Tree Reconciliation: Reconstruction of Species Phylogeny by Phylogenetic Gene Trees

It is well known that phylogenetic trees derived from different protein families are often incongruent. This is explained by mapping errors and by the essential processes of gene duplication, loss, and horizontal transfer. Therefore, the problem is to derive a consensus tree best fitting the given set of gene trees. This work presents a new method of deriving this tree. The method is different from the existing ones, since it considers not only the topology of the initial gene trees, but also the reliability of their branches. Thereby one can explicitly take into account the possible errors in the gene trees caused by the absence of reliable models of sequence evolution, by uneven evolution of different gene families and taxonomic groups, etc.     

Evolution of Orthologous Intronless and Intron-Bearing Globin Genes in Two Insect Species

While globin genes ctt-2β and ctt-9.1 in Chironomus thummi thummi each have a single intron, all of the other insect globin genes reported so far are intronless. We analyzed four globin genes linked to the two intron-bearing genes in C. th. thummi. Three have a single intron at the same position as ctt-2β and ctt-9.1; the fourth is intronless and lies between intron bearing genes. Finally, in addition to its intron, one gene (ctt-13RT) was recently interrupted by retrotransposition. Phylogenetic analyses show that the six genes in C. th. thummi share common ancestry with five globin genes in the distantly related species C. tentans, and that a 5-gene ancestral cluster predates the divergence of the two species. One gene in the ancestral cluster gave rise to ctn-ORFB in C. tentans, and duplicated in C. th. thummi to create ctt-11 and ctt-12. From parsimonious calculations of evolutionary distances since speciation, ctt-11, ctt-12, and ctn-ORFB evolved rapidly, while ctn-ORFE in C. tentans evolved slowly compared to other globin genes in the clusters. While these four globins are under selective pressure, we suggest that most chironomid globin genes were not selected for their unique function. Instead, we propose that high gene copy number itself was selected because conditions favored organisms that could synthesize more hemoglobin. High gene copy number selection to produce more of a useful product may be the basis of forming multigene families, all of whose members initially accumulate neutral substitutions while retaining essential function. Maintenance of a large family of globin genes not only ensured high levels of hemoglobin production, but may have facilitated the extensive divergence of chironomids into as many as 5000 species. Received: 31 December 1996 / Accepted: 16 May 1997     

脊椎动物DMRT基因家族的系统发生及同线性分析

利用本室克隆的DMRT／Dmrt基因以及多个基因数据库中收集的DMRT／Dmrt基因全(或部分)序列,构建了DMRT／Dmrt基因的系统发生树,DMRT／Dmrt基因明显地聚为7类(DMRT／Dmrt1-DMRT／Dmrt7)。以已克隆的斑马鱼Dmrt1基因序列及数据库中人和小鼠的DMRT／Dmrt基因序列,结合基因组数据的比对分析,发现脊椎动物DMRT／Dmrt基因家族成员在基因组中的定位呈现高度保守的同线性,主要集中于两大同线群,即DM-RT／Dmrt1-3和DMRT／Dmrt5∽6。     

氟污染区绿化树种的选择

前言凡使用含氟矿石(如冰晶石、磷矿石等)作原料的工厂,在碾磨、加热、酸化等过程中,以及利用含氟化合物作为接触剂、助熔剂的各种工艺过程的生产中,都会散发出大量的含氟废气与粉尘污染环境,给农林业生产及人     

以ND4L和ND4基因为标记探讨黑腹果蝇种组的系统发育关系

多年来的形态学、染色体组学以及DNA序列几个方面的研究均没有很好地阐明黑腹果蝇种组内的系统发育关系。本实验测定了33个样品的ND4和31个样品的ND4L基因序列,以D．obscuroides为外群,用最大简约法和Bayesian法分别构建进化树。结果表明两种方法构建的拓扑结构一致,而且大部分支系的支持率较高。整个黑腹果蝇种组分成三大谱系：1）montium种亚组;2）ananssae种亚组;3）Oriental种亚组（melanogaster、ficsphila、eugracilis、elegans、suzukii、takahashii）。montium是最早分化的种亚组。在第三谱系中,melanogaster分化得最早;然后依次是ficsphila,eugracilis,elegans;suzukii与takahashii为姐妹种亚组,最后分化。     

玉米与其他六种植物NBS类抗病基因的进化比较分析

具有核苷酸结合位点(nucleotide binding site,NBS)的抗病基因在植物抵抗各种病原菌侵染中起关键作用。对玉米全基因组中具有NBS结构的基因进行鉴定和分析,并结合水稻、高粱、拟南芥、百脉根、苜蓿和杨树的NBS类基因比较其在数量、复制、染色体定位和亲缘关系上的进化差异。发现玉米NBS类基因数量、复制数和成簇基因数均明显少于其他植物。低复制频率可能导致玉米NBS类基因较少,并推测可能导致其功能具有多样性。在基因染色体定位上,除高梁外,玉米与其他五种植物相似,呈不均衡分布。此外,进化树分析表明玉米NBS类基因与高粱的亲缘关系最近,与拟南芥的最远,在物种间表现出较高的保守性。结果对掲示玉米NBS基因的进化特点与发掘有益的NBS类抗病基因提供了重要的理论依据。     

Evolution of Functional Genes in Cetaceans Driven by Natural Selection on a Phylogenetic and Population Level

Cetaceans represent an evolutionary lineage marked by drastic morphological and physiological changes during their adaptation to an exclusively marine existence. In addition, several cetacean species exhibit geographical ranges that encompass different marine environments, with genetic breaks being sometimes consistent with environmental breaks. As such, genes that underwent adaptation during the land-sea transition can also be potential candidates for adaptation to different oceanic environments. In this study, we analysed 3 milk protein genes (β-casein, κ-casein, and α-lactalbumin) and 2 immunity related genes (MHC DQβ1 and γ-fibrinogen) for selection based on available phylogenetic datasets of both mammals and cetaceans, and used the results from this analysis to assess adaptation to different environments on a population level in the European common dolphin (Delphinus delphis). We found that evidence for positive selection could be detected in all genes in the phylogenetic analyses, with β-casein showing a further increase in selective pressure in the cetacean lineage. At the population level, both the immune system locus DQβ1 and β-casein genes showed patterns of variation consistent with divergent selection, and in each case the same populations showed differentiation. One of these populations was also differentiated at neutral markers, while the other was not. We discuss possible inference, and the potential for the further development of these ideas using genomic technologies.     

Phylogeny of the Malus (Apple Tree) Species,Inferred from the Morphological Traits and Molecular DNA Analysis

Some debated issues of the genus Malus (apple) taxonomy were examined using a variety of species from the collection of the Maikop Experimental Station, Vavilon Research Institute of Plant Industry (Krasnodar krai). Phylogenetic relationships among these species were studied using traditional analysis of morphological traits, RAPD, and complete sequencing of the 5"- internal transcribed spacer (ITS1), 5.8S rRNA, 3"- internal transcribed spacer (ITS2) (constituting a cluster of the rRNA genes), and the terminal fragment of the matK gene encoding chloroplast maturase. The results showed that the Sorbomalussection was polyphyletic; the American apple M. fusca was closely related to the species contributing to the East Asian center of the genus origin, and the American speciesM. angustifolia, M. coronaria, and M. ioensis were closely related to the M. trilobata relict species, whose assignment to the genus Malus is debated by some authors. Molecular analysis of the species relationships showed that the Middle Asian apple M. sieversii is the species from which apple domestication started.     

Delineation of the Species Haemophilus influenzae by Phenotype,Multilocus Sequence Phylogeny,and Detection of Marker Genes

To obtain more information on the much-debated definition of prokaryotic species, we investigated the borders of Haemophilus influenzae by comparative analysis of H. influenzae reference strains with closely related bacteria including strains assigned to Haemophilus haemolyticus, cryptic genospecies biotype IV, and the never formally validated species “Haemophilus intermedius”. Multilocus sequence phylogeny based on six housekeeping genes separated a cluster encompassing the type and the reference strains of H. influenzae from 31 more distantly related strains. Comparison of 16S rRNA gene sequences supported this delineation but was obscured by a conspicuously high number of polymorphic sites in many of the strains that did not belong to the core group of H. influenzae strains. The division was corroborated by the differential presence of genes encoding H. influenzae adhesion and penetration protein, fuculokinase, and Cu,Zn-superoxide dismutase, whereas immunoglobulin A1 protease activity or the presence of the iga gene was of limited discriminatory value. The existence of porphyrin-synthesizing strains (“H. intermedius”) closely related to H. influenzae was confirmed. Several chromosomally encoded hemin biosynthesis genes were identified, and sequence analysis showed these genes to represent an ancestral genotype rather than recent transfers from, e.g., Haemophilus parainfluenzae. Strains previously assigned to H. haemolyticus formed several separate lineages within a distinct but deeply branching cluster, intermingled with strains of “H. intermedius” and cryptic genospecies biotype IV. Although H. influenzae is phenotypically more homogenous than some other Haemophilus species, the genetic diversity and multicluster structure of strains traditionally associated with H. influenzae make it difficult to define the natural borders of that species.Bacterial diversity is usually expected to be organized into phenotypic and genetic clusters recognized as species. The diversity within species is thought to be confined by natural forces, although uncertainty exists as to the nature of the cohesion that constrains this diversity. There is increasing evidence that recombination occurs between distantly related bacteria and that barriers to this process, which could be used to define species naturally, are not always apparent (7, 11). As the bacterial species concept is central to taxonomy and evolutionary biology and has consequences for other disciplines such as the discrimination of pathogens from related bacteria with no pathogenic potential, there is a need to reevaluate to what extent accepted species are indeed coherent units.The gram-negative, nonmotile, facultatively anaerobic bacterium Haemophilus influenzae is a commensal organism of the pharynx frequently involved in localized infections of the respiratory tract, middle ear, and conjunctiva and sometimes in invasive infections such as meningitis or bacteremia. Presumptive identification is based on inability to synthesize NAD (V factor dependence) and porphyrin/hemin (X factor dependence). The latter characteristic is particularly notable as it is shared with few other microorganisms. Further metabolic characteristics of H. influenzae include fermentation of d-xylose, d-ribose, and d-galactose but not sucrose or d-mannose (17). By DNA analysis the X-factor-dependent species H. influenzae, Haemophilus aegyptius, and Haemophilus haemolyticus constitute a closely related group (4, 5, 14, 35), and housekeeping gene nucleotide dissimilarities between these species are exceeded by intraspecific nucleotide dissimilarities within the commensal species Haemophilus parainfluenzae (33).H. aegyptius was conceived as a species distinct from H. influenzae with a particular propensity to cause conjunctivitis (37). However, the existence of H. aegyptius as a separate species is controversial (5), and the designation H. influenzae biogroup aegyptius has been proposed to include traditional H. aegyptius and the closely related clones responsible for the invasive infection known as Brazilian purpuric fever (3), although formally the epithet aegyptius has priority. H. haemolyticus is distinguished from H. influenzae primarily by its hemolytic action on erythrocytes. A recent characterization of a large number of presumptive H. influenzae isolates from the respiratory tract of patients with chronic obstructive airway disease demonstrated that 102 of 258 strains clustered with the type strain of H. haemolyticus by 16S rRNA gene sequence, although many of the isolates were nonhemolytic. In contrast to H. influenzae, the atypical isolates were not associated with exacerbations of the disease (31), emphasizing the need to discriminate between the two species.Genetic methods have identified unnamed taxa of Haemophilus related to H. influenzae. Variant strains isolated from the genitourinary tract were first reported from Canada (1) and have been further studied by Quentin and coworkers (13, 39). These “cryptic genospecies biotype IV” strains (negative for tryptophanase/indole production and positive for urease and ornithine decarboxylase) are distinguishable from typical strains of H. influenzae by multilocus enzyme electrophoresis, 16S rRNA gene sequence, and DNA hybridization. However, only some biotype IV strains belong to the cryptic genospecies, and the lack of phenotypic characters enabling discrimination from H. influenzae has been an obstacle to the formal validation as a species. Another taxon, “Haemophilus intermedius,” was suggested (but never validly published) by Burbach (4). By DNA hybridization and by selected phenotypic traits, these strains take up an intermediate position between H. influenzae and H. parainfluenzae. Two subspecies were described, “Haemophilus intermedius subsp. intermedius,” capable of synthesizing porphyrin from δ-aminolevulinic acid and of fermenting sucrose, and “Haemophilus intermedius subsp. gazogenes,” characterized by the fermentation of mannose and the production of gas from glucose.A number of investigations have addressed the population structure of H. influenzae with assessment of particular virulence traits associated with specific subgroups or clades (9, 26, 32, 41). In the present study we attempted to define the borders of the species by performing phenotypic characterization, 16S rRNA sequence comparison, multilocus housekeeping gene sequence phylogeny, and detection of putative virulence and marker genes on a collection of 42 strains of H. influenzae and representatives of the above-mentioned closely related bacteria.     

基于同源基因的病原菌鉴定和分型靶位点的功能基因组学研究

利用病原菌序列差异,对病原菌特定基因和位点进行检测,可以快速发现和鉴别病原菌的分类和特征,对传染病快速诊断和溯源具有基础性意义和重要价值.本文旨在覆盖中国重要传染病的103种病原菌,寻找各分类阶元中特有的同源基因,并从中挑选出适合用于病原菌鉴定、分型的候选基因.利用生物信息学和基因组学方法,对已有全基因组序列的275株病原菌的836415个基因进行比对分析,进一步明确菌株的门、纲、目、科、属各分类阶元中特有的同源基因集合;通过COG功能分类方法,对同源基因集合进行功能注释,并分析在不同分类阶元内的保守基因功能的变化规律.本研究寻找到适合鉴定和分型的不同分类阶元（门、纲、目、科、属）的同源基因集合共19563个（门2891个、纲1016个、目3601个、科10130个、属1925个）.对同源基因功能的分析表明,适合对病原菌进行鉴定的基因在不同分类阶元中,表现的功能存在较大差异.革兰氏阳性和阴性病原菌在不同分类阶元中,同源基因表现出的功能也存在差异.该结果将为对在中国广泛存在的病原菌进行检测所涉及的探针、芯片设计提供理论依据,加快目标探针的筛选工作.同时,研究也是首次将世界范围内的全基因组数据和中国重大传染病涉及的病原菌紧密联系结合,为利用功能基因组学开展区域性、有针对性的病原检测和监测,提供候选基因和位点筛选的新方法.相关结果在细菌的元基因组学研究中也具有一定的应用价值.     

Tree Species Richness Strengthens Relationships between Ants and the Functional Composition of Spider Assemblages in a Highly Diverse Forest

In species‐rich ecosystems, such as subtropical and tropical forests, higher trophic level interactions are key mediators of ecosystem functioning. Plant species loss may alter these interactions, but the effects of plant diversity might be modified by intraguild interactions, particularly among predators. We analyzed the relationships between spiders and ants, two dominant predatory arthropod taxa, on tree saplings across a gradient from medium to high woody plant species richness in a subtropical forest in Southeast China. Neither ant nor spider total biomass was significantly related to plant species richness. By contrast, the biomass distribution of web‐building and hunting spiders changed and spider family richness increased in the presence of ants, resulting in more web builder‐dominated assemblages. However, these relationships depended on the plant communities, and were stronger in plots with higher plant species richness. Our results indicate that in addition to potential effects of ants on hunting spiders in particular, ants could indirectly influence intraguild interactions within spider assemblages. The observed shifts in the spider assemblages with increasing ant presence and plant species richness may have functional consequences, as web‐building and hunting spiders have distinct prey spectra. The relationships among ants, spiders, and plant species richness might contribute to explaining the non‐significant relationship between the overall effects of predators and plant diversity previously observed in the same forest plots. Our findings thus give insight into the complexity of biotic interactions in such species‐rich ecosystems.     

厦门岛城市林业发展概况及优势树种选择

在对厦门城市森林调查研究的基础上,就厦门岛的林业发展现状和存在问题进行分析,并提出在厦门岛内城市林业发展中较具应用价值的优势树种。     

Phylogenetic Analysis of Phaeosphaeria Species Using Mating Type Genes and Distribution of Mating Types in Iran

Phaeosphaeria species are pathogenic on wheat, barley and a wide range of wild grasses. To analyze mating type loci of the Phaeosphaeria species and investigate mating type distribution in Iran, we sequenced mating type loci of 273 Phaeosphaeria isolates including 67 isolates obtained from symptomatic leaves and ears of wheat, barley, and wild grasses from two wheat-growing region in Iran as well as 206 isolates from our collection from other regions in Iran which were isolated in our previous studies. Mating type genes phylogeny was successfully used to determine the species identity and relationships among isolates within the Phaeosphaeria spp. complex. In this study, we reported seven new host records for Phaeosphaeria species and the Phaeosphaeria avenaria f. sp. tritici 3 group was first reported from Iran in this study. Mating type distribution among Phaeosphaeria species was determined. Both mating types were present in all sampling regions from Iran. We observed skewed distribution of mating types in one region (Kohgiluyeh va Boyer-Ahmad) and equal distribution in the other region (Bushehr). However, when considering our entire dataset of 273 Iranian Phaeosphaeria isolates, the ratio of mating types was not deviated significantly from 1:1 suggesting possibilities for isolates of opposite mating type to interact and reproduce sexually, although the sexual cycle may infrequently occur in some regions especially when the climatic conditions are unfavorable for teleomorph development.     

Phylogenetic Analyses on the Diversity of Aspergillus fumigatus Sensu Lato Based on Five Orthologous Loci

One hundred isolates of Aspergillus fumigatus sensu lato mainly from China, as well as from Australia, France, India, Indonesia, Ireland, UK, and USA were analyzed to infer their sequence types (STs) and population diversity based on partial calmodulin, calcineurin regulatory subunit B, beta-tubulin, cytochrome C and calcineurin catalytic subunit A genes as well as their mating types, using ClonalFrame, Structure and MEGA software. Our results inferred 48 STs and showed that most of the STs or lineages evolved independently and without clear population structure among them. Whereas one lineage was recognized that could be a true population and in which one clade might diverge into another distinct lineage, namely, a cryptic species, A. neoellipticus. In addition, we found that mutation, parasexual, and sexual recombination could, respectively, play specific roles in the evolution of these fungi. Our results also showed that MAT1-1/MAT1-2 mating type ratios of A. fumigatus sensu lato was biased to nearly 1:1.4 (20/28) when clone-corrected, but when not clone-corrected, the ratio of MAT1-1/MAT1-2 was so biased as near 1:2 (35/65), which might mean that isolates with MAT1-2 are in the process of losing sexual ability preceding those with MAT1-1.