents this constraint: it is achieved not only at the external surface of the bone shaft, but also within cavities included in the bone cortex as it grows centrifugally. Our approach contributes to the unification of historicism, functionalism, and structuralism toward a more integrated evolutionary biology.     

Circularity,evolution, systematics … and circularity

Many have argued strongly that incorporation of evolutionary theory into systematics is dangerously circular, while others have maintained that such an integrated approach increases the accuracy of phylogenetic inference. Here, it is demonstrated that such blanket statements regarding exclusion or inclusion of evolutionary principles in systematics fail to distinguish between two very different types of principles. ‘Phylogeny-neutral’ evolutionary principles are those inferred without any recourse to specific phylogenetic hypotheses (e.g. via developmental genetics, biomechanics). In contrast, ‘phylogeny-dependent’ principles are those which can only be inferred on the basis of specific phylogenetic hypotheses (e.g. character associations detected via ‘comparative methods’). Inclusion of phylogeny-neutral principles in systematic studies as a priori assumptions can be justified, since these principles have (often strong) external empirical support from other spheres of investigation. However, inclusion of phylogeny-dependent principles in systematic studies is circular, since such principles have no external empirical support but are themselves derived from systematic studies. Advocating inclusion or exclusion of all (or as many as possible) evolutionary principles from phylogenetic analysis is therefore misguided. Rather, phylogeny-neutral principles are independently supported and can be included, while phylogeny-dependent principles are unjustified assumptions and should be excluded to avoid circularity. However, integration of complex phylogeny-neutral principles in systematics can create operational problems, even though there are no methodological reasons against their inclusion.     

Evolution at the system level: the natural history of protein interaction networks

Recent work leading to new insights into the molecular architecture underlying complex cellular phenotypes enables researchers to investigate evolutionary processes in unprecedented detail. Protein interaction network data, which are now available for an increasing number of species, promise new insights and there have been many recent studies investigating evolutionary aspects of these interaction networks, from mathematical studies of growing networks to detailed phylogenetic surveys of proteins in their interaction network context. Here, we review the spectrum of such approaches, and assess issues associated with analyzing such data from an evolutionary perspective. Currently, such analyses are statistically challenging, but could link present initiatives in systems biology with results and methodologies that have developed in evolutionary biology over the past 60 years.     

Molecules,morphology, and phylogeny

A complicated, almost conflicting situation exists in contemporary biology, i.e., there are two scientific concepts in existence that solve some phylogenetic problems in a different way. These concepts are evolutionary morphology and molecular biology. Modern biology urgently needs these contradictions to be examined and removed.     

A phylogenetic comparative method for evaluating trait coevolution across two phylogenies for sets of interacting species

Evaluating trait correlations across species within a lineage via phylogenetic regression is fundamental to comparative evolutionary biology, but when traits of interest are derived from two sets of lineages that coevolve with one another, methods for evaluating such patterns in a dual‐phylogenetic context remain underdeveloped. Here, we extend multivariate permutation‐based phylogenetic regression to evaluate trait correlations in two sets of interacting species while accounting for their respective phylogenies. This extension is appropriate for both univariate and multivariate response data, and may use one or more independent variables, including environmental covariates. Imperfect correspondence between species in the interacting lineages can also be accommodated, such as when species in one lineage associate with multiple species in the other, or when there are unmatched taxa in one or both lineages. For both univariate and multivariate data, the method displays appropriate type I error, and statistical power increases with the strength of the trait covariation and the number of species in the phylogeny. These properties are retained even when there is not a 1:1 correspondence between lineages. Finally, we demonstrate the approach by evaluating the evolutionary correlation between traits in fig species and traits in their agaonid wasp pollinators. R computer code is provided.     

Atomism, transformism and the fossil record

The modern debate between exponents of classical evolutionary classification and of cladistic analysis of phylogenetic relationships mirrors to some extent the arguments that were put forward in the debate between Cuvier and Geoffroy Saint-Hilaire in 1830. Put into a historical perspective the problems of comparative biology centre around two complementary traditions, atomism and transformism.     

TRIBUTE: In Goethe's Wake: Marvalee Wake's conceptual contributions to the development and evolution of a science of morphology

Decrying the typological approach in much of the teaching of morphology, from the outset of her career Marvalee Wake advocated a synthetic, mechanistic and pluralistic developmental and evolutionary morphology. In this short essay, I do not evaluate Wake's contributions to our knowledge of the morphology of caecilians, nor her contributions to viviparity, both of which are seminal and substantive, nor do I examine her role as mentor, supervisor and collaborator, but assess her broader conceptual contributions to the development and evolution of morphology as a science. One of the earliest morphologists to take on board the concept of constraint, she viewed constraint explicitly in relation to adaptation and diversity. Her approach to morphology as a science was hierarchical – measure form and function in a phylogenetic context; seek explanations at developmental, functional, ecological, evolutionary levels of the biological hierarchy; integrate those explanations to the other levels. The explanatory power of morphology thus practised allows morphology to inform evolutionary biology and evolutionary theory, and paves the way for the integrative biology Wake has long championed.     

Old trees, new trees--is there any progress?

The amount of comparative data for phylogenetic analyses is constantly increasing. Data come from different directions such as morphology, molecular genetics, developmental biology and paleontology. With the increasing diversity of data and of analytical tools, the number of competing hypotheses on phylogenetic relationships rises, too. The choice of the phylogenetic tree as a basis for the interpretation of new data is important, because different trees will support different evolutionary interpretations of the data investigated. I argue here that, although many problematic aspects exist, there are several phylogenetic relationships that are supported by the majority of analyses and may be regarded as something like a robust backbone. This accounts, for example, for the monophyly of Metazoa, Bilateria, Deuterostomia, Protostomia (= Gastroneuralia), Gnathifera, Spiralia, Trochozoa and Arthropoda and probably also for the branching order of diploblastic taxa (“Porifera”, Trichoplax adhaerens, Cnidaria and Ctenophora). Along this “backbone”, there are several problematic regions, where either monophyly is questionable and/or where taxa “rotate” in narrow regions of the tree. This is illustrated exemplified by the probable paraphyly of Porifera and the phylogenetic relationships of basal spiralian taxa. Two problems span wider regions of the tree: the position of Arthropoda either as the sister taxon of Annelida (= Articulata) or of Cycloneuralia (= Ecdysozoa) and the position of tentaculate taxa either as sister taxa of Deuterostomia (= Radialia) or within the taxon Spiralia. The backbone makes it possible to develop a basic understanding of the evolution of genes, molecules and structures in metazoan animals.     

Dogs,cats, and kin: A molecular species-level phylogeny of Carnivora

Phylogenies underpin comparative biology as high-utility tools to test evolutionary and biogeographic hypotheses, inform on conservation strategies, and reveal the age and evolutionary histories of traits and lineages. As tools, most powerful are those phylogenies that contain all, or nearly all, of the taxa of a given group. Despite their obvious utility, such phylogenies, other than summary ‘supertrees’, are currently lacking for most mammalian orders, including the order Carnivora. Carnivora consists of about 270 extant species including most of the world’s large terrestrial predators (e.g., the big cats, wolves, bears), as well as many of man’s favorite wild (panda, cheetah, tiger) and domesticated animals (dog, cat). Distributed globally, carnivores are highly diverse ecologically, having occupied all major habitat types on the planet and being diverse in traits such as sociality, communication, body/brain size, and foraging ecology. Thus, numerous studies continue to address comparative questions within the order, highlighting the need for a detailed species-level phylogeny. Here we present a phylogeny of Carnivora that increases taxon sampling density from 28% in the most detailed primary-data study to date, to 82% containing 243 taxa (222 extant species, 17 subspecies). In addition to extant species, we sampled four extinct species: American cheetah, saber-toothed cat, cave bear and the giant short-faced bear. Bayesian analysis of cytochrome b sequences data-mined from GenBank results in a phylogenetic hypothesis that is largely congruent with prior studies based on fewer taxa but more characters. We find support for the monophyly of Carnivora, its major division into Caniformia and Feliformia, and for all but one family within the order. The only exception is the placement of the kinkajou outside Procyonidae, however, prior studies have already cast doubt on its family placement. In contrast, at the subfamily and genus level, our results indicate numerous problems with current classification. Our results also propose new, controversial hypotheses, such as the possible placement of the red panda (Ailuridae) sister to canids (Canidae). Our results confirm previous findings suggesting that the dog was domesticated from the Eurasian wolf (Canis lupus lupus) and are congruent with the Near East domestication of the cat. In sum, this study presents the most detailed species-level phylogeny of Carnivora to date and a much needed tool for comparative studies of carnivoran species. To demonstrate one such use, we perform a phylogenetic analysis of evolutionary distinctiveness (EDGE), which can be used to help establish conservation priorities. According with those criteria, and under one of the many possible sets of parameters, the highest priority Carnivora species for conservation of evolutionary diversity include: monk seals, giant and red panda, giant otter, otter civet, Owston’s palm civet, sea otter, Liberian mongoose, spectacled bear, walrus, binturong, and the fossa.     

Evolution and patterning of the ovule in seed plants

The ovule and its developmental successor, the seed, together represent a highly characteristic feature of seed plants that has strongly enhanced the reproductive and dispersal potential of this diverse group of taxa. Ovules encompass multiple tissues that perform various roles within a highly constrained space, requiring a complex cascade of genes that generate localized cell proliferation and programmed cell death during different developmental stages. Many heritable morphological differences among lineages reflect relative displacement of these tissues, but others, such as the second (outer) integuments of angiosperms and Gnetales, represent novel and apparently profound and independent innovations. Recent studies, mostly on model taxa, have considerably enhanced our understanding of gene expression in the ovule. However, understanding its evolutionary history requires a comparative and phylogenetic approach that is problematic when comparing extant angiosperms not only with phylogenetically distant extant gymnosperms but also with taxa known only from fossils. This paper reviews ovule characters across a phylogenetically broad range of seed plants in a dynamic developmental context. It discusses both well-established and recent theories of ovule and seed evolution and highlights potential gaps in comparative data that will usefully enhance our understanding of evolutionary transitions and developmental mechanisms.     

Parallel genotypic adaptation: when evolution repeats itself

Until recently, parallel genotypic adaptation was considered unlikely because phenotypic differences were thought to be controlled by many genes. There is increasing evidence, however, that phenotypic variation sometimes has a simple genetic basis and that parallel adaptation at the genotypic level may be more frequent than previously believed. Here, we review evidence for parallel genotypic adaptation derived from a survey of the experimental evolution, phylogenetic, and quantitative genetic literature. The most convincing evidence of parallel genotypic adaptation comes from artificial selection experiments involving microbial populations. In some experiments, up to half of the nucleotide substitutions found in independent lineages under uniform selection are the same. Phylogenetic studies provide a means for studying parallel genotypic adaptation in non-experimental systems, but conclusive evidence may be difficult to obtain because homoplasy can arise for other reasons. Nonetheless, phylogenetic approaches have provided evidence of parallel genotypic adaptation across all taxonomic levels, not just microbes. Quantitative genetic approaches also suggest parallel genotypic evolution across both closely and distantly related taxa, but it is important to note that this approach cannot distinguish between parallel changes at homologous loci versus convergent changes at closely linked non-homologous loci. The finding that parallel genotypic adaptation appears to be frequent and occurs at all taxonomic levels has important implications for phylogenetic and evolutionary studies. With respect to phylogenetic analyses, parallel genotypic changes, if common, may result in faulty estimates of phylogenetic relationships. From an evolutionary perspective, the occurrence of parallel genotypic adaptation provides increasing support for determinism in evolution and may provide a partial explanation for how species with low levels of gene flow are held together.     

Eco‐oncology: Applying ecological principles to understand and manage cancer

Cancer is a disease of single cells that expresses itself at the population level. The striking similarities between initiation and growth of tumors and dynamics of biological populations, and between metastasis and ecological invasion and community dynamics suggest that oncology can benefit from an ecological perspective to improve our understanding of cancer biology. Tumors can be viewed as complex, adaptive, and evolving systems as they are spatially and temporally heterogeneous, continually interacting with each other and with the microenvironment and evolving to increase the fitness of the cancer cells. We argue that an eco‐evolutionary perspective is essential to understand cancer biology better. Furthermore, we suggest that ecologically informed therapeutic approaches that combine standard of care treatments with strategies aimed at decreasing the evolutionary potential and fitness of neoplastic cells, such as disrupting cell‐to‐cell communication and cooperation, and preventing successful colonization of distant organs by migrating cancer cells, may be effective in managing cancer as a chronic condition.     

禾本科系统学与演化研究的进展

：综合近年来禾本科不同分支学科的研究进展,对当前禾本科研究的4个热点进行讨论：1．禾本科内不同阶元系统的种系发育研究方法,有传统的、实验的、历史的、分支的4种分析方法;2．性系统的演化,涉及自交亲和繁育方式的优势、偏离正常性比的发育模式、性别决定的分子生物学基础3个方面;3．花序演化的形态学、遗传学、发育形态学研究;4．禾本科的起源时间。总的看来,不同性状的数据比较和不同研究方法的综合已构成现代禾本科系统学研究的必然趋势,建立一个反映植物系统发育历史的分类是禾本科系统学研究的最终目标。