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Coevolution

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https://www.readbyqxmd.com/read/29221892/coevolution-of-nonlinear-group-interactions-and-strategies-in-well-mixed-and-structured-populations
#1
Lei Zhou, Aming Li, Long Wang
In microbial populations and human societies, the rule of nonlinear group interactions strongly affects the intraspecific evolutionary dynamics, which leads to the variation of the strategy composition eventually. The consequence of such variation may retroact to the rule of the interactions. This correlation indicates that the rule of nonlinear group interactions may coevolve with individuals' strategies. Here, we develop a model to investigate such coevolution in both well-mixed and structured populations...
December 5, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29215005/disentangling-eco-evolutionary-dynamics-of-predator-prey-coevolution-the-case-of-antiphase-cycles
#2
Ellen van Velzen, Ursula Gaedke
The impact of rapid predator-prey coevolution on predator-prey dynamics remains poorly understood, as previous modelling studies have given rise to contradictory conclusions and predictions. Interpreting and reconciling these contradictions has been challenging due to the inherent complexity of model dynamics, defying mathematical analysis and mechanistic understanding. We develop a new approach here, based on the Geber method for deconstructing eco-evolutionary dynamics, for gaining such understanding. We apply this approach to a co-evolutionary predator-prey model to disentangle the processes leading to either antiphase or ¼-lag cycles...
December 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29213355/draft-genome-sequence-of-venturia-carpophila-the-causal-agent-of-peach-scab
#3
Chunxian Chen, Clive H Bock, Bruce W Wood
Venturia carpophila causes peach scab, a disease that renders peach (Prunus persica) fruit unmarketable. We report a high-quality draft genome sequence (36.9 Mb) of V. carpophila from an isolate collected from a peach tree in central Georgia in the United States. The genome annotation is described and a phylogenetic analysis of the pathogen is presented. The genome sequence will be a useful resource for various studies on the pathogen, including the biology and ecology, taxonomy and phylogeny, host interaction and coevolution, isolation and characterization of genes of interest, and development of molecular markers for genotyping and mapping...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/29206201/selection-on-the-major-color-gene-melanocortin-1-receptor-shaped-the-evolution-of-the-melanocortin-system-genes
#4
Linda Dib, Luis M San-Jose, Anne-Lyse Ducrest, Nicolas Salamin, Alexandre Roulin
Modular genetic systems and networks have complex evolutionary histories shaped by selection acting on single genes as well as on their integrated function within the network. However, uncovering molecular coevolution requires the detection of coevolving sites in sequences. Detailed knowledge of the functions of each gene in the system is also necessary to identify the selective agents driving coevolution. Using recently developed computational tools, we investigated the effect of positive selection on the coevolution of ten major genes in the melanocortin system, responsible for multiple physiological functions and human diseases...
December 5, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29205373/coexistence-via-coevolution-driven-by-reduced-allelochemical-effects-and-increased-tolerance-to-competition-between-invasive-and-native-plants
#5
Fangfang Huang, Richard Lankau, Shaolin Peng
Coevolution can promote long-term coexistence of two competing species if selection acts to reduce the fitness inequality between competitors and/or strengthen negative frequency dependence within each population. However, clear coevolution between plant competitors has been rarely documented. Plant invasions offer opportunities to capture the process of coevolution. Here we investigated how the developing relationship between an invasive forb, Alliaria petiolata, and a native competitor, Pilea pumila, may affect their long-term coexistence, by testing the competitive effects of populations of varying lengths of co-occurrence on each other across a chronosequence of invasion history...
December 4, 2017: New Phytologist
https://www.readbyqxmd.com/read/29194650/evolution-on-the-bright-side-of-life-microorganisms-and-the-evolution-of-mutualism
#6
REVIEW
Kristina Linnea Hillesland
Mutualistic interactions, where two interacting species have a net beneficial effect on each other's fitness, play a crucial role in the survival and evolution of many species. Despite substantial empirical and theoretical work in past decades, the impact of these interactions on natural selection is not fully understood. In addition, mutualisms between microorganisms have been largely ignored, even though they are ecologically important and can be used as tools to bridge the gap between theory and empirical work...
November 30, 2017: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/29178135/demographically-idiosyncratic-responses-to-climate-change-and-rapid-pleistocene-diversification-of-the-walnut-genus-juglans-juglandaceae-revealed-by-whole-genome-sequences
#7
Wei-Ning Bai, Peng-Cheng Yan, Bo-Wen Zhang, Keith E Woeste, Kui Lin, Da-Yong Zhang
Whether species demography and diversification are driven primarily by extrinsic environmental changes such as climatic oscillations in the Quaternary or by intrinsic biological interactions like coevolution between antagonists is a matter of active debate. In fact, their relative importance can be assessed by tracking past population fluctuations over considerable time periods. We applied the pairwise sequentially Markovian coalescent approach on the genomes of 11 temperate Juglans species to estimate trajectories of changes in effective population size (Ne ) and used a Bayesian-coalescent based approach that simultaneously considers multiple genomes (G-PhoCS) to estimate divergence times between lineages...
November 27, 2017: New Phytologist
https://www.readbyqxmd.com/read/29170530/identification-and-analysis-of-seven-effector-protein-families-with-different-adaptive-and-evolutionary-histories-in-plant-associated-members-of-the-xanthomonadaceae
#8
Renata de A B Assis, Lorraine Cristina Polloni, José S L Patané, Shalabh Thakur, Érica B Felestrino, Julio Diaz-Caballero, Luciano Antonio Digiampietri, Luiz Ricardo Goulart, Nalvo F Almeida, Rafael Nascimento, Abhaya M Dandekar, Paulo A Zaini, João C Setubal, David S Guttman, Leandro Marcio Moreira
The Xanthomonadaceae family consists of species of non-pathogenic and pathogenic γ-proteobacteria that infect different hosts, including humans and plants. In this study, we performed a comparative analysis using 69 fully sequenced genomes belonging to this family, with a focus on identifying proteins enriched in phytopathogens that could explain the lifestyle and the ability to infect plants. Using a computational approach, we identified seven phytopathogen-enriched protein families putatively secreted by type II secretory system: PheA (CM-sec), LipA/LesA, VirK, and four families involved in N-glycan degradation, NixE, NixF, NixL, and FucA1...
November 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29169316/coevolution-of-siglec-11-and-siglec-16-via-gene-conversion-in-primates
#9
Toshiyuki Hayakawa, Zahra Khedri, Flavio Schwarz, Corinna Landig, Suh-Yuen Liang, Hai Yu, Xi Chen, Naoko T Fujito, Yoko Satta, Ajit Varki, Takashi Angata
BACKGROUND: Siglecs-11 and -16 are members of the sialic acid recognizing Ig-like lectin family, and expressed in same cells. Siglec-11 functions as an inhibitory receptor, whereas Siglec-16 exhibits activating properties. In humans, SIGLEC11 and SIGLEC16 gene sequences are extremely similar in the region encoding the extracellular domain due to gene conversions. Human SIGLEC11 was converted by the nonfunctional SIGLEC16P allele, and the converted SIGLEC11 allele became fixed in humans, possibly because it provides novel neuroprotective functions in brain microglia...
November 23, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29166834/the-entomopathogenic-fungus-metarhizium-robertsii-communicates-with-the-insect-host-galleria-mellonella-during-infection
#10
Krishnendu Mukherjee, Andreas Vilcinskas
Parasitic fungi are the only pathogens that can infect insect hosts directly through their proteinaceous exoskeleton. Penetration of the cuticle requires the release of fungal enzymes, including proteinases, which act as virulence factors. Insects can sense fungal infections and activate innate immune responses, including the synthesis of antifungal peptides and proteinase inhibitors that neutralize the incoming proteinases. This well-studied host response is epigenetically regulated by histone acetylation/deacetylation...
November 23, 2017: Virulence
https://www.readbyqxmd.com/read/29166166/coevolution-between-mutualists-and-parasites-in-symbiotic-communities-may-lead-to-the-evolution-of-lower-virulence
#11
Paul G Nelson, Georgiana May
Most eukaryotes harbor a diverse community of parasitic, mutualistic, and commensal microbial symbionts. Although the diversity of these microbial symbiotic communities has recently drawn considerable attention, theory regarding the evolution of interactions among symbionts and with the host is still in its nascent stages. Here we evaluate the role of interactions among coinfecting symbionts in the evolution of symbiont virulence toward the host. To do so, we place the virulence-transmission trade-off into a community context and model the evolution of symbiont trophic modes along the continuum from parasitism (virulence) to mutualism (negative virulence)...
December 2017: American Naturalist
https://www.readbyqxmd.com/read/29158553/the-architecture-of-mutualistic-networks-as-an-evolutionary-spandrel
#12
Sergi Valverde, Jordi Piñero, Bernat Corominas-Murtra, Jose Montoya, Lucas Joppa, Ricard Solé
Mutualistic networks have been shown to involve complex patterns of interactions among animal and plant species, including a widespread presence of nestedness. The nested structure of these webs seems to be positively correlated with higher diversity and resilience. Moreover, these webs exhibit marked measurable structural patterns, including broad distributions of connectivity, strongly asymmetrical interactions and hierarchical organization. Hierarchical organization is an especially interesting property, since it is positively correlated with biodiversity and network resilience, thus suggesting potential selection processes favouring the observed web organization...
November 20, 2017: Nature Ecology & Evolution
https://www.readbyqxmd.com/read/29155606/a-new-framework-for-analysis-of-coevolutionary-systems-directed-graph-representation-and-random-walks
#13
Siang Yew Chong, Peter Tiňo, Jun He, Xin Yao
Studying coevolutionary systems in the context of simplified models (i.e. games with pairwise interactions between coevolving solutions modelled as self plays) re-mains an open challenge since the rich underlying structures associated with pairwise-comparison-based fitness measures are often not taken fully into account. Although cyclic dynamics have been demonstrated in several contexts (such as intransitivity in coevolutionary problems), there is no complete characterization of cycle structures and their effects on coevolutionary search...
November 20, 2017: Evolutionary Computation
https://www.readbyqxmd.com/read/29155284/the-dynamic-evolution-of-drosophila-innubila-nudivirus
#14
Tom Hill, Robert L Unckless
Viruses coevolve with their hosts to overcome host resistance and gain the upper hand in the evolutionary arms race. Drosophila innubila nudivirus (DiNV) is a double stranded DNA virus, closely related to Oryctes rhinoceros nudivirus (OrNV) and Kallithea virus. DiNV is the first DNA virus found to naturally infect Drosophila and therefore has the potential to be developed as a model for DNA virus immune defense and host/virus coevolution within its well-studied host system. Here we sequence and annotate the genome of DiNV and identify signatures of adaptation, revealing clues for genes involved in host-parasite coevolution...
November 16, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29145803/unraveling-the-evolution-and-coevolution-of-small-regulatory-rnas-and-coding-genes-in-listeria
#15
Franck Cerutti, Ludovic Mallet, Anaïs Painset, Claire Hoede, Annick Moisan, Christophe Bécavin, Mélodie Duval, Olivier Dussurget, Pascale Cossart, Christine Gaspin, Hélène Chiapello
BACKGROUND: Small regulatory RNAs (sRNAs) are widely found in bacteria and play key roles in many important physiological and adaptation processes. Studying their evolution and screening for events of coevolution with other genomic features is a powerful way to better understand their origin and assess a common functional or adaptive relationship between them. However, evolution and coevolution of sRNAs with coding genes have been sparsely investigated in bacterial pathogens. RESULTS: We designed a robust and generic phylogenomics approach that detects correlated evolution between sRNAs and protein-coding genes using their observed and inferred patterns of presence-absence in a set of annotated genomes...
November 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29144443/a-genomic-survey-of-scpp-family-genes-in-fishes-provides-novel-insights-into-the-evolution-of-fish-scales
#16
Yunyun Lv, Kazuhiko Kawasaki, Jia Li, Yanping Li, Chao Bian, Yu Huang, Xinxin You, Qiong Shi
The family of secretory calcium-binding phosphoproteins (SCPPs) have been considered vital to skeletal tissue mineralization. However, most previous SCPP studies focused on phylogenetically distant animals but not on those closely related species. Here we provide novel insights into the coevolution of SCPP genes and fish scales in 10 species from Otophysi. According to their scale phenotypes, these fishes can be divided into three groups, i.e., scaled, sparsely scaled, and scaleless. We identified homologous SCPP genes in the genomes of these species and revealed an absence of some SCPP members in some genomes, suggesting an uneven evolutionary history of SCPP genes in fishes...
November 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29144205/lessons-in-effector-and-nlr-biology-of-plant-microbe-systems
#17
Aleksandra Białas, Erin K Zess, Juan Carlos De la Concepcion, Marina Franceschetti, Helen G Pennington, Kentaro Yoshida, Jessica L Upson, Emilie Chanclud, Chih-Hang Wu, Thorsten Langner, Abbas Maqbool, Freya A Varden, Lida Derevnina, Khaoula Belhaj, Koki Fujisaki, Hiromasa Saitoh, Ryohei Terauchi, Mark J Banfield, Sophien Kamoun
A diversity of plant-associated organisms secrete effectors-proteins and metabolites that modulate plant physiology to favor host infection and colonization. However, effectors can also activate plant immune receptors, notably nucleotide-binding domain and leucine-rich repeat region (NLR)-containing proteins, enabling plants to fight off invading organisms. This interplay between effectors, their host targets, and the matching immune receptors is shaped by intricate molecular mechanisms and exceptionally dynamic coevolution...
November 16, 2017: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29143083/the-polyphyletic-origins-of-primase-helicase-bifunctional-proteins
#18
Ankita Gupta, Supriya Patil, Ramya Vijayakumar, Kiran Kondabagil
We studied the evolutionary relationships of different primase-helicase bifunctional proteins, found mostly in viruses, virophages, plasmids, and organellar genomes, by phylogeny and correlation analysis. Our study suggests independent origins of primase-helicase bifunctional proteins resulting from multiple fusion events between genes encoding primase and helicase domains of different families. The correlation analysis further indicated strong functional dependencies of domains in the bifunctional proteins that are part of smaller genomes and plasmids...
November 15, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29132402/efficient-high-throughput-molecular-method-to-detect-ehrlichia-ruminantium-in-ticks
#19
Nídia Cangi, Valérie Pinarello, Laure Bournez, Thierry Lefrançois, Emmanuel Albina, Luís Neves, Nathalie Vachiéry
BACKGROUND: Ehrlichia ruminantium is the causal agent of heartwater, a fatal tropical disease affecting ruminants with important economic impacts. This bacterium is transmitted by Amblyomma ticks and is present in sub-Saharan Africa, islands in the Indian Ocean and the Caribbean, where it represents a threat to the American mainland. METHODS: An automated DNA extraction method was adapted for Amblyomma ticks and a new qPCR targeting the pCS20 region was developed to improve E...
November 13, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/29125597/phage-mobility-is-a-core-determinant-of-phage-bacteria-coexistence-in-biofilms
#20
Matthew Simmons, Knut Drescher, Carey D Nadell, Vanni Bucci
Many bacteria are adapted for attaching to surfaces and for building complex communities, termed biofilms. The biofilm mode of life is predominant in bacterial ecology. So too is the exposure of bacteria to ubiquitous viral pathogens, termed bacteriophages. Although biofilm-phage encounters are likely to be common in nature, little is known about how phages might interact with biofilm-dwelling bacteria. It is also unclear how the ecological dynamics of phages and their hosts depend on the biological and physical properties of the biofilm environment...
November 10, 2017: ISME Journal
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