免疫系统在动物系统发育过程中的发生和发展

动物免疫系统的发生和发展是一个漫长的过程,是在生物长期进化和适应发展的过程中逐渐形成并不断发展和完善的。无脊椎动物只具有非特异性免疫;脊椎动物在非特异性免疫的基础上形成了强大的特异性免疫;到了人类,免疫系统得到了充分发展,其结构完善、其功能更为强大。

DNA条形码及其在动物系统发育中的应用

自C．V．Linne提出双名法以来，分类学一直是生物学的基础。最初的分类学一直依靠的是形态学和解剖学等提供的依据，对分类学家的知识和经验依赖较大。随着分子生物学技术的发展，特别是PCR和测序技术的进步，越来越多的分类学研究则依靠物种的核基因或线粒体基因序列。

动物演化学说的新突破——软体动物外套腔形成真体腔假说

人类是真体腔动物的一种。真体腔的起源一直遵循一百多年前提出的"肠体腔囊假说"和"裂体腔假说"。本文作者提出了一种新的假说,软体动物"外套腔法形成真体腔"以及"软体动物为真体腔动物起源"。这种假说与近几年国内外基于比较基因组学产生的新研究观点非常吻合合。并且能够弥补经典假说很多不足,是动物演化学说新的突破。

Notch信号转导与调控

Notch是一个进化上十分保守的跨膜受体蛋白家族 ,它可以通过与表达配体的相邻细胞间的相互作用转导信号 ,从而决定动物系统发育过程中多种细胞的“命运” .Notch信号转导过程包括Notch受体与配体的结合、Notch受体的酶切活化、可溶性NICD转移至细胞核并与CSLDNA结合蛋白相互作用 ,从而调控靶基因的表达 .Notch活性水平、时间和空间分布受到包括配体、蛋白质转运、泛素化降解等多水平内源性和外源性诱导因素的调节 .系统介绍了Notch信号转导通路的分子组成、Notch信号激活的生化机制、Notch信号的多水平调节以及与部分相关疾病的关系 .

PHYLOGENY AND ZOOGEOGRAPHY OF THE CYPRINID GENUS Spinibarbus (Pisces: Cyprinidae)

The cyprinid genus Spinibarbus consists of 5 species. They form into a monophyly by three synapomorphies. Based on 19 external and skeletal characters, the most parsimonious cladogram is constructed for Spinibarbus fishes. Sister groups A (S. hollandi) and B-E (S. sinensis + S. denticulatus + S. yunnanensis + S. polylepis) represent the first phyletic branching within the genus Spinibarbus. The phyletic division of second sister groups B (S. sinensis) and C-E (S. denticulatus + S. yunnanensis + S. polylepis) is supposed to be resulted from the upheaval of Yunnan-Guizhou Plateau and the subsequent drainages' division. The phyletic division of third sister groups C (S. denticulatus) and D^E (S. yunnanensis + S. polylepis) is supposed to be resulted from the environmental differentiation between Yunnan-Guizhou Plateau and the lowlands of middle and lower Pearl and Yuanjiang Rivers.

Molecular phylogeny of oligotrich genera Omegastrombidium and Novistrombidium(Protozoa,Ciliophora) for the systematical relationships within Family Strombidiidae

The phylogeny of the oligotrich ciliates is currently a hot debate despite the availability of both morphological and molecular data.In the present paper,further small subunit rRNA(SS rRNA) genes were analyzed from the Genera Omegastrombidium and Novistrombidium,as well as from Strombidium,and combined with three new SS rRNA sequences from Strombidium basimorphum,S.sulcatum population QD-1,and Novistrombidium testaceum population GD.The phylogenetic positions of these organisms were inferred using Bayesian inference,Maximum Likelihood,and Maximum Parsimony methods.The main results are:(1) the SS rRNA gene sequence analyses match the recent findings about the molecular evolution of oligotrichs,indicating that the family Strombidiidae is paraphyletic;(2) the Genus Omegastrombidium is separated from the Genus Strombidium,as shown in recent cladistic analyses;(3) morphospecies in Genus Novistrombidium,based on similarity of somatic ciliature,are separated from each other in all topological trees,indicating that this genus could be a paraphyletic group;(4) the molecular data indicate a possibility of paraphyly for the genus Strombidium;and(5) the similarities of the SS rRNA gene of specimens identified as S.sulcatum and S.inclinatum are 99.8%-100%.However,present knowledge on the oligotrichs sensu stricto is still insufficient and further studies based on both molecular and other technologies are required.

Phylogeny of subclass Scuticociliatia(Protozoa,Ciliophora) using combined data inferred from genetic,morphological,and morphogenetic evidence

Gene sequence-based genealogies of scuticociliates are different from those produced by morphological analyses.For this reason,11 representative scuticociliates and two ambiguously related genera were chosen to test the ability of combined phylogenetic analyses using both gene sequences and morphological/morphogenetic characteristics.Analyses of both the SSrRNA gene sequences and the combined datasets revealed a consistent branching pattern.While the terminal branches and the order level relationships were generally well resolved,the family level relationships remain unresolved.However,two other trees based on ITS1-5.8S-ITS2 region sequences and morphological/morphogenetic characters showed limited information,due to a lack of informative sites in these two datasets.Our data suggest,however,that the combined analysis of morphological/morphogenetic characters and gene sequences did produce some changes to the phylogenetic estimates of this group.

The origin of the vertebrate jaw:Intersection between developmental biology-based model and fossil evidence

The origin of the vertebrate jaw has been reviewed based on the molecular,developmental and paleontological evidences.Advances in developmental genetics have accumulated to propose the heterotopy theory of jaw evolution,i.e.the jaw evolved as a novelty through a heterotopic shift of mesenchyme-epithelial interaction.According to this theory,the disassociation of the nasohypophyseal complex is a fundamental prerequisite for the origin of the jaw,since the median position of the nasohypophyseal placode in cyclostome head development precludes the forward growth of the neural-crest-derived craniofacial ectomesenchyme.The potential impacts of this disassociation on the origin of the diplorhiny are also discussed from the molecular perspectives.Thus far,our study on the cranial anatomy of galeaspids,a 435-370-million-year-old 'ostracoderm' group from China and northern Vietnam,has provided the earliest fossil evidence for the disassociation of nasohypophyseal complex in vertebrate phylogeny.Using Synchrotron Radiation X-ray Tomography,we further show some derivative structures of the trabeculae(e.g.orbitonasal lamina,ethmoid plate) in jawless galeaspids,which provide new insights into the reorganization of the vertebrate head before the evolutionary origin of the jaw.These anatomical observations based on new techniques highlight the possibility that galeaspids are,in many respects,a better proxy than osteostracans for reconstructing the pre-gnathostome condition of the rostral part of the braincase.The cranial anatomy of galeaspids reveals a number of derived characters uniquely shared with gnathostomes.This raises the potential possibility that galeaspids might be the closest jawless relatives of jawed vertebrates.Our study provides an intriguing example of intersection between developmental biology-based model and fossil evidence.

Primate phylogeny:molecular evidence for a pongid clade excluding humans and a prosimian clade containing tarsiers

Unbiased readings of fossils are well known to contradict some of the popular molecular groupings among primates,particularly with regard to great apes and tarsiers.The molecular methodologies today are however flawed as they are based on a mistaken theoretical interpretation of the genetic equidistance phenomenon that originally started the field.An improved molecular method the 'slow clock' was here developed based on the Maximum Genetic Diversity hypothesis,a more complete account of the unified changes in genotypes and phenotypes.The method makes use of only slow evolving sequences and requires no uncertain assumptions or mathematical corrections and hence is able to give definitive results.The findings indicate that humans are genetically more distant to orangutans than African apes are and separated from the pongid clade ～17.6 million years ago.Also,tarsiers are genetically closer to lorises than simian primates are.Finally,the fossil times for the radiation of mammals at the K/T boundary and for the Eutheria-Metatheria split in the Early Cretaceous were independently confirmed from molecular dating calibrated using the fossil split times of gorilla-orangutan,mouse-rat,and opossum-kangaroo.Therefore,the re-established primate phylogeny indicates a remarkable unity between molecules and fossils.

Evolutionary annotation of conserved long non-coding RNAs in major mammalian species

Mammalian genomes contain tens of thousands of long non-coding RNAs(lnc RNAs) that have been implicated in diverse biological processes. However, the lnc RNA transcriptomes of most mammalian species have not been established, limiting the evolutionary annotation of these novel transcripts. Based on RNA sequencing data from six tissues of nine species, we built comprehensive lnc RNA catalogs(4,142–42,558 lnc RNAs) covering the major mammalian species. Compared to protein-coding RNAs, expression of lnc RNAs exhibits striking lineage specificity. Notably, although 30%–99% human lnc RNAs are conserved across different species on DNA locus level, only 20%–27% of these conserved lnc RNA loci are detected to transcription, which represents a stark contrast to the proportion of conserved protein-coding genes(48%–80%). This finding provides a valuable resource for experimental scientists to study the mechanisms of lnc RNAs. Moreover, we constructed lnc RNA expression phylogenetic trees across nine mammals and demonstrated that lnc RNA expression profiles can reliably determine phylogenic placement in a manner similar to their coding counterparts. Our data also reveal that the evolutionary rate of lnc RNA expression varies among tissues and is significantly higher than those for protein-coding genes. To streamline the processes of browsing lnc RNAs and detecting their evolutionary statuses, we integrate all the data produced in this study into a database named Phylo NONCODE(http://www.bioinfo.org/phylo Noncode). Our work starts to place mammalian lnc RNAs in an evolutionary context and represent a rich resource for comparative and functional analyses of this critical layer of genome.