Personality in the context of social networks

There is great interest in environmental effects on the development and evolution of animal personality traits. An important component of an individual's environment is its social environment. However, few studies look beyond dyadic relationships and try to place the personality of individuals in the context of a social network. Social network analysis provides us with many new metrics to characterize the social fine-structure of populations and, therefore, with an opportunity to gain an understanding of the role that different personalities play in groups, communities and populations regarding information or disease transmission or in terms of cooperation and policing of social conflicts. The network position of an individual is largely a consequence of its interactive strategies. However, the network position can also shape an individual's experiences (especially in the case of juveniles) and therefore can influence the way in which it interacts with others in future. Finally, over evolutionary time, the social fine-structure of animal populations (as quantified by social network analysis) can have important consequences for the evolution of personalities-an approach that goes beyond the conventional game-theoretic analyses that assumed random mixing of individuals in populations.     

Mining the genome and regulatory networks

A report on the 16th International Conference on Genome Informatics (GIW 2005), Yokohama, Japan, 19-21 December 2005.     

The zebrafish genome in context: ohnologs gone missing

Some zebrafish genes appear to lack an ortholog in the human genome and researchers often call them "novel" genes. The origin of many so-called "novel" genes becomes apparent when considered in the context of genome duplication events that occurred during evolution of the phylum Chordata, including two rounds at about the origin of the subphylum Vertebrata (R1 and R2) and one round before the teleost radiation (R3). Ohnologs are paralogs stemming from such genome duplication events, and some zebrafish genes said to be "novel" are more appropriately interpreted as "ohnologs gone missing", cases in which ohnologs are preserved differentially in different evolutionary lineages. Here we consider ohnologs present in the zebrafish genome but absent from the human genome. Reasonable hypotheses are that lineage-specific loss of ohnologs can play a role in establishing lineage divergence and in the origin of developmental innovations. How does the evolution of ohnologs differ from the evolution of gene duplicates arising from other mechanisms, such as tandem duplication or retrotransposition? To what extent do different major vertebrate lineages or different teleost lineages differ in ohnolog content? What roles do differences in ohnolog content play in the origin of developmental mechanisms that differ among lineages? This review explores these questions.     

Arabidopsis genome: life without notch

The complete genome sequence of the flowering plant Arabidopsis thaliana has been determined. New insights have come from comparisons between this sequence and genome sequences of other species, including those of cyanobacteria, yeast, worms and flies.     

Body mass dynamics of Daphnia in the context of life history theory: an approach based on contribution analysis

In this paper, we elaborate on the method of contribution analysis in relation to body mass dynamics which has been proposed recently (Polishchuk, Vijverberg, 2005. Oecologia. V. 144. P. 268-277). We suggest that contribution analysis as applied to body mass dynamics makes a bridge between production-energetic approach and life history theory. Production is conventionally divided into somatic and reproductive components, and our approach shows how to estimate the role (i.e. contributions) of these components in body mass dynamics. The pattern of contributions is further interpreted in terms of life history. The approach is applied to study body mass dynamics of the cladoceran Daphnia galeata in response to improving trophic conditions. The performance of the method is found to depend on the resolution of food concentrations, that is, on how many food concentrations are examined and how far they are spaced on the food concentration axis. When resolution is fine, a shift in resource allocation priorities is detected - from somatic component attracting more resources under harsh food conditions to reproduction attracting more resources under favorable conditions. However, when resolution is poor this pattern remains hidden. In that case, we observe roughly equal contributions of somatic and reproductive components to body mass dynamics.     

Analysis of the Thermotoga maritima genome combining a variety of sequence similarity and genome context tools

The proliferation of genome sequence data has led to the development of a number of tools and strategies that facilitate computational analysis. These methods include the identification of motif patterns, membership of the query sequences in family databases, metabolic pathway involvement and gene proximity. We re-examined the completely sequenced genome of Thermotoga maritima by employing the combined use of the above methods. By analyzing all 1877 proteins encoded in this genome, we identified 193 cases of conflicting annotations (10%), of which 164 are new function predictions and 29 are amendments of previously proposed assignments. These results suggest that the combined use of existing computational tools can resolve inconclusive sequence similarities and significantly improve the prediction of protein function from genome sequence.     

The origin of life in a cosmic context

The significance of examinations of the planets and their satellites, asteroids, comets and the interplanetary medium for the origin of life is assessed. It appears that the deprovincialization of biology must await the search for extraterrestrial life.     

A genome alignment algorithm based on compression

Background  

Traditional genome alignment methods consider sequence alignment as a variation of the string edit distance problem, and perform alignment by matching characters of the two sequences. They are often computationally expensive and unable to deal with low information regions. Furthermore, they lack a well-principled objective function to measure the performance of sets of parameters. Since genomic sequences carry genetic information, this article proposes that the information content of each nucleotide in a position should be considered in sequence alignment. An information-theoretic approach for pairwise genome local alignment, namely XMAligner, is presented. Instead of comparing sequences at the character level, XMAligner considers a pair of nucleotides from two sequences to be related if their mutual information in context is significant. The information content of nucleotides in sequences is measured by a lossless compression technique.     

基于密码对使用的基因组进化

以密码对使用偏好性和密码对中二核苷酸频率分别构建了系统发育树。发现用40种模式生物编码序列中密码对的二核苷酸频率构建的系统发育树,明显将生物按进化分成细菌,古菌,真核生物;用密码对使用偏好性指标构建的系统发育树与基于密码对中二核苷酸频率的系统发育树基本一致。结果表明密码对中二核苷酸组分是密码对偏好的决定因素之一。     

How the genome got a life span

In the space of little more than a decade, ideas of the human genome have shifted significantly, with the emergence of the notion that the genome of an individual changes with development, age, disease, environmental inputs, and time. This paper examines the emergence of the genome with a life span, one that experiences drift, instability, and mutability, and a host of other temporal changes. We argue that developments in chromatin biology have provided the basis for this genomic embodiment of experience and exposure. We analyze how time has come to matter for the genome through chromatin, providing analysis of examples in which the human life course is being explored as a set of material changes to chromatin. A genome with a life span aligns the molecular and the experiential in new ways, shifting ideas of life stages, their interrelation, and the temporality of health and disease.     

Knowledge diffusion and collaboration networks on life cycle assessment

Purpose  

The interest in life cycle assessment (LCA) studies has increased over the years, and one of the main ways of disseminating these studies is through the publication of articles in scientific journals. Coauthorship relations form a social network where it is possible to identify how research is organized and structured in a specific field of knowledge. This paper aims to show the spread of these studies and the configuration of a collaboration network based on coauthorship relations between researchers of LCA considering some properties of social networks.     

Gene sharing and genome evolution: networks in trees and trees in networks

Frequent lateral genetic transfer undermines the existence of a unique “tree of life” that relates all organisms. Vertical inheritance is nonetheless of vital interest in the study of microbial evolution, and knowing the “tree of cells” can yield insights into ecological continuity, the rates of change of different cellular characters, and the evolutionary plasticity of genomes. Notwithstanding within-species recombination, the relationships most frequently recovered from genomic data at shallow to moderate taxonomic depths are likely to reflect cellular inheritance. At the same time, it is clear that several types of ‘average signals’ from whole genomes can be highly misleading, and the existence of a central tendency must not be taken as prima facie evidence of vertical descent. Phylogenetic networks offer an attractive solution, since they can be formulated in ways that mitigate the misleading aspects of hybrid evolutionary signals in genomes. But the connections in a network typically show genetic relatedness without distinguishing between vertical and lateral inheritance of genetic material. The solution may lie in a compromise between strict tree-thinking and network paradigms: build a phylogenetic network, but identify the set of connections in the network that are potentially due to vertical descent. Even if a single tree cannot be unambiguously identified, choosing a subnetwork of putative vertical connections can still lead to drastic reductions in the set of candidate vertical hypotheses.     

Backbone phylogeny of Salix based on genome skimming dataOA

The genus Salix is a common component of the Northern Hemisphere dendroflora with important ecological and economic value. However, taxonomy and systematics of Salix is extremely difficult and relationships between main lineages, especially deep phylogenies, remain largely unresolved. In this study, we used genome-skimming, plastome assembly, and single-copy orthologs(SCOs) from 66 Salix accessions, along with publicly available plastome and sequence read archive(SRA) datasets to obtain a robust backbone phylogeny of Salix, clarify relationships between its main lineages, and gain a more precise understanding of the origin and diversification of this species-rich genus. The plastome and SCO datasets resolved Salix into two robust clades, with plastome-based phylogenies lacking inner resolution and SCO offering fully resolved phylogenies. Our results support the classification of Salix into five subgenera: Salix, Urbaniana, Triandrae, Longifoliae and Vetrix. We observed a significant acceleration in the diversification rate within the Chamaetia-Vetrix clade, while Salix exhibited increased rates of diversification spanning from the early Oligocene to the late Miocene. These changes coincided with contemporaneous tectonic and climate change events. Our results provide a foundation for future systematic and evolutionary studies of Salix. Additionally, we showed that genome skimming data is an efficient, rapid, and reliable approach for obtaining extensive genomic data for phylogenomic studies,enabling the comprehensive elucidation of Salix relationships.     

Self-similarity analysis of eubacteria genome based on weighted graph

We introduce a weighted graph model to investigate the self-similarity characteristics of eubacteria genomes. The regular treating in similarity comparison about genome is to discover the evolution distance among different genomes. Few people focus their attention on the overall statistical characteristics of each gene compared with other genes in the same genome. In our model, each genome is attributed to a weighted graph, whose topology describes the similarity relationship among genes in the same genome. Based on the related weighted graph theory, we extract some quantified statistical variables from the topology, and give the distribution of some variables derived from the largest social structure in the topology. The 23 eubacteria recently studied by Sorimachi and Okayasu are markedly classified into two different groups by their double logarithmic point-plots describing the similarity relationship among genes of the largest social structure in genome. The results show that the proposed model may provide us with some new sights to understand the structures and evolution patterns determined from the complete genomes.