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Evolutionary dynamics

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https://www.readbyqxmd.com/read/28109326/from-the-evolution-of-protein-sequences-able-to-resist-self-assembly-to-the-prediction-of-aggregation-propensity
#1
F Bemporad, M Ramazzotti
Folding of polypeptide chains into biologically active entities is an astonishingly complex process, determined by the nature and the sequence of residues emerging from ribosomes. While it has been long believed that evolution has pressed genomes so that specific sequences could adopt unique, functional three-dimensional folds, it is now clear that complex protein machineries act as quality control system and supervise folding. Notwithstanding that, events such as erroneous folding, partial folding, or misfolding are frequent during the life of a cell or a whole organism, and they can escape controls...
2017: International Review of Cell and Molecular Biology
https://www.readbyqxmd.com/read/28108681/re-emergence-of-methicillin-susceptibility-in-a-resistant-lineage-of-staphylococcus-aureus
#2
Alice Ledda, James R Price, Kevin Cole, Martin J Llewelyn, Angela M Kearns, Derrick W Crook, John Paul, Xavier Didelot
OBJECTIVES: MRSA is a leading cause of hospital-associated infection. Acquired resistance is encoded by the mecA gene or its homologue mecC, but little is known about the evolutionary dynamics involved in gain and loss of resistance. The objective of this study was to obtain an expanded understanding of Staphylococcus aureus methicillin resistance microevolution in vivo, by focusing on a single lineage. METHODS: We compared the whole-genome sequences of 231 isolates from a single epidemic lineage [clonal complex 30 (CC30) and spa-type t018] of S...
January 20, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28108445/multi-rate-poisson-tree-processes-for-single-locus-species-delimitation-under-maximum-likelihood-and-markov-chain-monte-carlo
#3
P Kapli, S Lutteropp, J Zhang, K Kobert, P Pavlidis, A Stamatakis, T Flouri
MOTIVATION: In recent years, molecular species delimitation has become a routine approach for quantifying and classifying biodiversity. Barcoding methods are of particular importance in large-scale surveys as they promote fast species discovery and biodiversity estimates. Among those, distance-based methods are the most common choice as they scale well with large datasets; however, they are sensitive to similarity threshold parameters and they ignore evolutionary relationships. The recently introduced "Poisson Tree Processes" (PTP) method is a phylogeny-aware approach that does not rely on such thresholds...
January 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28108306/bone-remodeling-as-a-spatial-evolutionary-game
#4
Marc D Ryser, Kevin A Murgas
Bone remodeling is a complex process involving cell-cell interactions, biochemical signaling and mechanical stimuli. Early models of the biological aspects of remodeling were non-spatial and focused on the local dynamics at a fixed location in the bone. Several spatial extensions of these models have been proposed, but they generally suffer from two limitations: first, they are not amenable to analysis and are computationally expensive, and second, they neglect the role played by bone-embedded osteocytes. To address these issues, we developed a novel model of spatial remodeling based on the principles of evolutionary game theory...
January 17, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28108305/efficient-dynamic-programming-algorithm-with-prior-knowledge-for-protein-%C3%AE-strand-alignment
#5
Mostafa Sabzekar, Mahmoud Naghibzadeh, Javad Sadri
One of the main tasks towards the prediction of protein β-sheet structure is to predict the native alignment of β-strands. The alignment of two β-strands defines similar regions that may reflect functional, structural, or evolutionary relationships between them. Therefore, any improvement in β-strands alignment not only reduces the computational search space but also improves β-sheet structure prediction accuracy. To define the alignment scores, previous studies utilized predicted residue-residue contacts (contact maps)...
January 17, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28107053/diversity-and-coevolutionary-dynamics-in-high-dimensional-phenotype-spaces
#6
Michael Doebeli, Iaroslav Ispolatov
We study macroevolutionary dynamics by extending microevolutionary competition models to long timescales. It has been shown that for a general class of competition models, gradual evolutionary change in continuous phenotypes (evolutionary dynamics) can be nonstationary and even chaotic when the dimension of the phenotype space in which the evolutionary dynamics unfold is high. It has also been shown that evolutionary diversification can occur along nonequilibrium trajectories in phenotype space. We combine these lines of thinking by studying long-term coevolutionary dynamics of emerging lineages in multidimensional phenotype spaces...
February 2017: American Naturalist
https://www.readbyqxmd.com/read/28106109/center-of-mass-in-complex-networks
#7
Chuanji Fu, Yachun Gao, Shimin Cai, Hongchun Yang, Chun Yang
Network dynamics is always a big challenge in nonlinear dynamics. Although great advancements have been made in various types of complex systems, an universal theoretical framework is required. In this paper, we introduce the concept of center of 'mass' of complex networks, where 'mass' stands for node importance or centrality in contrast to that of particle systems, and further prove that the phase transition and evolutionary state of the system can be characterized by the activity of center of 'mass'. The steady states of several complex networks (gene regulatory networks and epidemic spreading systems) are then studied by analytically calculating the decoupled equation of the dynamic activity of center of 'mass', which is derived from the dynamic equation of the complex networks...
January 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28104906/interrogating-open-issues-in-cancer-precision-medicine-with-patient-derived-xenografts
#8
Annette T Byrne, Denis G Alférez, Frédéric Amant, Daniela Annibali, Joaquín Arribas, Andrew V Biankin, Alejandra Bruna, Eva Budinská, Carlos Caldas, David K Chang, Robert B Clarke, Hans Clevers, George Coukos, Virginie Dangles-Marie, S Gail Eckhardt, Eva Gonzalez-Suarez, Els Hermans, Manuel Hidalgo, Monika A Jarzabek, Steven de Jong, Jos Jonkers, Kristel Kemper, Luisa Lanfrancone, Gunhild Mari Mælandsmo, Elisabetta Marangoni, Jean-Christophe Marine, Enzo Medico, Jens Henrik Norum, Héctor G Palmer, Daniel S Peeper, Pier Giuseppe Pelicci, Alejandro Piris-Gimenez, Sergio Roman-Roman, Oscar M Rueda, Joan Seoane, Violeta Serra, Laura Soucek, Dominique Vanhecke, Alberto Villanueva, Emilie Vinolo, Andrea Bertotti, Livio Trusolino
Patient-derived xenografts (PDXs) have emerged as an important platform to elucidate new treatments and biomarkers in oncology. PDX models are used to address clinically relevant questions, including the contribution of tumour heterogeneity to therapeutic responsiveness, the patterns of cancer evolutionary dynamics during tumour progression and under drug pressure, and the mechanisms of resistance to treatment. The ability of PDX models to predict clinical outcomes is being improved through mouse humanization strategies and the implementation of co-clinical trials, within which patients and PDXs reciprocally inform therapeutic decisions...
January 20, 2017: Nature Reviews. Cancer
https://www.readbyqxmd.com/read/28103791/high-virulence-does-not-necessarily-impede-viral-adaptation-to-a-new-host-a-case-study-using-a-plant-rna-virus
#9
Anouk Willemsen, Mark P Zwart, Santiago F Elena
BACKGROUND: Theory suggests that high virulence could hinder between-host transmission of microparasites, and that virulence therefore will evolve to lower levels. Alternatively, highly virulent microparasites could also curtail host development, thereby limiting both the host resources available to them and their own within-host effective population size. In this case, high virulence might restrain the mutation supply rate and increase the strength with which genetic drift acts on microparasite populations...
January 19, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28103248/effect-of-the-latent-reservoir-on-the-evolution-of-hiv-at-the-within-and-between-host-levels
#10
Hilje M Doekes, Christophe Fraser, Katrina A Lythgoe
The existence of long-lived reservoirs of latently infected CD4+ T cells is the major barrier to curing HIV, and has been extensively studied in this light. However, the effect of these reservoirs on the evolutionary dynamics of the virus has received little attention. Here, we present a within-host quasispecies model that incorporates a long-lived reservoir, which we then nest into an epidemiological model of HIV dynamics. For biologically plausible parameter values, we find that the presence of a latent reservoir can severely delay evolutionary dynamics within a single host, with longer delays associated with larger relative reservoir sizes and/or homeostatic proliferation of cells within the reservoir...
January 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28100827/insights-into-resource-consumption-cross-feeding-system-collapse-stability-and-biodiversity-from-an-artificial-ecosystem
#11
Yu Liu, David Sumpter
Community ecosystems at very different levels of biological organization often have similar properties. Coexistence of multiple species, cross-feeding, biodiversity and fluctuating population dynamics are just a few of the properties that arise in a range of ecological settings. Here we develop a bottom-up model of consumer-resource interactions, in the form of an artificial ecosystem 'number soup', which reflects basic properties of many bacterial and other community ecologies. We demonstrate four key properties of the number soup model: (i) communities self-organize so that all available resources are fully consumed; (ii) reciprocal cross-feeding is a common evolutionary outcome, which evolves in a number of stages, and many transitional species are involved; (iii) the evolved ecosystems are often 'robust yet fragile', with keystone species required to prevent the whole system from collapsing; (iv) non-equilibrium dynamics and chaotic patterns are general properties, readily generating rich biodiversity...
January 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28100817/mechanical-sensitivity-and-the-dynamics-of-evolutionary-rate-shifts-in-biomechanical-systems
#12
Martha M Muñoz, Philip S L Anderson, S N Patek
The influence of biophysical relationships on rates of morphological evolution is a cornerstone of evolutionary theory. Mechanical sensitivity-the correlation strength between mechanical output and the system's underlying morphological components-is thought to impact the evolutionary dynamics of form-function relationships, yet has rarely been examined. Here, we compare the evolutionary rates of the mechanical components of the four-bar linkage system in the raptorial appendage of mantis shrimp (Order Stomatopoda)...
January 25, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28100168/effects-of-pleistocene-sea-level-fluctuations-on-mangrove-population-dynamics-a-lesson-from-sonneratia-alba
#13
Yuchen Yang, Jianfang Li, Shuhuan Yang, Xinnian Li, Lu Fang, Cairong Zhong, Norman C Duke, Renchao Zhou, Suhua Shi
BACKGROUND: A large-scale systematical investigation of the influence of Pleistocene climate oscillation on mangrove population dynamics could enrich our knowledge about the evolutionary history during times of historical climate change, which in turn may provide important information for their conservation. RESULTS: In this study, phylogeography of a mangrove tree Sonneratia alba was studied by sequencing three chloroplast fragments and seven nuclear genes. A low level of genetic diversity at the population level was detected across its range, especially at the range margins, which was mainly attributed to the steep sea-level drop and associated climate fluctuations during the Pleistocene glacial periods...
January 18, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28099782/back-to-basics-using-colour-polymorphisms-to-study-evolutionary-processes
#14
Erik I Svensson
Here, I suggest that colour polymorphic study systems have been underutilized to answer general questions about evolutionary process, such as morph frequency-dynamics between generations and population divergence in morph frequencies. Colour polymorphisms can be used to study fundamental evolutionary processes like frequency-dependent selection, gene flow, recombination and correlational selection for adaptive character combinations. However, many previous studies of colour polymorphism often suffer from weak connections to population genetic theory...
January 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28098244/stochastic-evolution-in-populations-of-ideas
#15
Robin Nicole, Peter Sollich, Tobias Galla
It is known that learning of players who interact in a repeated game can be interpreted as an evolutionary process in a population of ideas. These analogies have so far mostly been established in deterministic models, and memory loss in learning has been seen to act similarly to mutation in evolution. We here propose a representation of reinforcement learning as a stochastic process in finite 'populations of ideas'. The resulting birth-death dynamics has absorbing states and allows for the extinction or fixation of ideas, marking a key difference to mutation-selection processes in finite populations...
January 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28096484/evolutionary-dynamics-of-pandemic-methicillin-sensitive-staphylococcus-aureus-st398-and-its-international-spread-via-routes-of-human-migration
#16
Anne-Catrin Uhlemann, Paul R McAdam, Sean B Sullivan, Justin R Knox, Hossein Khiabanian, Raul Rabadan, Peter R Davies, J Ross Fitzgerald, Franklin D Lowy
: Methicillin-susceptible Staphylococcus aureus (MSSA) accounts for the majority of S. aureus infections globally, and yet surprisingly little is known about its clonal evolution. We applied comparative whole-genome sequencing (WGS) analyses to epidemiologically and geographically diverse ST398-MSSA, a pandemic lineage affecting both humans and livestock. Bayesian phylogenetic analysis predicted divergence of human-associated ST398-MSSA ~40 years ago. Isolates from Midwestern pigs and veterinarians differed substantially from those in New York City (NYC)...
January 17, 2017: MBio
https://www.readbyqxmd.com/read/28094438/environmental-niche-conservatism-explains-the-accumulation-of-species-richness-in-mediterranean-hotspot-plant-genera
#17
Alexander Skeels, Marcel Cardillo
The causes of exceptionally high plant diversity in Mediterranean-climate biodiversity hotspots are not fully understood. We asked whether a mechanism similar to the tropical niche conservatism hypothesis could explain the diversity of four large genera (Protea, Moraea, Banksia, and Hakea) with distributions within and adjacent to the Greater Cape Floristic Region (South Africa) or the Southwest Floristic Region (Australia). Using phylogenetic and spatial data we estimated the environmental niche of each species, and reconstructed the mode and dynamics of niche evolution, and the geographic history, of each genus...
January 17, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28093338/a-virus-like-particle-vaccination-strategy-expands-its-tolerance-to-h3n2-antigenic-drift-by-enhancing-neutralizing-antibodies-against-hemagglutinin-stalk
#18
Ji-Rong Yang, Chieh-Yu Cheng, Chih-Yuan Chen, Chao-Hua Lin, Chuan-Yi Kuo, Hsiang-Yi Huang, Fu-Ting Wu, Yu-Chih Yang, Chia-Ying Wu, Ming-Tsan Liu, Pei-Wen Hsiao
Seasonal influenza viruses impact public health annually due to their continual evolution. However, the current inactivated seasonal vaccines provide poor protection against antigenically drifted viruses and require periodical reformulation through hit-and-miss predictions about which strains will circulate during the next season. To reduce the impact caused by vaccine mismatch, we investigated the drift-tolerance of virus-like particles (VLP) as an improved vaccine candidate. The cross-protective humoral immunity elicited by the H3N2-VLP vaccine constructed for the 2011-2012 season was examined against viruses isolated from 2010 to 2015 in Taiwan evolving chronologically through clades 1, 4, 5, 3B and 3C, as well as viruses that were circulating globally in 2005, 2007 and 2009...
January 13, 2017: Antiviral Research
https://www.readbyqxmd.com/read/28092596/a-general-framework-of-dynamic-constrained-multiobjective-evolutionary-algorithms-for-constrained-optimization
#19
Sanyou Zeng, Ruwang Jiao, Changhe Li, Xi Li, Jawdat S Alkasassbeh
A novel multiobjective technique is proposed for solving constrained optimization problems (COPs) in this paper. The method highlights three different perspectives: 1) a COP is converted into an equivalent dynamic constrained multiobjective optimization problem (DCMOP) with three objectives: a) the original objective; b) a constraint-violation objective; and c) a niche-count objective; 2) a method of gradually reducing the constraint boundary aims to handle the constraint difficulty; and 3) a method of gradually reducing the niche size aims to handle the multimodal difficulty...
January 16, 2017: IEEE Transactions on Cybernetics
https://www.readbyqxmd.com/read/28092573/environment-sensitivity-based-cooperative-co-evolutionary-algorithms-for-dynamic-multi-objective-optimization
#20
Biao Xu, Yong Zhang, Dunwei Gong, Yinan Guo, Miao Rong
Dynamic multi-objective optimization problems (DMOPs) not only involve multiple conflicting objectives, but these objectives may also vary with time, raising a challenge for researchers to solve them. This paper presents a cooperative co-evolutionary strategy based on environment sensitivities for solving DMOPs. In this strategy, a new method that groups decision variables is first proposed, in which all the decision variables are partitioned into two subcomponents according to their interrelation with environment...
January 16, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
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