毛冠菊属的系统学研究

　　毛冠菊属是菊科21个“有问题”属中的一个，主要分布于青藏高原地区。按照林镕、陈艺林的概念，它包含了Nannoglottis、．Stereosanthus、Vierhapperia、Senecio和Doronicum5个属的成员。它曾先后被放入旋覆花族、千里光族和紫菀族，在上述三族中的亚族位置也不确定。它的许多重要性状，如舌片颜色、染色体数目等等，人们所知甚少。由于缺乏野外工作以及看不到大多数名字的模式，林镕、陈艺林对该属的修订有待深入的研究。本文研究了该属的外部形态学、微形态学、解剖学、孢粉学、细胞学、生态学以及ITS序列，确定了毛冠菊属的分类位置，并建立了一个新的属下分类系统。 1．外部形态 在检查大量标本（包括大多数模式）和野外居群考察的基础上，分析了主要外部形态学性状的变异式样及其对划定物种范围的价值。共确认以下9个种：青海毛冠菊、厚毛毛冠菊、狭舌毛冠菊、虎克毛冠菊、宽苞毛冠菊、大果毛冠菊、毛冠菊、玉龙毛冠菊和云南毛冠菊。川西毛冠菊被处理成狭舌毛冠菊的异名。 2．微形态学 在光镜下检查了毛冠菊属9种和紫菀族2个代表属的花柱的形状、花药顶端不育附属物、花药基部、花药基部、花盘、花丝领、药室内壁细胞等微形态性状。除了花柱基外，其他的微形态学在属内一致。管状花的花柱形态支持将毛冠菊属放在紫菀族，但其药室内壁细胞两极加厚式样表明它和广义的旋覆花有某些联系。 3．叶表皮研究 在光镜和电镜下检查了毛冠菊属8个种的叶表皮特征。．所有种的气孔器都为不规则型。青海毛冠菊表皮细胞的为多边形，而其他种都为不规则型。青海毛冠菊表皮角质层的加厚方式也与其他种明显不同。 4．扫描电镜下的舌片和花柱分枝特征 在扫描电镜下观察毛冠菊属8种和紫菀族7个代表种的舌片近轴面表皮细胞。发现毛冠菊属的舌片近轴面表皮细胞都为板状，并且沿细胞中央特征性加厚，这与紫菀族类型的表皮细胞一致，但毛冠菊属表皮细胞的角质层主要是纵向条纹或皱纹，而紫菀族总是横向的条纹或皱纹，明显不同。 在扫描电镜下又检查了毛冠菊属8种和紫菀族8个代表种的管状花花柱分枝近轴面的结构，结果在毛冠菊属管状花花柱分枝的近轴面都发现了柱头毛状的突起，而在紫菀族8种中没有发现。从突起的形状和位置判断，它可能是残存的、未充分发育的柱头毛。这表明雌性不育管状花可能刚刚从两性管状花演化而来。 也在扫描电镜下观察了毛冠菊属6种和紫菀族8个代表种的舌状花和丝状花的花柱分枝的远轴面，结果在毛冠菊属4种中发现了类似扫集毛状的突起。从这种突起的位置和形状判断，它可能是残余的扫集毛。这种突起在除雏菊以外的其他紫菀族代表种中缺失。 5．细胞学 检查了毛冠菊属8种的细胞学性状。结果发现毛冠菊属所有种的染色体基数都为x -9。染色体长度大约4um-lOum。核型公式：毛冠菊、厚毛毛冠菊、狭舌毛冠菊、宽苞毛冠菊和云南毛冠菊都为2n=14m+2sm+2st;玉龙毛冠菊、大果毛冠菊和青海毛冠菊都为2n=12m+4sm+2st。A1、A2值在属内没有明显差异。所有种的核型都是2A型。这表明在物种形成的过程中没有多倍化参与，毛冠菊属宜放在紫菀族而不是千里光族。细胞学证据支持毛冠菊属为一单系类群。 6．分子生物学 测定了毛冠菊属7种的ITS序列，并从基因库里下载了46个ITS序列，涵盖紫菀族14个亚属和旋覆花族、春黄菊族、金盏菊族。以旋覆花族、春黄菊族、金盏菊族为外类群。简约性分析显示，毛冠菊属在紫菀族中，并有较高的bootstrap值，在紫菀族中处于基部位置。Olearia和Chiliotrichum两个Hinterhuberinae亚族的代表属与毛冠菊属密切相关。在属下系统发育分析中，Olearia和Chiliotrichum被选做外类群。652个性状中，共有7】个信息位点（31个在ITSI，33个在ITS2，7个在5.8S）。简约性分析时只获得一棵最简约树。树上有两个明显的进化支，一支仅有青海毛冠菊一种，另一支包含其他种类。这种分支方式也得到形态学和生态学证据的支持。 7．毛冠菊属的系统学 从上述结果可以看出，毛冠菊属宜放入紫菀族中，在紫菀族中处于基部位置，与Hinterhuberinae亚族关系密切。综合上述研究结果，提出一个新的属下 分类系统： 毛冠菊属的新系统 组I单头组Sect. Monocephala T.G.Gao et YL.Chen Sect nov. 青海毛冠菊Nannoglottis ravida (C.Winkl.)Y.L.Chen 组II毛冠菊组Sect. Nannoglottis 系1．长舌系Ser. Delavayanae Ling et YL.Chen 厚毛毛冠菊Nannoglottis delavayi(Franch.)Ling et Y.L.Chen 狭舌毛冠菊Nannoglottis gynura(C.Winkl.) Ling et YL.Chen 虎克毛冠菊Nannoglottis hookeri (C.B.Clarke ex Hook.f.)Kitam. 宽苞毛冠菊Nannoglottis latisquama Ling et Y.L.Chen 大果毛冠菊Nannoglottis macrocarpa Ling et YL.Chen 系2．短舌系Ser. Nannoglottis 毛冠菊Nannoglottis carpesioides Maxim. 玉龙毛冠菊Nannoglottis hieraciphylla (Hand.-Mzt.)Ling et YL.Chen 云南毛冠菊Nannoglottis yuennanensis (Hand.-Mzt.) Hand.-Mzt.

Phylogenetic relationships among two species of golden monkey and three species of leaf monkey inferred from rDNA variation

Restriction maps of rDNA repeats of five species of Colobinae and three outgroup taxa, Hylobates leucogenys, Macaca mulatta, and Macaca irus, were constructed using 15 restriction endonucleases and cloned 18S and 28S rRNA gene probes. The site variation between Rhinopithecus roxellana and Rhinopithecus bieti is comparable to that between Presbytis francoisi and Presbytis phayrei, implying that R. bieti is a valid species rather than a subspecies of R. roxellana. Phylogenetic analysis on the 47 informative sites supports the case for Rhinopithecus being an independent genus and closely related to Presbytis. Furthermore, branch lengths of the tree seem to support the hypothesis that the leaf monkeys share some ancestral traits as well as some automorphic characters.

系统发育研究中"长枝吸引"假象概述

下载PDF阅读器系统发育研究(phylogeny)不仅有助于重建地球所有生物体的进化历史,而且还可以揭示进化生物学领域中的一些基本问题.清晰了解各生物物种进化历程及不同物种之间的进化关系,是进一步研究和探索生物学其他学科的基础.但是现今广泛应用的所有系统发育分析方法都存在一定的局限性,在一定程度上不能有效消除各种误差,从而不能客观地处理和分析数据,也就不能成功重建生物进化历程,真实反映物种进化关系.系统发育研究中,"长枝吸引"(Long-branch Attraction,LBA)假象是最为困扰研究者的问题.文章从"长枝吸引"问题的产生原由、检测方法以及消除策略等多个方面进行详尽概述,并通过列举典型实例,阐述了解决"长枝吸引"问题的途径.

Episodic evolution of prolactin receptor gene in mammals: coevolution with its ligand

Divergence of proteins in signaling pathways requires ligand and receptor coevolution to maintain or improve binding affinity and/or specificity. In this paper we show a clear case of coevolution between the prolactin (PRL) gene and its receptor (prolactin receptor, PRLR) in mammals. First we observed episodic evolution of the extracellular and intracellular domains of the PRLR, which is closely consistent with that seen in PRL. Correlated evolution was demonstrated both between PRL and its receptor and between the two domains of the PRLR using Pearson's correlation coefficient. On comparing the ratio of the nonsynonymous substitution rate to synonymous substitution rate (omega=d(N)/d(S)) for each branch of the star phylogeny of mammalian PRLRs, separately for the extracellular domain (ECD) and the transmembrane domain/intracellular domain (TMD/ICD), we observed a lower omega ratio for ECD than TMD/ICD along those branches leading to pig, dog and rabbit but a higher ratio for ECD than TMD/ICD on the branches leading to primates, rodents and ruminants, on which bursts of rapid evolution were observed. These observations can be best explained by coevolution between PRL and its receptor and between the two domains of the PRLR.

Phylogenetic analyses of Fringillidae (Aves : Passeriformes) using mitochondrial tRNA gene sequences and secondary structure

Fringillidae is a large and diverse family of Passeriformes. So far, however, Fringillidae relationships deduced from morphological features and by a number of molecular approaches have remained unproven. Recently, much attention has been attracted to mitochondrial tRNA genes, whose sequence and secondary structural characteristics have shown to be useful for Acrodont Lizards and deep-branch phylogenetic studies. In order to identify useful phylogenetic markers and test Fringillidae relationships, we have sequenced three major clusters of mitochondrial tRNA genes from 15 Fringillidae, taxa. A coincident tree, with coturnix as outgroup, was obtained through Maximum-likelihood method using combined dataset of 11 mitochondrial tRNA gene sequences. The result was similar to that through Neighbor-joining but different from Maximum-parsimony methods. Phylogenetic trees constructed with stem-region sequences of 11 genes had many different topologies and lower confidence than with total sequences. On the other hand, some secondary structural characteristics may provide phylogenetic information on relatively short internal branches at under-genus level. In summary, our data indicate that mitochondrial tRNA genes can achieve high confidence on Fringillidae phylogeny at subfamily level, and stem-region sequences may be suitable only at above-family level. Secondary structural characteristics may also be useful to resolve phylogenetic relationship between different genera of Fringillidae with good performance.

Phylogeny and biogeography of the Petaurista philippensis complex (Rodentia : Sciuridae), inter- and intraspecific relationships inferred from molecular and morphometric analysis

With modified DNA extraction and Purification protocols, the complete cytochrome b gene sequences (1140 bp) were determined from degraded museum specimens. Molecular analysis and morphological examination of cranial characteristics of the giant flying squirrels of Petaurista philippensis complex (P. grandis, P. hainana, and P. yunanensis) and other Petaurista species yielded new insights into long-standing controversies in the Petaurista systematics. Patterns of genetic variations and morphological differences observed in this study indicate that P. hainana, P. albiventer, and P. yunanensis can be recognized as distinct species, and P. grandis and P. petaurista are conspecific populations. Phylogenetic relationships reconstructed by using parsimony, likelihood, and Bayesian methods reveal that, with P. leucogenys as the basal branch, all Petaurista groups formed two distinct clades. Petaurista philippensis, P. hainana, P. yunanensis, and P. albiventer are clustered in the same clade, while P. grandis shows a close relationship to P. petaurista. Deduced divergence times based on Bayesian analysis and the transversional substitution at the third codon suggest that the retreating of glaciers and upheavals or movements of tectonic plates in the Pliocene-Pleistocene were the major factors responsible for the present geographical distributions of Petaurista groups. (c) 2005 Elsevier Inc. All rights reserved.

Adaptive evolution of energy metabolism genes and the origin of flight in bats

Bat flight poses intriguing questions about how flight independently developed in mammals. Flight is among the most energy-consuming activities. Thus, we deduced that changes in energy metabolism must be a primary factor in the origin of flight in bats. The respiratory chain of the mitochondrial produces 95% of the adenosine triphosphate (ATP) needed for locomotion. Because the respiratory chain has a dual genetic foundation, with genes encoded by both the mitochondrial and nuclear genomes, we examined both genomes to gain insights into the evolution of flight within mammals. Evidence for positive selection was detected in 23.08% of the mitochondrial-encoded and 4.90% of nuclear-encoded oxidative phosphorylation (OXPHOS) genes, but in only 2.25% of the nuclear-encoded nonrespiratory genes that function in mitochondria or 1.005% of other nuclear genes in bats. To address the caveat that the two available bat genomes are of only draft quality, we resequenced 77 OXPHOS genes from four species of bats. The analysis of the resequenced gene data are in agreement with our conclusion that a significantly higher proportion of genes involved in energy metabolism, compared with background genes, show evidence of adaptive evolution specific on the common ancestral bat lineage. Both mitochondrial and nuclear-encoded OXPHOS genes display evidence of adaptive evolution along the common ancestral branch of bats, supporting our hypothesis that genes involved in energy metabolism were targets of natural selection and allowed adaptation to the huge change in energy demand that were required during the origin of flight.

中鲤亚属的分支系统学分析

基于外部形态特征和内部骨骼特征对鲤科鲤属中鲤亚属进行了分支系统学分析。内群包括中鲤亚属的全部5种和鲤亚属的2种鱼类，外群采用乌原鲤。在鲤属鱼类和外群间共有48个性状存在变化。系统发育分析采用PAUP~(*)软件的Parsimony和Bootstrap两种方式的Branch-and-Bound算法。排除不能极化的特征和特有离征之后，还有28个特征可用，由这28个特征可得到唯一的系统树，树长69，一致性系数0.7246，排除无用特征的一致性系数0.6122，保留系数0.6346。由5种中鲤组成的中鲤亚属明显不构成一个单系群。结果表明：中鲤亚属是一个复系群，该类元应该被撤销。

Phylogenetic positions of several amitochondriate protozoa - Evidence from phylogenetic analysis of DNA topoisomerase II

Several groups of parasitic protozoa, as represented by Giardia, Trichomonas, Entamoeba and Microsporida, were once widely considered to be the most primitive extant eukaryotic group - Archezoa. The main evidence for this is their 'lacking mitochondria' and possessing some other primitive features between prokaryotes and eukaryotes, and being basal to all eukaryotes with mitochondria in phylogenies inferred from many molecules. Some authors even proposed that these organisms diverged before the endosymbiotic origin of mitochondria within eukaryotes. This view was once considered to be very significant to the study of origin and evolution of eukaryotic cells (eukaryotes). However, in recent years this has been challenged by accumulating evidence from new studies. Here the sequences of DNA topoisomerase 11 in G lamblia, T vaginalis and E histolytica were identified first by PCR and sequencing, then combining with the sequence data of the microsporidia Encephalitozoon cunicul and other eukaryotic groups of different evolutionary positions from GenBank, phylogenetic trees were constructed by various methods to investigate the evolutionary positions of these amitochondriate protozoa. Our results showed that since the characteristics of DNA topoisomerase 11 make it avoid the defect of 'long-branch attraction' appearing in the previous phylogenetic analyses, our trees can not only reflect effectively the relationship of different major eukaryotic groups, which is widely accepted, but also reveal phylogenetic positions for these amitochondriate protozoa, which is different from the previous phylogenetic trees. They are not the earliest-branching eukaryotes, but diverged after some mitochondriate organisms such as kinetoplastids and mycetozoan; they are not a united group but occupy different phylogenetic positions. Combining with the recent cytological findings of mitochondria-like organelles in them, we think that though some of them (e.g. diplomonads, as represented by Giardia) may occupy a very low evolutionary position, generally these organisms are not as extremely primitive as was thought before; they should be polyphyletic groups diverging after the endosymbiotic origin of mitochondrion to adapt themselves to anaerobic parasitic life.

Identification, characteristic and phylogenetic analysis of type II DNA topoisomerase gene in Giardia lamblia

The genes encoding type II DNA topoisomerases were investigated in Giardia lamblia genome, and a type IIA gene, GlTop 2 was identified. It is a single copy gene with a 4476 by long ORF without intron. The deduced amino acid sequence shows strong homology to eukaryotic DNA Top 2. However, some distortions were found, such as six insertions in the ATPase domain and the central domain, a similar to 100 as longer central domain; a similar to 200 as shorter C-terminal domain containing rich charged residues. These features revealed by comparing with Top 2 of the host, human, might be helpful in exploiting drug selectivity for antigiardial therapy. Phylogenetic analysis of eukaryotic enzymes showed that kinetoplastids, plants, fungi, and animals were monophyletic groups, and the animal and fungi lineages shared a more recent common ancestor than either did with the plant lineage; microsporidia grouped with fungi. However, unlike many previous phylogenetic analyses, the "amitochondriate" G. lamblia was not the earliest branch but diverged after mitochondriate kinetoplastids in our trees. Both the finding of typical eukaryotic type IIA topoisomerase and the phylogenetic analysis suggest G. lamblia is not possibly as primitive as was regarded before and might diverge after the acquisition of mitochondria. This is consistent with the recent discovery of mitochondrial remnant organelles in G. lamblia.

Intergroup interactions in Tibetan macaques at Mt. Emei, China

Data on intergroup-interactions (I-I) were collected in 5 seasonally provisioned groups (A, B, D, D-1, and E) of Tibetan macaques (Macaca Thibetana) at Mt. Emei in three 70-day periods between 1991 April-June (P1), September-November (P2), December-1992 February (P3). The I-I were categorized as forewarning made by high-ranking males (including Branch Shaking and/or Loud Calls), long-distance interactions in space (specified by changes in their foraging movements), and close encounters (with Affinitive Behavior, Male's Herding Female, Sexual Interaction, Severe Conflict, Adult Male-male Conflict, Opportunistic Advance and Retreat, etc. performed by different age-sex classes). From periods Fl to P3, the I-I rate decreased with reduction in population density as a positive correlate of food clumpedness or the number of potential feeders along a pedestrian trail. On the other hand, from the birth season (BS, represented by P1 and P3) to the mating season (MS, represented by P2) the dominance relation between groups, which produced a winner and a loser in the encounters, became obscure; the proportion of close encounters in the I-I increased; the asymmetry (local groups over intruders) of forewarning signals disappeared; the rate of branch shaking decreased; and sometimes intergroup cohesion appeared. Considering that sexual interactions also occurred between the encountering groups, above changes in intergroup behaviors may be explained with a model of the way in which the competition for food (exclusion) and the sexual attractiveness between opposite sexes were in a dynamic equilibrium among the groups, with the former outweighing the latter in the BS, and conversely in the MS. Females made 93% of severe conflicts, which occurred in 18% of close encounters. Groups fissioned in the recent past shared the same home range, and showed the highest hostility to each other by females. In conspicuous contrast with females' great interest in intergroup food/range competition, adult male-male conflicts that were normally without body contact occurred in 66% bf close encounters; high-ranking male herding of females, which is typical in baboons, appeared in 83% of close encounters, and showed no changes with season and sexual weight-dimorphism; peripheral juvenile and subadult males were the main performers of the affinitive behaviors, opportunistic advance and retreat, and guarding at the border. In brief, all males appeared to "sit on the fence" at the border, likely holding out hope of gaining the favor of females both within and outside the group. Thus, females and males attempted to maximize reproductive values in different ways, just as expected by Darwin-Trivers' theory of sexual selection. In addition, group fission was observed in the largest and highest-ranking group for two times (both in the MS) when its size increased to a certain level, and the mother group kept their dominant position in size and rank among the groups that might encounter, suggesting that fission takes a way of discarding the "superfluous part" in order to balance the cost of competition for food and mates within a group, and the benefit of cooperation to access the resources for animals in the mother group. (C) 1997 Wiley-Liss, Inc.

Secondary structures of mRNAs and splicing of introns in eukaryotes.

After analyzing the secondary structures of 68 exon-intron-exon and the corresponding exon-exon sequence segments, it is found that about 90% of 5' and 3' terminal bases G (splicing sites) of introns are situated in the loops of secondary structures or at the ends of stems near the loops, and most of "G" s in loops are closed to the ends of loops. Approximately 92% of the connecting sites of the adjoining exons also show the similar features. About 82% of the branch point "A" s are situated in loops or at the ends of stems near the loops. Splicing sites and branch points approach each other in space because of the folding.

Establishment of a Chinese sturgeon Acipenser sinensis tail-fin cell line and its susceptibility to frog iridovirus

Chinese sturgeon Acipenser sinensis, a cartilaginous ganoid, is a 'living fossil' on a deeply isolated evolutionary branch. A cell line was established from Chinese sturgeon tail-fin tissue (CSTF) . These epithelial CSTF cells grew well in Dulbecco's modified Eagle's medium at 25 degrees C. Karyotypic analysis revealed a normal diploid karyotype with 2n = 264 and large numbers of punctate chromosomes. A strain of frog iridoviruses [Rana grylio virus (RGV)] was used to test the susceptibility of this cell line to infection. Infection was confirmed by cytopathic effect, immunofluorescence and electron-microscope observations, which detected the viral antigens or particles in the cytoplasm of RGV-infected cells. Molecular analysis further suggested that c. 550 bp DNA fragment could be cloned from the RGV-infected CSTF cells' DNA with major capsid protein gene polymerase chain reaction primers. Furthermore, after transfection with pEGFP vector DNA, the CSTF cell line produced significant fluorescent signals indicating its utility in exogenous studies.

Inhibition of no tail (ntl) gene expression in zebrafish by external guide sequence (EGS) technique

External guide sequence (EGS) technique, a branch of ribozyme strategy, can be enticed to cleave the target mRNA by forming a tRNA-like structure. In the present study, no tail gene (ntl), a key gene participating in the formation of normal tail, was used as a target for ribonuclease (RNase) P-mediated gene disruption in zebrafish in vivo. Transient expression of pH1-m3/4 ntl-EGS or pH1-3/4 ntl-EGS produced the full no tail phenotype at long-pec stage in proportion as 24 or 35%, respectively. As is expected that the full-length ntl mRNA of embryos at 50% epiboly stage decreased relative to control when injected the embryos with 3/4 EGS or m3/4 EGS RNA. Interestingly, ntl RNA transcripts, including the cleaved by EGS and the untouched, increased. Taken together, these results indicate that EGS strategy can work in zebrafish in vivo and becomes a potential tool for degradation of targeted mRNAs.

Characterization of two genes encoding leucine-rich repeat-containing proteins in grass carp Ctenopharyngodon idellus

The cDNAs and genes of two different types of leucine- rich repeat-containing proteins from grass carp ( Ctenopharyngodon idellus) were cloned. Homology search revealed that the two genes, designated as GC-GARP and GC-LRG, have 37% and 32% deduced aminoacid sequence similarities with human glycoprotein A repetitions predominant precursor ( GARP) and leucine-rich alpha2-glycoprotein (LRG), respectively. The cDNAs of GC-GARP and GC-LRG encoded 664 and 339 amino acid residues, respectively. GC-GARP and GC-LRG contain many distinct structural and/or functional motifs of the leucine- rich repeat (LRR) subfamily, such as multiple conserved 11-residue segments with the consensus sequence LxxLxLxxN/CxL ( x can be any amino acid). The genes GC-GARP and GC-LRG consist of two exons, with 4,782 bp and 2,119 bp in total length, respectively. The first exon of each gene contains a small 5'-untranslated region and partial open reading frame. The putative promoter region of GC-GARP was found to contain transcription factor binding sites for GATA-1, IRF4, Oct-1, IRF-7, IRF-1, AP1, GATA-box and NFAT, and the promoter region of GC-LRG for MYC-MAX, MEIS1, ISRE, IK3, HOXA9 and C/EBP alpha. Phylogenetic analysis showed that GC-GARP and mammalian GARPs were clustered into one branch, while GC-LRG and mammalian LRGs were in another branch. The GC-GARP gene was only detected in head kidney, and GC-LRG in the liver, spleen and heart in the copepod ( Sinergasilus major)- infected grass carp, indicating the induction of gene expression by the parasite infection. The results obtained in the present study provide insight into the structure of fish LRR genes, and further study should be carried out to understand the importance of LRR proteins in host - pathogen interactions.