Phylogenetic relationships and biogeography of xantusiid lizards, inferred from mitochondrial DNA sequences.

Portions of two mitochondrial genes (12S ribosomal RNA and cytochrome b) were sequenced in seven species to examine phylogenetic relationships within the lizard family Xantusiidae. Phylogenies derived from these sequences (709 total bp) are concordant and indicate that the Cuban species Cricosaura typica is the sister group to all other xantusiids. The Middle American genus Lepidophyma is the closest relative of Xantusia, and X. riversiana (California Islands) the closest relative of X. vigilis (mainland). These findings are not in agreement either with the results of a recent morphological analysis that united Cricosaura and Lepidophyma as closest relatives or with past studies that have recognized X. riversiana as a separate genus. Levels of sequence divergence, as well as the age and affinities of some mainland fossil taxa, suggest that the origin of Cricosaura was associated with the tectonic evolution of the Greater Antilles in the late Cretaceous. These results further demonstrate that significant resolution of phylogenies can be obtained with relatively short DNA sequences and that these mitochondrial genes are concordant in their estimation of phylogeny.     

The Closest BLAST Hit Is Often Not the Nearest Neighbor

It is well known that basing phylogenetic reconstructions on uncorrected genetic distances can lead to errors in their reconstruction. Nevertheless, it is often common practice to report simply the most similar BLAST (Altschul et al. 1997) hit in genomic reports that discuss many genes (Ruepp et al. 2000; Freiberg et al. 1997). This is because BLAST hits can provide a rapid, efficient, and concise analysis of many genes at once. These hits are often interpreted to imply that the gene is most closely related to the gene or protein in the databases that returned the closest BLAST hit. Though these two may coincide, for many genes, particularly genes with few homologs, they may not be the same. There are a number of circumstances that can account for such limitations in accuracy (Eisen 2000). We stress here that genes appearing to be the most similar based on BLAST hits are often not each others closest relative phylogenetically. The extent to which this occurs depends on the availability of close relatives present in the databases. As an example we have chosen the analysis of the genomes of a crenarcheaota species Aeropyrum pernix, an organism with few close relatives fully sequenced, and Escherichia coli, an organism whose closest relative, Salmonella typhimurium, is completely sequenced.     

Basananthe aciphylla (Passifloraceae), a new species from Somalia

The new species Basananthe aciphylla , a thorny shrublet from central Somalia, is described and illustrated. Its closest relative is the likewise spinescent NE African endemic B. berberoides .     

A new Pharus (Poaceae) endemic to Ecuador

The new species Pharus ecuadoricus , endemic to the Pacific lowlands of Ecuador, is described, illustrated, and compared with its closest relative, P. parvifolius.     

Phylogenetic analysis of the pathogenic anaerobe Clostridium perfringens using the 16S rRNA nucleotide sequence.

Clostridium perfringens, the first pathogenic clostridium examined, was placed in the nonmycoplasma subgroup of the low-dG+dC-content gram-positive cluster on the basis of the results of a phylogenetic analysis in which we used 16S rRNA comparisons. The closest relative that has been identified to date is Clostridium pasteurianum.     

文昌鱼特异的基因倍增

进化生物学和发育生物学的结合产生了一门新兴学科——进化发育生物学,近年来该领域研究取得了丰硕的成果。头索动物文昌鱼是现存生物中最近似于脊椎动物直接祖先的生物,在与脊椎动物分化后形态改变很小,其基因组未曾经历大规模的基因组倍增,在一定程度上反映了脊椎动物祖先型基因组的特征,但在漫长的独立进化历程中基因组自身还是经历了一些变化。本文介绍了在几例在文昌鱼支系中独立发生的基因倍增事件(Hox; Evx; HNF-3; Calmodulin-like),有力地揭示了文昌鱼虽然与脊椎动物直接祖先极其接近,但其基因组有其自身特性,不能简单地将之等同于脊椎动物直接祖先。Abstract: The union of the two complementary disciplines, developmental biology and evolutionary biology resulted in a new division of evolutionary developmental biology, namely “Evo-Devo”. Recently, the research on this field has been fruitful in understanding the origin and development of vertebrates. The cephalochordate amphioxus, which remains in relatively invariant morphology since the divergence from the vertebrate lineage, is the closest living relative to vertebrates. The vertebrate-like simple body plan and preduplicative genome provide amphioxus genes the privilege to serve as key landmark to understand morphological evolution. However, the amphioxus genome has not escaped evolution. In this paper several examples of independent gene (Hox; Evx; HNF-3 and Calmodulin-like) duplications in the cephalochordate lineage were summarized. These particularities and oddities remind the fact that amphioxus is not an immediate ancestor of the vertebrates but ‘only’ the closest living relative to the ancestor, with a mix of prototypical and amphioxus-specific features in its genome.     

Phylogeny and molecular evolution in primates

Statistical methods for estimating the branching order and the branching dates from DNA sequence data, taking into account of the rate variation among lineages, are reviewed. An application of the methods to data from primates suggests that chimpanzee is the closest relative of man, and further suggests that these two species diverged about 4-5 million years ago.     

New species of Habracanthus (Acanthaceae) from Mexico

A new species,Habracanthus harleyi from Guerrero, is described, illustrated, and compared with its closest relative,Hansteinia monolopha.     

Molecular Genetic Polymorphism of the Yeast Kluyveromyces dobzhanskii

Microbiology - Based on strains of various ecological and geographical origins, we studied intraspecific polymorphism of the wild yeast Kluyveromyces dobzhanskii, the closest relative of the...     

Estrogens and progesterone during gestation in Dolichotis patagona

During pregnancy, a progesterone-binding plasma protein is present and is similar in several respects to the binding protein reported in other hystricomorphs. These findings establish estradiol-17 beta as the predominant estrogen of pregnancy and that progesterone rises during pregnancy and does not decline until after parturition. Gestation length is 96 days. This study establishes similarities between the mara and its closest relative, the guinea pig.     

Whole genome sequence of an unusual Borrelia burgdorferi sensu lato isolate

Human Lyme disease is caused by a number of related Borrelia burgdorferi sensu lato species. We report here the complete genome sequence of Borrelia sp. isolate SV1 from Finland. This isolate is to date the closest known relative of B. burgdorferi sensu stricto, but it is sufficiently genetically distinct from that species that it and its close relatives warrant its candidacy for new-species status. We suggest that this isolate should be named "Borrelia finlandensis."     

Rap1 signalling: adhering to new models

Ras-like GTPases are ubiquitously expressed, evolutionarily conserved molecular switches that couple extracellular signals to various cellular responses. Rap1, the closest relative of Ras, has attracted much attention because of the possibility that it regulates Ras-mediated signalling. Rap1 is activated by extracellular signals through several regulatory proteins, and it might function in diverse processes, ranging from modulation of growth and differentiation to secretion, integrin-mediated cell adhesion and morphogenesis.     

耐辐射黑色酵母状真菌的筛选和特性研究

【目的】确定辐射污染土样中分离筛选获得的一批黑色酵母状真菌的分类学地位和抗逆特性。【方法】通过菌落形态和菌丝特征观察,结合LSU rDNA D1/D2区序列的系统发育分析,并进行了菌株的60Coγ射线照射、紫外线照射和对等重金属离子以及NaCl生长压力实验。【结果】上述菌株均为Aureobasidium属菌,其中菌株F99和F134均与A.pullulans var.subglaciale CBS 123388T具有最大同源性,为100%;菌株F19与A.pullulans var.melaogenum CBS 105.22T具有最大同源性,为99.8%;上述菌株均具有极强的抗逆特性。【结论】为了解耐辐射真菌抗逆机理提供了重要的研究材料。     

Molecular phylogenetics and historical biogeography of Hawaiian Dryopteris (Dryopteridaceae)

The fern genus Dryopteris (Dryopteridaceae) is represented in the Hawaiian Islands by 18 endemic taxa and one non-endemic, native species. The goals of this study were to determine whether Dryopteris in Hawai'i is monophyletic and to infer the biogeographical origins of Hawaiian Dryopteris by determining the geographical distributions of their closest living relatives. We sequenced two chloroplast DNA fragments, rbcL and the trnL-F intergenic spacer (IGS), for 18 Hawaiian taxa, 45 non-Hawaiian taxa, and two outgroup species. For individual fragments, we estimated phylogenetic relationships using Bayesian inference and maximum parsimony. We performed a combined analysis of both cpDNA fragments employing Bayesian inference, maximum parsimony, and maximum likelihood. These analyses indicate that Hawaiian Dryopteris is not monophyletic, and that there were at least five separate colonizations of the Hawaiian Islands by different species of dryopteroid ferns, with most of the five groups having closest relatives in SE Asia. The results suggest that one colonizing ancestor, perhaps from SE Asia, gave rise to eight endemic taxa (the glabra group). Another colonizing ancestor, also possibly from SE Asia, gave rise to a group of five endemic taxa (the exindusiate group). Dryopteris fusco-atra and its two varieties, which are endemic to Hawai'i, most likely diversified from a SE Asian ancestor. The Hawaiian endemic Nothoperanema rubiginosum has its closest relatives in SE Asia, and while the remaining two species, D. wallichiana and D. subbipinnata, are sister species, their biogeographical origins could not be determined from these analyses due to the widespread distributions of D. wallichiana and its closest non-Hawaiian relative.     

The genomics of wild yeast populations sheds light on the domestication of man's best (micro) friend

The domestication of plants, animals and microbes by humans are the longest artificial evolution experiments ever performed. The study of these long‐term experiments can teach us about the genomics of adaptation through the identification of the genetic bases underlying the traits favoured by humans. In laboratory evolution, the characterization of the molecular changes that evolved specifically in some lineages is straightforward because the ancestors are readily available, for instance in the freezer. However, in the case of domesticated species, the ancestor is often missing, which leads to the necessity of going back to nature in order to infer the most likely ancestral state. Significant and relatively recent examples of this approach include wolves as the closest wild relative to domestic dogs (Axelsson et al. 2013) and teosinte as the closest relative to maize (reviewed in Hake & Ross‐Ibarra 2015). In both cases, the joint analysis of domesticated lineages and their wild cousins has been key in reconstructing the molecular history of their domestication. While the identification of closest wild relatives has been done for many plants and animals, these comparisons represent challenges for micro‐organisms. This has been the case for the budding yeast Saccharomyces cerevisiae, whose natural ecological niche is particularly challenging to define. For centuries, this unicellular fungus has been the cellular factory for wine, beer and bread crafting, and currently for bioethanol and drug production. While the recent development of genomics has lead to the identification of many genetic elements associated with important wine characteristics, the historical origin of some of the domesticated wine strains has remained elusive due to the lack of knowledge of their close wild relatives. In this issue of Molecular Ecology, Almeida et al. (2015) identified what is to date the closest known wild population of the wine yeast. This population is found associated with oak trees in Europe, presumably its natural host. Using population genomics analyses, Almeida and colleagues discovered that the initial divergence between natural and domesticated wine yeasts in the Mediterranean region took place around the early days of wine production. Surprisingly, genomic regions that are key to wine production today appeared not to be derived from these natural populations but from genes gained from other yeast species.     

Cryptococcus zeae, a new yeast species associated with Zea mays

A new yeast, Cryptococcus zeae (type strain HB 1207^T) is described. Six strains were isolated from corn and pests of corn in Austria. Microsatellite-primed polymerase chain reaction (MSP-PCR) fingerprints showed that the strains are members of the same species. Phylogenetical analyses of domains D1/D2 26S rDNA and ITS 1-5,8S–ITS 2 sequences showed C. zeae to have the closest relationship to C. luteolus. The D1/D2 sequences of C. zeae fit with three Korean Cryptococcus sp. strains (AF459690, AF459691, AF459692). The new species is separable from the closest relative C. luteolus using only two physiological tests.     

A new species in the intermedia-group and a new synonymy in the genus Pollenia Robineau-Desvoidy, 1830 (Diptera: Calliphoridae)

Abstract. An intermedia species-group is defined within Pollenia Robineau-Desvoidy. P.pseudintermedia sp.n. is described from Greece, Yugoslavia and Spain and compared with its closest relative P. intermedia Macquart. P.alajensis Rodendorf, stat.rev. is established as a new senior synonym of P.sytshevskajae Grunin, syn.n.     

产甾体皂甙华重楼内生菌的筛选与鉴定

从华重楼(Paris polyphyllavar.chinensisFranch)的地下块茎中分离筛选得到2株可能产生甾体皂甙的内生菌(SS01和SS02),薄层层析检测菌株SS01、SS02的发酵产物分别有3条和2条层析带与重楼总皂甙的层析带迁移率相当。形态和生理生化特征初步表明SS01和SS02分属于肠杆菌科(Enterobacteriaceae)和芽孢杆菌属(Bacillussp.)细菌。扩增、测序得到SS01和SS02的部分16S rDNA序列,GenBank接收号分别为AY842143和AY842144。用Blastn调出与菌株16SrDNA同源的序列,用Clustal W进行多重序列对比,用软件Phylip按Neighbor-Joining方法构建16SrDNA系统发育树。菌株SS01和SS02分别与Cedecea davisae DSM4568、Paenibacillus daejeonensis处于同一分支,相似性分别为98.9%和97.7%,将它们鉴定为Cedecea davisae SS01和Paenibacillus daejeonensis SS02。