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Evolutionary dynamics

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https://www.readbyqxmd.com/read/28327965/carbon-dating-cancer-defining-the-chronology-of-metastatic-progression-in-colorectal-cancer
#1
H Lote, I Spiteri, L Ermini, A Vatsiou, A Roy, A McDonald, N Maka, M Balsitis, N Bose, M Simbolo, A Mafficini, A Lampis, J C Hahne, F Trevisani, Z Eltahir, G Mentrasti, C Findlay, Eaj Kalkman, M Punta, B Werner, S Lise, A Aktipis, C Maley, M Greaves, C Braconi, J White, M Fassan, A Scarpa, A Sottoriva, N Valeri
Background: HASH(0x4907970) Patients often ask oncologists how long a cancer has been present before causing symptoms or spreading to other organs. The evolutionary trajectory of cancers can be defined using phylogenetic approaches but lack of chronological references makes dating the exact onset of tumours very challenging. Patients and Methods: HASH(0x49cfb48) Here we describe the case of a colorectal cancer patient presenting with synchronous lung metastasis and metachronous thyroid, chest wall and urinary tract metastases over the course of five years...
February 23, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28325942/comparative-genomics-reveals-contraction-in-olfactory-receptor-genes-in-bats
#2
Georgia Tsagkogeorga, Steven Müller, Christophe Dessimoz, Stephen J Rossiter
Gene loss and gain during genome evolution are thought to play important roles in adaptive phenotypic diversification. Among mammals, bats possess the smallest genomes and have evolved the unique abilities of powered flight and laryngeal echolocation. To investigate whether gene family evolution has contributed to the genome downsizing and phenotypic diversification in this group, we performed comparative evolutionary analyses of complete proteome data for eight bat species, including echolocating and non-echolocating forms, together with the proteomes of 12 other laurasiatherian mammals...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28325881/probabilistic-models-of-species-discovery-and-biodiversity-comparisons
#3
Stewart M Edie, Peter D Smits, David Jablonski
Inferring large-scale processes that drive biodiversity hinges on understanding the phylogenetic and spatial pattern of species richness. However, clades and geographic regions are accumulating newly described species at an uneven rate, potentially affecting the stability of currently observed diversity patterns. Here, we present a probabilistic model of species discovery to assess the uncertainty in diversity levels among clades and regions. We use a Bayesian time series regression to estimate the long-term trend in the rate of species description for marine bivalves and find a distinct spatial bias in the accumulation of new species...
March 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28323481/the-emergence-of-life-as-a-first-order-phase-transition
#4
Cole Mathis, Tanmoy Bhattacharya, Sara Imari Walker
It is well known that life on Earth alters its environment over evolutionary and geological timescales. An important open question is whether this is a result of evolutionary optimization or a universal feature of life. In the latter case, the origin of life would be coincident with a shift in environmental conditions. Here we present a model for the emergence of life in which replicators are explicitly coupled to their environment through the recycling of a finite supply of resources. The model exhibits a dynamic, first-order phase transition from nonlife to life, where the life phase is distinguished by selection on replicators...
March 2017: Astrobiology
https://www.readbyqxmd.com/read/28322874/reconstructing-the-genotype-to-fitness-map-for-the-bacterial-chemotaxis-network-and-its-emergent-behavioural-phenotypes
#5
Alberto Nakauma, G Sander van Doorn
The signal-transduction network responsible for chemotaxis in Escherichia coli has been characterised in extraordinary detail. Yet, relatively little is known about eco-evolutionary aspects of chemotaxis, such as how the network has been shaped by selection and to what extent natural populations may fine-tune their chemotactic behaviour to the ecological conditions. To address these questions, we here develop an evolutionary-systems-biology model of the chemotaxis network of E. coli, which we apply to estimate the resource accumulation rate (here used as a proxy for fitness) of wildtype and a large number of potential mutant genotypes...
March 18, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28322743/an-experimental-approach-to-the-immuno-modulatory-basis-of-host-parasite-local-adaptation-in-tapeworm-infected-sticklebacks
#6
Madeleine Hamley, Frederik Franke, Joachim Kurtz, Jörn Peter Scharsack
The evolutionary arms race of hosts and parasites often results in adaptations, which may differ between populations. Investigation of such local adaptation becomes increasingly important to understand dynamics of host-parasite interactions and co-evolution. To this end we performed an infection experiment involving pairs of three-spined sticklebacks and their tapeworm parasite Schistocephalus solidus from three geographically separated origins (Germany, Spain and Iceland) in a fully-crossed design for sympatric and allopatric host/parasite combinations...
March 18, 2017: Experimental Parasitology
https://www.readbyqxmd.com/read/28322313/the-epidemic-dynamics-of-hepatitis-c-virus-subtypes-4a-and-4d-in-saudi-arabia
#7
Ahmed A Al-Qahtani, Guy Baele, Nisreen Khalaf, Marc A Suchard, Mashael R Al-Anazi, Ayman A Abdo, Faisal M Sanai, Hamad I Al-Ashgar, Mohammed Q Khan, Mohammed N Al-Ahdal, Philippe Lemey, Bram Vrancken
The relatedness between viral variants sampled at different locations through time can provide information pertinent to public health that cannot readily be obtained through standard surveillance methods. Here, we use virus genetic data to identify the transmission dynamics that drive the hepatitis C virus subtypes 4a (HCV4a) and 4d (HCV4d) epidemics in Saudi Arabia. We use a comprehensive dataset of newly generated and publicly available sequence data to infer the HCV4a and HCV4d evolutionary histories in a Bayesian statistical framework...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28320902/a-global-optimization-perspective-on-molecular-clusters
#8
REVIEW
J M C Marques, F B Pereira, J L Llanio-Trujillo, P E Abreu, M Albertí, A Aguilar, F Pirani, M Bartolomei
Although there is a long history behind the idea of chemical structure, this is a key concept that continues to challenge chemists. Chemical structure is fundamental to understanding most of the properties of matter and its knowledge for complex systems requires the use of state-of-the-art techniques, either experimental or theoretical. From the theoretical view point, one needs to establish the interaction potential among the atoms or molecules of the system, which contains all the information regarding the energy landscape, and employ optimization algorithms to discover the relevant stationary points...
April 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/28319831/structure-based-prediction-of-host-pathogen-protein-interactions
#9
REVIEW
Rachelle Mariano, Stefan Wuchty
The discovery, validation, and characterization of protein-based interactions from different species are crucial for translational research regarding a variety of pathogens, ranging from the malaria parasite Plasmodium falciparum to HIV-1. Here, we review recent advances in the prediction of host-pathogen protein interfaces using structural information. In particular, we observe that current methods chiefly perform machine learning on sequence and domain information to produce large sets of candidate interactions that are further assessed and pruned to generate final, highly probable sets...
March 16, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28316618/an-evolutionary-method-for-financial-forecasting-in-microscopic-high-speed-trading-environment
#10
Chien-Feng Huang, Hsu-Chih Li
The advancement of information technology in financial applications nowadays have led to fast market-driven events that prompt flash decision-making and actions issued by computer algorithms. As a result, today's markets experience intense activity in the highly dynamic environment where trading systems respond to others at a much faster pace than before. This new breed of technology involves the implementation of high-speed trading strategies which generate significant portion of activity in the financial markets and present researchers with a wealth of information not available in traditional low-speed trading environments...
2017: Computational Intelligence and Neuroscience
https://www.readbyqxmd.com/read/28315870/the-hypermethylated-regions-in-avian-chromosomes
#11
Michael Schmid, Claus Steinlein
Chromosomal locations and amounts of 5-methylcytosine-rich chromosome regions were detected in the karyotypes of 13 bird species by indirect immunofluorescence using a monoclonal anti-5-methylcytosine antibody. These species belong to 7 orders and 10 families of modern (Neognathae) and primitive (Palaeognathae) birds and are characterized by macro- and microchromosomes as well as ZW sex chromosomes. In all 13 species, the hypermethylated chromosome segments are confined to constitutive heterochromatin. The chromosomal locations of hypermethylated DNA regions in the karyotypes are constant and species-specific...
March 18, 2017: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/28306137/empirical-phylogenies-and-species-abundance-distributions-are-consistent-with-pre-equilibrium-dynamics-of-neutral-community-models-with-gene-flow
#12
Anne-Sophie Bonnet-Lebrun, Andrea Manica, Anders Eriksson, Ana S L Rodrigues
Community characteristics reflect past ecological and evolutionary dynamics. Here, we investigate whether it is possible to obtain realistically shaped modelled communities - i.e., with phylogenetic trees and species abundance distributions shaped similarly to typical empirical bird and mammal communities - from neutral community models. To test the effect of gene flow, we contrasted two spatially explicit individual-based neutral models: one with protracted speciation, delayed by gene flow, and one with point mutation speciation, unaffected by gene flow...
March 17, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28302867/an-early-life-hypoxia-event-has-a-long-term-impact-on-protein-digestion-and-growth-in-european-sea-bass-juvenile
#13
José L Zambonino-Infante, David Mazurais, A Servili, C Cahu, G Vanderplancke, N Le Bayon, C Huelvan, Guy Claireaux
Ocean warming, eutrophication and consequent decrease in oxygen lead to smaller average fish size. Although such responses are well-known in an evolutionary context, involving multiple generations, it appears to be incompatible with current rapid environmental change. Rather, phenotypic plasticity could provide a means for marine fish to cope with rapid environmental changes. However, little is known about the mechanisms underlying plastic responses to environmental conditions that favour small phenotypes.Our aim was to investigate how and why European sea bass that had experienced a short episode of moderate hypoxia during their larval stage subsequently exhibited a growth depression at the juvenile stage compared to the control group...
March 16, 2017: Journal of Experimental Biology
https://www.readbyqxmd.com/read/28299519/insights-into-the-effects-of-glycosylation-and-the-monosaccharide-binding-activity-of-the-plant-lectin-cratabl
#14
Laercio Pol-Fachin
CrataBL is a glycoprotein isolated from Crataeva tapia bark, containing two N-glycosylation sites. It has been identified to present lectin activity with some specificity for binding glucose over galactose. However, to date, no information on the effects of glycosylation or CrataBL monosaccharide-binding sites and monosaccharide specificity has been obtained. Thus, molecular docking and molecular dynamics simulations were employed to characterize the glycosylated CrataBL conformation and dynamics in aqueous solutions, as well as the molecular basis for its binding specificity...
March 15, 2017: Glycoconjugate Journal
https://www.readbyqxmd.com/read/28298915/transcriptomic-analysis-reveals-mechanisms-of-sterile-and-fertile-flower-differentiation-and-development-in-viburnum-macrocephalum-f-keteleeri
#15
Zhaogeng Lu, Jing Xu, Weixing Li, Li Zhang, Jiawen Cui, Qingsong He, Li Wang, Biao Jin
Sterile and fertile flowers are an important evolutionary developmental (evo-devo) phenotype in angiosperm flowers, playing important roles in pollinator attraction and sexual reproductive success. However, the gene regulatory mechanisms underlying fertile and sterile flower differentiation and development remain largely unknown. Viburnum macrocephalum f. keteleeri, which possesses fertile and sterile flowers in a single inflorescence, is a useful candidate species for investigating the regulatory networks in differentiation and development...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28298465/geographic-divergence-and-colour-change-in-response-to-visual-backgrounds-and-illumination-intensity-in-bearded-dragons
#16
Viviana Cadena, Kathleen R Smith, John A Endler, Devi Stuart-Fox
Animals may improve camouflage by both dynamic colour change and local evolutionary adaptation of colour but we have little understanding of their relative importance in colour-changing species. We tested for differences in colour change in response to background colour and light intensity in two populations of central bearded dragon lizards (Pogona vitticeps) representing the extremes in body coloration and geographical range. We found that bearded dragons change colour in response to various backgrounds and that colour change is affected by illumination intensity...
March 15, 2017: Journal of Experimental Biology
https://www.readbyqxmd.com/read/28298080/unraveling-energy-and-dynamics-determinants-to-interpret-protein-functional-plasticity-the-limonene-1-2-epoxide-hydrolases-case-study
#17
Silvia Rinaldi, Alessandro Gori, Celeste Annovazzi, Erica Elisa Ferrandi, Daniela Monti, Giorgio Colombo
The balance between structural stability and functional plasticity in proteins that share common three-dimensional folds is the key factor that drives protein evolvability. The ability to distinguish the parts of homologous proteins that underlie common structural organization patterns from the parts acting as regulatory modules that can sustain modifications in response to evolutionary pressure may provide fundamental insights for understanding sequence-structure-dynamics relationships. In applicative terms, this would help develop rational protein design methods...
March 15, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28297894/evolution-of-cooperative-imitators-in-social-networks
#18
Yixiao Li
Many evolutionary game models for network reciprocity are based on an imitation dynamics, yet how semirational imitators prevail has seldom been explained. Here we use a model to investigate the coevolutionary dynamics of cooperation and partnership adjustment in a polygenic population of semirational imitators and rational payoff maximizers. A rational individual chooses a strategy best responding to its neighbors when updating strategy and switches to a new partner who can bring it the maximal payoff from all candidates when adjusting the partnership...
February 2017: Physical Review. E
https://www.readbyqxmd.com/read/28297717/the-true-tempo-of-evolutionary-radiation-and-decline-revealed-on-the-hawaiian-archipelago
#19
Jun Y Lim, Charles R Marshall
Establishing the relationship between rates of change in species richness and biotic and abiotic environmental change is a major goal of evolutionary biology. Although exquisite fossil and geological records provide insight in rare cases, most groups lack high-quality fossil records. Consequently, biologists typically rely on molecular phylogenies to study the diversity dynamics of clades, usually by correlating changes in diversification rate with environmental or trait shifts. However, inferences drawn from molecular phylogenies can be limited owing to the challenge of accounting for extinct species, making it difficult to accurately determine the underlying diversity dynamics that produce them...
March 15, 2017: Nature
https://www.readbyqxmd.com/read/28297706/phytoplankton-can-actively-diversify-their-migration-strategy-in-response-to-turbulent-cues
#20
Anupam Sengupta, Francesco Carrara, Roman Stocker
Marine phytoplankton inhabit a dynamic environment where turbulence, together with nutrient and light availability, shapes species fitness, succession and selection. Many species of phytoplankton are motile and undertake diel vertical migrations to gain access to nutrient-rich deeper layers at night and well-lit surface waters during the day. Disruption of this migratory strategy by turbulence is considered to be an important cause of the succession between motile and non-motile species when conditions turn turbulent...
March 15, 2017: Nature
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