Sharp changes in state, such as transitions from survival to extinction, are hallmarks of evolutionary dynamics in biological systems. These transitions can be explored using the techniques of statistical physics and the physics of nonlinear and complex systems. For example, a survival-to-extinction transition can be characterized as a non-equilibrium phase transition to an absorbing state. Here, we review the literature on phase transitions in evolutionary dynamics. We discuss directed percolation transitions in cellular automata and evolutionary models, and models that diverge from the directed percolation universality class. We explore in detail an example of an absorbing phase transition in an agent-based model of evolutionary dynamics, including previously unpublished data demonstrating similarity to, but also divergence from, directed percolation, as well as evidence for phase transition behavior at multiple levels of the model system's evolutionary structure. We discuss phase transition models of the error catastrophe in RNA virus dynamics and phase transition models for transition from chemistry to biochemistry, i.e., the origin of life. We conclude with a review of phase transition dynamics in models of natural selection, discuss the possible role of phase transitions in unraveling fundamental unresolved questions regarding multilevel selection and the major evolutionary transitions, and assess the future outlook for phase transitions in the investigation of evolutionary dynamics.

1.
Albano
,
E. V.
and
Monetti
,
R. A.
, “
Comment on ‘life at the edge of chaos,’
Phys. Rev. Lett.
75
(
5
),
981
(
1995
).
2.
Aldana
,
M.
,
Larralde
,
H.
, and
Vázquez
,
B.
, “
On the emergence of collective order in swarming systems: A recent debate
,”
Int. J. Mod. Phys. B
23
(
18
),
3661
3685
(
2009
).
3.
Alonso
,
J.
and
Fort
,
H.
, “
Error catastrophe for viruses infecting cells: Analysis of the phase transition in terms of error classes
,”
Philos. Trans. R. Soc. A
368
(
1933
),
5569
5582
(
2010
).
4.
Baake
,
E.
,
Baake
,
M.
, and
Wagner
,
H.
, “
Ising quantum chain is equivalent to a model of biological evolution
,”
Phys. Rev. Lett.
78
(
3
),
559
562
(
1997
).
5.
Baake
,
E.
and
Wagner
,
H.
, “
Mutation-selection models solved exactly with methods of statistical mechanics
,”
Genet. Res.
78
,
93
117
(
2001
).
6.
Bagchi
,
D.
and
Mohanty
,
P. K.
, “
Phase transition in an exactly solvable extinction model
,”
Phys. Rev. E
84
,
061921
(
2011
).
7.
Bahar
,
S.
,
The Essential Tension: Competition, Cooperation and Multilevel Selection in Evolution
. (
Springer
,
Dordrecht
,
2018
).
8.
Bak
,
P.
,
How Nature Works the Science of Self-Organized Criticality
(
Copernicus, Springer-Verlag
,
New York
,
1996
).
9.
Bak
,
P.
and
Sneppen
,
K.
, “
Punctuated equilibrium and criticality in a simple model of evolution
,”
Phys. Rev. Lett.
71
(
24
),
4083
4086
(
1993
).
10.
Bak
,
P.
,
Tang
,
C.
, and
Wiesenfeld
,
K.
, “
Self-organized criticality: An explanation of 1/f noise
,”
Phys. Rev. Lett.
59
(
4
),
381
384
(
1987
).
11.
Barghathi
,
H.
,
Tackkett
,
S.
, and
Vojta
,
T.
, “
Extinction transitions in a model of ecological and evolutionary dynamics
,”
Eur. Phys. J. B
90
,
129
(
2017
).
12.
Barton
,
N. H.
and
Coe
,
J. B.
, “
On the application of statistical physics to evolutionary biology
,”
J. Theor. Biol.
259
,
317
324
(
2009
).
13.
Bedau
,
M. A.
and
Packard
,
N. H.
, “
Evolution of evolvability via adaptation of mutation rates
,”
BioSystems
69
,
143
162
(
2003
).
14.
Bena
,
I.
,
Droz
,
M.
,
Szwabiński
,
J.
, and
Pękalski
,
A.
, “
Complex population dynamics as a competition between multiple-time-scale phenomena
,”
Phys. Rev. E
76
,
011908
(
2007
).
15.
Bhattacharjee
,
S. M.
and
Seno
,
F.
, “
A measure of data collapse for scaling
,”
J. Phys. A: Math. Gen.
34
,
6375
6380
(
2001
).
16.
Bi
,
D.
,
Yang
,
X.
,
Marchetti
,
M. C.
, and
Manning
,
M. L.
, “
Motility-driven glass and jamming transitions in biological tissues
,”
Phys. Rev. X
6
(
2
),
021011
(
2016
).
17.
Biebricher
,
C. K.
and
Eigen
,
M.
, “
The error threshold
,”
Virus Res.
107
,
117
127
(
2005
).
18.
Bull
,
J. J.
,
Meyers
,
L. A.
, and
Lachmann
,
M.
, “
Quasispecies made simple
,”
PLoS Comput. Biol.
1
(
6
),
e61
(
2005
).
19.
Buss
,
L. W.
,
The Evolution of Individuality
(
Princeton University Press
,
Princeton
,
1988
).
20.
Cavagna
,
A.
,
Cimarelli
,
A.
,
Giardina
,
I.
,
Parisi
,
G.
,
Santagati
,
R.
,
Stefanini
,
F.
, and
Viale
,
M.
, “
Scale-free correlations in starling flocks
,”
Proc. Natl. Acad. Sci. U.S.A.
107
(
26
),
11865
11870
(
2010
).
21.
Champagne-Ruel
,
A.
and
Charbonneau
,
P.
, “
A mutation threshold for cooperative takeover
,”
Life (Basel)
12
(
2
),
254
(
2022
).
22.
Choi
,
S.-S.
,
Jung
,
K.
, and
Kim
,
J. H.
, “
Phase transition in a random NK landscape model
,” in
Proceedings of the 2005 Conference on Genetic and Evolutionary Computation
(
ACM Press
,
New York
,
2005
), pp.
1241
1248
.
23.
Clar
,
S.
,
Monetti
,
R. A.
, and
Schwabl
,
F.
, “
Critical behavior of an evolution model
,” in
Fourth Granada Lectures in Computational Physics. Lecture Notes in Physics
, edited by
P. L.
Garrido
and
J.
Marro
(
Springer
,
Berlin
,
1997
), Vol. 493, pp. 287–288.
24.
Crotty
,
S.
,
Cameron
,
C. E.
, and
Andino
,
R.
, “
RNA virus error catastrophe direct molecular test by using ribavirin
,”
Proc. Natl. Acad. Sci. U.S.A.
98
,
6895
6900
(
2001
).
25.
Damuth
,
J.
and
Heisler
,
I. L.
, “
Alternative formulations of multilevel selection
,”
Biol. Philos.
3
,
407
430
(
1988
).
26.
Dapp
,
M. J.
,
Clouser
,
C. L.
,
Patterson
,
S.
, and
Mansky
,
L. M.
, “
5-Azacytidine can induce lethal mutagenesis in human immunodeficiency virus type 1
,”
J. Virol.
83
(
22
),
11950
11958
(
2009
).
27.
Dees
,
N. D.
and
Bahar
,
S.
, “
Noise-optimized speciation in an evolutionary model
,”
PLoS One
5
(
8
),
e11952
(
2010
).
28.
Delneri
,
D.
,
Colson
,
I.
,
Grammenoudi
,
S.
,
Roberts
,
I. N.
,
Louis
,
E. J.
, and
Oliver
,
S. G.
, “
Engineering evolution to study speciation in yeasts
,”
Nature
422
,
68
72
(
2003
).
29.
de Vladar
,
H. P.
and
Barton
,
N. H.
, “
The contribution of statistical physics to evolutionary biology
,”
Trends Ecol. Evol.
26
(
8
),
424
432
(
2011
).
30.
Domany
,
E.
and
Kinzel
,
W.
, “
Directed percolation in two dimensions: Numerical analysis and an exact solution
,”
Phys. Rev. Lett.
47
(
1
),
5
8
(
1981
).
31.
Domany
,
E.
and
Kinzel
,
W.
, “
Equivalence of cellular automata to ising models and directed pecolation
,”
Phys. Rev. Lett.
53
(
4
),
311
314
(
1984
).
32.
Drossel
,
B.
, “
Biological evolution and statistical physics
,”
Adv. Phys.
50
(
2
),
209
295
(
2001
).
33.
Duffy
,
S.
, “
Why are RNA virus mutation rates so damn high?
,”
PLoS Biol.
16
(
8
),
e3000003
(
2018
).
34.
Dyson
,
F. J.
,
Origins of Life
(
Cambridge University Press
,
Cambridge
,
1999
).
35.
Eigen
,
M.
, “
Self-organization of matter and evolution of biologial macromolecules
,”
Naturwissenschaften
58
,
465
523
(
1971
).
36.
Eigen
,
M.
, “
Natural selection: A phase transition?
,”
Biophys. Chem.
85
,
101
123
(
2000
).
37.
Eigen
,
M.
, “
Error catastrophe and antiviral strategy
,”
Proc. Natl. Acad. Sci. U.S.A.
99
(
21
),
13374
13376
(
2002
).
38.
Eigen
,
M.
,
McCaskill
,
J.
, and
Schuster
,
P.
, “
Molecular quasi-species
,”
J. Phys. Chem.
92
,
6881
6891
(
1988
).
39.
Eigen
,
M.
and
Schuster
,
P.
, “
The hypercycle. A principle of natural selforganization: Part A: Emergence of the hypercycle
,”
Naturwissenschaften
64
,
541
565
(
1977
).
40.
Eldredge
,
N.
and
Gould
,
S. J.
, “
Punctuated equilibria An alternative to phyletic gradualism
,” in
Models in Paleobiology
, edited by
T. J. M.
Schopf
(
Freeman, Cooper & Company
,
San Francisco
,
1972
), pp.
82
115
.
41.
Ferreira
,
C. P.
and
Fontanari
,
J. F.
, “
Nonequilibrium phase transitions in a model for the origin of life
,”
Phys. Rev. E
65
,
021902
(
2002
).
42.
Feshenfeld
,
K. M.
,
Dickman
,
R.
, and
Bernardes
,
A. T.
, “
Survival-extinction phase transition in a bit-string population with mutation
,”
Phys. Rev. E
67
,
031915
(
2003
).
43.
Fisher
,
D. S.
, “
Sliding charge-density waves as a dynamic critical phenomenon
,”
Phys. Rev. B
31
,
1396
1427
(
1985
).
44.
Flierl
,
G.
,
Grünbaum
,
D.
,
Levin
,
S.
, and
Olson
,
D.
, “
From individuals to aggregations: The interplay between behavior and physics
,”
J. Theor. Biol.
196
,
397
454
(
1999
).
45.
Floría
,
L. M.
,
Gracia-Lázaro
,
C.
,
Gómez-Gardeñes
,
J.
, and
Moreno
,
Y.
, “
Social network reciprocity as a phase transition in evolutionary cooperation
,”
Phys. Rev. E
79
,
026106
(
2009
).
46.
Galluccio
,
S.
, “
Exact solution of the quasispecies model in a sharply peaked fitness landscape
,”
Phys. Rev. E
56
(
4
),
4526
4539
(
1997
).
47.
Gao
,
Y.
and
Culberson
,
J.
, “
An analysis of phase transitions in NK landscapes
,”
J. Art. Intell. Res.
17
,
309
322
(
2002
).
48.
Giavazzi
,
F.
,
Paoluzzi
,
M.
,
Macchi
,
M.
,
Bi
,
D.
,
Scita
,
G.
,
Manning
,
L. M.
,
Cerbino
,
R.
, and
Marchetti
,
M. C.
, “
Flocking transitions in confluent tissues
,”
Soft Matter
14
(
18
),
3471
3477
(
2018
).
49.
Glavin
,
D. P.
,
Burton
,
A. S.
,
Elsila
,
J. E.
,
Aponte
,
J. C.
, and
Dworkin
,
J. P.
, “
The search for chiral asymmetry as a potential biosignature in our solar system
,”
Chem. Rev.
120
,
4660
4689
(
2020
).
50.
Gleiser
,
M.
and
Walker
,
S. I.
, “
An extended model for the evolution of prebiotic homochirality: A bottom-up approach to the origin of life
,”
Orig. Life Evol. Biosph.
38
,
293
315
(
2008
).
51.
Gould
,
S. J.
,
Wonderful Life: The Burgess Shale and the Nature of History
(
Cambridge University Press
,
Cambridge
,
1989
).
52.
Gould
,
S. J.
,
The Structure of Evolutionary Theory
(
The Belknap Press of Harvard University Press
,
Cambridge, MA
,
2002
).
53.
Gould
,
S. J.
and
Eldredge
,
N.
, “
Punctuated equilibria: The tempo and mode of evolution reconsidered
,”
Paleobiology
3
(
2
),
115
151
(
1977
).
54.
Graci
,
J. D.
and
Cameron
,
C.
, “
Quasispecies, error catastrophe, and the antiviral activity of ribavirin
,”
Virology
298
,
175
180
(
2002
).
55.
Grant
,
P. R.
and
Grant
,
B. R.
, “
Speciation undone
,”
Nature
507
,
178
179
(
2014
).
56.
Grassberger
,
P.
, “
On phase transitions in Schlögl's second model
,”
Z. Phys. B
47
,
365
374
(
1982
).
57.
Grassberger
,
P.
, “
The Bak-Sneppen model for punctuated evolution
,”
Phys. Lett. A
200
,
277
282
(
1995
).
58.
Gravner
,
J.
,
Pitman
,
D.
, and
Gavrilets
,
S.
, “
Percolation on fitness landscapes: Effects of correlation, phenotype, and incompatibilities
,”
J. Theor. Biol.
248
,
627
645
(
2007
).
59.
Gu
,
C.-J.
,
Zheng
,
C.-Y.
,
Zhang
,
Q.
,
Shi
,
L.-L.
,
Li
,
Y.
, and
Qu
,
S.-F.
, “
An antiviral mechanism investigated with ribavirin as an RNA virus mutagen for foot-and-mouth disease virus
,”
J. Biochem. Mol. Biol.
39
(
1
),
9
15
(
2006
).
60.
Hart
,
G. R.
and
Ferguson
,
A. L.
, “
Error catastrophe and phase transition in the empirical fitness landscape of HIV
,”
Phys. Rev. E
91
(
3
),
032705
(
2015
).
61.
Heffern
,
E. F. W.
,
Huelskamp
,
H.
,
Bahar
,
S.
, and
Inglis
,
R. F.
, “
Phase transitions in biology: From bird flocks to population dynamics
,”
Proc. R. Soc. B
288
(
1961
),
20211111
(
2021
).
62.
Hein
,
J.
,
Schierup
,
M. H.
, and
Wiuf
,
C.
,
Gene Genealogies, Variation and Evolution: A Primer in Coalescent Theory
(
Oxford University Press Inc.
,
New York
,
2005
).
63.
Henkel
,
M.
,
Hinrichsen
,
H.
, and
Lübeck
,
S.
,
Non-Equilibrium Phase Transitions Volume I: Absorbing Phase Transitions
(
Springer
,
Dordrecht
,
2008
).
64.
Hinrichsen
,
H.
, “
Non-equilibrium critical phenomena and phase transitions into absorbing states
,”
Adv. Phys.
49
(
7
),
815
958
(
2000
).
65.
Houchmandzadeh
,
B.
and
Vallade
,
M.
, “
Clustering in neutral ecology
,”
Phys. Rev. Lett.
68
,
061912
(
2003
).
66.
Hubbell
,
S. P.
,
The Unified Neutral Theory of Biodiversity and Biogeography
(
Princeton University Press
,
Princeton
,
2001
).
67.
Inui
,
N.
and
Tretiakov
,
A.
, “
Nonequilibrium phase transition of contact processes with the kauffman NK model
,”
Phys. Rev. E
85
,
021123
(
2012
).
68.
Janssen
,
H. K.
, “
On the nonequilibrium phase transition in reaction-diffusion systems with an absorbing stationary state
,”
Z. Phys. B
42
,
151
154
(
1981
).
69.
Jeancolas
,
C.
,
Malaterre
,
C.
, and
Nghe
,
P.
, “
Thresholds in origin of life scenarios
,”
iScience
23
(
11
),
101756
(
2020
).
70.
Jovanović
,
B.
,
Buldyrev
,
S. V.
,
Havlin
,
S.
, and
Stanley
,
H. E.
, “
Punctuated equilibrium and ‘history-dependent’ percolation
,”
Phys. Rev. E
50
(
4
),
R2403
R2406
(
1994
).
71.
Kabinger
,
F.
,
Stiller
,
C.
,
Schmitzová
,
J.
,
Dienemann
,
C.
,
Kokic
,
G.
,
Hillen
,
H. S.
,
Höbartner
,
C.
, and
Cramer
,
P.
, “
Mechanism of molnupiravir-induced SARS-CoV-2 mutagenesis
,”
Nat. Struct. Molec. Biol.
28
,
740
746
(
2021
).
72.
Karev
,
G. P.
,
Berezovskaya
,
F. S.
, and
Koonin
,
E. V.
, “
Modeling genome evolution with a diffusion approximation of a birth-and-death process
,”
Bioinformatics
21
(
Suppl. 3
),
iii12
19
(
2005
).
73.
Kauffman
,
S. A.
, “
Autocatalytic sets of proteins
,”
J. Theor. Biol.
119
(
1
),
1
24
(
1986
).
74.
Kauffman
,
S. A.
,
The Origins of Order: Self-Organization and Selection in Evolution
(
Oxford University Press
,
New York
,
1993
).
75.
Kauffman
,
S. A.
, “
Approaches to the origin of life on earth
,”
Life (Basel)
1
(
1
),
34
48
(
2011
).
76.
Killingback
,
T.
,
Blok
,
H. J.
, and
Doebeli
,
M.
, “
Scale-free extinction dynamics in spatially structured host-parasitoid systems
,”
J. Theor. Biol.
241
,
745
750
(
2006
).
77.
Kimura
,
M.
, “
Evolutionary rate at the molecular level
,”
Nature
217
,
624
626
(
1968
).
78.
Kimura
,
M.
,
The Neutral Theory of Molecular Evolution
(
Cambridge University Press
,
Cambridge
,
1983
).
79.
King
,
D. M.
, “
Evolutionary dynamics of speciation and extinction
,”
Ph.D. dissertation
(
University of Missouri St. Louis/Missouri University of Science and Technology
,
2015
), see https://scholarsmine.mst.edu/doctoral_dissertations/2464/
80.
King
,
D. M.
,
Scott
,
A. D.
, and
Bahar
,
S.
, “
Multiple phase transitions in an agent-based evolutionary model with neutral fitness
,”
R. Soc. Open Sci.
4
(
4
),
170005
(
2017
).
81.
Kleindorfer
,
S.
,
O’Connor
,
J. A.
,
Dudaniec
,
R. Y.
,
Myers
,
S. A.
,
Robertson
,
J.
, and
Sulloway
,
F. J.
, “
Speciation collapse via hybridization in Darwin’s tree finches
,”
Am. Nat.
183
(
3
),
325
341
(
2014
).
82.
Kuhr
,
J. T.
,
Leisner
,
M.
, and
Frey
,
E.
, “
Range expansion with mutation and selection: Dynamical phase transition in a two-species eden model
,”
New J. Phys.
13
,
113013
(
2011
).
83.
Kussell
,
E.
,
Leibler
,
S.
, and
Grosberg
,
A.
, “
Polymer-population mapping and localization in the space of phenotypes
,”
Phys. Rev. Lett.
97
,
068101
(
2006
).
84.
Kussell
,
E.
and
Vucelja
,
M.
, “
Non-equilibrium physics and evolution—Adaptation extinction, and ecology: A key issues review
,”
Rep. Prog. Phys.
77
,
102602
(
2014
).
85.
Laurent
,
G.
,
Lacoste
,
D.
, and
Gaspard
,
P.
, “
Emergence of homochirality in large molecular systems
,”
Proc. Natl. Acad. Sci. U.S.A.
118
(
3
),
e201274118
(
2021
).
86.
Lavrentovich
,
M. O.
,
Korolev
,
K. S.
, and
Nelson
,
D. R.
, “
Radial Domany-Kinzel models with mutation and selection
,”
Phys. Rev. E
87
,
012103
(
2013
).
87.
Lawton-Keister
,
E.
and
Manning
,
M. L.
, “
Jamming and arrest of cell motion in biological tissues
,”
Curr. Opin. Cell. Biol.
72
,
146
155
(
2021
).
88.
Leuthäusser
,
I.
, “
An exact correspondence between eigen’s evolution model and a two-dimensional Ising system
,”
J. Chem. Phys.
84
,
1884
1885
(
1986
).
89.
Leuthäusser
,
I.
, “
Statistical-mechanics of eigen evolution model
,”
J. Stat. Phys.
48
,
343
360
(
1987
).
90.
Lewontin
,
R. C.
, “
The units of selection
,”
Ann. Rev. Ecol. System.
1
,
1
18
(
1970
).
91.
Lipowski
,
A.
and
Łopata
,
M.
, “
Model of biological evolution with threshold dynamics and infinitely many absorbing states
,”
Phys. Rev. E
60
(
2
),
1516
1519
(
1999
).
92.
Loeb
,
L. A.
,
Essigmann
,
J. M.
,
Kazazi
,
F.
,
Zhang
,
J.
,
Rose
,
K. D.
, and
Mullins
,
J. I.
, “
Lethal mutagenesis of HIV with mutagenic nucleoside analogs
,”
Proc. Natl. Acad. Sci. U. S. A.
96
(
4
),
1492
1497
(
1999
).
93.
López
,
C.
,
Ramos
,
F.
, and
Hernández-García
,
E.
, “
An absorbing phase transition from a structured active particle phase
,”
J. Phys.: Cond. Matt.
19
(
6
),
065133
(
2007
).
94.
Luz-Burgoa
,
K.
,
de Oliveira
,
S. M.
,
Schwämmle
,
V.
, and
Sá Martins
,
J. S.
, “
Thermodynamic behavior of a phase transition in a model for sympatric speciation
,”
Phys. Rev. E
74
,
021910
(
2006
).
95.
Marshall
,
C.
, “
Explaining the Cambrian ‘explosion’ of animals
,”
Ann. Rev. Earth Planet. Sci.
34
,
355
384
(
2006
).
96.
Mathis
,
C.
,
Bhattacharya
,
T.
, and
Walker
,
S. I.
, “
The emergence of life as a first-order phase transition
,”
Astrobiology
17
(
3
),
266
276
(
2017
).
97.
Maynard Smith
,
J.
and
Szathmáry
,
E.
,
The Major Transitions in Evolution
(
Oxford University Press
,
Oxford
,
1998
).
98.
McKinnon
,
J. S.
and
Taylor
,
E. B.
, “
Species choked and blended
,”
Nature
482
,
313
314
(
2012
).
99.
Mendonça
,
J. R. G.
and
de Oliveira
,
M. J.
, “
An extinction-survival-type phase transition in the probabilistic cellular automaton p182-q200
,”
J. Phys. A: Math. Theor.
44
,
155001
(
2011
).
100.
Meyer
,
M.
,
Havlin
,
S.
, and
Bunde
,
A.
, “
Clustering of independently diffusing individuals by birth and death processes
,”
Phys. Rev. E
54
(
5
),
5567
5570
(
1996
).
101.
Michod
,
R. E.
and
Nedelcu
,
A. M.
, “
On the reorganization of fitness during evolutionary transitions in individuality
,”
Integr. Comp. Biol.
43
,
64
73
(
2003
).
102.
Michod
,
R. E.
and
Roze
,
D.
, “
Cooperation and conflict in the evolution of individuality. III. Transitions in the unit of fitness
,” in
Mathematical and Computational Biology: Computational Morphogenesis, Hierarchical Complexity, and Digital Evolution
, edited by
C. L.
Nehaniv
(
American Mathematical Society
,
Providence, RI
,
1999
), Vol. 26, pp. 47–92.
103.
Mullins
,
J. I.
,
Heath
,
L.
,
Hughes
,
J. P.
,
Kicha
,
J.
,
Styrchak
,
S.
,
Wong
,
K. G.
,
Rao
,
U.
,
Hansen
,
A.
,
Harris
,
K. S.
,
Laurent
,
J.-P.
,
Li
,
D.
,
Simpson
,
J. H.
,
Essigmann
,
J. M.
,
Loeb
,
L. A.
, and
Parkins
,
J.
, “
Mutation of HIV-1 genomes in a clinical population treated with the mutagenic nucleoside KP1461
,”
PLoS One
6
(
1
),
e15135
(
2011
).
104.
Nichol
,
S.
, “
Life on the edge of catastrophe
,”
Nature
384
,
218
219
(
1996
).
105.
Nowak
,
M.
, “
Five rules for the evolution of cooperation
,”
Science
314
(
5805
),
1560
1563
(
2006
).
106.
Nowak
,
M.
and
Ohtsuki
,
H.
, “
Prevolutionary dynamics and the origin of evolution
,”
Proc. Natl. Acad. Sci. U.S.A.
105
(
39
),
14924
14927
(
2008
).
107.
Oborny
,
B.
,
Meszéna
,
G.
, and
Szabó
,
G.
, “
Dynamics of populations on the verge of extinction
,”
Oikos
109
,
291
296
(
2005
).
108.
Ojosnegros
,
S.
,
Perales
,
C.
,
Mas
,
A.
, and
Domingo
,
E.
, “
Quasispecies as a matter of fact: Viruses and beyond
,”
Vir. Res.
162
,
203
215
(
2011
).
109.
Okasha
,
S.
,
Evolution and the Levels of Selection
(
Oxford University Press
,
New York
,
2006
).
110.
Ordway
,
S. W.
, “
Critical behavior in evolutionary and population dynamics
,”
Ph.D. dissertation
(
University of Missouri St. Louis/Missouri University of Science and Technology
,
2021
), see https://irl.umsl.edu/dissertation/1120.
111.
Ordway
,
S. W.
,
King
,
D. M.
,
Friend
,
D.
,
Noto
,
C.
,
Phu
,
C.
,
Huelskamp
,
H.
,
Inglis
,
R. F.
,
Olivas
,
W.
, and
Bahar
,
S.
, “
Phase transitions in yeast and bacterial populations under stress
,”
R. Soc. Open Sci.
7
(
7
),
192211
(
2020
).
112.
Paczuski
,
M.
,
Maslov
,
S.
, and
Bak
,
P.
, “
Field theory for a model of self-organized criticality
,”
Europhys. Lett.
27
(
2
),
97
102
(
1994
).
113.
Pastor-Satorras
,
R.
and
Solé
,
R. V.
, “
Field theory for a reaction-diffusion model of quasispecies dynamics
,”
Phys. Rev. E
64
(
5 Pt 1
),
051909
(
2001
).
114.
Peichel
,
C. L.
,
Nereng
,
K. S.
,
Ohgi
,
K. A.
,
Cole
,
B. L.
,
Colosimo
,
P. F.
,
Buerkle
,
C. A.
,
Schluter
,
D.
, and
Kingsley
,
D. M.
, “
The genetic architecture of divergence between threespine stickleback species
,”
Nature
414
(
6866
),
901
905
(
2001
).
115.
Quer
,
J.
,
Huerta
,
R.
,
Novella
,
I. S.
,
Tsimring
,
L.
,
Domingo
,
E.
, and
Holland
,
J. J.
, “
Reproducible nonlinear population dynamics and critical points during replicative competitions of RNA virus quasispecies
,”
J. Mol. Biol.
264
,
465
471
(
1996
).
116.
Ramos
,
F.
,
López
,
C.
,
Hernández-García
,
E.
, and
Muñoz
,
M. A.
, “
Crystallization and melting of bacteria colonies and Brownian bugs
,”
Phys. Rev. E
77
,
021102
(
2008
).
117.
Ray
,
T. S.
and
Jan
,
N.
, “
Anomalous approach to the self-organized critical state in a model for ‘life at the edge of chaos,’
Phys. Rev Lett.
72
(
25
),
4045
4048
(
1994
).
118.
Ray
,
T. S.
and
Jan
,
N.
, “
Ray and Jan reply
,”
Phys. Rev. Lett.
75
(
5
),
982
(
1995
).
119.
Ribeiro
,
F.
and
Caticha
,
N.
, “
Emergence and loss of assortative mating in sympatric speciation
,”
J. Theor. Biol.
258
,
465
477
(
2009
).
120.
Roze
,
D.
and
Michod
,
R. E.
, “
Mutation, multilevel selection, and the evolution of propagule size during the origin of multicellularity
,”
Am. Nat.
158
(
6
),
638
654
(
2001
).
121.
Rudman
,
S. M.
and
Schluter
,
D.
, “
Ecological impacts of reverse speciation in threespine stickleback
,”
Curr. Biol.
26
,
490
495
(
2016
).
122.
Saakian
,
D. B.
,
Biebricher
,
C. K.
, and
Hu
,
C.-K.
, “
Phase diagram for the eigen quasispecies theory with a truncated fitness landscape
,”
Phys. Rev. E
79
,
041905
(
2009
).
123.
Sardanyés
,
J.
and
Elena
,
S. F.
, “
Error threshold in RNA quasispecies models with complementation
,”
J. Theor. Biol.
265
(
3
),
278
286
(
2010
).
124.
Sardanyés
,
J.
and
Solé
,
R. V.
, “
Bifurcations and phase transitions in spatially extended two-member hypercycles
,”
J. Theor. Biol.
234
,
468,482
(
2006
).
125.
Sarkar
,
N.
, “
Active-to-absorbing phase transition in an evolving population with mutation
,”
Phys. Rev. E
92
,
042110
(
2015
).
126.
Scheffer
,
M.
,
Bascompte
,
J.
,
Brock
,
W. A.
,
Brovkin
,
V.
,
Carpenter
,
S. R.
,
Dakos
,
V.
,
Held
,
H.
,
van Nes
,
E. H.
,
Rietkerk
,
M.
, and
Sugihara
,
G.
, “
Early-warning signals for critical transitions
,”
Nature
461
,
53
59
(
2009
).
127.
Scheffer
,
M.
,
Carpenter
,
S. R.
,
Lenton
,
T. M.
,
Bascompte
,
J.
,
Brock
,
W.
,
Dakos
,
V.
,
van de Koppel
,
J.
,
van d Leemput
,
I. A.
,
Levin
,
S. A.
,
van Nes
,
E. H.
,
Pascual
,
M.
, and
Vandermeer
,
J.
, “
Anticipating critical transitions
,”
Science
338
,
344
348
(
2012
).
128.
Schuster
,
P.
, “
How do RNA molecules and viruses explore their worlds?
,” in
Complexity Metaphors, Models and Reality (Santa Fe Institute Series)
, edited by
G.
Cowan
,
D.
Pines
, and
D.
Meltzer
(
Addison Wesley
,
1994
), pp.
383
418
.
129.
Scott
,
A. D.
, “
Speciation dynamics of an agent-based evolution model in phenotype space
,”
Ph.D. dissertation
(
University of Missouri St. Louis/Missouri University of Science and Technology
,
2014
), see http://scholarsmine.mst.edu/doctoral_dissertations/2270/
130.
Scott
,
A. D.
,
King
,
D. M.
,
Marić
,
N.
, and
Bahar
,
S.
, “
Clustering and phase transitions on a neutral landscape
,”
Europhys. Lett.
102
(
6
),
68003
(
2013
).
131.
Shelton
,
D. E.
and
Michod
,
R. E.
, “
Group and individual selection during evolutinary transitions in individuality
,”
Philos. Trans. R. Soc. B
375
,
20190364
(
2020
).
132.
Skanata
,
A.
and
Kussell
,
E.
, “
Evolutionary phase transitions in random environments
,”
Phys. Rev. Lett.
117
,
038104
(
2016
).
133.
Smith
,
E.
and
Morowitz
,
H.
, “
The phase transition paradigm for emergence
,” in
The Origin and Nature of Life on Earth The Emergence of the Fourth Geosphere
(
Cambridge University Press
,
Cambridge
,
2016
), pp.
424
538
.
134.
Smith
,
H. H.
,
Hyde
,
A. S.
,
Simkus
,
D. N.
,
Libby
,
E.
,
Maurer
,
E.
,
Graham
,
H. V.
,
Kempes
,
C. P.
,
Sherwood Lollar
,
B.
,
Chou
,
L.
,
Ellington
,
A. D.
,
Fricke
,
G. M.
,
Girguis
,
P. R.
,
Grefenstette
,
N. M.
,
Pozarycki
,
C. I.
,
House
,
C. H.
, and
Johnson
,
S. S.
, “
The grayness of the origin of life
,”
Life
11
(
6
),
498
(
2021
).
135.
Sneppen
,
K.
,
Bak
,
P.
,
Flyvberg
,
H.
, and
Jensen
,
M. H.
, “
Evolution as a self-organized critical phenomenon
,”
Proc. Natl. Acad. Sci. U.S.A.
92
,
5209
5213
(
1995
).
136.
Solé
,
R. V.
,
Manrubia
,
S. C.
,
Benton
,
M.
,
Kauffman
,
S.
, and
Bak
,
P.
, “
Criticality and scaling in evolutionary ecology
,”
Trends Evol. Ecol.
14
(
4
),
156
160
(
1999
).
137.
Sornette
,
D.
and
Dornic
,
I.
, “
Parallel Bak-Sneppen model and directed percolation
,”
Phys. Rev. E
54
(
4
),
3334
3338
(
1996
).
138.
Strefler
,
J.
,
Erdmann
,
U.
, and
Schimansky-Geier
,
L.
, “
Swarming in three dimensions
,”
Phys. Rev. E
78
,
031927
(
2008
).
139.
Suki
,
B.
, “
The major transitions of life from a network perspective
,”
Front. Physiol.
3
,
94
(
2012
).
140.
Summers
,
J.
and
Litwin
,
S.
, “
Examining the theory of error catastrophe
,”
J. Virol.
80
(
1
),
20
26
(
2006
).
141.
Swetina
,
J.
and
Schuster
,
P.
, “
Self-replication with errors: A model for polynucleotide replication
,”
Biophys. Chem.
16
,
329
345
(
1982
).
142.
Szabó
,
B.
,
Szöllösi
,
G. J.
,
Gönci
,
B.
,
Jurányi
,
Z. S.
,
Selmeczi
,
D.
, and
Vicsek
,
T.
, “
Phase transition in the collective migration of tissue cells: Experiment and model
,”
Phys. Rev. E
74
,
061908
(
2006
).
143.
Szathmáry
,
E.
, “
Toward major evolutionary transitions theory 2.0
,”
Proc. Natl. Acad. Sci. U.S.A.
112
(
33
),
10104
10111
(
2015
).
144.
Takeuchi
,
K. A.
,
Kuroda
,
M.
,
Chaté
,
H.
, and
Sano
,
M.
, “
Experimental realization of directed percolation criticality in turbulent liquid crystals
,”
Phys. Rev. E
80
(
5
),
051116
(
2009
).
145.
Tannenbaum
,
E.
,
Deeds
,
E. J.
, and
Shakhnovich
,
E. I.
, “
Equilibrium distribution of mutators in the single fitness peak model
,”
Phys. Rev. Lett.
91
(
13
),
138105
(
2003
).
146.
Tarazona
,
P.
, “
Error threshold for molecular quasispecies as phase transitions: From simple landscapes to spin-glass models
,”
Phys. Rev. A
45
,
6038
6050
(
1992
).
147.
Tlusty
,
T.
, “
A model for the emergence of the genetic code as a transition in a noisy information channel
,”
J. Theor. Biol.
249
(
2
),
331
342
(
2007
).
148.
Tlusty
,
T.
, “
A colorful origin for the genetic code: Information theory, statistical mechanics and the emergence of molecular codes
,”
Phys. Life Rev.
7
(
3
),
362
376
(
2010
).
149.
Tüzel
,
E.
and
Sevim
,
V.
, “
And Erzan A., ‘strategies for the evolution of sex
,”
Phys. Rev. E
64
,
061908
(
2001
).
150.
Vanchurin
,
V.
,
Wolf
,
Y. I.
,
Koonin
,
E. V.
, and
Katsnelson
,
M. I.
, “
Thermodynamics of evolution and the origin of life
,”
Proc. Natl. Acad. Sci. U.S.A.
119
(
6
),
e2120042119
(
2022
).
151.
Vicsek
,
T.
,
Czirók
,
A.
,
Ben-Jacob
,
E.
,
Cohen
,
I.
, and
Shochet
,
O.
, “
Novel type of phase transition in a system of self-driven particles
,”
Phys. Rev. Lett.
75
(
6
),
1226
1229
(
1995
).
152.
Volkenstein
,
M. V.
, “
Punctualism, non-adaptationism, neutralism and evolution
,”
BioSystems
20
(
3
),
289
304
(
1987
).
153.
Volkenstein
,
M. V.
and
Livshits
,
M. A.
, “
Speciation and bifurcations
,”
BioSystems
23
(
1
),
1
5
(
1989
).
154.
Vonlanthen
,
P.
,
Bittner
,
D.
,
Hudson
,
A. G.
,
Young
,
K. A.
,
Müller
,
R.
,
Lundsgaard-Hansen
,
B.
,
Roy
,
D.
,
Di Piazza
,
S.
,
Largiader
,
C. R.
, and
Seehausen
,
O.
, “
Eutrophication causes speciation reversal in whitefish adaptive radiations
,”
Nature
482
,
357
362
(
2012
).
155.
Waclaw
,
B.
,
Allen
,
R. J.
, and
Evans
,
M. R.
, “
Dynamical phase transition in a model for evolution with migration
,”
Phys. Rev. Lett.
105
,
268101
(
2010
).
156.
Wakeley
,
J.
,
Coalescent Theory: An Introduction
(
Colorado Roberts & Company
,
Greenwood Village
,
2009
).
157.
Wallace
,
R.
, “
A new formal perspective on ‘Cambrian explosions’
,”
Comptes Rend. Biol.
337
,
1
5
(
2014
).
158.
Weinberger
,
E.
, “
A model of natural selection that exhibits a dynamic phase transition
,”
J. Stat. Phys.
49
(
5/6
),
1011
1028
(
1987
).
159.
Wilke
,
C. O.
, “
Quasispecies theory in the context of population genetics
,”
BMC Evol. Biol.
5
,
44
(
2005
).
160.
Wolfe
,
K.
, “
Speciation reversal
,”
Nature
422
,
25
26
(
2003
).
161.
Woo
,
H.-J.
and
Wallqvist
,
A.
, “
Nonequilibrium phase transitions associated with DNA replication
,”
Phys. Rev. Lett.
106
,
060601
(
2011
).
162.
Wu
,
M.
and
Higgs
,
P. G.
, “
The origin of life is a spatially localized stochastic transition
,”
Biol. Dir.
7
,
42
(
2012
).
163.
Young
,
W. R.
,
Roberts
,
A. J.
, and
Stuhne
,
G.
, “
Reproductive pair correlations and the clustering of organisms
,”
Nature
412
,
328
331
(
2001
).
You do not currently have access to this content.