Evolution of gene regulatory networks by means of selection and random genetic drift

被引:0
作者
Papadadonakis, Stefanos [1 ,2 ]
Kioukis, Antonios [3 ]
Karageorgiou, Charikleia [4 ]
Pavlidis, Pavlos [1 ,2 ]
机构
[1] Fdn Res & Technol Hellas, Inst Comp Sci, Iraklion, Crete, Greece
[2] Univ Crete, Dept Biol, Iraklion, Crete, Greece
[3] Univ Crete, Sch Med, Iraklion, Crete, Greece
[4] Univ Buffalo, Dept Biol Sci, New York, NY USA
关键词
Evolution; Simulation; Selection; Gene regulatory networks; Random genetic drift; ROBUSTNESS; DISCOVERY; SWEEPS; MODELS;
D O I
10.7717/peerj.17918
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
The evolution of a population by means of genetic drift and natural selection operating on a gene regulatory network (GRN) of an individual has not been scrutinized in depth. Thus, the relative importance of various evolutionary forces and processes on shaping genetic variability in GRNs is understudied. In this study, we implemented a simulation framework, called EvoNET, that simulates forward-in- time the evolution of GRNs in a population. The fi tness effect of mutations is not constant, rather fi tness of each individual is evaluated on the phenotypic level, by measuring its distance from an optimal phenotype. Each individual goes through a maturation period, where its GRN may reach an equilibrium, thus deciding its phenotype. Afterwards, individuals compete to produce the next generation. We examine properties of the GRN evolution, such as robustness against the deleterious effect of mutations and the role of genetic drift. We are able to confirm fi rm previous hypotheses regarding the effect of mutations and we provide new insights on the interplay between random genetic drift and natural selection.
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页数:18
相关论文
共 22 条
[1]   Selective Sweep at a Quantitative Trait Locus in the Presence of Background Genetic Variation [J].
Chevin, Luis-Miguel ;
Hospital, Frederic .
GENETICS, 2008, 180 (03) :1645-1660
[2]   Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel [J].
Gerdol, Marco ;
Moreira, Rebeca ;
Cruz, Fernando ;
Gomez-Garrido, Jessica ;
Vlasova, Anna ;
Rosani, Umberto ;
Venier, Paola ;
Naranjo-Ortiz, Miguel A. ;
Murgarella, Maria ;
Greco, Samuele ;
Balseiro, Pablo ;
Corvelo, Andre ;
Frias, Leonor ;
Gut, Marta ;
Gabaldon, Toni ;
Pallavicini, Alberto ;
Canchaya, Carlos ;
Novoa, Beatriz ;
Alioto, Tyler S. ;
Posada, David ;
Figueras, Antonio .
GENOME BIOLOGY, 2020, 21 (01) :275
[3]   Soft sweeps: Molecular population genetics of adaptation from standing genetic variation [J].
Hermisson, J ;
Pennings, PS .
GENETICS, 2005, 169 (04) :2335-2352
[4]   Wagner's canalization model [J].
Huerta-Sanchez, Emilia ;
Durrett, Rick .
THEORETICAL POPULATION BIOLOGY, 2007, 71 (02) :121-130
[5]   A statistical method for alignment-free comparison of regulatory sequences [J].
Kantorovitz, Miriam R. ;
Robinson, Gene E. ;
Sinha, Saurabh .
BIOINFORMATICS, 2007, 23 (13) :I249-I255
[6]   Motif-Blind, Genome-Wide Discovery of cis-Regulatory Modules in Drosophila and Mouse [J].
Kantorovitz, Miriam R. ;
Kazemian, Majid ;
Kinston, Sarah ;
Miranda-Saavedra, Diego ;
Zhu, Qiyun ;
Robinson, Gene E. ;
Goettgens, Berthold ;
Halfon, Marc S. ;
Sinha, Saurabh .
DEVELOPMENTAL CELL, 2009, 17 (04) :568-579
[7]   Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison [J].
Kazemian, Majid ;
Zhu, Qiyun ;
Halfon, Marc S. ;
Sinha, Saurabh .
NUCLEIC ACIDS RESEARCH, 2011, 39 (22) :9463-9472
[8]  
Kioukis A, 2018, bioRxiv, DOI [10.1101/449645, 10.1101/449645, DOI 10.1101/449645]
[9]   Evolution of gene regulatory networks: Robustness as an emergent property of evolution [J].
Krishnan, Arun ;
Tomitaa, Masaru ;
Giuliani, Alessandro .
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, 2008, 387 (8-9) :2170-2186
[10]   Modelling genotype-phenotype relationships and human disease with genetic interaction networks [J].
Lehner, Ben .
JOURNAL OF EXPERIMENTAL BIOLOGY, 2007, 210 (09) :1559-1566