对于早期鸟类起源与演化过程中一些疑问的个人见解

鸟类起源问题在学术界仍然存在分歧 ,现在大多数古生物学家都支持鸟类起源于恐龙之说。虽然化石证据表明恐龙和早期鸟类之间确实存在很多相似之处 ,但是仍有一些疑问无法得到合理解释 ,那么鸟类是否起源于恐龙呢？很多学者认为霸王龙和驰龙类同鸟类具有较近的亲缘关系 ,但是却无法解释这类进步的恐龙为何出现在比中生代早期化石鸟类更晚的地层之中？笔者认为霸王龙及驰龙类的始祖同鸟类最终始祖之间可能存在较近的亲缘关系 ,可以认为霸王龙及驰龙类在它们的演化过程中除体型以外在其他方面同其始祖之间并无较大区别 ,笔者认为霸王龙可能处于…     

核基因在鸟类分子系统发育学研究中的应用

核基因作为一种新的遗传标记,近年来被广泛应用于鸟类分子系统发育研究中.核基因与线粒体基因位于不同的遗传载体上,因此被引入到系统发育学研究中为物种树的重建提供独立的证据.常用的外显子标记为重组激活基因1(RAG-1),重组激活基因2(RAG-2),癌基因c-myc,原癌基因c-mos,它们由于缓慢的进化速率而被用于鸟类高级分类阶元的系统学研究中.常用的内含子标记是β纤维蛋白原基因内含子7(β-fibrinogen intron7,β-fibint7),肌红蛋白基因内含子Ⅱ(myoglobin intionⅡ).内含子标记通常与线粒体序列联合使用,形成具有互补系统发育信号的数据集,应用于各种分类阶元的系统学研究中.     

水生甲虫系统发育研究进展

简要回顾了水生甲虫近十几年来各个分类阶元水平系统关系的研究历史,对代表性的水生甲虫类高级阶元系统发育关系进行了比较分析,总结了普遍存在的共识和争议.在研究进展中还介绍了分子生物学方法在水生甲虫系统发育研究中的尝试,虽然其研究结果还未能完全解决上述问题,但必将是对现有研究方法的补充.     

杜鹃花科白珠树属分子系统学和生物地理学研究进展

白珠树属(Gaultheria)在杜鹃花科(Ericaceae)系统演化中占有十分重要的地位,其系统位置和演化关系一直备受争议.最近的分子系统学研究认为,白珠树属已经不再属于传统上的越橘亚科(Vaccinioideae)的綟木族(Andromedeae),而是与一些相关属组成了白珠树族(Gaultherieae).对白珠树属产于美洲的类群和相关类群的分子系统学的初步研究则表明,该属与Diplycosia、Tepuia和Pernettya等属(均为"常绿类群")关系密切,可能应将这几个属并入到白珠树属中,但其属下分类系统关系还需要对产于亚洲的类群进行深入的研究后才能确定.白珠树属与其近缘属的进化历史和生物地理学关系较为复杂,与杜鹃花科其他大多数属不同,白珠树属为典型的环太平洋分布.关于白珠树属的起源问题存在两种不同的推测:一种观点认为该属起源于南半球的冈瓦纳古陆;另一种观点则认为其起源于北半球的劳亚古大陆.本文概述了近年来白珠树属的分子系统学和生物地理学研究进展,并对该属尚存的一些问题进行了讨论.     

中国鸟类的DNA分类及系统发育研究概述

鸟类分类是鸟类学其他研究领域的基础,近年来分子技术的发展,以及计算机技术的应用为鸟类分类学和鸟类系统演化研究提供了新的研究手段,给传统的系统分类研究带来了新的机遇.Tautz等于2002年首先提出运用DNA序列作为生物分类系统的主要平台,即DNA分类学(DNA Taxonomy).而Hebert等于2003年则首次提出了DNA条形码(DNA Barcoding)的概念,并对其物种分类和鉴定意义予以肯定,建议利用线粒体细胞色素C氧化酶亚单位Ⅰ(COI)的特定区段来做DNA条形编码的基础.在鸟类DNA分类方面,国内学者应用线粒体基因Cut b,COI,c-mos,c-myc,12s rRNA,16s rRNA,ND2,ND3,CR,RAG-1以及核基因myoglobin introⅡ等不同片段对很多类群进行了分类探讨和系统发育研究.但是主要集中在鸡形目及雀形目鸟类.中国是鸟类多样性极其丰富的国家,近年来很多亚种、种及以上分类阶元依然存在问题,因此,中国鸟类物种的分类地位、系统发育与演化关系等依然有很多问题等待深入研究.目前国内基于COI的鸟类分类及系统发育研究有了一些报道,但是真正的DNA条形码工作尚需继续、深入地开展.     

云南南涧凤凰山秋季夜间迁移鸟类多样性分析

2002年9月16日至11月28日、2003年4月6日至26日、2003年9月9日至11月26日,对云南南涧凤凰山秋季夜间迁移鸟类进行了研究。共网捕迁移鸟176种6677只,分属13目29科,其中红喉姬、红点颏、蓝歌鸲等雀形目鸟类数量优势度十分显著,表明该地迁移鸟类以雀形目等中小型鸟类为主。对网捕迁移鸟进行多样性分析,Shannon-Weaner指数为3·89,G指数为4·13,总的F指数为25·56,表明该地迁移鸟在种、属、科等分类阶元的多样性均较丰富。2002和2003年迁移鸟类多样性t检验结果表明,年间、月份间的多样性差异明显,即凤凰山迁移鸟类动态变化明显。     

海菜花属的分支学研究

本文选取了与海菜花属系统发育有重要关系的19个性状,采用分支分析方法,研究了代表中国海菜花属全部已知分类群的18个居群的系统发育关系;根据简约性原则,构建了18个居群的分支图。结果表明,18个居群可划分为4类,它们分别对应于现知的4个分类学种,而与数值分类学研究中的Q分析结果基本一致;在分类群的划分上,分支分析与Q分析一样有效,并能反映系统发育关系。本文最后对海菜花属的起源和演化作了探索性推测,认为本属可能最迟在白垩纪末起源于冈瓦纳古陆的热带湖沼地区,此后分化成沉水叶多花支、沉水叶单花支和浮水叶单花支繁衍演化。     

中国(鱼兆)科(鱼匽)(鱼兆)群系统发育与地理分布格局研究进展

中国鮡科鰋鮡群鱼类至今已记录8属23种(亚种),但分布于云南澜沧江、怒江等水系的一些种类及分布于四川西南地区的属和石爬属的一些种的有效性仍存疑问或争议,值得进一步研究。分子生物学证据为解决种级阶元分类地位的争议,或者为系统发育研究提供了微观证据。但形态学之间、形态学与分子生物学之间、分子生物学之间的研究结果均不完全吻合,甚至同一作者不同年代形态学与分子生物学的研究结果也相互矛盾。鱼类的分布格局及不同阶元的分化与青藏高原的3次隆升有着密不可分的关系。鰋鮡鱼类的分化不仅体现在各大水系之间,也体现在同一水系的不同支流或上下游之间。该类群的分化既包括了自然阻障形成导致的分类阶元的隔离分化过程,也包括了同一阶元在同一水系扩散分化的生态适应过程。这两个过程的交织,使得鰋鮡鱼类的分化和分布异常复杂。尽可能收全鰋鮡鱼类现生种类,发现更多的分类学证据,形态特征与分子证据的有机结合,是今后鰋鮡鱼类分类、系统发育和地理分布格局研究的发展方向。     

四川省鸟类种数的最新统计

依据郑光美<中国鸟类分类与分布名录>的分类系统,在前人的研究基础之上,结合近年来发现的新分布记录,对四川的鸟类重新进行了统计.结果 表明,四川省鸟类有21目80科683种,分别占全国鸟类目的87.50%,科的79.21%,种的51.28%,其中非雀形目有20目42科273种,雀形目有38科410种.四川省有国家Ⅰ级重点保护鸟类17种,Ⅱ级保护鸟类80种;CITES(2007)附录Ⅰ有9种,附录Ⅱ有62种;IUCN(2007)红色名录有42种;中国鸟类特有种37种,占全国鸟类特有种的52.1%.     

B染色体起源的研究进展

B染色体(简写为Bs)起源的传统观点是认为它起源于携带者所在物种的基因组.目前又发现了许多新的证据来推测Bs的起源.它可能具有两种起源:种内起源和种间起源(起源于另一物种的基因组),且有证据表明同一物种的Bs可能是多次起源,同时对Bs的起源机制也作了总结.认为B8起源的研究已取得了一定的进展,但要给Bs起源下一个确切的结论仍需要大量的实验证据.     

Systematics of fossil platanoids and hamamelids

The data on fossil platanoids and hamamelids are generalized, their morphological diversity and probable patterns of the establishment of the extant families Platanaceae and Hamamelidaceae are analyzed. It is shown that morphological and epidermal characters of polymorphic leaves of typical platanoid appearance were formed in the Late Albian and remained essentially invariable to the present time, indicating the morphological stasis of these leaves combined with a wide variation range. In view of association with essentially different reproductive structures, it is proposed to classify these leaves by the morphological system irrespective of the natural system of angiosperms. A new system of extinct platanoids and hamamelids, which is based on reproductive structures and includes two orders, Hamamelidales and Sarbaicarpales ordo. nov., is proposed. Hamamelidales comprises two extant families, Platanaceae (with the subfamilies Platanoideae subfam. nov. and Gynoplatananthoideae subfam. nov.) and Hamamelidaceae, and the extinct family Bogutchanthaceae fam. nov.; the new extinct order Sarbaicarpales ordo. nov. consists of two new families, Sarbaicarpaceae fam. nov. and Kasicarpaceae fam. nov. In a system of flowering plants that is based on molecular data, the families Platanaceae and Hamamelidaceae are assigned to remote orders, excluding close relationship (APG, 2003). At the same time, the system of APG II often contradicts morphological and paleontological data, while traditional ideas of morphologists concerning the common origin of these families have recently been supported by paleobotanic evidence. Probable origin of the families Platanaceae and Hamamelidaceae from a common polymorphic ancestral group is discussed.     

Molecular phylogeny of Kalyptorhynchia (Rhabdocoela,Platyhelminthes) inferred from ribosomal sequence data

With 556 species described to date, Kalyptorhynchia includes about one‐third of all species of rhabdocoel flatworms. In this study, we present the first molecular phylogenetic analysis of this taxon. The final analysis comprises 110 species. These represent 11 of the 17 known families. The largest family (241 known species), Polycystididae, is represented by nine of 10 subfamilies and 33 of the 58 genera. Sequence data from 18S rDNA and 28S rDNA were analysed using maximum likelihood and Bayesian approaches. Of the two taxa traditionally recognised within Kalyptorhynchia, Eukalyptorhynchia and Schizorhynchia, only Schizorhynchia is monophyletic. All eukalyptorhynch families, except Cicerinidae, are monophyletic. On the other hand, two of the three schizorhynch families included are not monophyletic. Within Polycystididae, the traditional taxonomy was not reflected in our phylogenetic analyses and most subfamilies are polyphyletic. These results suggest that current classification, mostly based on characters of the genital system, suffers from homoplasy. Where possible, a revised classification, taking into account these new findings, is given.     

Estimating number of families for an urban fox population by using two public data sets

The number of families in the urban fox population of Sapporo, Japan, was estimated from two sets of data reported by the public to government: records of road-killed foxes (information-A) and records of complaints about foxes (information-B). We assumed that fox populations consist of families that have exclusive home ranges, i.e., territories, during the period between gestation and dispersal. The urban area was then divided into hexagons that correspond to the territories. The locations from the two sets of records during the territorial period were plotted on the map. The number of fox families for which information-A and/or B was reported was estimated by counting the number of hexagons that include the record. The total number of families was estimated by using a double-observation method. We adopted Chapman’s unbiased estimator which is based on the hypergeometric distribution that corresponds to the conditional likelihood. We demonstrated the possibility of estimating the abundance of animals from government data such as road kill and complaints if the animals have territories. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The systematic distribution of tannins in the leaves of angiosperms: A tool for ecological studies

The systematic distribution of tannins in foliar tissues has not been comprehensively reviewed for the Angiosperms in over 20 years. Here their systematic distribution is assessed using data based on protein precipitation or chemically specific tests. Fewer families are characterized by the typical presence of tannins than has previously been reported, and a greater variation in the occurrence of tannins in species sampled from within single plant families has been detected. This study presents the proportion of tannin-containing species in angiosperm families arranged according to the system of Cronquist for the first time. The potential utility of these data in testing ecological ideas about the distribution of tannins, such as those based on plant habit or life-history, is discussed.     

CHS基因起源初探及其在被子植物中的进化分析

利用PCR与TAlL-PCR方法,从半月苔(Lunularia cructata(L.)Dum.ex Lindb)中获得了一段长约l 000 bp的基因片段,它与已知的CHS基因在核苷酸水平上的相似性大于56%,在氨基酸水平上的相似性大于60%,所推断的氨基酸序列中酶反应的4个催化位点与已知晶体结构的紫花苜蓿MCHS2A上的催化位点相同,首次证明了苔类植物中可能存在类CHS基因,将CHS基因的起源时间推到苔藓类植物出现之前.以该序列和两种蕨类植物(Psilotumnudum(L.)Griseb.和Equisetum arvense L.)的CHS序列作为外类群,应用邻接法、最大简约法和最大似然法分别构建了被子植物的CHS的分子系统树.结果表明,大部分科中的CHS分布在不同的分支上,而十字花科、可科和禾本科各自聚成一个单系类群.以邻接树为依据,对茄科、旋花科和菊科的CHS基因进行了相对碱基替换速率的检测,发现这三个科内或科间序列的替换速率不一致.被子植物的CHS基因在基因拷贝数目、碱基替换速率以及重复/丢失事件的发生上都存在较大的差异,这种差异可能与被子植物的生活史、生活环境、花的特性以及对外界的防御系统等的多样性相关.     

CHS基因起源初探及其在被子植物中的进化分析

利用PCR与TAIL-PCR方法,从半月苔(Lunulariacruciata(L.)Dum.exLindb.)中获得了一段长约1000bp的基因片段,它与已知的CHS基因在核苷酸水平上的相似性大于56%,在氨基酸水平上的相似性大于60%,所推断的氨基酸序列中酶反应的4个催化位点与已知晶体结构的紫花苜蓿MCHS2A上的催化位点相同,首次证明了苔类植物中可能存在类CHS基因,将CHS基因的起源时间推到苔藓类植物出现之前。以该序列和两种蕨类植物(Psilotumnudum(L.)Griseb.和EquisetumarvenseL.)的CHS序列作为外类群,应用邻接法、最大简约法和最大似然法分别构建了被子植物的CHS的分子系统树。结果表明,大部分科中的CHS分布在不同的分支上,而十字花科、豆科和禾本科各自聚成一个单系类群。以邻接树为依据,对茄科、旋花科和菊科的CHS基因进行了相对碱基替换速率的检测,发现这三个科内或科间序列的替换速率不一致。被子植物的CHS基因在基因拷贝数目、碱基替换速率以及重复/丢失事件的发生上都存在较大的差异,这种差异可能与被子植物的生活史、生活环境、花的特性以及对外界的防御系统等的多样性相关。     

Constructing ontology-driven protein family databases

MOTIVATION: Protein family databases provide a central focus for scientific communities as well as providing useful resources to aide research. However, such resources require constant curation and often become outdated and discontinued. We have developed an ontology-driven system for capturing and managing protein family data that addresses the problems of maintenance and sustainability. RESULTS: Using protein phosphatases and ABC transporters as model protein families, we constructed two protein family database resources around a central DAML+OIL ontology. Each resource contains specialist information about each protein family, providing specialized domain-specific resources based on the same template structure. The formal structure, combined with the extraction of biological data using GO terms, allows for automated update strategies. Despite the functional differences between the two protein families, the ontology model was equally applicable to both, demonstrating the generic nature of the system. AVAILABILITY: The protein phosphatase resource, PhosphaBase, is freely available on the internet (http://www.bioinf.man.ac.uk/phosphabase). The DAML+OIL ontology for the protein phosphatases and the ABC transporters is available on request from the authors. CONTACT: kwolstencroft@cs.man.ac.uk.     

Comparing Families of Dynamic Causal Models

Mathematical models of scientific data can be formally compared using Bayesian model evidence. Previous applications in the biological sciences have mainly focussed on model selection in which one first selects the model with the highest evidence and then makes inferences based on the parameters of that model. This “best model” approach is very useful but can become brittle if there are a large number of models to compare, and if different subjects use different models. To overcome this shortcoming we propose the combination of two further approaches: (i) family level inference and (ii) Bayesian model averaging within families. Family level inference removes uncertainty about aspects of model structure other than the characteristic of interest. For example: What are the inputs to the system? Is processing serial or parallel? Is it linear or nonlinear? Is it mediated by a single, crucial connection? We apply Bayesian model averaging within families to provide inferences about parameters that are independent of further assumptions about model structure. We illustrate the methods using Dynamic Causal Models of brain imaging data.     

The Transporter Classification (TC) System, 2002

The Transporter Classification (TC) system is a functional/phylogenetic system designed for the classification of all transmembrane transport proteins found in living organisms on Earth. It parallels but differs from the strictly functional EC system developed decades ago by the Enzyme Commission of the International Union of Biochemistry and Molecular Biology (IUBMB) for the classification of enzymes. Recently, the TC system has been adopted by the IUBMB as the internationally acclaimed system for the classification of transporters. Here we present the characteristics of the nearly 400 families of transport systems included in the TC system and provide statistical analyses of these families and their constituent proteins. Specifically, we analyze the transporter types for size and topological differences and analyze the families for the numbers and organismal sources of their constituent members. We show that channels and carriers exhibit distinctive structural and topological features. Bacterial-specific families outnumber eukaryotic-specific families about 2 to 1, while ubiquitous families, found in all three domains of life, are about half as numerous as eukaryotic-specific families. The results argue against appreciable horizontal transfer of genes encoding transporters between the three domains of life over the last 2 billion years.     

The transporter classification (TC) system, 2002

The Transporter Classification (TC) system is a functional/phylogenetic system designed for the classification of all transmembrane transport proteins found in living organisms on Earth. It parallels but differs from the strictly functional EC system developed decades ago by the Enzyme Commission of the International Union of Biochemistry and Molecular Biology (IUBMB) for the classification of enzymes. Recently, the TC system has been adopted by the IUBMB as the internationally acclaimed system for the classification of transporters. Here we present the characteristics of the nearly 400 families of transport systems included in the TC system and provide statistical analyses of these families and their constituent proteins. Specifically, we analyze the transporter types for size and topological differences and analyze the families for the numbers and organismal sources of their constituent members. We show that channels and carriers exhibit distinctive structural and topological features. Bacterial-specific families outnumber eukaryotic-specific families about 2 to 1, while ubiquitous families, found in all three domains of life, are about half as numerous as eukaryotic-specific families. The results argue against appreciable horizontal transfer of genes encoding transporters between the three domains of life over the last 2 billion years.