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Polygene-based evolution

Shuaiqiang Wang, Byron J. Gao, Shuangling Wang, Guibao Cao, Yilong Yin
2012 Proceedings of the 21st ACM international conference on Information and knowledge management - CIKM '12  
In this paper, we introduce polygene-based evolution, a novel framework for evolutionary algorithms (EAs) that features distinctive operations in the evolution process.  ...  In polygene-based evolutionary algorithms (PGEAs), the evolution unit is polygene, i.e., a set of co-regulated genes.  ...  In conventional EAs, the primitive evolution unit is gene, where genes are independent components during evolution. In this paper, we introduce a novel polygene-based evolution framework.  ... 
doi:10.1145/2396761.2398616 dblp:conf/cikm/WangGWCY12 fatcat:4bzeusimtzf3lci5gjisgagkza

EVOLUTIONARY INSIGHT FROM THE MOLECULAR LANDSCAPE

Charles B. Fenster
2011 Evolution  
On a more intimate evolutionary scale, Arnold's chapter demonstrates the power of the evolutionary design algorithm, a.k.a., directed evolution, a method utilizing artificial selection concepts to engineer  ...  Based on ISI searches, roughly five of the top 100 cited papers for the topic "evolution" for any journal that typically publishes on evolution (including Evolution, Nature, etc.) will be on human or primate  ... 
doi:10.1111/j.1558-5646.2011.01304.x fatcat:nik342xtkjfw3lvsurkno7bd5e

Enrichment of genetic markers of recent human evolution in educational and cognitive traits

Saurabh Srinivasan, Francesco Bettella, Oleksandr Frei, W. David Hill, Yunpeng Wang, Aree Witoelar, Andrew J. Schork, Wesley K. Thompson, Gail Davies, Rahul S. Desikan, Ian J. Deary, Ingrid Melle (+5 others)
2018 Scientific Reports  
This provides a rare opportunity to gain novel insight into the evolutionary processes in humans.  ...  Specifically, we investigated the enrichment of associations concurrent with the evolutionary affiliations in a covariate-modulated statistical framework 61 .  ...  To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.  ... 
doi:10.1038/s41598-018-30387-9 pmid:30135563 pmcid:PMC6105609 fatcat:svrntcg3lbhg5pn3b3dd6ws2fe

An Ancient Evolutionary Origin of Genes Associated with Human Genetic Diseases

T. Domazet-Loso, D. Tautz
2008 Molecular biology and evolution  
Using a phylostratigraphic approach, we have studied the evolutionary emergence of such genes at 19 phylogenetic levels.  ...  Several thousand genes in the human genome have been linked to a heritable genetic disease.  ...  We thank Michael Nachmann for discussion and comments on the manuscript. Literature Cited  ... 
doi:10.1093/molbev/msn214 pmid:18820252 pmcid:PMC2582983 fatcat:epbjjfyylnacfhj6zin5cjta64

Evolution in the Anthropocene: Informing Governance and Policy

Peter Søgaard Jørgensen, Carl Folke, Scott P. Carroll
2019 Annual Review of Ecology, Evolution and Systematics  
The five challenges are: ( a) evolutionary feedbacks, ( b) maintaining resilience, ( c) alleviating constraints, ( d) coevolutionary disruption, and ( e) biotechnology.  ...  Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 50 is November 4, 2019.  ...  STATE OF APPLICATION IN GOVERNANCE Previous reviews of applied evolutionary biology have highlighted a diverse set of applications, including directed evolution and algorithms (Bull & Wichman 2001) ;  ... 
doi:10.1146/annurev-ecolsys-110218-024621 fatcat:rp23c6sstzg4vcsprtbh2tquxe

Can Modern Evolutionary Theory Explain Macroevolution? [chapter]

Douglas J. Futuyma
2015 Interdisciplinary Evolution Research  
accounts for macroevolution, or evolution above the species level.  ...  Ever since the Evolutionary Synthesis of the 1930s and 1940s, some biologists have expressed doubt that the Synthetic Theory, based principally on mutation, genetic variation, and natural selection, adequately  ...  of the relationship of developmental biology to the Evolutionary Synthesis, and to two anonymous reviewers for suggestions and queries.  ... 
doi:10.1007/978-3-319-15045-1_2 fatcat:qe5rw6qpwbgwphjdlbdde4fjyi

A generalist pathogen view of plant evolution [article]

Celine Caseys, Gongjun Shi, Nicole Soltis, Raoni Gwinner, Jason Corwin, Susanna Atwell, Daniel Kliebenstein
2018 bioRxiv   pre-print
Here, we use a collection of 98 isolates of Botrytis cinerea to address how this generalist necrotroph perceive plant evolution across 90 plant genotypes from eight Eudicot species.  ...  AbstractPlant-pathogen interactions are largely modeled as co-evolutionary arms races based on specialist pathogens. Less is known about how generalist pathogens interact with diverse hosts.  ...  In the arms-race model, defense innovation in the host rapidly selects a novel counter mechanism in the pathogen and virulence is driven by evolution in large effect genes linked to this interaction.  ... 
doi:10.1101/507491 fatcat:ql6q6ktbnfbgblmcxnrmqzteia

Increasing the power of genome wide association studies in natural populations using repeated measures - evaluation and implementation

Lars Rönnegård, S. Eryn McFarlane, Arild Husby, Takeshi Kawakami, Hans Ellegren, Anna Qvarnström, Robert Freckleton
2016 Methods in Ecology and Evolution  
The method was evaluated in a simulation study based on observed genotypes from a long-term study of collared flycatchers in Sweden. 3.  ...  Our method fits fixed SNP effects in a linear mixed model that can include both random polygenic effects and permanent environmental effects.  ...  Acknowledgements We thank € Orjan Carlborg and Allison Kwok for useful comments on earlier versions of the manuscript.  ... 
doi:10.1111/2041-210x.12535 pmid:27478587 pmcid:PMC4950150 fatcat:moh3htpkinfhfbkxtki3mv5g44

Novel computational method for predicting polytherapy switching strategies to overcome tumor heterogeneity and evolution

Vanessa D. Jonsson, Collin M. Blakely, Luping Lin, Saurabh Asthana, Nikolai Matni, Victor Olivas, Evangelos Pazarentzos, Matthew A. Gubens, Boris C. Bastian, Barry S. Taylor, John C. Doyle, Trever G. Bivona
2017 Scientific Reports  
For identification of focal amplification, the signals targeting BRAF, MET and EGFR were compared to Centromere 6 (CEP6) signal as in Supplemental Fig. 1 with a ratio greater than 2 considered evidence  ...  J.C.D. provided funding for V.D.J. and N.M.  ...  Here, we present a novel approach that combines a mathematical model of the evolution of tumor cell populations with parameters identified from our experimental data and an engineering framework for the  ... 
doi:10.1038/srep44206 pmid:28287179 pmcid:PMC5347024 fatcat:h3evw6572rgj3e63op3llhvtiy

Genome resequencing reveals rapid, repeated evolution in the Colorado potato beetle, Leptinotarsa decemlineata [article]

Benjamin Pélissié, Yolanda H Chen, Zachary P. Cohen, Michael S. Crossley, David Hawthorne, Sean D Schoville
2021 bioRxiv   pre-print
Despite expectations, we do not find support for strong selection on novel mutations, or rapid evolution from selection on regulatory genes.  ...  Conclusion: CPB evolves insecticide resistance repeatedly across agricultural regions, and oftentimes at the same loci, supporting a prominent role of polygenic evolution from standing genetic variation  ...  Given multiple data sources, overlap in gene identity and 798 function provides a measure of support for repeated evolution and polygenic adaptation.  ... 
doi:10.1101/2021.02.09.430453 fatcat:gtz73eohdzfcpiosqfxcrc3a5a

Understanding rare and common diseases in the context of human evolution

Lluis Quintana-Murci
2016 Genome Biology  
In this review, I discuss how theoretical and empirical population genetics studies, using both modern and ancient DNA data, are a powerful tool for obtaining new insight into the genetic basis of severe  ...  Models of adaptive evolution based on positive or balancing selection apply to a few Mendelian traits or disorders, most notably, but not exclusively, those related to malaria resistance (reviewed in  ...  [156] for a review).  ... 
doi:10.1186/s13059-016-1093-y pmid:27821149 pmcid:PMC5098287 fatcat:ojvzo3m73vbsjksblx65uoptk4

Genome variation, diversity and evolution

2008 Genomic Medicine  
Genetics plays a major role in determining performance and success of an individual in a sport.  ...  Elite athletic performance, a complex trait is said to largely depend on complex interactions of multiple genetic and environmental factors with inter-individual and inter-population differences.  ...  Thangaraj, 1 Lalji Singh The non-recombining, uniparentally transmitting human Y chromosome and mitochondrial DNA are useful tools for tracing population history.  ... 
doi:10.1007/s11568-009-9096-3 pmid:19449171 pmcid:PMC2694881 fatcat:ndwdo3hzknhepopkrufdavxde4

New frontiers in the study of human cultural and genetic evolution

Cody T Ross, Peter J Richerson
2014 Current Opinion in Genetics and Development  
We begin by briefly describing the framework of gene-culture coevolutionary (or dual-inheritance) models for human evolutionary change.  ...  We then describe some exciting new directions in the empirical study of gene-culture coevolution, and conclude with a discussion of the role of gene-culture evolutionary models in the future integration  ...  organic evolutionary theory does for biology.  ... 
doi:10.1016/j.gde.2014.08.014 pmid:25218864 fatcat:z25c6f5kunbhfdy6ykt2ywvp3y

The evolution of hyperactivity, impulsivity and cognitive diversity

Jonathan Williams, Eric Taylor
2005 Journal of the Royal Society Interface  
However, previous suggestions of evolutionary roles for ADHD have not accounted for its confinement to a substantial minority.  ...  Simulations of the Changing Food group task show that unpredictable behaviour by a minority optimizes results for the group.  ...  DISCUSSION Based on a review of the literature, we have presented a multifactorial view of the evolutionary status of ADHD-HI.  ... 
doi:10.1098/rsif.2005.0102 pmid:16849269 pmcid:PMC1578754 fatcat:j26urvxjrfcvfkrvjzokvvch5i

PopNet: A Markov Clustering Approach to Study Population Genetic Structure

Javi Zhang, Asis Khan, Andrea Kennard, Michael E. Grigg, John Parkinson
2017 Molecular biology and evolution  
These relationships are subsequently visualized within a network by a novel implementation of chromosome painting.  ...  Here we present PopNet, a novel computational method that identifies regions of shared ancestry in the chromosomes of related strains through clustering patterns of genetic variation.  ...  M.E.G. is a scholar of the Canadian Institute for Advanced Research (CIFAR) Integrated Microbial Biodiversity Program. Computing resources were provided by the SciNet HPC Consortium.  ... 
doi:10.1093/molbev/msx110 pmid:28383661 pmcid:PMC5850731 fatcat:k42bhuf3tzdk7ghm7kxnwsa2du
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