Exploring the diversity and molecular evolution of shrews (family Soricidae) using mtDNA cytochrome b data

The taxonomy of the shrews (family Soricidae) is primarily underpinned by the analysis of morphology characters. These morphological characters are, however, often plesiomorphic and difficult to interpret in an evolutionarily meaningful way. Recent molecular studies have provided some clarity at lower-taxonomic levels, but studies giving resolution to deeper levels of the soricid phylogeny are lacking. By constructing the most taxonomically inclusive molecular phylogeny for this cosmopolitan family, this study aims to test the utility of the routinely used mitochondrial cytochrome b gene to resolve the higher-level relationships within the Soricidae. Given the life history characteristics of shrews (high metabolic rate in Soricinae, small body size, fast generation time and generally short life span), the metabolic theory predicts accelerated nucleotide turnover in this family. By examining the molecular evolution of the cytochrome b molecule, this study identifies both lineage- and codon-specific mutational rate differences.We suggest that codon-specific mutational rate patterns are best explained by unique selective regimes operating on the different codon positions, while lineage-specific rate variation among genera belonging to Soricidae may reflect differences in the mode and speed of speciation events which generated species.     

Genetic variation among spiny-footed lizards in the Acanthodactylus pardalis group from North Africa

The systematics of the genus Acanthodactylus was classically based on external morphological traits, osteological characters and morphology of the hemipenes. Although the identification of species complexes is relatively easy, the distinction within some groups is difficult due to a high variability of the external morphology. Partial mitochondrial (12S and 16S rRNA) sequences (371 and 499 base pairs, respectively) were analysed from 32 specimens of the A. pardalis group from northern Africa including the described species A. busacki, A. maculatus, A. mechriguensis and A. pardalis. Several highly distinct genetic units were resolved, but with little support for relationships between them. These units did not coincide with current taxonomic units, but showed geographic structuring. Although the A. pardalis group displays significant variation, the present taxonomy of the group must be considered unsatisfactory since it is not supported by genetic evidence. For some forms, such as A. mechriguensis there is no support and it is suggested that it should be synonymized with A. maculatus. More data are clearly needed for other forms. Complex microevolutionary patterns due to the recent contraction/ expansion phases of the Sahara Desert probably are related with the phylogenetic patterns observed.     

A class-wide phylogenetic assessment of Dothideomycetes

We present a comprehensive phylogeny derived from 5 genes, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, for 356 isolates and 41 families (six newly described in this volume) in Dothideomycetes. All currently accepted orders in the class are represented for the first time in addition to numerous previously unplaced lineages. Subclass Pleosporomycetidae is expanded to include the aquatic order Jahnulales. An ancestral reconstruction of basic nutritional modes supports numerous transitions from saprobic life histories to plant associated and lichenised modes and a transition from terrestrial to aquatic habitats are confirmed. Finally, a genomic comparison of 6 dothideomycete genomes with other fungi finds a high level of unique protein associated with the class, supporting its delineation as a separate taxon.     

Evolution of CDC42, a putative virulence factor triggering meristematic growth in black yeasts

The cell division cycle gene (CDC42) controlling cellular polarization was studied in members of Chaetothyriales. Based on ribosomal genes, ancestral members of the order exhibit meristematic growth in view of their colonization of inert surfaces such as rock, whereas in derived members of the order the gene is a putative virulence factor involved in expression of the muriform cell, the invasive phase in human chromoblastomycosis. Specific primers were developed to amplify a portion of the gene of 32 members of the order with known position according to ribosomal phylogeny. Phylogeny of CDC42 proved to be very different. In all members of Chaetohyriales the protein sequence is highly conserved. In most species, distributed all over the phylogenetic tree, introns and 3^rd codon positions are also invariant. However, a number of species had paralogues with considerable deviation in non-coding exon positions, and synchronous variation in introns, although non-synonomous variation had remained very limited. In some strains both orthologues and paralogues were present. It is concluded that CDC42 does not show any orthologous evolution, and that its paralogues haves the same function but are structurally relaxed. The variation or absence thereof could not be linked to ecological changes, from rock-inhabiting to pathogenic life style. It is concluded that eventual pathogenicity in Chaetothyriales is not expressed at the DNA level in CDC42 evolution.     

A rock-inhabiting ancestor for mutualistic and pathogen-rich fungal lineages

Rock surfaces are unique terrestrial habitats in which rapid changes in the intensity of radiation, temperature, water supply and nutrient availability challenge the survival of microbes. A specialised, but diverse group of free-living, melanised fungi are amongst the persistent settlers of bare rocks. Multigene phylogenetic analyses were used to study relationships of ascomycetes from a variety of substrates, with a dataset including a broad sampling of rock dwellers from different geographical locations. Rock-inhabiting fungi appear particularly diverse in the early diverging lineages of the orders Chaetothyriales and Verrucariales. Although these orders share a most recent common ancestor, their lifestyles are strikingly different. Verrucariales are mostly lichen-forming fungi, while Chaetothyriales, by contrast, are best known as opportunistic pathogens of vertebrates (e.g. Cladophialophora bantiana and Exophiala dermatitidis, both agents of fatal brain infections) and saprophytes. The rock-dwelling habit is shown here to be key to the evolution of these two ecologically disparate orders. The most recent common ancestor of Verrucariales and Chaetothyriales is reconstructed as a non-lichenised rock-inhabitant. Ancestral state reconstructions suggest Verrucariales as one of the independent ascomycetes group where lichenisation has evolved on a hostile rock surface that might have favored this shift to a symbiotic lifestyle. Rock-inhabiting fungi are also ancestral to opportunistic pathogens, as they are found in the early diverging lineages of Chaetothyriales. In Chaetothyriales and Verrucariales, specific morphological and physiological traits (here referred to as extremotolerance) evolved in response to stresses in extreme conditions prevailing on rock surfaces. These factors facilitated colonisation of various substrates including the brains of vertebrates by opportunistic fungal pathogens, as well as helped establishment of a stable lichen symbiosis.     

金丝猴生态学和分子生物学研究进展

金丝猴(Rhinopithecus)是典型的经历快速辐射和近期物种形成事件的进化类群,分为川金丝猴(Rhinopithecus roxellanae)、黔金丝猴(Rhinopithecus brelichi)、滇金丝猴(Rhinopithecus bieti)、越南金丝猴(Rhinopithecus avunculus)和缅甸金丝猴(Rhinopithecus strykeri)5个种。它们共同占据着东南亚的森林和林地生态位,是非人灵长类重要物种,国内外学者在它们的宏观和微观方面都做了大量研究工作,文章就5种金丝猴各自的生态学和分子生物学研究现状进行综述,并对存在的问题提出相应的建议。     

一种油茶新炭疽病原的多基因系统发育分析鉴定

为明确我国油茶炭疽病病原菌的种类,对采集自我国6个省市油茶产区的炭疽病样本进行病原菌分离,通过形态学特征并结合多基因谱系分析方法构建系统发育树进行比较分析.结果表明共分离到能引起油茶叶出现炭疽病症状的病原菌23株.病原菌在PDA培养基上28 ℃培养7 d后,菌落圆形,初期白色,逐渐变为灰色,最终为灰黑色;分生孢子堆橘黄色,分生孢子椭圆形、单胞、无色,大小为(16.8±0.7) μm×(5.7±0.4) μm;菌丝附着孢椭圆形,褐色,边缘光滑、完整,大小为(9.5±1.5) μm×(6.1±0.6) μm.多基因系统发育树显示,这23株病原菌与包括模式菌株ICMP 18581在内的所有果生刺盘孢菌Colletotrichum fructicola菌株序列聚为一个进化枝,置信度高达100%.根据形态特征及多基因系统发育树,鉴定这23株病原菌为果生刺盘孢菌C.fructicola,为国内油茶上果生刺盘孢菌的首次报道.     

Improving Potato virus Y strain nomenclature: lessons from comparing isolates obtained over a 73‐year period

Biological and whole genome properties were compared between eight historical European (1943–1984) and five Australian (2003–2012) Potato virus Y (PVY) isolates. Based on eliciting hypersensitivity genes Nc, Ny or Nz, the former belonged to biological strain groups PVY^C (CT, CRM1), PVY^O (CRN, KE, RS) or PVY^Z (CM2, CRM2, DS). The latter were inoculated to differential and other potato cultivars, tobacco and tomato. Two belonged to PVY^O (BL, DEL3), one to PVY^Z (ATL1), and one (KIP1) to suggested strain group (PVY^D) which elicited putative hypersensitivity gene Nd. Tomato isolate CN1 (and unsequenced CN2), which were poorly adapted to infect potato, were not grouped. Next‐generation sequencing (NGS) of samples containing all isolates except CN2, yielded 13 complete sequences of 9592–9700 nucleotides (nt), and one partial sequence of 9002 nt, none being recombinants. Comparing the former with 60 other PVY complete genomes, found one (CRM2) in phylogenetic subgroup Y^O, eight in Y^O5 (CM2, CRN, DS, KE, RS, ATL1, BL, DEL3), three in Y^C2 (CRM1, CT, KIP1) and one in Y^C1 (CN1). Thus, biologically defined PVY^O (5) and PVY^Z (4) isolates were within phylogenetic subgroups Y^O or Y^O5, biological PVY^C isolates (2) within Y^C2, biological PVY^D isolate KIP1 in Y^C2 and tomato isolate CN1 in Y^C1. NGS identified KIP1 and partial sequence KIP from mixed infection. KIP was in Y^O5. Grouping of four PVY^Z isolates within phylogenetic PVY^O, and the PVY^D isolate within phylogenetic PVY^C, reveals disagreement between current biological and phylogenetic PVY nomenclature systems. Using Latinized numerals for phylogenetic group names resolved this.