Adami C (1998) Introduction to artificial life. Springer, New York
Book
Google Scholar
Adami C, Ofria C, Collier TC (2000) Evolution of biological complexity. Proc Natl Acad Sci 97:4463–4468
CAS
PubMed
Article
Google Scholar
Aita T, Morinaga S, Husimi Y (2004) Thermodynamical interpretation of evolutionary dynamics on a fitness landscape in a evolution reactor. I Bull Math Biol 66:1371–1403
PubMed
Article
Google Scholar
Barton NH (1995) A general model for the evolution of recombination. Genet Res 65:123–145
CAS
PubMed
Article
Google Scholar
Barton NH, Coe JB (2009) On the application of statistical physics to evolutionary biology. J Theor Biol 259:317–324
CAS
PubMed
Article
Google Scholar
Beerenwinkel N, Pachter L, Sturmfels B, Elena SF, Lenski RE (2007) Analysis of epistatic interactions and fitness landscapes using a new geometric approach. BMC Evol Biol 7:60
PubMed
PubMed Central
Article
Google Scholar
Bonhoeffer S, Chappey C, Parkin NT, Whitcomb JM, Petropoulos CJ (2004) Evidence for positive epistasis in HIV-1. Science 306:1547–1550
CAS
PubMed
Article
Google Scholar
Bull JJ, Sanjuan R, Wilke CO (2007) Theory of lethal mutagenesis for viruses. J Virol 81:2930–2939
CAS
PubMed
PubMed Central
Article
Google Scholar
Burch CL, Chao L (2004) Epistasis and its relationship to canalization in the RNA virus phi 6. Genetics 167:559–567
PubMed
PubMed Central
Article
Google Scholar
Charlesworth B (1976) Recombination modification in a fluctuating environment. Genetics 83:181–195
CAS
PubMed
PubMed Central
Google Scholar
de Visser JA, Hoekstra RF, van den Ende H (1997) An experimental test for synergistic epistasis and its application in chlamydomonas. Genetics 145:815–819
PubMed
Google Scholar
Elena SF, Lenski R (1997) Test of synergistic interactions among deleterious mutations in bacteria. Nature 390:395–397
CAS
PubMed
Article
Google Scholar
Franklin J, LaBar T, Adami C (2019) Mapping the peaks: fitness landscapes of the fittest and the flattest. Artif Life 25:250–262
PubMed
Article
Google Scholar
Gibson G, Wagner G (2000) Canalization in evolutionary genetics: a stabilizing theory? BioEssays 22:372–380
CAS
PubMed
Article
Google Scholar
Goyal S, Balick DJ, Jerison ER, Neher RA, Shraiman BI, Desai MM (2012) Dynamic mutation-selection balance as an evolutionary attractor. Genetics 191:1309–1319
PubMed
PubMed Central
Article
Google Scholar
Gros P-A, Le Nagard H, Tenaillon O (2009) The evolution of epistasis and its links with genetic robustness, complexity and drift in a phenotypic model of adaptation. Genetics 182:277–293
CAS
PubMed
PubMed Central
Article
Google Scholar
Haigh J (1978) The accumulation of deleterious genes in a population—Muller’s ratchet. Theor Popul Biol 14:251–267
CAS
PubMed
Article
Google Scholar
Iwasa Y (1988) Free fitness that always increases in evolution. J Theor Biol 135:265–281
CAS
PubMed
Article
Google Scholar
Jasnos L, Korona R (2007) Epistatic buffering of fitness loss in yeast double deletion strains. Nat Genet 39:550–554
CAS
PubMed
Article
Google Scholar
Kirby LE, Koslowsky D (2017) Mitochondrial dual-coding genes in Trypanosoma brucei. PLoS Negl Trop Dis 11:e0005989
PubMed
PubMed Central
Article
CAS
Google Scholar
Koffi M, De Meeûs T, Bucheton B, Solano P, Camara M, Kaba D, Cuny G, Ayala FJ, Jamonneau V (2009) Population genetics of Trypanosoma brucei gambiense, the agent of sleeping sickness in western africa. Proc Natl Acad Sci USA 106:209–214
CAS
PubMed
Article
Google Scholar
Kondrashov AS (1982) Selection against harmful mutations in large sexual and asexual populations. Genet Res 40:325–332
CAS
PubMed
Article
Google Scholar
Kondrashov AS (1988) Deleterious mutations and the evolution of sexual reproduction. Nature 336:435–440
CAS
PubMed
Article
Google Scholar
Kondrashov AS (1994) Muller’s ratchet under epistatic selection. Genetics 136:1469–1473
CAS
PubMed
PubMed Central
Google Scholar
LaBar T, Adami C (2017) Evolution of drift robustness in small populations of digital organisms. Nat Commun 8:1012
PubMed
PubMed Central
Article
CAS
Google Scholar
Lan Y, Trout A, Weinreich D M, Wylie C S (2017) Natural selection can favor the evolution of ratchet robustness over evolution of mutational robustness. bioRxiv 122087
Lynch M, Bürger R, Butcher D, Gabriel W (1993) The mutational meltdown in asexual populations. J Hered 84:339–344
CAS
PubMed
Article
Google Scholar
McCandlish DM, Stoltzfus A (2014) Modeling evolution using the probability of fixation: history and implications. Q Rev Biol 89:225–252
PubMed
Article
Google Scholar
Meurer A, Smith CP, Paprocki M, Čertík O, Kirpichev SB, Rocklin M, Kumar A, Ivanov S, Moore JK, Singh S, Rathnayake T, Vig S, Granger BE, Muller RP, Bonazzi F, Gupta H, Vats S, Johansson F, Pedregosa F, Curry MJ, Terrel AR, Roučka Š, Saboo A, Fernando I, Kulal S, Cimrman R, Scopatz A (2017) SymPy: symbolic computing in Python. PeerJ Comput Sci 3:e103
Article
Google Scholar
Oberle M, Balmer O, Brun R, Roditi I (2010) Bottlenecks and the maintenance of minor genotypes during the life cycle of Trypanosoma brucei. PLoS Pathog 6:e1001023
PubMed
PubMed Central
Article
CAS
Google Scholar
Ofria C, Bryson DM, Wilke CO (2009) Avida: a software platform for research in computational evolutionary biology. In: Komosinski M, Adamatzky A (eds) Artificial life models in software. Springer, London, pp 3–35
Chapter
Google Scholar
Oliphant TE (2006) A guide to NumPy. Trelgol Publishing, New York
Google Scholar
Østman B, Hintze A, Adami C (2012) Impact of epistasis and pleiotropy on evolutionary adaptation. Proc R Soc B 279:247–256
PubMed
Article
Google Scholar
Python Software Foundation (2019) The Python language reference. Python Software Foundation, Wilmington
Google Scholar
R Core Team (2019) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna
Google Scholar
Sanjuán R, Cuevas JM, Moya A, Elena SF (2005) Epistasis and the adaptability of an RNA virus. Genetics 170:1001–1008
PubMed
PubMed Central
Article
CAS
Google Scholar
Sanjuán R, Cuevas JM, Furió V, Holmes EC, Moya A (2007) Selection for robustness in mutagenized RNA viruses. PLoS Genet 3:e93
PubMed
PubMed Central
Article
CAS
Google Scholar
Scharloo W (1991) Canalization: genetic and developmental aspects. Annu Rev Ecol Syst 22:65–93
Article
Google Scholar
Sella G, Hirsh AE (2005) The application of statistical physics to evolutionary biology. Proc Natl Acad Sci USA 102:9541–9546
CAS
PubMed
Article
Google Scholar
Speijer D (2006) Is kinetoplastid pan-editing the result of an evolutionary balancing act? IUBMB Life 58:91–96
CAS
PubMed
Article
Google Scholar
Tenaillon O, Silander OK, Uzan J-P, Chao L (2007) Quantifying organismal complexity using a population genetic approach. PLoS ONE 2:e217
PubMed
PubMed Central
Article
Google Scholar
Westy SA, Lively CM, Read AF (1999) A pluralist approach to sex and recombination. J Evol Biol 12:1003–1012
Article
Google Scholar
Wickham H, Averick M, Bryan J, Chang W, D’Agostino McGowan L, François R, Grolemund G, Hayes A, Henry L, Hester J, Kuhn M, Lin Pedersen T, Miller E, Milton Bache S, Müller K, Ooms J, Robinson D, Paige Seidel D, Spinu V, Takahashi K, Vaughan D, Wilke C, Woo K, Yutani H (2019) Welcome to the tidyverse. J Open Source Softw 4:1686
Article
Google Scholar
Wilke CO, Adami C (2001) Interaction between directional epistasis and average mutational effects. Proc R Soc Lond B 268:1469–1474
CAS
Article
Google Scholar
Wilke CO, Adami C (2003) Evolution of mutational robustness. Mutat Res 522:3–11
CAS
PubMed
Article
Google Scholar
Wilke CO, Wang JL, Ofria C, Lenski RE, Adami C (2001) Evolution of digital organisms at high mutation rates leads to survival of the flattest. Nature 412:331–333
CAS
PubMed
PubMed Central
Article
Google Scholar
Wolf JB, Brodie ED III, Wade MJ (eds) (2000) Epistasis and the evolutionary process. Oxford University Press, Oxford
Google Scholar