锦鸡儿属种系发生关系重建的探讨

基于形态学、染色体、花粉形态24个特征,采用分支系统学方法研究锦鸡儿属（Caragana）的种系发生关系。根据分支图结果,将锦鸡儿属72种排列成12系5组。分支图也表达出分类群演化关系,对Moore(1968)种系发生方案提出了修改,重建了本属的种系发生关系。     

被子植物起源和早期演化研究的回顾与展望

近年来,被子植物起源和早期演化研究,由于手段和技术的更新,资料大量积累,取得了许多重要进展,成为植物学领域的一大热点。本文对过去近五十年的研究作了回顾,并从分子系统学、分支系统学、花原基发生的形态学、花发育的分子遗传学及白垩纪花和其它生殖结构化石研究等五个方面对该领域在最近十几年的研究进展进行综述,最后,对今后如何开展这方面的工作作了简要评论。     

鹅观草属的系统发育分析

根据分支系统学的原理和方法, 对禾本科鹅观草属进行了系统发育分析。鹅观草属传统分类上的18 个系被确定为终端类群, 来自形态学、解剖学、细胞学和孢粉学的23 个性状被选作建立矩阵的依据;雀麦族中的短柄草属作为外类群被用于外部性状的极性识别, 过去分析过的性状资料被用于微观特征的极性判断;采用PAUP 程序对矩阵进行运算, 共获得6 个同等简约的谱系分支图, 其中具最低f-比值的图被选作分支分析的基础。结果表明, 分支图上显示的组、系划分与传统分类的基本一致, 各类群间的演化关系与过去凭借单一证据所作的零散推断也基本吻合。所不同的是半颖组各支类群不是共祖起源, 可能具有复杂的内部组成;在个别系间, 分支图展现的类群位置与宏观分析的存在差异。     

木贼类和真蕨类是与种子植物关系最近的单元类群

苔藓类、蕨类和种子植物发生发展的过程构成了陆地植物四亿七千万年演化历史的主要内容。在九千万年以前 ,被子植物诞生并发展成为陆地生态系统中的优势类群。随着多基因序列分析的开展 ,我们对于被子植物系统发育的认识 ,特别是它们早期演化路线分支系统的认识不断丰富和提高。对泥盆纪 (距今约四亿年 )以来的维管植物所有主要演化路线相互关系的重建至今依然是个挑战。本文报道了对陆地植物所有主要演化路线的35种代表类群的形态学特征和四个基因的资料所进行的综合系统学分析。通过对这些植物的两个基因组的四个基因 :质体ａｔｐＢ ,ｒｂ…     

分支系统学当前的理论和方法概述及华东地区山胡椒属十二个种的…

本概述了当前分支系统学研究中涉及的主要理论和方法,包括性状的选取、性状状态和极性的确定、数据矩阵的分析计算、结果分支图的处理、分支图可靠性的评价及分支图的应用。本同时以华东地区樟科山胡椒属Ｌｉｎｄｅｒａ１２个种的分支系统学研究为例,讨论了用形态性状进行分支系统学研究中可能遇到的问题,也揭示了一些分支系统学与传统的系统学在应用性状推导进化关系上的不同点。对这１２个种的分支系统学研究得出了一些不同     

蕨类植物起源与系统发生关系研究进展

蕨类植物是一群非常古老的植物,在其漫长的演化历史中丢失了大量的系统发生信息,因此重建其系统演化关系是蕨类植物学家所面临的重要任务之一。近年来的分子系统学研究已经确立了一些类群的系统关系,但现存的蕨类分类系统和系统发生关系还有很多谜团有待揭开。化石记录表明蕨类植物最早出现于大约4亿多年前,但大部分现代真蕨类缺少足够的化石证据。它们的起源时间和方式及其内部各类群的系统发生关系等诸多问题的解决,还有待于大量形态学和不同分子水平上的实验数据的进一步积累,并结合其直接的化石证据进行综合研究。     

毛茛科分子系统发育研究进展

毛茛科(Ranunculaceae)在被子植物的系统演化中占有十分重要的地位,其系统位置和科下演化关系一直备受争议。近20多年的分子系统学研究表明,以往基于形态学的分类系统与分子系统学研究结果存在巨大差异。通过形态学性状界定的绝大多数亚科都没有得到分子系统学支持。此外,通过形态学确定的一些属如升麻属(Cimicifuga)、黄三七属(Souliea)、獐耳细辛属(Hepatica)、白头翁属(Pulsatilla)和水毛茛属(Batrachium)等,根据分子系统学研究均应予以归并。而分子系统学研究也确立了一些类群的属级地位,如露蕊乌头属(Gymnaconitum)等。以中国分布的毛茛科植物为例,通过以往分子系统学研究,共有10个属被归并,2个属新被确立。然而,毛茛科分子系统学研究对于科下许多类群之间的关系目前仍然没有得到很好的解决,如毛茛亚科和翠雀族等类群的系统发育关系仍需要进行深入研究后方能确定。该文对近年来国内外有关毛茛科的分子系统学研究进展进行了综述,并对该科尚存的一些问题和未来的研究方向进行了讨论。     

蕨类植物起源与系统发生关系研究进展

蕨类植物是一群非常古老的植物,在其漫长的演化历史中丢失了大量的系统发生信息,因此重建其系统演化关系是蕨类植物学家所面临的重要任务之一.近年来的分子系统学研究已经确立了一些类群的系统关系,但现存的蕨类分类系统和系统发生关系还有很多谜团有待揭开.化石记录表明蕨类植物最早出现于大约4亿多年前,但大部分现代真蕨类缺少足够的化石证据.它们的起源时间和方式及其内部各类群的系统发生关系等诸多问题的解决,还有待于大量形态学和不同分子水平上的实验数据的进一步积累,并结合其直接的化石证据进行综合研究.     

中国特有蕨属扇蕨属（水龙骨科）的系统学研究

扇蕨属（Neocheiropteris）为中国蕨类植物4个特有属之一。自Christ建属以来,不同的分类学者对本属的范畴以及系统位置一直存有争议。本研究对扇蕨属和盾蕨属进行了形态解剖观察,并对扇蕨属及其近缘类群共14个种的4个叶绿体DNA片段：rbcL、rpS4 ＆ rpS4-trnS IGS、trnL intron ＆ trnL-trnF IGS以及atpB ＆ atpB-rbcL IGS进行测序,应用最大简约法（Maximum-parsimony）、最大似然法（Maximum-likeli-hood）和贝叶斯推断（Bayesian inference）对序列进行联合矩阵分析,并构建系统树。该研究从形态学和分子系统学方面都提出了支持扇蕨属和盾蕨属分立的证据。形态学研究显示扇蕨属和盾蕨属叶片分裂方式、叶被和侧脉特征迥异,支持扇蕨属和盾蕨属的分立;但两属根状茎鳞片的共同特征则反映了两属问的紧密联系。分子系统学研究表明扇蕨属与毛鳞蕨属和鳞果星蕨属构成姐妹群,其集合与盾蕨属构成姐妹群。综合形态学和分子系统学的证据,对扇蕨属的系统位置以及范畴进行了深入探讨,扇蕨属包括扇蕨和三出扇蕨,结合形态学和分子系统学证据对三出扇蕨的系统位置进行了初步探讨。     

云南食植瓢虫族的系统位置及属间关系

本文对云南食植瓢虫族昆虫形态学,特别是跗爪基齿,上颚侧齿,雌、雄性外生殖器等性状的研究,讨论了本族的属间关系;应用分支系统学的原理和方法,对本族系统位置的研究进行了尝试。采用最大同步法对本族5个属8个性状状态进行了分支分析,其结果与传统分类结果有一定的差异。结论支持将食植瓢虫属分为3个亚属,其中2个为新亚属。     

Macroevolution of panicoid inflorescences: a history of contingency and order of trait acquisition

Background and Aims

Inflorescence forms of panicoid grasses (Panicoideae s.s.) are remarkably diverse and they look very labile to human eyes; however, when performing a close inspection one can identify just a small subset of inflorescence types among a huge morphospace of possibilities. Consequently, some evolutionary constraints have restricted, to some extent, the diversification of their inflorescence. Developmental and genetic mechanisms, the photosynthetic type and plant longevity have been postulated as candidate constraints for angiosperms and panicoids in particular; however, it is not clear how these factors operate and which of these have played a key role during the grass inflorescence evolution. To gain insight into this matter the macroevolutionary aspects of panicoid inflorescences are investigated.

Methods

The inflorescence aspect (lax versus condensed), homogenization, truncation of the terminal spikelet, plant longevity and photosynthetic type were the traits selected for this study. Maximum likelihood and Bayesian Markov chain Monte Carlo methods were used to test different models of evolution and to evaluate the existence of evolutionary correlation among the traits. Both, models and evolutionary correlation were tested and analysed in a phylogenetic context by plotting the characters on a series of trees. For those cases in which the correlation was confirmed, test of contingency and order of trait acquisition were preformed to explore further the patterns of such co-evolution.

Key Results

The data reject the independent model of inflorescence trait evolution and confirmed the existence of evolutionary contingency. The results support the general trend of homogenization being a prerequisite for the loss of the terminal spikelet of the main axis. There was no evidence for temporal order in the gain of homogenization and condensation; consequently, the homogenization and condensation could occur simultaneously. The correlation between inflorescence traits with plant longevity and photosynthetic type is not confirmed.

Conclusions

The findings indicate that the lability of the panicoid inflorescence is apparent, not real. The results indicate that the history of the panicoids inflorescence is a combination of inflorescence trait contingency and order of character acquisition. These indicate that developmental and genetic mechanisms may be important constraints that have limited the diversification of the inflorescence form in panicoid grasses.Key words: Inflorescence, morphology, evolution, panicoids, Panicoideae, Poaceae     

Phylogeny-based developmental analyses illuminate evolution of inflorescence architectures in dogwoods (Cornus s. l., Cornaceae)

? Inflorescence architecture is important to angiosperm reproduction, but our knowledge of the developmental basis underlying the evolution of inflorescence architectures is limited. Using a phylogeny-based comparative analysis of developmental pathways, we tested the long-standing hypothesis that umbel evolved from elongated inflorescences by suppression of inflorescence branches, while head evolved from umbels by suppression of pedicels. ? The developmental pathways of six species of Cornus producing different inflorescence types were characterized by scanning electron microscopy (SEM) and histological analysis. Critical developmental events were traced over the molecular phylogeny to identify evolutionary changes leading to the formation of umbels and heads using methods accounting for evolutionary time and phylogenetic uncertainty. ? We defined 24 developmental events describing the developmental progression of the different inflorescence types. The evolutionary transition from paniculate cymes to umbels and heads required alterations of seven developmental events occurring at different evolutionary times. ? Our results indicate that heads and umbels evolved independently in Cornus from elongated forms via an umbellate dichasium ancestor and this process involved several independent changes. Our findings shed novel insights into head and umbel evolution concealed by outer morphology. Our work illustrates the importance of combining developmental and phylogenetic data to better define morphological evolutionary processes.     

Systematics and Evolution of Subfam. Panicoideae (Gramineae)

Subfam. Panicoideae consists of 230 genera and 3000 species, about 1/3 of the total number of Gramineae. The evolution in Gramineae (Poaceae) is considered to have been proceeding in the direction of simplification. Three major lineages in Panicoideae are recognized based on analysis of characters, geographical distribution and ecological preferences. They are represented respectively by three supertribes i.e. Panicatae, Andropogonatae and Maydatae. The first supertribe has well-developed florets, fertile lemma indurate, but is awnless and thus is the primitive group in the subfamily. In the second supertribe spikelets are well-developed, the lower glume is larger than the florets and embraces them, the florets are awned. Particularly significant is the evolution of spikelets from solitary to paired, from the two spikelets of each pair both bisexual and alike in form to heterogamous pair of spikelets in which the sessile one is fertile and the pedicelled one sterile and further to homogamous pair of spikelets at base of inflorescence. In this lineage occurs an inflorescence protected by a large sheathing bract. It is the most flourishing by developed evolutionary branch. In the third supertribe raches are developed, thick, inflorescences have become pillar-shaped with spikelets sunken in the raches. The reduction of spikelets from bisexual to unisexual has taken place and they occur on separte inflorescenes, bringing about subsequent sexual differentiation of inflorescences. Raches have also evolved from solitary to united. The supertribe Maydatae is likely to be one of the most advanced group in Gramineae. Subfam. Panicoideae occurs in the tropics and subtropics, and these three supertribes have apparently followed three lines of development under different environmental conditions. The supertribe Panicatae adapts to hot moist conditions, the supertribe Andropogonatae adapts to a monsoon climate, occurring in savannas, the supertribe Maydatae occurs in monsoon moist conditions.     

Lineage diversification and morphological evolution in a large-scale continental radiation: the neotropical ovenbirds and woodcreepers (aves: Furnariidae)

Patterns of diversification in species-rich clades provide insight into the processes that generate biological diversity. We tested different models of lineage and phenotypic diversification in an exceptional continental radiation, the ovenbird family Furnariidae, using the most complete species-level phylogenetic hypothesis produced to date for a major avian clade (97% of 293 species). We found that the Furnariidae exhibit nearly constant rates of lineage accumulation but show evidence of constrained morphological evolution. This pattern of sustained high rates of speciation despite limitations on phenotypic evolution contrasts with the results of most previous studies of evolutionary radiations, which have found a pattern of decelerating diversity-dependent lineage accumulation coupled with decelerating or constrained phenotypic evolution. Our results suggest that lineage accumulation in tropical continental radiations may not be as limited by ecological opportunities as in temperate or island radiations. More studies examining patterns of both lineage and phenotypic diversification are needed to understand the often complex tempo and mode of evolutionary radiations on continents.     

Les Ammonoïdes (Mollusca,Cephalopoda) : avancées et contributions récentes à la paléobiologie évolutive

Ammonoids ruled the seas for 335 Myr and present themselves as an especially suitable model when analyzing biological evolution. This synthetic paper focuses on (1): the phylogenetic place of ammonoids within cephalopods and the choice of an extant reference model; (2): the establishment of phenotypic spaces supplying relevant insights into biological evolution; (3): the concordances and discordances between phylogenetic reconstructions and the fossil record, and (4): the postcrisis recoveries, as models to study large-scale evolution. It appears from these topics that ammonoids can be used as case studies for many themes in Paleontology (biodiversity dynamics, phylogenetics, analysis of the fossil record) that offered and continues to offer a better understanding of evolutionary patterns and processes, especially in the context of large-scale studies.     

Diversification of inflorescence development in the PCK clade (Poaceae: Panicoideae: Paniceae)

In grasses, inflorescence diversification and its correlation with species evolution are intriguing and not well understood. Part of this problem lies in our lack of comprehension about the inflorescence morphological complexity of grasses. We focused our study on the PCK clade (named for phosphoenol pyruvate carboxykinase), a well-supported monophyletic group for which the relationships among its taxa are not well resolved. Interestingly, the PCK clade has an extensive diversity of adult inflorescence forms. A comparative developmental approach can help us to understand the basis of such morphological differences as well as provide characters that can be used in phylogenetic studies of the group. Using SEM studies, we demonstrate that inflorescence morphology in this clade is even more complex than what is typically observed in adult forms. We describe a number of new characters, and some classical features previously used for taxonomic purposes are redefined on the basis of development. We also define four morphological groups combining adult inflorescence form and development, and we discuss some of the evolutionary aspects of inflorescence diversification in the PCK clade. Taxonomic delimitation among genera in the PCK clade remains confusing and unclear where molecular and morphological studies support different classifications.     

ECOD: An Evolutionary Classification of Protein Domains

Understanding the evolution of a protein, including both close and distant relationships, often reveals insight into its structure and function. Fast and easy access to such up-to-date information facilitates research. We have developed a hierarchical evolutionary classification of all proteins with experimentally determined spatial structures, and presented it as an interactive and updatable online database. ECOD (Evolutionary Classification of protein Domains) is distinct from other structural classifications in that it groups domains primarily by evolutionary relationships (homology), rather than topology (or “fold”). This distinction highlights cases of homology between domains of differing topology to aid in understanding of protein structure evolution. ECOD uniquely emphasizes distantly related homologs that are difficult to detect, and thus catalogs the largest number of evolutionary links among structural domain classifications. Placing distant homologs together underscores the ancestral similarities of these proteins and draws attention to the most important regions of sequence and structure, as well as conserved functional sites. ECOD also recognizes closer sequence-based relationships between protein domains. Currently, approximately 100,000 protein structures are classified in ECOD into 9,000 sequence families clustered into close to 2,000 evolutionary groups. The classification is assisted by an automated pipeline that quickly and consistently classifies weekly releases of PDB structures and allows for continual updates. This synchronization with PDB uniquely distinguishes ECOD among all protein classifications. Finally, we present several case studies of homologous proteins not recorded in other classifications, illustrating the potential of how ECOD can be used to further biological and evolutionary studies.     

Evolution of “determinants” in sex-determination: A novel hypothesis for the origin of environmental contingencies in avian sex-bias

Sex-determination is commonly categorized as either “genetic” or “environmental”—a classification that obscures the origin of this dichotomy and the evolution of sex-determining factors. The current focus on static outcomes of sex-determination provides little insight into the dynamic developmental processes by which some mechanisms acquire the role of sex determinants. Systems that combine “genetic” pathways of sex-determination (i.e., sex chromosomes) with “environmental” pathways (e.g., epigenetically induced segregation distortion) provide an opportunity to examine the evolutionary relationships between the two classes of processes and, ultimately, illuminate the evolution of sex-determining systems. Taxa with sex chromosomes typically undergo an evolutionary reduction in size of one of the sex chromosomes due to suppressed recombination, resulting in pronounced dimorphism of the sex chromosomes, and setting the stage for emergence of epigenetic compensatory mechanisms regulating meiotic segregation of heteromorphic sex chromosomes. Here we propose that these dispersed and redundant regulatory mechanisms enable environmental contingency in genetic sex-determination in birds and account for frequently documented context-dependence in avian sex-determination. We examine the evolution of directionality in such sex-determination as a result of exposure of epigenetic regulators of meiosis to natural selection and identify a central role of hormones in integrating female reproductive homeostasis, resource allocation to oocytes, and offspring sex. This approach clarifies the evolutionary relationship between sex-specific molecular genetic mechanisms of sex-determination and non-sex-specific epigenetic regulators of meiosis and demonstrates that both can determine sex. Our perspective shows how non-sex-specific mechanisms can acquire sex-determining function and, by establishing the explicit link between physiological integration of oogenesis and sex-determination, opens new avenues to the studies of adaptive sex-bias and sex-specific resource allocation in species with genetic sex-determination.     

Evolution of heteromorphic sex chromosomes in the order Aulopiformes

The fish order Aulopiformes contains both synchronously hermaphroditic and gonochoristic species. From the cytogenetic viewpoint, few reports show that gonochoristic Aulopiformes have heteromorphic sex chromosomes. Because fish in this order give us a unique opportunity to elucidate the evolution of sex chromosomes, it is important to examine a phylogenetic relationship in Aulopiformes by both molecular evolutionary and cytogenetic methods. Thus, we conducted molecular phylogenetic and cytogenetic studies of six Aulopiform species. Our results suggested that hermaphroditic species were evolutionarily derived from gonochoristic species. It follows that the hermaphroditic species might have lost the heteromorphic sex chromosomes during evolution. Here, we suggest a possibility that heteromorphic sex chromosomes can disappear from the genome, even if they have appeared once in evolution. Taking into account Ohno's hypothesis that heteromorphic sex chromosomes might have emerged from autosomes, we propose the hypothesis that heteromorphic sex chromosomes may have undergone repeated events of appearance and disappearance during the course of fish evolution.     

Mitochondrial gene rearrangements: new paradigm in the evolutionary biology and systematics

Mitochondrial (mt) genomic study may reveal significant insight into the molecular evolution and several other aspects of genome evolution such as gene rearrangements evolution, gene regulation, and replication mechanisms. Other questions such as patterns of gene expression mechanism evolution, genomic variation and its correlation with physiology, and other molecular and biochemical mechanisms can be addressed by the mt genomics. Rare genomic changes have attracted evolutionary biology community for providing homoplasy free evidence of phylogenetic relationships. Gene rearrangements are considered to be rare evolutionary events and are being used to reconstruct the phylogeny of diverse group of organisms. Mt gene rearrangements have been established as a hotspot for the phylogenetic and evolutionary analysis of closely as well as distantly related organisms.