Hox基因及其进化机制的研究进展

Hox基因是生物体内一类重要的发育调控基因家族.Hox基因高度保守,通常成簇存在,编码一类转录因子,在个体胚胎发育中起着重要的调控作用.近期研究表明,基因复制、基因序列变异及选择压力对Hox基因簇的产生和进化有重要作用,同时调节元件和协同进化对Hox基因的进化也有重要影响.     

Olfactory Receptor Multigene Family in Vertebrates: From the Viewpoint of Evolutionary Genomics

Olfaction is essential for the survival of animals. Diverse odor molecules in the environment are detected by the olfactory receptors (ORs) in the olfactory epithelium of the nasal cavity. There are ~400 and ~1,000 OR genes in the human and mouse genomes, respectively, forming the largest multigene family in mammals. The relationships between ORs and odorants are multiple-to-multiple, which allows for discriminating almost unlimited number of different odorants by a combination of ORs. However, the OR-ligand relationships are still largely unknown, and predicting the quality of odor from its molecular structure is unsuccessful.Extensive bioinformatic analyses using the whole genomes of various organisms revealed a great variation in number of OR genes among species, reflecting the diversity of their living environments. For example, higher primates equipped with a well-developed vision system and dolphins that are secondarily adapted to the aquatic life have considerably smaller numbers of OR genes than most of other mammals do. OR genes are characterized by extremely frequent gene duplications and losses. The OR gene repertories are also diverse among human individuals, explaining the diversity of odor perception such as the specific anosmia.OR genes are present in all vertebrates. The number of OR genes is smaller in teleost fishes than in mammals, while the diversity is higher in the former than the latter. Because the genome of amphioxus, the most basal chordate species, harbors vertebrate-like OR genes, the origin of OR genes can be traced back to the common ancestor of the phylum Chordata.     

Downsized Dinosaurs: The Evolutionary Transition to Modern Birds

Living birds are the most diverse land vertebrates and the heirs of a rich chapter in the evolution of life. The origin of modern birds from animals similar to Tyrannosaurus rex is among the most remarkable examples of an evolutionary transition. A wealth of recently discovered fossils has finally settled the century-old controversy about the origin of birds and it has made the evolutionary saga toward modern birds one of the best documented transitions in the history of life. This paper reviews the evidence in support of the origin of birds from meat-eating dinosaurs, and it highlights the array of fossils that connect these fearsome animals with those that fly all around us.     

Evolutionary Patterns of Gene Families Generated in the Early Stage of Vertebrates

In this paper we have analyzed 49 vertebrate gene families that were generated in the early stage of vertebrates and/or shortly before the origin of vertebrates, each of which consists of three or four member genes. We have dated the first (T₁) and second (T₂) gene duplications of 26 gene families with 3 member genes. The means of T₁ (594 mya) and T₂ (488 mya) are largely consistent to a well-cited version of two-round (2R) genome duplication theory. Moreover, in most cases, the time interval between two successive gene duplications is large enough that the fate of duplicate genes generated by the first gene duplication was likely to be determined before the second one took place. However, the phylogenetic pattern of 23 gene families with 4 members is complicated; only 5 of them are predicted by 2R model, but 11 families require an additional gene (or genome) duplication. For the rest (7 families), at least one gene duplication event had occurred before the divergence between vertebrate and Drosophila, indicating a possible misleading of the 4:1 rule (member gene ratio between vertebrates and invertebrates). Our results show that Ohno's 2R conjecture is valid as a working hypothesis for providing a most parsimonious explanation. Although for some gene families, additional gene duplication is needed, the credibility of the third genome duplication (3R) remains to be investigated. Received: 13 December 1999 / Accepted: 7 April 2000     

The Origin of the Vertebrate Eye

In his considerations of “organs of extreme perfection,” Charles Darwin described the evidence that would be necessary to support the evolutionary origin of the eye, namely, demonstration of the existence of “numerous gradations” from the most primitive eye to the most perfect one, where each such tiny change had provided a survival advantage (however slight) to the organism possessing the subtly altered form. In this paper, we discuss evidence indicating that the vertebrate eye did indeed evolve through numerous subtle changes. The great majority of the gradual transitions that did occur have not been preserved to the present time, either in the fossil record or in extant species; yet clear evidence of their occurrence remains. We discuss the remarkable “eye” of the hagfish, which has features intermediate between a simple light detector and an image-forming camera-like eye and which may represent a step in the evolution of our eye that can now be studied by modern methods. We also describe the important clues to the evolutionary origin of the vertebrate eye that can be found by studying the embryological development of our own eye, by examining the molecular genetic record preserved in our own genes and in the genes of other vertebrates, and through consideration of the imperfections (or evolutionary “scars”) in the construction of our eye. Taking these findings together, it is possible to discuss in some detail how the vertebrate eye evolved.     

山东植物区系的演变和来源

1　现代植物区系山东省位于我国东部、黄河下游 ,北濒渤海 ,东临黄海 ,地理范围介于北纬 34°2 3′～38°2 4′,东经 1 1 4°4 8′～ 1 2 2°4 3′之间。全省总面积为 1 5.72万 km2 ,占全国总面积的 1 .6%。属暖温带季风气候 ,沿海比较湿润 ,地带性植被主要是暖温带落叶阔叶林和松、栎类针阔叶混交林。山东省在中国植物区系的分区地位隶属于泛北极植物区、中国 -日本森林植物亚区、华北植物地区 [1 ]。据最近研究统计 ,现有野生维管植物 1 47科、61 4属 ,约 1 547种 (包括变种 ,下同 )。其中蕨类植物 2 4科 39属 1 0 5种 ,裸子植物 3科 3属 …     

Evolutionary Transitions Among Dinosaurs: Examples from the Jurassic of China

Dinosaurs have captured the popular imagination more than any other extinct group of organisms and are therefore a powerful tool in teaching evolutionary biology. Most students are familiar with a wide variety of dinosaurs and the relative suddenness of their extinction, but few are aware of the tremendous longevity of their time on Earth and the richness of their fossil record. We first review some of the best-known groups of dinosaurs and discuss how their less-specialized relatives elucidate the path through which each evolved. We then discuss our recent discovery of Yinlong downsi, a distant relative of Triceratops, and other fossils from Jurassic deposits in China to exemplify how the continuing discovery of fossils is filling out the dinosaur family tree.     

The sequence of a cytoplasmic intermediate filament (IF) protein from theannelid Lumbricus terrestris emphasizes a distinctive feature of protostomic IF proteins

The complete cDNA clone for a cytoplasmic intermidiatefilament (IF) protein from the annelid Lumbricus terrestris reported here, shows an extra 42 residues in the coil 1b subdomain of the central rod, as do the IF proteins from nematodes and moluscs. These extra six heptads are also present in all nuclear lamins but not in any known vertebrate cytoplasmic IF protein. Thus, it seems that protostomic metazoa conserve a lamin-like structural element in their cytoplasmic IF proteins, which was lost in the deuterostomic metazoan branch leading to the vertebrates.     

From prebiotic chemistry to cellular metabolism--the chemical evolution of metabolism before Darwinian natural selection

It is generally assumed that the complex map of metabolism is a result of natural selection working at the molecular level. However, natural selection can only work on entities that have three basic features: information, metabolism and membrane. Metabolism must include the capability of producing all cellular structures, as well as energy (ATP), from external sources; information must be established on a material that allows its perpetuity, in order to safeguard the goals achieved; and membranes must be able to preserve the internal material, determining a selective exchange with external material in order to ensure that both metabolism and information can be individualized. It is not difficult to understand that protocellular entities that boast these three qualities can evolve through natural selection. The problem is rather to explain the origin of such features under conditions where natural selection could not work. In the present work we propose that these protocells could be built by chemical evolution, starting from the prebiotic primordial soup, by means of chemical selection. This consists of selective increases of the rates of certain specific reactions because of the kinetic or thermodynamic features of the process, such as stoichiometric catalysis or autocatalysis, cooperativity and others, thereby promoting their prevalence among the whole set of chemical possibilities. Our results show that all chemical processes necessary for yielding the basic materials that natural selection needs to work may be achieved through chemical selection, thus suggesting a way for life to begin.     

The phytogeographical studies of Thermopsis (Fabaceae)

The present article is the first comprehensive treatment of phytogeography of Thermopsis (Fabaceae) in the world. Thermopsis is one of the few genera within Fabaceae with the distribution pattern of the East Asia-North American disjunction. The distribution patterns of 5 recognized sections (including a new one) covering 21 species in Thermopsis are analyzed, and the results show four centres of frequency of the genus: the Eastern Asiatic Region (9 spp. / 3 sects., including 4 endemic species), the Irano-Turanian Region (7 spp./3 sects., including 3 endemic species), the Rocky Mountain Region (7 spp./2 sects., all endemic), and the Atlantic North American Region (3 spp. / 1 sect., all endemic). In the light of the fact that most species and sections, a number of phylogenetic series of the genus, and the most primitive sections and most advanced sections in Thermopsis occur in the East Asia, the Eastern Asiatic Region might be the centre of diversity of the genus. As the Irano-Turanian Region and the Rocky Mountain Region were just second to that of Eastern Asiatic Region in number of sections and species, and many polyploids appeared in these regions, they were considered as the secondary centres of distribution and speciation of the genus. The speciation looks to be frequent and complex in these regions, and many new taxa have been described from there while many new reduced or incorporated taxa have happened over there. However, recent molecular data has shown that two reduced taxa of Thermopsis are distinct in these regions. Based on the modern distribution patterns and evolutionary trends in morphological characters of the genus, and available fossil record of the genus and the historical geology, we speculate that Thermopsis had already existed on Eurasia and North America before the Late Miocene, and probably originated from an ancestral form of Sophora-like taxa with lupine alkaloids somewhere in the Laurasia in the Early Tertiary or Late Cretaceous. After the separation of the two continents, species on different continents developed distinctly under influences of different evolutionary factors. In Asia, the late Tertiary orogeny, disappearing of the Tethys and aridity and freezing caused by the Quaternary glaciation were the main forces to promote the speciation and evolutionary processes, whereas in North America it was the Quaternary glaciation and the orogeny of partial area to promote evolution of the genus. According to the evolutionary trends in Thermopsis and the distribution pattern of the primitive taxa, Sino-Japanese Subregion of Eastern Asiatic Region may be considered asthe centre of primitive forms of Thermopsis.     

柽柳科柽柳属的植物地理研究

柽柳属是典型的旧世界温带分布属。对柽柳属3组68种的分布进行了分析,发现本属3个频度分布中心依次为伊朗—吐兰区的西亚亚区(30种／3组,其中特有种13种),中亚亚区(20种／2组,其中特有种6种)和地中海区(12种／3组,其中特有种6种)。由于伊朗—吐兰地区的西亚亚区存在本属最多的组与种、特有种多且可以见到柽柳属系统发育系列,因而认为该亚区是现存本属植物的现代分布中心和分化中心。地中海地区包含的组、种数仅次于伊朗—吐兰区,并且特有种为6种,带有新特有种的性质,全是系统发育上相对年轻、进步的类型,被认为是本属的一个次级分布中心,另一个次级分布中心在中亚亚区,尤其是中国西北干旱地区。根据柽柳属植物的现代地理分布、化石资料及地质历史资料,推测柽柳属起源于古地中海热带成分盛行的早第三纪始新世,具有起源古老的性质,并且随着晚第三纪古地中海的退缩、气候逐渐干旱而得到进一步发展,产生许多新的以温带成分为主适应旱生环境的现代柽柳属种类。柽柳属起源之后,首先繁衍、散布到以伊朗为中心的现代分布中心,其后以伊朗为廊道向西、向东扩散,在地中海沿岸、东非、阿拉伯半岛、非洲西南部及亚洲中部的荒漠地区得到发展。     

The Evolution of Evolutionary Thinking in Chile

The scientific study of evolution in Chile has experienced periods of diversification and stasis, depending upon the social and political context at different times. In the eighteenth century, most of the natural history research consisted of systematics and taxonomy and, as in most of South America, this task was performed mainly by natural historian theologists. Later, the immigration of European scientists to Chile after independence from Spain in 1810 improved substantially its knowledge of the local biota and stimulated the diversification of naturalists in the country. Research in modern biology and the teaching of genetics in Chile can be traced back to Giovanni Noe, an Italian zoologist who had a profound impact in the first third of the twentieth century. In the 1960s–70s, Danko Brncic, a population geneticist educated in the tradition of Dobzhansky and the modern synthesis, led the most important diversification process in the study of evolutionary biology in the country. However, the military coup in 1973 brought this radiation to a sudden stop and produced a stasis period associated with the subsequent 17-year dictatorship. Evolutionary biology recovered its status after the re-establishment of democracy, and it is currently experiencing an exciting and renewed diversification period that has led to the foundation of the Chilean Society of Evolutionary Biology, the only scientific society for the study of evolution in Latin America. One of the missions of the Society is to bridge the gap between scientists and science educators in order to improve the teaching of evolution at different levels both in secular and religious schools. Even though the Roman Catholic Church has been a pivotal institution in the development of Chilean society, debate on evolutionism—creationism issues has been largely absent both in public and academic discussions. The influence of religion on science education has been sporadic, and mostly related to omission rather than tergiversation of scientific information in biology textbooks. Currently, schools are obliged by law to teach the basics of evolution in K-12 and K-16 levels (or their local equivalents). Because of this, there is little at present that suggests an organized creationist or intelligent design movement surge in the near future. Nevertheless, the high percentage of religiosity in Chile, together with the observation that the moral values of Chilean society are among the most conservative in the world, provide good reasons to remain vigilant.     

Evolutionary modification of T-brain (tbr) expression patterns in sand dollar

The sand dollars are a group of irregular echinoids that diverged from other regular sea urchins approximately 200 million years ago. We isolated two orthologs of T-brain (tbr), Smtbr and Pjtbr, from the indirect developing sand dollar Scaphechinus mirabilis and the direct developing sand dollar Peronella japonica, respectively. The expression patterns of Smtbr and Pjtbr during early development were examined by whole mount in situ hybridization. The expression of Smtbr was first detected in micromere descendants in early blastula stage, similar to tbr expression in regular sea urchins. However, unlike in regular sea urchin, Smtbr expression in middle blastula stage was detected in micromere-descendent cells and a subset of macromere-descendant cells. At gastrula stage, expression of Smtbr was detected in part of the archenteron as well as primary mesenchyme cells. A similar pattern of tbr expression was observed in early Peronella embryos. A comparison of tbr expression patterns between sand dollars and other echinoderm species suggested that broader expression in the endomesoderm is an ancestral character of echinoderms. In addition to the endomesoderm, Pjtbr expression was detected in the apical organ, the animal-most part of the ectoderm.     

The Classification and Distribution of the Genus Calligonum L. in China

The genus Calligonum L. includes a total number of 35 species in the world, of which 24 are in China. They are grouped into four sections, of which Sect. Calliphysae (Fisch. et Mey.) Borszcz. is the most primitive and Sect. Medusae Sosk. et Alexender. is the most progressive. The Calligonum L. is an ancient genus in the arid desert flora, and central Asia is the place of its origin. Some species migrated to the Middle Asia and Iran, developing into a second center there. Also, some newly occurred species of the Middle Asia emigrated eastwards to central Asia, so the genus Calligonum L. in China comprises components of both central Asia and the Middle Asia. The genus Calligonum L. is distributed in North Africa, south Europa and Asia, and China is the eastmost part of the distribution range. They grow in Nei Monggol, Gansu, Qinghai and Xinjiang. There are 12 species in the Zhuengar Basin, covering 50 percent of the total number of species in China, amd thus the genus is the most abundant there.     

Science and the Concept of Evolution: From the Big Bang to the Origin and Evolution of Life

The common thread of evolution runs through all science disciplines, and the concept of evolution enables students to better understand the nature of the universe and our origins. “Science and the Concept of Evolution” is one of two interdisciplinary science Core courses taken by Dowling College undergraduates as part of their General Education requirements. The course examines basic principles and methods of science by following the concept of evolution from the big bang to the origin and evolution of life. Case studies of leading scientists illustrate how their ideas developed and contributed to the evolution of our understanding of the world. Evidences for physical, chemical, and biological evolution are explored, and students learn to view the evolution of matter and of ideas as a natural process of change over space and time.     

miR-106-363基因簇在脊椎动物中的进化分析

microRNA(miRNA)是一类在真核生物体内广泛表达的非编码小分子RNA,在生物体生长、发育以及疾病发生等过程中都起着极其重要的作用。miR-106-363基因簇是一个高度保守的基因簇,编码miR-106、miR-18、miR-20、miR-19、miR-92和miR-363等6个miRNA。本文通过对miRBase数据库检索以及同源搜索的方法在16种脊椎动物中搜索到了miR-106-363基因簇。该miRNA基因簇在高等脊椎动物中高度保守,稳定存在。系统进化树分析表明,miR-106-363基因簇与miR-17-92基因簇有着共同的祖先,且在进化上miR-17-92基因簇有着更早的起源。     

The nonhistone chromosomal proteins of vertebrate liver and kidney: A comparative study by gel electrophoresis

Summary The nonhistone chromosomal proteins (NHC proteins) probably include enzymes of chromosomal metabolism, general structural proteins, and possibly control elements. In theory, these proteins may have been strongly conserved during evolution, as the histones have. We have used sodium dodecyl sulfate (SDS) disc gel electrophoresis to analyze and compare the NHC proteins of two tissues, liver and kidney, from rat, cat, cow, chicken, turtle, and frog. The gel patterns indicate that the NHC proteins have changed much more during evolution than have the histones; the total pattern of NHC proteins has not been conserved. However, there does appear to be a conservation of a subset of bands for each tissue investigated. Further chemical analysis will be required to establish the significance of the results.Recipient of NIH Career Development Award NIH AI-20388     

Comparative Characterization of Two Marine Alginate Lyases from Zobellia galactanivorans Reveals Distinct Modes of Action and Exquisite Adaptation to Their Natural Substrate

Cell walls of brown algae are complex supramolecular assemblies containing various original, sulfated, and carboxylated polysaccharides. Among these, the major marine polysaccharide component, alginate, represents an important biomass that is successfully turned over by the heterotrophic marine bacteria. In the marine flavobacterium Zobellia galactanivorans, the catabolism and uptake of alginate are encoded by operon structures that resemble the typical Bacteroidetes polysaccharide utilization locus. The genome of Z. galactanivorans contains seven putative alginate lyase genes, five of which are localized within two clusters comprising additional carbohydrate-related genes. This study reports on the detailed biochemical and structural characterization of two of these. We demonstrate here that AlyA1_PL7 is an endolytic guluronate lyase, and AlyA5 cleaves unsaturated units, α-l-guluronate or β-d-manuronate residues, at the nonreducing end of oligo-alginates in an exolytic fashion. Despite a common jelly roll-fold, these striking differences of the mode of action are explained by a distinct active site topology, an open cleft in AlyA1_PL7, whereas AlyA5 displays a pocket topology due to the presence of additional loops partially obstructing the catalytic groove. Finally, in contrast to PL7 alginate lyases from terrestrial bacteria, both enzymes proceed according to a calcium-dependent mechanism suggesting an exquisite adaptation to their natural substrate in the context of brown algal cell walls.