Adaptive multiscapes: an up-to-date metaphor to visualize molecular adaptation.

PubWeight™: 0.77‹?›

🔗 View Article (PMID 28245845)

Published in Biol Direct on February 28, 2017

Authors

Pablo Catalán1,2, Clemente F Arias1, Jose A Cuesta1,2,3,4, Susanna Manrubia5,6

Author Affiliations

1: Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain.
2: Departamento de Matemáticas, Universidad Carlos III de Madrid, Madrid, Spain.
3: Institute for Biocomputation and Physics of Complex Systems, Zaragoza, Spain.
4: UC3M-BS Institute of Financial Big Data (IFiBiD), Madrid, Spain.
5: Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain smanrubia@cnb.csic.es.
6: Departamento de Biología de Sistemas, Centro Nacional de Biotecnología (CSIC), Madrid, Spain.

Articles cited by this

Evolution in Mendelian Populations. Genetics (1931) 138.42

HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy. Science (1995) 18.40

The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers (1990) 10.92

Enzyme recruitment in evolution of new function. Annu Rev Microbiol (1976) 6.95

The distribution of fitness effects of new mutations. Nat Rev Genet (2007) 6.42

Turning a hobby into a job: how duplicated genes find new functions. Nat Rev Genet (2008) 6.07

From sequences to shapes and back: a case study in RNA secondary structures. Proc Biol Sci (1994) 6.01

Epochal evolution shapes the phylodynamics of interpandemic influenza A (H3N2) in humans. Science (2006) 6.01

The evolution of gene duplications: classifying and distinguishing between models. Nat Rev Genet (2010) 5.75

The 'evolvability' of promiscuous protein functions. Nat Genet (2004) 5.41

Natural selection and the concept of a protein space. Nature (1970) 5.21

The frailty of adaptive hypotheses for the origins of organismal complexity. Proc Natl Acad Sci U S A (2007) 4.96

Plasticity, evolvability, and modularity in RNA. J Exp Zool (2000) 3.98

Evolution of digital organisms at high mutation rates leads to survival of the flattest. Nature (2001) 3.92

Smoothness within ruggedness: the role of neutrality in adaptation. Proc Natl Acad Sci U S A (1996) 3.67

Continuity in evolution: on the nature of transitions. Science (1998) 3.40

Robustness and evolvability: a paradox resolved. Proc Biol Sci (2008) 3.08

Innovation and robustness in complex regulatory gene networks. Proc Natl Acad Sci U S A (2007) 2.70

In the light of directed evolution: pathways of adaptive protein evolution. Proc Natl Acad Sci U S A (2009) 2.66

One sequence, two ribozymes: implications for the emergence of new ribozyme folds. Science (2000) 2.53

Recruitment of enzymes as lens structural proteins. Science (1987) 2.25

Subclonal components of consensus fitness in an RNA virus clone. J Virol (1994) 2.09

Initial mutations direct alternative pathways of protein evolution. PLoS Genet (2011) 2.01

fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences. Nucleic Acids Res (2006) 1.94

Generic properties of combinatory maps: neutral networks of RNA secondary structures. Bull Math Biol (1997) 1.85

Latent evolutionary potentials under the neutral mutational drift of an enzyme. HFSP J (2007) 1.75

Modelling 'evo-devo' with RNA. Bioessays (2002) 1.71

Exploring phenotype space through neutral evolution. J Mol Evol (1996) 1.68

How are model protein structures distributed in sequence space? Biophys J (1997) 1.67

Neutral genetic drift can alter promiscuous protein functions, potentially aiding functional evolution. Biol Direct (2007) 1.61

Evolution and speciation on holey adaptive landscapes. Trends Ecol Evol (1997) 1.59

Shaping space: the possible and the attainable in RNA genotype-phenotype mapping. J Theor Biol (1998) 1.50

From fitness landscapes to seascapes: non-equilibrium dynamics of selection and adaptation. Trends Genet (2009) 1.50

Percolation on the fitness hypercube and the evolution of reproductive isolation. J Theor Biol (1997) 1.45

A latent capacity for evolutionary innovation through exaptation in metabolic systems. Nature (2013) 1.38

The fittest versus the flattest: experimental confirmation of the quasispecies effect with subviral pathogens. PLoS Pathog (2006) 1.35

Neutral networks in protein space: a computational study based on knowledge-based potentials of mean force. Fold Des (1997) 1.29

The look-ahead effect of phenotypic mutations. Biol Direct (2008) 1.28

Patterns of Epistasis between beneficial mutations in an antibiotic resistance gene. Mol Biol Evol (2013) 1.24

Enumerating Designing Sequences in the HP Model. J Biol Phys (2002) 1.20

The ascent of the abundant: how mutational networks constrain evolution. PLoS Comput Biol (2008) 1.20

Predictability of evolutionary trajectories in fitness landscapes. PLoS Comput Biol (2011) 1.12

Topological structure of the space of phenotypes: the case of RNA neutral networks. PLoS One (2011) 1.05

Neutral network sizes of biological RNA molecules can be computed and are not atypically small. BMC Bioinformatics (2008) 1.05

The effect of phenotypic plasticity on evolution in multipeaked fitness landscapes. J Evol Biol (2006) 1.04

On the structural repertoire of pools of short, random RNA sequences. J Theor Biol (2008) 1.04

Connectivity of neutral networks, overdispersion, and structural conservation in protein evolution. J Mol Evol (2003) 0.98

Genotype networks, innovation, and robustness in sulfur metabolism. BMC Syst Biol (2011) 0.94

The arrival of the frequent: how bias in genotype-phenotype maps can steer populations to local optima. PLoS One (2014) 0.91

Tempo and mode of plant RNA virus escape from RNA interference-mediated resistance. J Virol (2011) 0.88

Fitness distributions in exponentially growing asexual populations. Phys Rev Lett (2003) 0.87

Evolutionary dynamics on networks of selectively neutral genotypes: effects of topology and sequence stability. Phys Rev E Stat Nonlin Soft Matter Phys (2009) 0.86

Evolutionary dynamics in a simple model of self-assembly. Phys Rev E Stat Nonlin Soft Matter Phys (2011) 0.86

Mutation-induced fold switching among lattice proteins. J Chem Phys (2011) 0.84

Pre-existence and emergence of drug resistance in a generalized model of intra-host viral dynamics. Epidemics (2012) 0.84

toyLIFE: a computational framework to study the multi-level organisation of the genotype-phenotype map. Sci Rep (2014) 0.81

Evolution at increased error rate leads to the coexistence of multiple adaptive pathways in an RNA virus. BMC Evol Biol (2013) 0.79

The organization of biological sequences into constrained and unconstrained parts determines fundamental properties of genotype-phenotype maps. J R Soc Interface (2015) 0.79

The structure of the genotype-phenotype map strongly constrains the evolution of non-coding RNA. Interface Focus (2015) 0.79

Secondary structural entropy in RNA switch (Riboswitch) identification. BMC Bioinformatics (2015) 0.79

One RNA plays three roles to provide catalytic activity to a group I intron lacking an endogenous internal guide sequence. Nucleic Acids Res (2009) 0.77

Quantifying the similarity of monotonic trajectories in rough and smooth fitness landscapes. Mol Biosyst (2013) 0.77

Evolution on neutral networks accelerates the ticking rate of the molecular clock. J R Soc Interface (2015) 0.77

RNAdualPF: software to compute the dual partition function with sample applications in molecular evolution theory. BMC Bioinformatics (2016) 0.76

Tipping points and early warning signals in the genomic composition of populations induced by environmental changes. Sci Rep (2015) 0.75

Articles by these authors

Distribution of genotype network sizes in sequence-to-structure genotype-phenotype maps. J R Soc Interface (2017) 0.75