RHR转录因子家族起源、功能以及进化机制的研究进展

转录因子是一类能够通过与基因特异性序列进行结合,从而调控基因转录与表达的蛋白质,对细胞的生物学活性具有重要的调节作用。RHR (Rel-homology region,RHR)转录因子家族属于IF (immunoglobulin fold)转录因子超家族最主要的成员,其成员含有保守的Rel结构域和IPT (immunoglobulin-like fold)结构域。作为古老的转录因子家族,RHR家族成员随着物种演化,通过基因的复制、突变和沉默,不断分化出新型同源基因的同时也伴随着基因的丢失。自然选择导致了各家族成员不同的进化速率,并且在一些功能结构域上展现出了特殊的进化机制。然而,目前有关RHR家族起源和分化的综述比较少见。本文综述了RHR家族各成员的分布、分类、功能及家族进化等方面的研究成果,以期为研究整个转录因子家族的演化机制和物种之间的进化关系提供参考和新的思路。     

The other facets of family life and their role in the evolution of animal sociality

Family life forms an integral part of the life history of species across the animal kingdom and plays a crucial role in the evolution of animal sociality. Our current understanding of family life, however, is almost exclusively based on studies that (i) focus on parental care and associated family interactions (such as those arising from sibling rivalry and parent‐offspring conflict), and (ii) investigate these phenomena in the advanced family systems of mammals, birds, and eusocial insects. Here, we argue that these historical biases have fostered the neglect of key processes shaping social life in ancestral family systems, and thus profoundly hamper our understanding of the (early) evolution of family life. Based on a comprehensive survey of the literature, we first illustrate that the strong focus on parental care in advanced social systems has deflected scrutiny of other important social processes such as sibling cooperation, parent–offspring competition and offspring assistance. We then show that accounting for these neglected processes – and their changing role over time – could profoundly alter our understanding of the origin and subsequent evolution of family life. Finally, we outline how this ‘diachronic’ perspective on the evolution of family living provides novel insights into general processes driving the evolution of animal sociality. Overall, we infer that the explicit consideration of thus‐far neglected facets of family life, together with their study across the whole diversity of family systems, are crucial to advance our understanding of the processes that shape the evolution of social life.     

Signatures of selection and sex-specific expression variation of a novel duplicate during the evolution of the Drosophila desaturase gene family

The tempo and mode of evolution of loci with a large effect on adaptation and reproductive isolation will influence the rate of evolutionary divergence and speciation. Desaturase loci are involved in key biochemical changes in long-chain fatty acids. In insects, these have been shown to influence adaptation to starvation or desiccation resistance and in some cases act as important pheromones. The desaturase gene family of Drosophila is known to have evolved by gene duplication and diversification, and at least one locus shows rapid evolution of sex-specific expression variation. Here, we examine the evolution of the gene family in species representing the Drosophila phylogeny. We find that the family includes more loci than have been previously described. Most are represented as single-copy loci, but we also find additional examples of duplications in loci which influence pheromone blends. Most loci show patterns of variation associated with purifying selection, but there are strong signatures of diversifying selection in new duplicates. In the case of a new duplicate of desat1 in the obscura group species, we show that strong selection on the coding sequence is associated with the evolution of sex-specific expression variation. It seems likely that both sexual selection and ecological adaptation have influenced the evolution of this gene family in Drosophila.     

Plastomic data shed new light on the phylogeny,biogeography, and character evolution of the family Crassulaceae

Crassulaceae is a mid-sized family of angiosperms, most species of which are herbaceous succulents, usually with 5-merous flowers and one or two whorls of stamens. Although previous phylogenetic studies revealed seven major “clades” in Crassulaceae and greatly improved our understanding of the evolutionary history of the family, relationships among major clades are still contentious. In addition, the biogeographic origin and evolution of important morphological characters delimiting infrafamilial taxa have not been subject to formal biogeographic and character evolution analyses based on a well-supported phylogeny backbone. In this study, we used plastomic data of 52 species, representing all major clades revealed in previous studies to reconstruct a robust phylogeny of Crassulaceae, based on which we unraveled the spatiotemporal framework of diversification of the family. We found that the family may originate in southern Africa and then dispersed to the Mediterranean, from there to eastern Asia, Macaronesia, and North America. The crown age of Crassulaceae was dated at ca. 63.93 million years ago, shortly after the Cretaceous–Paleogene (K-Pg) boundary. We also traced the evolution of six important morphological characters previously used to delimit infrafamilial taxa and demonstrated widespread parallel and convergent evolution of both vegetative (life form and phyllotaxis) and floral characters (number of stamen whorls, petals free or fused, and flower merism). Our results provide a robust backbone phylogeny as a foundation for further investigations, and also some important new insights into biogeography and evolution of the family Crassulaceae.     

Exploring the common dynamics of homologous proteins. Application to the globin family

We present a procedure to explore the global dynamics shared between members of the same protein family. The method allows the comparison of patterns of vibrational motion obtained by Gaussian network model analysis. After the identification of collective coordinates that were conserved during evolution, we quantify the common dynamics within a family. Representative vectors that describe these dynamics are defined using a singular value decomposition approach. As a test case, the globin heme-binding family is considered. The two lowest normal modes are shown to be conserved within this family. Our results encourage the development of models for protein evolution that take into account the conservation of dynamical features.     

Trophic specialization influences the rate of environmental niche evolution in damselfishes (Pomacentridae)

The rate of environmental niche evolution describes the capability of species to explore the available environmental space and is known to vary among species owing to lineage-specific factors. Trophic specialization is a main force driving species evolution and is responsible for classical examples of adaptive radiations in fishes. We investigate the effect of trophic specialization on the rate of environmental niche evolution in the damselfish, Pomacentridae, which is an important family of tropical reef fishes. First, phylogenetic niche conservatism is not detected in the family using a standard test of phylogenetic signal, and we demonstrate that the environmental niches of damselfishes that differ in trophic specialization are not equivalent while they still overlap at their mean values. Second, we estimate the relative rates of niche evolution on the phylogenetic tree and show the heterogeneity among rates of environmental niche evolution of the three trophic groups. We suggest that behavioural characteristics related to trophic specialization can constrain the evolution of the environmental niche and lead to conserved niches in specialist lineages. Our results show the extent of influence of several traits on the evolution of the environmental niche and shed new light on the evolution of damselfishes, which is a key lineage in current efforts to conserve biodiversity in coral reefs.     

Tobacco to tomatoes: a phylogenetic perspective on fruit diversity in the Solanaceae

The Solanaceae contains many species of agricultural importance. Several of these are cultivated for their fruits, such as the tomato, the pepper and the aubergine. The family is very diverse in fruit type with capsules, drupes, pyrenes, berries, and several sorts of dehiscent non-capsular fruits occurring in the 90+ genera. In this paper, recent work on fruit type evolution in angiosperms is reviewed in relation to dispersal agents and habitat ecology. Defining fruit types in the Solanaceae in a simple five state system, then mapping them onto a previously published molecular phylogeny based on chloroplast DNA allows discussion of the evolution of these fruit types in a phylogenetic framework. Capsules are plesiomorphic in the family, and although berries are a synapomorphy (shared derived character) for a large clade including the genus Solanum (tomatoes and aubergines), they have arisen several times in the family as a whole. Problems with homology of drupes and pyrenes are discussed, and areas for future investigation of fruit structure homology identified. The distribution of fruit types in the large and diverse genus Solanum is also discussed in the light of monophyletic groups identified using chloroplast gene sequences. This variety is related to recent advances in the understanding of the molecular biology of fruit development. Finally, several key areas of future comparative, phylogenetic investigation into fruit type evolution in the family are highlighted.     

Molecular phylogeny and evolution of the plant-specific seven-transmembrane MLO family

Homologues of barley Mlo encode the only family of seven-transmembrane (TM) proteins in plants. Their topology, subcellular localization, and sequence diversification are reminiscent of those of G-protein coupled receptors (GPCRs) from animals and fungi. We present a computational analysis of MLO family members based on 31 full-size and 3 partial sequences, which originate from several monocot species, the dicot Arabidopsis thaliana, and the moss Ceratodon purpureus. This enabled us to date the origin of the Mlo gene family back at least to the early stages of land plant evolution. The genomic organization of the corresponding genes supports a monophyletic origin of the Mlo gene family. Phylogenetic analysis revealed five clades, of which three contain both monocot and dicot members, while two indicate class-specific diversification. Analysis of the ratio of nonsynonymous-to-synonymous changes in coding sequences provided evidence for functional constraint on the evolution of the DNA sequences and purifying selection, which appears to be reduced in the first extracellular loop of 12 closely related orthologues. The 31 full-size sequences were examined for potential domain-specific intramolecular coevolution. This revealed evidence for concerted evolution of all three cytoplasmic domains with each other and the C-terminal cytoplasmic tail, suggesting interplay of all intracellular domains for MLO function.     

Positive selection of three chitinase genes of the family 18 of glycoside hydrolases in mammals

The digestive enzyme chitinase degrades chitin, and is found in a wide range of organisms, from prokaryotes to eukaryotes. Although mammals cannot synthesize or assimilate chitin, several proteins of the glycoside hydrolase (GH) chitinase family GH18, including some with enzymatic activity, have recently been identified from mammalian genomes. Consequently, there is growing interest in molecular evolution of this family of proteins. Here we report on the use of maximum likelihood methods to test for evidence of positive selection in three genes of the chitinase family GH18, all of which are found in mammals. These focal genes are CHIA, CHIT1 and CHI3L1, which encode the chitinase proteins acidic mammalian chitinase, chitotriosidase and cartilage protein 39, respectively. The results of our analyses indicate that each of these genes has undergone independent selective pressure in their evolution. Additionally, we have found evidence of a signature of positive natural selection, with most sites identified as being subject to adaptive evolution located in the catalytic domain. Our results suggest that positive selection on these genes stems from their function in digestion and/or immunity.     

对金缕梅科现代分类系统的评述

为了进一步研究金缕梅科的系统与进化,作者详细介绍了该科的分类历史及各个分类系统;根据现代植物系统学研究的原理和方法,着重对金缕梅科的５个现代主要分类系统,Ｈａｒｍｓ（１９３０）,张宏达（１９７３,１９７９）,Ｂｏｇｌｅｅｔａｌ．（１９８０）,Ｅｎｄｒｅｓｓ（１９８９）和李建华（Ｌｉ,１９９７）进行了详细的分析、比较和评述,在此基础上提出自己的观点,认为李建华的分类系统有一定合理性,但他对个别属的处理和族的划分仍有不妥之处     

蕨类植物MADS盒基因研究概况

MADS盒基因是生物重要的调控基因家族.简述了MADS盒基因的分类、分布和功能及种子植物MADS盒基因研究及一种苔藓植物的MADS盒基因概况,对目前从蕨类植物中分离定性的MADS盒基因与种子植物相比具有的特点及其演化关系进行了重点介绍.     

The molecular evolution of pituitary growth hormone prolactin and placental lactogen: A protein family showing variable rates of evolution

Summary Pituitary growth hormone and prolactin, together with the homologous placental hormones, comprise a family of related protein hormones. Complete or partial amino acid sequences of seven mammalian growth hormones, six mammalian prolactins and one placental lactogen are available, and have been compared. A phylogenetic tree has been constructed which describes the relationships within the family. At least two gene duplications have occurred during the evolution of these proteins. Rates of evolution in the family have been quite variable, the overall rate of evolution having been apparently fairly slow, but having increased markedly on several occasions, most notably in the evolution of human (and, on the basis of immunological relationships, probably other primate) growth hormones and rat (and possibly other rodent) prolactins.     

Species-specific evolution of immune receptor tyrosine based activation motif-containing CEACAM1-related immune receptors in the dog

Background  

Although the impact of pathogens on the evolution of the mammalian immune system is still under debate, proteins, which both regulate immune responses and serve as cellular receptors for pathogens should be at the forefront of pathogen-driven host evolution. The CEA (carcinoembryonic antigen) gene family codes for such proteins and indeed shows tremendous species-specific variation between human and rodents. Since little is known about the CEA gene family in other lineages of placental mammals, we expected to gain new insights into the evolution of the rapidly diverging CEA family by analyzing the CEA family of the dog.     

Recent duplication and positive selection of the <Emphasis Type="Italic">GAGE</Emphasis> gene family

We report that the GAGE gene family of human Cancer/testis antigen (CTA) genes is likely to be in an early stage of its evolution. Members of this gene family are tandemly arranged on the X chromosome only in human, chimpanzee and macaque genomes and share a very high similarity. Phylogenetic trees show that the GAGE gene family began to duplicate after the split of human and chimpanzee. The estimated ages of the duplication events range from 4 million years ago to the present. The Ka/Ks values between the duplicates are significantly greater than 1, indicating that the mutation rate is higher in coding regions than non-coding regions of the genes, which suggests that the GAGE gene family is under positive selection. These findings indicate that the GAGE gene family may be a newly formed gene family undergoing rapid functional evolution. Yang Liu and Qiyun Zhu contributed equally to this work.     

A genome-wide phylogenetic reconstruction of family 1 UDP-glycosyltransferases revealed the expansion of the family during the adaptation of plants to life on land

For almost a decade, our knowledge on the organisation of the family 1 UDP‐glycosyltransferases (UGTs) has been limited to the model plant A. thaliana. The availability of other plant genomes represents an opportunity to obtain a broader view of the family in terms of evolution and organisation. Family 1 UGTs are known to glycosylate several classes of plant secondary metabolites. A phylogeny reconstruction study was performed to get an insight into the evolution of this multigene family during the adaptation of plants to life on land. The organisation of the UGTs in the different organisms was also investigated. More than 1500 putative UGTs were identified in 12 fully sequenced and assembled plant genomes based on the highly conserved PSPG motif. Analyses by maximum likelihood (ML) method were performed to reconstruct the phylogenetic relationships existing between the sequences. The results of this study clearly show that the UGT family expanded during the transition from algae to vascular plants and that in higher plants the clustering of UGTs into phylogenetic groups appears to be conserved, although gene loss and gene gain events seem to have occurred in certain lineages. Interestingly, two new phylogenetic groups, named O and P, that are not present in A. thaliana were discovered.     

Testing the phylogenetic position of a parasitic plant (Cuscuta, Convolvulaceae, asteridae): Bayesian inference and the parametric bootstrap on data drawn from three genomes

Previous findings on structural rearrangements in the chloroplast genome of Cuscuta (dodder), the only parasitic genus in the morning-glory family, Convolvulaceae, were attributed to its parasitic life style, but without proper comparison to related nonparasitic members of the family. Before molecular evolutionary questions regarding genome evolution can be answered, the phylogenetic problems within the family need to be resolved. However, the phylogenetic position of parasitic angiosperms and their precise relationship to nonparasitic relatives are difficult to infer. Problems are encountered with both morphological and molecular evidence. Molecular data have been used in numerous studies to elucidate relationships of parasitic taxa, despite accelerated rates of sequence evolution. To address the question of the position of the genus Cuscuta within Convolvulaceae, we generated a new molecular data set consisting of mitochondrial (atpA) and nuclear (RPB2) genes, and analyzed these data together with an existing chloroplast data matrix (rbcL, atpB, trnL-F, and psbE-J), to which an additional chloroplast gene (rpl2) was added. This data set was analyzed with an array of phylogenetic methods, including Bayesian analysis, maximum likelihood, and maximum parsimony. Further exploration of data was done by using methods of phylogeny hypothesis testing. At least two nonparasitic lineages are shown to diverge within the Convolvulaceae before Cuscuta. However, the exact sister group of Cuscuta could not be ascertained, even though many alternatives were rejected with confidence. Caution is therefore warranted when interpreting the causes of molecular evolution in Cuscuta. Detailed comparisons with nonparasitic Convolvulaceae are necessary before firm conclusions can be reached regarding the effects of the parasitic mode of life on patterns of molecular evolution in Cuscuta.