An evolutionary analysis of the relationship between spite and altruism

We investigate the selective pressures on a social trait when evolution occurs in a population of constant size. We show that any social trait that is spiteful simultaneously qualifies as altruistic. In other words, any trait that reduces the fitness of less related individuals necessarily increases that of related ones. Our analysis demonstrates that the distinction between "Hamiltonian spite" and "Wilsonian spite" is not justified on the basis of fitness effects. We illustrate this general result with an explicit model for the evolution of a social act that reduces the recipient's survival ("harming trait"). This model shows that the evolution of harming is favoured if local demes are of small size and migration is low (philopatry). Further, deme size and migration rate determine whether harming evolves as a selfish strategy by increasing the fitness of the actor, or as a spiteful/altruistic strategy through its positive effect on the fitness of close kin.     

Phylogenetic and evolutionary analysis of the PLUNC gene family

The PLUNC family of human proteins are candidate host defense proteins expressed in the upper airways. The family subdivides into short (SPLUNC) and long (LPLUNC) proteins, which contain domains predicted to be structurally similar to one or both of the domains of bactericidal/permeability-increasing protein (BPI), respectively. In this article we use analysis of the human, mouse, and rat genomes and other sequence data to examine the relationships between the PLUNC family proteins from humans and other species, and between these proteins and members of the BPI family. We show that PLUNC family clusters exist in the mouse and rat, with the most significant diversification in the locus occurring for the short PLUNC family proteins. Clear orthologous relationships are established for the majority of the proteins, and ambiguities are identified. Completion of the prediction of the LPLUNC4 proteins reveals that these proteins contain approximately a 150-residue insertion encoded by an additional exon. This insertion, which is predicted to be largely unstructured, replaces the structure homologous to the 40s hairpin of BPI. We show that the exon encoding this region is anomalously variable in size across the LPLUNC proteins, suggesting that this region is key to functional specificity. We further show that the mouse and human PLUNC family orthologs are evolving rapidly, which supports the hypothesis that these proteins are involved in host defense. Intriguingly, this rapid evolution between the human and mouse sequences is replaced by intense purifying selection in a large portion of the N-terminal domain of LPLUNC4. Our data provide a basis for future functional studies of this novel protein family.     

Phylogenetic and evolutionary analysis of Vibrio parahaemolyticus and Vibrio alginolyticus isolates based on toxR gene sequence

The Vibrio genus contains a large number of closely related bacterial species differing, in some cases, less than 1% in 16S rRNA gene sequence. The present study evaluated the usefulness of toxR gene for phylogenetic and evolution analysis on Vibrio isolates of environmental or clinical origin belonging to the two closely related species V. parahaemolyticus and V. alginolyticus. The phylogenetic analysis based on toxR gene, contrary to 16S rRNA gene, allowed a clear differentiation of the isolates belonging to the two species and showed the presence of two separate, statistically supported clusters in V. alginolyticus (subgroup A and B). Such division, partially reflected in the biochemical features of the isolates, could not be explained by spatial and/or temporal distance in the isolation, leading to the hypothesis of two distinct, co-existing clusters in the V. alginolyticus isolates analysed. The evolutionary analysis on the toxR sequence showed that while the substitutions inferred from the alignment of V. parahaemolyticus are best explained by the negative/neutral selection model, in V. alginolyticus--and particularly in subgroup B--is acting a positive evolutionary pressure. The site detected as under diversifying selection (P164L) could be related to conformational changes of ToxR protein.     

16SrDNA同源性所揭示的双歧杆菌与有关细菌的亲缘关系

本研究测定了低ＧＣ含量的双歧杆菌（Ｂｉｆｉｄｏｂａｃｔｅｒｉｕｍ ｉｎｏｐｉｎａｔｕｍ）和新种Ｂ。ｔｈｅｒｍｏｃｉ．ｄｏｐｈｉｌｕｍ的１６ＳｒＤＮＡ全序列,在同另外１９个双歧杆菌及８个相关细菌的１６ＳｒＮＡ同源笥分析的基础上构建了系统发育树。结果表明：除低ＧＣ含蜈的Ｂ．ｉｎｏｐｉｎａｔｕｍ外,所有双杆菌的种在１６ＳｒＤＮＡ序列相似性≥８２％的水平上聚类为一个簇群。尽管Ｂ．ｉｎｏｐｉｎａｉｕｍ与其它     

Phylogenetic analyses and evolutionary timescale of Coleoptera based on mitochondrial sequence

Coleopteran phylogeny was analysed using mitochondrial genome (mitogenome) sequence. The optimal tree topology was given by the dataset consisted of all coding genes except for the exclusion of the 3rd codon sites (mtDNA12) using Bayesian Inference Method. This topology supports the monophyly of four suborders, and the sister group relationship between Adephaga and Myxophaga and between Polyphaga and Archostemata. In Polyphaga, Cucujiformia and Elateroidea formed independent node respectively, the remaining species grouped together except for Cyphon sp, among which, only Cucujiformia and Scarabaeiformia were supported as monophyletic group, respectively. Within Cucujiformia, the monophyly of Chrysomeloidea, Curculionoidea and Tenebrionoidea were supported respectively, among which Tenebrionoidea occupied the basal position of Cucujiformia. Cleroidea grouped together with Bothrideridae and Coccinellidae, and formed an independent node, which lead to the paraphyly of Cucujoidea. The monophyly of Elateriformia was not supported because of the division of Scirtoidea and Buprestoidea. Furthermore, using a Bayesian relaxed clock calibrated with fossil data, we estimated that most superfamilies within Polyphaga originated in the Jurassic period.     

Phylogenetic analysis based evolutionary study of 16S rRNA in known Pseudomonas sp

Molecular evolution analysis of 16S rRNA sequences of native Pseudomonas strains and different fluorescent pseudomonads wereconducted on the basis of Molecular Evolutionary Genetics Analysis version 5.2 (MEGA5.2). Topological evaluations showcommon origin for native strains with other known strains with available sequences at GenBank database. Phylogenetic affiliationof different Pseudomonas sp based on 16S rRNA gene shows that molecular divergence contributes to the genetic diversity ofPseudomonas sp. Result indicate direct dynamic interactions with the rhizospheric pathogenic microbial community. The selectionpressure acting on 16S rRNA gene was related to the nucleotide diversity of Pseudomonas sp in soil rhizosphere community amongdifferent agricultural crops. Besides, nucleotide diversity among the whole population was very low and tajima test statistic value(D) was also slightly positive (Tajima׳s test statistics D value 0.351). This data indicated increasing trends of infection of soil-bornepathogens under gangetic-alluvial regions of West Bengal due to high degree of nucleotide diversity with decreased population ofplant growth promoting rhizobacteria like fluorescent Pseudomonads in soil.     

Phylogenetic and evolutionary analysis of the septin protein family in metazoan

Septins, a conserved family of cytoskeletal GTP-binding proteins, were presented in diverse eukaryotes. Here, a comprehensive phylogenetic and evolutionary analysis for septin proteins in metazoan was carried out. First, we demonstrated that all septin proteins in metazoan could be clustered into four subgroups, and the representative homologue of every subgroup was presented in the non-vertebrate chordate Ciona intestinalis, indicating that the emergence of the four septin subgroups should have occurred prior to divergence of vertebrates and invertebrates, and the expansion of the septin gene number in vertebrates was mainly by the duplication of pre-existing genes rather than by the appearance of new septin subgroup. Second, the direct orthologues of most human septins existed in zebrafish, which suggested that human septin gene repertoire was mainly formed by as far as before the split between fishes and land vertebrates. Third, we found that the evolutionary rate within septin family in mammalian lineage varies significantly, human SEPT1, SEPT 10, SEPT 12, and SEPT 14 displayed a relative elevated evolutionary rate compared with other septin members. Our data will provide new insights for the further function study of this protein family.     

Phylogenetic concordance analysis shows an emerging pathogen is novel and endemic

Distinguishing whether pathogens are novel or endemic is critical for controlling emerging infectious diseases, an increasing threat to wildlife and human health. To test the endemic vs. novel pathogen hypothesis, we present a unique analysis of intraspecific host-pathogen phylogenetic concordance of tiger salamanders and an emerging Ranavirus throughout Western North America. There is significant non-concordance of host and virus gene trees, suggesting pathogen novelty. However, non-concordance has likely resulted from virus introductions by human movement of infected salamanders. When human-associated viral introductions are excluded, host and virus gene trees are identical, strongly supporting coevolution and endemism. A laboratory experiment showed an introduced virus strain is significantly more virulent than endemic strains, likely due to artificial selection for high virulence. Thus, our analysis of intraspecific phylogenetic concordance revealed that human introduction of viruses is the mechanism underlying tree non-concordance and possibly disease emergence via artificial selection.     

分子绝对进化速率与物种分歧时间之间的定量关系

通过对美国国家生物技术信息中心数据库Gen Bank提供的一些蛋白质和核苷酸序列进行比对和分析,发现生物分子绝对进化速率k与进化时间或物种分歧时间t之间存在下列定量关系:lnk=-Ea/Rt+lnK0,式中Ea为位点突变活化能,k0为分子极限绝对进化速率,R为常数,并对其生物学意义进行了初步的探讨;数据分析还揭示出物种的分子极限绝对进化速率与进化时间或物种分歧时间之间也服从相似的定量公式,也就是说生物分子进化过程可能同时受到序列位点突变和控制物种分子极限绝对进化速率进化的两个"分子钟"作用,即存在"双重分子钟"现象。     

Phylogenetic analysis and evolutionary origins of DNA polymerase X-family members

Mammalian DNA polymerase (pol) β is the founding member of a large group of DNA polymerases now termed the X-family. DNA polymerase β has been kinetically, structurally, and biologically well characterized and can serve as a phylogenetic reference. Accordingly, we have performed a phylogenetic analysis to understand the relationship between pol β and other members of the X-family of DNA polymerases. The bacterial X-family DNA polymerases, Saccharomyces cerevisiae pol IV, and four mammalian X-family polymerases appear to be directly related. These enzymes originated from an ancient common ancestor characterized in two Bacillus species. Understanding distinct functions for each of the X-family polymerases, evolving from a common bacterial ancestor is of significant interest in light of the specialized roles of these enzymes in DNA metabolism.     

Revisit on the evolutionary relationship between alternative splicing and gene duplication

Gene duplications and alternative splicing (AS) isoforms are two widespread types of genetic variations that can facilitate diversification of protein function. A number of studies claimed that after gene duplication, two AS isoforms with differential functions can be 'fixed', respectively, in each of the duplicate copies. This simple 'functional-sharing' hypothesis was recently challenged by Roux and Robinson-Rechavi (2011). Instead, they proposed a more sophisticated hypothesis, invoking that less alternative splicing genes tend to be duplicated more frequently, and single-copy genes are younger than duplicate genes, or the 'duplicability-age' hypothesis for short. In this letter, we show that all these genome-wide analyses of AS isoforms actually did not provide clear-cut evidence to nullify the basic idea of functional-sharing hypothesis. After updating our understanding of genome-wide alternative splicing, duplicability and CNV (copy number variation), we argue that the foundation of the duplicability-age hypothesis remains to be justified carefully. Finally, we suggest that a better approach to resolving this controversy is the correspondence analysis of indels (insertions and deletions) between duplicate genes to the genomic exon-intron structure, which can be used to experimentally test the effect of functional-sharing hypothesis.     

Phylogenetic analysis based on spectral methods

Whole-genome or multiple gene phylogenetic analysis is of interest since single gene analysis often results in poorly resolved trees. Here, the use of spectral techniques for analyzing multigene data sets is explored. The protein sequences are treated as categorical time series, and a measure of similarity between a pair of sequences, the spectral covariance, is based on the common periodicity between these two sequences. Unlike the other methods, the spectral covariance method focuses on the relationship between the sites of genetic sequences. By properly scaling the dissimilarity measures derived from different genes between a pair of species, we can use the mean of these scaled dissimilarity measures as a summary statistic to measure the taxonomic distances across multiple genes. The methods are applied to three different data sets, one noncontroversial and two with some dispute over the correct placement of the taxa in the tree. Trees are constructed using two distance-based methods, BIONJ and FITCH. A variation of block bootstrap sampling method is used for inference. The methods are able to recover all major clades in the corresponding reference trees with moderate to high bootstrap support. Through simulations, we show that the covariance-based methods effectively capture phylogenetic signal even when structural information is not fully retained. Comparisons of simulation results with the bootstrap permutation results indicate that the covariance-based methods are fairly robust under perturbations in sequence similarity but more sensitive to perturbations in structural similarity.     

基于细胞色素b基因序列的东亚鳜类系统发育关系

鳜类为东亚特有类群。为验证东亚鳜类的单系起源,解决其分类划分的争议,本文采用特异性引物PCR扩增法获得了鳜类中鳜、大眼鳜、斑鳜、暗鳜、波纹鳜、长体鳜细胞色素b基因的全长序列,结合GenBank中日本少鳞鳜、朝鲜少鳞鳜和中国少鳞鳜的序列,初步构建了东亚鳜类种间的系统发育关系。NJ树和MP树均一致表明,鳜类为单系类群,可分为两支:鳜鱼群和少鳞鳜群。长体鳜未单独成群,而与鳜鱼属聚为一支,不支持将长体鳜单独设属,而应归入鳜鱼属。鳜鱼群中,MP树推测的长体鳜、暗鳜较为原始,鳜、大眼鳜、斑鳜和波纹鳜为特化种类的系统关系假设与其形态、生态特征表型进化较为一致。少鳞鳜群中,中国少鳞鳜与朝鲜少鳞鳜为姐妹种,再与日本少鳞鳜构成姐妹群的系统关系与其地理分布格局较为一致。本研究结果可为深入探讨鳜类物种有效性、系统分类位置及生物地理学提供依据。     

Phylogenetic relationship between Dermanyssus gallinae populations in European countries based on mitochondrial COI gene sequences

Phylogenetic analysis of Dermanyssus gallinae mites originating from UK, France and Italy was performed using partial amplification of the mitochondrial COI gene. Results showed that UK samples reveal the greatest variation and diversity and are linked to one of the French populations highlighting North–South genetic transitions in European red mite populations. Intra-farm variations between mite samples highlighted the diversity between national populations and possibly its origin from the different chemical strategies used in each country.     

The Tic20 gene family: Phylogenetic analysis and evolutionary considerations

Tic20 is a polytopic protein of the inner envelope membrane of chloroplasts, and it is proposed to act as a translocation channel during chloroplast protein import. By analyzing 29 sequences from diverse organisms, it was evident that Tic20-related proteins form two distinct clades, termed Group 1 and Group 2. The former group includes canonical Tic20 proteins that are essential for chloroplast development, while members of the latter are of unknown function. An increased evolutionary rate, in connection with adaptation to terrestrial life, was detected in Group 1. Interestingly, the sub-cellular (genomic) localization of genes coding for Group 1 proteins differs between evolutionary lineages.Key words: Arabidopsis, chloroplast protein import, plastids, protein targeting, Tic20     

Phylogenetical relationship based on groE genes among phenotypically related Enterobacter,Pantoea, Klebsiella,Serratia and Erwinia species

In an attempt to define the phylogenetical relationship among 17 phenotypically related species of genera Enterobacter, Pantoea, Serratia, Klebsiella and Erwinia, we determined almost all of their groE operon sequences using the polymerase chain reaction direct sequencing method. The number of nucleotide substitutions per site was 0.12+/-0.030. The value was 3.6-fold higher than that of 16S rDNA. As a result, we were successful in constructing molecular phylogenetic trees which had a finer resolution than that based on the 16S rDNA sequences. The phylogenetic trees based on the nucleotide sequences and deduced amino acid sequences of groE operons indicated that the members of genera Enterobacter, Pantoea and Klebsiella were closely related to each other, while Serratia and Erwinia species except Erwinia carotovora, made distinct clades. The close relationship between Enterobacter aerogenes and Klebsiella pneumoniae, that had been suggested by biochemical tests and DNA hybridization, was also supported by our molecular phylogenetic trees.     

Phylogenetic analysis and molecular signatures defining a monophyletic clade of heterocystous cyanobacteria and identifying its closest relatives

Detailed phylogenetic and comparative genomic analyses are reported on 140 genome sequenced cyanobacteria with the main focus on the heterocyst-differentiating cyanobacteria. In a phylogenetic tree for cyanobacteria based upon concatenated sequences for 32 conserved proteins, the available cyanobacteria formed 8–9 strongly supported clades at the highest level, which may correspond to the higher taxonomic clades of this phylum. One of these clades contained all heterocystous cyanobacteria; within this clade, the members exhibiting either true (Nostocales) or false (Stigonematales) branching of filaments were intermixed indicating that the division of the heterocysts-forming cyanobacteria into these two groups is not supported by phylogenetic considerations. However, in both the protein tree as well as in the 16S rRNA gene tree, the akinete-forming heterocystous cyanobacteria formed a distinct clade. Within this clade, the members which differentiate into hormogonia or those which lack this ability were also separated into distinct groups. A novel molecular signature identified in this work that is uniquely shared by the akinete-forming heterocystous cyanobacteria provides further evidence that the members of this group are specifically related and they shared a common ancestor exclusive of the other cyanobacteria. Detailed comparative analyses on protein sequences from the genomes of heterocystous cyanobacteria reported here have also identified eight conserved signature indels (CSIs) in proteins involved in a broad range of functions, and three conserved signature proteins, that are either uniquely or mainly found in all heterocysts-forming cyanobacteria, but generally not found in other cyanobacteria. These molecular markers provide novel means for the identification of heterocystous cyanobacteria, and they provide evidence of their monophyletic origin. Additionally, this work has also identified seven CSIs in other proteins which in addition to the heterocystous cyanobacteria are uniquely shared by two smaller clades of cyanobacteria, which form the successive outgroups of the clade comprising of the heterocystous cyanobacteria in the protein trees. Based upon their close relationship to the heterocystous cyanobacteria, the members of these clades are indicated to be the closest relatives of the heterocysts-forming cyanobacteria.     

Phylogenetic analysis and evolutionary studies of plant carotenoid cleavage dioxygenase gene

The oxidative breakdown of carotenoid evidences the formation of apocarotenoids through carotenoid cleavage dioxygenases (CCDs). Numerous CCDs and apocarotenoids have been identified and characterized in plants. Using available sequence data, a study was performed to investigate the phylogenetic relationship among CCD genes and to statistically estimate the sequence conservation and functional divergence. In total, 77 genes were identified from 39 species belonging to 21 families. Our result of phylogenetic analysis indicated the existence of well-conserved subfamilies. Moreover, comparative genomic analysis showed that the gene structures of the CCDs were highly conserved across some different lineage species. Through functional divergence analysis, a substantial divergence was found between CCD subfamilies. In addition, examination of the site-specific profile revealed the critical amino acid residues accounting for functional divergence. This study mainly focused on the evolution of CCD genes and their functional divergence which may deliver an initial step for further experimental verifications.     

Phylogenetic and evolutionary analysis of NBS-encoding genes in Rosaceae fruit crops

Phylogenetic relationships of the nucleotide binding site (NBS)-encoding resistance gene homologues (RGHs) among 12 species in five genera of Rosaceae fruit crops were evaluated. A total of 228 Rosaceous RGHs were deeply separated into two distinct clades, designated as TIR (sequences within this clade containing a Toll Interleukin-1 Receptor domain) and NonTIR (sequences lacking a TIR domain). Most Rosaceous RGH genes were phylogenetically distinct from Arabidopsis, Rice or Pine genes, except for a few Rosaceous members which grouped closely with Arabidopsis genes. Within Rosaceae, sequences from multiple species were often phylogenetically clustered together, forming heterogenous groups, however, apple- and chestnut rose-specific groups really exist. Gene duplication followed by sequence divergence were proposed as the mode for the evolution of a large number of distantly or closely related RGH genes in Rosaceae, and this mode may play a role in the generation of new resistance specificity. Positively selected sites within NBS-coding region were detected and thus nucleotide variation within NBS domain may function in determining disease resistance specificity. This study also discusses the synteny of a genomic region that encompass powdery mildew resistance locus among Malus, Prunus and Rosa, which may have potential use for fruit tree disease breeding and important gene cloning.