Correlation of fruit tree rhizosphere soils with entomopathogenic fungi

Entomopathogenic fungi are microorganisms that control the density of host insects in nature; they are being studied as environmentally friendly alternatives to chemical insecticides for controlling insect pests. The main habitat of entomopathogenic fungi is soil, and the correlation between the distribution of entomopathogenic fungi and the physicochemical characteristics of soils planted with different trees, including vine (outdoor, greenhouse, and greenhouse shine musket), apple, peach, and pear, were analyzed. The entomopathogenic fungi of the genera Beauveria, Metarhizium, and Purpureocillium investigated in this study were all found in soil samples from vine-greenhouse, apple, and peach trees. Purpureocillium and Beauveria abundances were positively correlated with soil properties; however, Metarhizium abundances were not correlated with soil properties. The Metarhizium isolates discovered in this study showed pathogenicity to cotton aphids (an agricultural pest) and can be employed as sources for biological studies in the future. This study provides data on the diversity and abundance of entomopathogenic fungi related with soil properties, as well as the molecular, biological, and insecticidal characteristics of Metarhizium isolates.     

Evolution of fruit characters and dispersal modes in the tropical family Rubiaceae

We investigated the evolution of fruit characters, animals versus abiotic dispersal modes, life forms and geographical distribution, in the large, mostly tropical, family Rubiaceae. As a basis for our analysis we used a phylogenetic tree derived from chloroplast DNA variation. Fleshy fruits have evolved independently at least 12 times in the family. Most of these originations appear to have occurred during Eocene to Oligocene, i.e. the radiation period for some animal taxa (bird families, mammal orders) comprising most extant dispersers of Rubiaceae fruits. Changes of dispersal modes may be of more recent origin in a few cases, e.g. evolution of drupes in some lineages, and shifts from drupes to nuts. The distribution of fruit characters suggested that in several lineages animal-dispersed fruits, such as berries and drupes have remained largely unaltered since the time of origination. This is in contrast to the occurrence of winged seeds in capsules, and pterophylls, i.e. enlarged calyx lobes promoting wind dispersal of fruits, which apparently have shifted more frequently during evolution, indicating a difference in 'phylogenetic plasticity' between modes of animal and wind dispersal.
Animal dispersal was over-represented among genera dominated by shrubs, whereas abiotic dispersal was most prevalent among herbaceous genera. Drupes were over-represented in groups with transoceanic distributions, and on islands, indicating dispersal over long distances, probably by birds. In contrast, no evidence was found to support the view that animal dispersal in general enhances long distance dispersal. We also analysed geographical patterns on the tribal level but these were too complex to yield any resolved area cladograms due to the occurrence of many widespread taxa and area redundancy.     

A review of the pelvic girdle of acanthomorph fishes, with comments on hypotheses of acanthomorph intrarelationships

The anatomy of the pelvic girdle of acanthomorph fishes is reviewed. Derived morphological features of the pelvic complex are identified and discussed as evidence for the recognition of a monophyletic Acanthomorpha, Acanthopterygii and Percomorpha. Within the Percomorpha, evidence is presented to support the grouping of the Holocentridae with the remaining percomorph assemblage. An additional sub-grouping of "higher percomorphs" is also proposed.     

一株马冠状病毒的分离鉴定及遗传演化分析

马冠状病毒病是由马冠状病毒(equine coronavirus, ECoV)引起的一种马新发胃肠道病毒病,成年马感染后主要出现发烧、腹痛和腹泻等症状。1975年,马冠状病毒感染首次在美国出现,此后在多个国家和地区均有流行,此前我国仅从山东腹泻驴的小肠样品中分离得到了一株重组马冠状病毒。【目的】了解ECoV中国毒株的基因组成、亲缘关系以及生物学特性,可以为我国ECoV流行现状和遗传演化趋势提供依据,为ECoV防控产品的研发提供材料。【方法】对湖北省武汉市黄陂区腹泻马匹的粪便样品进行RT-PCR检测,对检测阳性样品进行病毒分离,并利用靶向ECoV S1蛋白的单克隆抗体通过间接免疫荧光试验(indirect immunofluorescence assay, IFA)对分离的病毒进行验证。根据ECoV-JL株全基因组测序结果,对全基因组、N基因和NS2基因进行了基因组系统发育分析和同源性比较。【结果】成功分离到一株ECoV,并命名为ECoV-JL。透射电镜(transmission electron microscopy, TEM)观察分离到的病毒颗粒呈球状,且具有囊膜和冠状病毒典型的纤突结构。该分离株感染HRT-18细胞72 h后病毒滴度可到达峰值,半数组织培养感染剂量(tissue culture infectious dose 50%, TCID₅₀)约为10^6.16 TCID₅₀/mL。ECoV-JL毒株可以在人回盲肠癌(human ileocecal cancer-18, HRT-18)细胞、人结直肠腺癌(human colorectal adenocarcinoma-2, Caco-2)细胞和人肝癌(human liver cancer cells, Huh7)细胞上稳定传代。ECoV-JL株与GenBank中现有的ECoV全基因组序列相似性为97.9%-99.0%,系统发育分析发现ECoV-JL株属于单独的演化分支,与其他毒株的亲缘关系较远,说明ECoV-JL株可能是重组变异而来,其中NS2基因突变较多,NS2基因编码的差异是造成ECoV-JL株与其他毒株同源性较差的主要原因。【结论】本研究从腹泻马的粪便样品中成功分离并鉴定了一株ECoV,将其命名为ECoV-JL株,对该毒株生物学特性和亲缘关系的研究反映了湖北地区流行毒株的特点,为我国ECoV流行现状和演化趋势提供重要依据。     

The complete chloroplast genomes of three Hamamelidaceae species: Comparative and phylogenetic analyses

Hamamelidaceae is an important group that represents the origin and early evolution of angiosperms. Its plants have many uses, such as timber, medical, spice, and ornamental uses. In this study, the complete chloroplast genomes of Loropetalum chinense (R. Br.) Oliver, Corylopsis glandulifera Hemsl., and Corylopsis velutina Hand.‐Mazz. were sequenced using the Illumina NovaSeq 6000 platform. The sizes of the three chloroplast genomes were 159,402 bp (C. glandulifera), 159,414 bp (C. velutina), and 159,444 bp (L. chinense), respectively. These chloroplast genomes contained typical quadripartite structures with a pair of inverted repeat (IR) regions (26,283, 26,283, and 26,257 bp), a large single‐copy (LSC) region (88,134, 88,146, and 88,160 bp), and a small single‐copy (SSC) region (18,702, 18,702, and 18,770 bp). The chloroplast genomes encoded 132–133 genes, including 85–87 protein‐coding genes, 37–38 tRNA genes, and 8 rRNA genes. The coding regions were composed of 26,797, 26,574, and 26,415 codons, respectively, most of which ended in A/U. A total of 37–43 long repeats and 175–178 simple sequence repeats (SSRs) were identified, and the SSRs contained a higher number of A + T than G + C bases. The genome comparison showed that the IR regions were more conserved than the LSC or SSC regions, while the noncoding regions contained higher variability than the gene coding regions. Phylogenetic analyses revealed that species in the same genus tended to cluster together. Chunia Hung T. Chang, Mytilaria Lecomte, and Disanthus Maxim. may have diverged early and Corylopsis Siebold & Zucc. was closely related to Loropetalum R. Br. This study provides valuable information for further species identification, evolution, and phylogenetic studies of Hamamelidaceae plants.     

Evolutionary Processes in the Emergence and Recent Spread of the Syphilis Agent,Treponema pallidum

The incidence of syphilis has risen worldwide in the last decade in spite of being an easily treated infection. The causative agent of this sexually transmitted disease is the bacterium Treponema pallidum subspecies pallidum (TPA), very closely related to subsp. pertenue (TPE) and endemicum (TEN), responsible for the human treponematoses yaws and bejel, respectively. Although much focus has been placed on the question of the spatial and temporary origins of TPA, the processes driving the evolution and epidemiological spread of TPA since its divergence from TPE and TEN are not well understood. Here, we investigate the effects of recombination and selection as forces of genetic diversity and differentiation acting during the evolution of T. pallidum subspecies. Using a custom-tailored procedure, named phylogenetic incongruence method, with 75 complete genome sequences, we found strong evidence for recombination among the T. pallidum subspecies, involving 12 genes and 21 events. In most cases, only one recombination event per gene was detected and all but one event corresponded to intersubspecies transfers, from TPE/TEN to TPA. We found a clear signal of natural selection acting on the recombinant genes, which is more intense in their recombinant regions. The phylogenetic location of the recombination events detected and the functional role of the genes with signals of positive selection suggest that these evolutionary processes had a key role in the evolution and recent expansion of the syphilis bacteria and significant implications for the selection of vaccine candidates and the design of a broadly protective syphilis vaccine.     

Placing Ancient DNA Sequences into Reference Phylogenies

Joint phylogenetic analysis of ancient DNA (aDNA) with modern phylogenies is hampered by low sequence coverage and post-mortem deamination, often resulting in overconservative or incorrect assignment. We provide a new efficient likelihood-based workflow, pathPhynder, that takes advantage of all the polymorphic sites in the target sequence. This effectively evaluates the number of ancestral and derived alleles present on each branch and reports the most likely placement of an ancient sample in the phylogeny and a haplogroup assignment, together with alternatives and supporting evidence. To illustrate the application of pathPhynder, we show improved Y chromosome assignments for published aDNA sequences, using a newly compiled Y variation data set (120,908 markers from 2,014 samples) that significantly enhances Y haplogroup assignment for low coverage samples. We apply the method to all published male aDNA samples from Africa, giving new insights into ancient migrations and the relationships between ancient and modern populations. The same software can be used to place samples with large amounts of missing data into other large non-recombining phylogenies such as the mitochondrial tree.     

Phylogenetic Relationships of Globodera millefolii,G. artemisiae,and Cactodera salina Based on ITS Region of Ribosomal DNA

Globodera millefolii and G. artemisiae are interesting because their type localities (Estonia and Russia, respectively) are geographically distant from those of the potato cyst nematodes and other Globodera species that seem to have originated in the Western world, and because the type host for each is a member of Compositae rather than Solanaceae. Sequence data for ITS1, ITS2, and 5.8S ribosomal DNA (ITS rDNA) for G. millefolii and G. artemisiae were nearly identical to sequence data for Cactodera salina from the rhizosphere of the estuary plant Salicornia bigelovii in Sonora, Mexico. The ITS rDNA sequences of these three species were all about 94% similar to those of two other Cactodera species for which ITS rDNA data were obtained. Phylogenetic analysis indicated that, based on the ITS rDNA data, G. millefolii and G. artemisiae are more closely related phylogenetically to the Cactodera species than to other nominal Globodera species. The molecular data further suggest that the genus Cactodera may comprise two or more morphologically similar but separate groups.     

晚三叠世泡孔类苔藓动物Casianopora及其种系发生关系

本文描述了窄唇纲苔藓动物的一个新种Ｃａｓｉａｎｏｐｏｒａｈｅｉｓｐ．ｎｏｖ．,此新种发现于我国滇西北宁蒗彝族自治县松桂组１５层（菊石Ｍａｌａｙｉｔｅｓ－Ｐｓｅｕｄｏｃａｒｄｉｏｃｅｒａｓ带）,是迄今已知的全球三叠纪泡孔类的一个最新代表。重新确定了Ｃａｓｉａｎｏｐｏｒａ属（卡尼中期－诺利早期）的分类位置,它和Ｃｙｓｔｉｔｒｙｐａ属（卡尼早期）都归入Ｆｉｓｔｕｌｉｐｏｒｉｄａｅ科。这两个三叠纪的属,与古生代和古生代后的一些泡孔类的种系发生关系的初步探讨表明,所有古生代后的窄唇纲的各个目（除环口目外）,可能都是从同一演化根系上发展而来的。