Kinetics of node splitting in evolving complex networks

Copyright @ 2012 Elsevier B.V. All rights reserved. This is a preprint version of the published article which can be accessed at the link below.We introduce a collection of complex networks generated by a combination of preferential attachment and a previously unexamined process of "splitting" nodes of degree k into k nodes of degree 1. Four networks are considered, each evolves at each time step by either preferential attachment, with probability p, or splitting with probability 1-p. Two methods of attachment are considered; first, attachment of an edge between a newly created node and an existing node in the network, and secondly by attachment of an edge between two existing nodes. Splitting is also considered in two separate ways; first by selecting each node with equal probability and secondly, selecting the node with probability proportional to its degree. Exact solutions for the degree distributions are found and scale-free structure is exhibited in those networks where the candidates for splitting are chosen with uniform probability, those that are chosen preferentially are distributed with a power law with exponential cut-off.Engineering and Physical Sciences Research Counci

Local rewiring rules for evolving complex networks

ERC is grateful for the nancial support of the EPSRC

Complex scale-free networks with tunable power-law exponent and clustering

This article is made available through the Brunel Open Access Publishing Fund. It is distributed under a Creative Commons License (http://creativecommons.org/licenses/by/3.0/). Copyright @ 2013 Elsevier B.V.We introduce a network evolution process motivated by the network of citations in the scientific literature. In each iteration of the process a node is born and directed links are created from the new node to a set of target nodes already in the network. This set includes mm “ambassador” nodes and ll of each ambassador’s descendants where mm and ll are random variables selected from any choice of distributions plpl and qmqm. The process mimics the tendency of authors to cite varying numbers of papers included in the bibliographies of the other papers they cite. We show that the degree distributions of the networks generated after a large number of iterations are scale-free and derive an expression for the power-law exponent. In a particular case of the model where the number of ambassadors is always the constant mm and the number of selected descendants from each ambassador is the constant ll, the power-law exponent is (2l+1)/l(2l+1)/l. For this example we derive expressions for the degree distribution and clustering coefficient in terms of ll and mm. We conclude that the proposed model can be tuned to have the same power law exponent and clustering coefficient of a broad range of the scale-free distributions that have been studied empirically.EPSR

Observational evidence of European summer weather patterns predictable from spring

Forecasts of summer weather patterns months in advance would be of great value for a wide range of applications. However, seasonal dynamical model forecasts for European summers have very little skill, particularly for rainfall. It has not been clear whether this low skill reflects inherent unpredictability of summer weather or, alternatively, is a consequence of weaknesses in current forecast systems. Here we analyze atmosphere and ocean observations and identify evidence that a specific pattern of summertime atmospheric circulation--the summer East Atlantic (SEA) pattern--is predictable from the previous spring. An index of North Atlantic sea-surface temperatures in March-April can predict the SEA pattern in July-August with a cross-validated correlation skill above 0.6. Our analyses show that the sea-surface temperatures influence atmospheric circulation and the position of the jet stream over the North Atlantic. The SEA pattern has a particularly strong influence on rainfall in the British Isles, which we find can also be predicted months ahead with a significant skill of 0.56. Our results have immediate application to empirical forecasts of summer rainfall for the United Kingdom, Ireland, and northern France and also suggest that current dynamical model forecast systems have large potential for improvement

Evidence for Horizontal Gene Transfer of Anaerobic Carbon Monoxide Dehydrogenases

Carbon monoxide (CO) is commonly known as a toxic gas, yet both cultivation studies and emerging genome sequences of bacteria and archaea establish that CO is a widely utilized microbial growth substrate. In this study, we determined the prevalence of anaerobic carbon monoxide dehydrogenases ([Ni,Fe]-CODHs) in currently available genomic sequence databases. Currently, 185 out of 2887, or 6% of sequenced bacterial and archaeal genomes possess at least one gene encoding [Ni,Fe]-CODH, the key enzyme for anaerobic CO utilization. Many genomes encode multiple copies of [Ni,Fe]-CODH genes whose functions and regulation are correlated with their associated gene clusters. The phylogenetic analysis of this extended protein family revealed six distinct clades; many clades consisted of [Ni,Fe]-CODHs that were encoded by microbes from disparate phylogenetic lineages, based on 16S rRNA sequences, and widely ranging physiology. To more clearly define if the branching patterns observed in the [Ni,Fe]-CODH trees are due to functional conservation vs. evolutionary lineage, the genomic context of the [Ni,Fe]-CODH gene clusters was examined, and superimposed on the phylogenetic trees. On the whole, there was a correlation between genomic contexts and the tree topology, but several functionally similar [Ni,Fe]-CODHs were found in different clades. In addition, some distantly related organisms have similar [Ni,Fe]-CODH genes. Thermosinus carboxydivorans was used to observe horizontal gene transfer (HGT) of [Ni,Fe]-CODH gene clusters by applying Kullback–Leibler divergence analysis methods. Divergent tetranucleotide frequency and codon usage showed that the gene cluster of T. carboxydivorans that encodes a [Ni,Fe]-CODH and an energy-converting hydrogenase is dissimilar to its whole genome but is similar to the genome of the phylogenetically distant Firmicute, Carboxydothermus hydrogenoformans. These results imply that T carboxydivorans acquired this gene cluster via HGT from a relative of C. hydrogenoformans

Social dilemmas in an online social network: the structure and evolution of cooperation

We investigate two paradigms for studying the evolution of cooperation--Prisoner's Dilemma and Snowdrift game in an online friendship network obtained from a social networking site. We demonstrate that such social network has small-world property and degree distribution has a power-law tail. Besides, it has hierarchical organizations and exhibits disassortative mixing pattern. We study the evolutionary version of the two types of games on it. It is found that enhancement and sustainment of cooperative behaviors are attributable to the underlying network topological organization. It is also shown that cooperators can survive when confronted with the invasion of defectors throughout the entire ranges of parameters of both games. The evolution of cooperation on empirical networks is influenced by various network effects in a combined manner, compared with that on model networks. Our results can help understand the cooperative behaviors in human groups and society.Comment: 14 pages, 7 figure

Paleocene to Pliocene low-latitude, high-elevation basins of southern Tibet: implications for tectonic models of India-Asia collision, Cenozoic climate, and geochemical weathering

The elevation history of the Tibetan Plateau promises insight into the mechanisms and dynamics that develop and sustain high topography over tens of millions of years. We present the first nearly continuous Cenozoic elevation history from two sedimentary basins on the southern Tibetan Plateau within the latest Cretaceous to Eocene Gangdese arc. Oxygen-isotope and Δ47 clumped-isotope compositions of nonmarine carbonates allow us to constrain carbonate formation temperature and reconstruct the paleoprecipitation record of the Eocene to Pliocene Oiyug Basin and Paleocene to Eocene Penbo Basin. We exploit the systematic decrease of surface temperature and meteoric water δ18O values with elevation to derive paleoelevation estimates for these basins. Minimally altered and unaltered pedogenic and lacustrine carbonates from the Oiyug Basin yield Δ47, CDES (relative to the carbon dioxide equilibrium scale [CDES]) values of 0.625‰ to 0.755‰, which correspond to temperatures of 1−30 °C using a Δ47 thermometer for low-temperature carbonates. Similarly, the Penbo Basin yielded Δ47, CDES values of 0.701‰ to 0.726‰, corresponding to temperatures of 6−12 °C. The apparent evidence for survival of primary clumped-isotope values in the face of substantial burial and heating is an important result for the field of carbonate clumped-isotope thermometry. Our paleoelevation estimates for the Eocene to Pliocene Oiyug Basin (∼6.5−4.1 km) support previous evidence that high elevations were attained in southern Tibet by at least ca. 30 Ma. Stable-isotope results allow for the possibility of significant topographic subsidence during the Miocene as a result of regional extension. In the Penbo Basin, our paleoelevation estimates for the Paleocene to Eocene Nianbo Formation (4.4 +1.3/−1.7 km) and Eocene Pana Formation (4.1 +1.2/−1.6 km) extend the altitude record of the southern Tibetan Plateau to pre−India-Asia collision. These results support the “Lhasaplano” model of an Andean-type continental margin tectonic system. The rise of the Himalayas and Tibet is often invoked to understand isotopic proxies for global chemical weathering in the Cenozoic and has constrained the debate on the nature of CO2−climate−weathering feedbacks. The nature of the Tibetan paleoelevations from pre- to postcollision, as presented here, indicates that high relief at low latitude prevailed on the Asian margin much earlier than previously thought. Thus, high topography alone at low latitude is not sufficient to account for the Cenozoic weathering proxy record

Complete Genome Sequence of the Aerobic CO-Oxidizing Thermophile Thermomicrobium roseum

In order to enrich the phylogenetic diversity represented in the available sequenced bacterial genomes and as part of an “Assembling the Tree of Life” project, we determined the genome sequence of Thermomicrobium roseum DSM 5159. T. roseum DSM 5159 is a red-pigmented, rod-shaped, Gram-negative extreme thermophile isolated from a hot spring that possesses both an atypical cell wall composition and an unusual cell membrane that is composed entirely of long-chain 1,2-diols. Its genome is composed of two circular DNA elements, one of 2,006,217 bp (referred to as the chromosome) and one of 919,596 bp (referred to as the megaplasmid). Strikingly, though few standard housekeeping genes are found on the megaplasmid, it does encode a complete system for chemotaxis including both chemosensory components and an entire flagellar apparatus. This is the first known example of a complete flagellar system being encoded on a plasmid and suggests a straightforward means for lateral transfer of flagellum-based motility. Phylogenomic analyses support the recent rRNA-based analyses that led to T. roseum being removed from the phylum Thermomicrobia and assigned to the phylum Chloroflexi. Because T. roseum is a deep-branching member of this phylum, analysis of its genome provides insights into the evolution of the Chloroflexi. In addition, even though this species is not photosynthetic, analysis of the genome provides some insight into the origins of photosynthesis in the Chloroflexi. Metabolic pathway reconstructions and experimental studies revealed new aspects of the biology of this species. For example, we present evidence that T. roseum oxidizes CO aerobically, making it the first thermophile known to do so. In addition, we propose that glycosylation of its carotenoids plays a crucial role in the adaptation of the cell membrane to this bacterium's thermophilic lifestyle. Analyses of published metagenomic sequences from two hot springs similar to the one from which this strain was isolated, show that close relatives of T. roseum DSM 5159 are present but have some key differences from the strain sequenced

Coveting thy neighbors fitness as a means to resolve social dilemmas

In spatial evolutionary games the fitness of each individual is traditionally determined by the payoffs it obtains upon playing the game with its neighbors. Since defection yields the highest individual benefits, the outlook for cooperators is gloomy. While network reciprocity promotes collaborative efforts, chances of averting the impending social decline are slim if the temptation to defect is strong. It is therefore of interest to identify viable mechanisms that provide additional support for the evolution of cooperation. Inspired by the fact that the environment may be just as important as inheritance for individual development, we introduce a simple switch that allows a player to either keep its original payoff or use the average payoff of all its neighbors. Depending on which payoff is higher, the influence of either option can be tuned by means of a single parameter. We show that, in general, taking into account the environment promotes cooperation. Yet coveting the fitness of one's neighbors too strongly is not optimal. In fact, cooperation thrives best only if the influence of payoffs obtained in the traditional way is equal to that of the average payoff of the neighborhood. We present results for the prisoner's dilemma and the snowdrift game, for different levels of uncertainty governing the strategy adoption process, and for different neighborhood sizes. Our approach outlines a viable route to increased levels of cooperative behavior in structured populations, but one that requires a thoughtful implementation.Comment: 10 two-column pages, 5 figures; accepted for publication in Journal of Theoretical Biolog