mathematics
Article
Modelling Functional Shifts in Two-Species Hypercycles
Bernat Bassols 1, * , Ernest Fontich 2 , Daniel Oro 3 , David Alonso 3






Citation: Bassols, B.; Fontich, E.; Oro,
D.; Alonso, D.; Sardanyés, J.
Modelling Functional Shifts in
Two-Species Hypercycles.
Mathematics 2021, 9, 1809. https://
doi.org/10.3390/math9151809
Academic Editors: Jan Awrejcewicz
and José A. Tenreiro Machado
Received: 2 July 2021
Accepted: 23 July 2021
Published: 30 July 2021
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Copyright: © 2021 by the authors.
Licensee MDPI, Basel, Switzerland.
This article is an open access article
distributed under the terms and
conditions of the Creative Commons
Attribution (CC BY) license (https://
creativecommons.org/licenses/by/
4.0/).
Mathematics 2021, 9, 1809. https://doi.org/10.3390/math9151809
and Josep Sardanyés 4, *
1 Department of Mathematics, Imperial College London, London SW7 2AZ, UK
2 Departament de Matemàtiques i Informàtica, Universitat de Barcelona (UB), Gran Via de les
Corts Catalanes 585, 08007 Barcelona, Spain; fontich@ub.edu
3 Theoretical and Computational Ecology Laboratory, Center for Advanced Studies of Blanes (CEAB-CSIC),
Accés Cala Sant Francesc 14, 17300 Blanes, Spain; d.oro@csic.es (D.O.); dalonso@ceab.csic.es (D.A.)
4 Centre de Recerca Matemàtica, Edicici C, Campus de Bellatera, 08193 Cerdanyola del Vallès, Spain
* Correspondence: bb420@ic.ac.uk (B.B.); jsardanyes@crm.cat (J.S.)
Abstract: Research on hypercycles focuses on cooperative interactions among replicating species,
including the emergence of catalytic parasites and catalytic shortcircuits. Further interactions may be
expected to arise in cooperative systems. For instance, molecular replicators are subject to mutational
processes and ecological species to behavioural shifts due to environmental and ecological changes.
Such changes could involve switches from cooperative to antagonistic interactions, in what we call a
functional shift. In this article, we investigate a model for a two-member hypercycle model, considering
that one species performs a functional shift. First, we introduce the model dynamics without
functional shifts to illustrate the dynamics only considering obligate and facultative cooperation.
Then, two more cases maintaining cross-catalysis are considered: (i) a model describing the dynamics
of ribozymes where a fraction of the population of one replicator degrades the other molecular
species while the other fraction still receives catalytic aid; and (ii) a system in which a given fraction
of the population predates on the cooperating species while the rest of the population still receives
aid. We have characterised the key bifurcation parameters determining extinction, survival, and
coexistence of species. We show that predation, regardless of the fraction that benefits from it, does
not significantly change dynamics with respect to the degradative case (i), thus conserving dynamics
and bifurcations. Their biological significance is interpreted, and their potential implications for the
dynamics of early replicators and ecological species are outlined.
Keywords: cooperation; dynamical systems; functional shifts; ribozymes; origins of life; behavioural
ecology
1. Introduction
Hypercycles are catalytic networks of self-replicating species able to catalyse the
replication of another single species as they all form a closed loop (see Figure 1a,b) [1,2].
Originally, the hypercycle was suggested to allow for the cooperative selection of compet-
ing replicators in the origins of life, ensuring the stability of broad contents of information,
contrarily to non-catalytically joint replicators, i.e., quasispecies [3,4]. Hypercycles have
been suggested as a possible molecular network of prebiotic replicators involving a crucial
step from the transition from inanimate to living chemistry [3,4] due to their potential
capacity of maintaining larger stable genetic contents as compared to quasispecies popula-
tions under large mutations [1,3]. The interest in hypercycles goes beyond the origin of life
problem, being a canonical model to investigate different dynamical systems, including
cooperation. The generality of the hypercycle replicator equations has allowed using this
model to explore virus replication dynamics [5–8], neural networks [9,10], the immune
system [11], or the emergence of language [12]. Moreover, several hypercycle-like systems
have been implemented experimentally. These include coiled-coil peptides [13], yeast cell
populations [14], and engineered bacteria growing with catalytic parasites [15].
https://www.mdpi.com/journal/mathematics
Mathematics 2021, 9, 1809 2 of 22

It has been argued that hypercycle units may need two minimal conditions to be
evolutionary stable [4,16], namely, catalytic activity and capacity to store information.
Good candidates fulfilling these two conditions are catalytic RNA molecules (ribozymes).
RNAs with stem and loop structures, similar to transference RNAs [17], are known to be
resistant to hydrolysis [18] and also have replicability potential [19,20]. Ribozymes are short
RNA molecules with catalytic activity similar to protein enzymes [21,22] and have been
considered as potential candidates for forming the first autonomous, self-replicating molec-
ular systems involved in the origins of life [4,16,19,23–26]. Different activities have been
described for natural and in vitro (e.g., peptide-bond formation [27]) evolved ribozymes.
Certain introns can catalyse their own excision (self-cleavage) from single-stranded RNA
(ssRNA) [20] and ligase reactions by RNA catalysts can occur even with short RNA se-
quences [28]. Moreover, the same RNA sequences can catalyse trans-esterification reactions
for the elongation of one monomer [20], ligation of two independent ssRNAs [29,30], and
cleavage of RNA into smaller sequences [20,22,31,32] (see also [26,33] for reviews). Recent
experiments have revealed that the combination of RNAs with cold-adaptative mutations
enabled catalysing the synthesis of an RNA sequence longer than itself (adding about
200 nucleotides) [34]. Other experiments have shown the spontaneous formation of cat-
alytic cycles and networks from mixtures of RNA fragments able to self-assemble into
self-replicating ribozymes [35], providing evidence for selective advantage of cooperative
systems composed of ribozymes.
Hypercycle equations have also been suggested as a suitable modelling framework to
investigate the dynamics of cooperation in complex ecosystems [36]. More recently, the
hypercycle theory and the spatio-temporal dynamics of cooperative ecological interactions
have been reviewed in the framework of landscape ecology [37]. Cooperation arises in a
multitude of ecological systems [38–42]. These include alarm calls, coalition formation,
predator inspection, cooperative breeding, protection against attacks by predators or
conspecifics, or cooperative hunting, among others. Examples of intra-specific cooperation
(individuals of the same species cooperate) are found, for instance, in females of the
vampire species Desmodus rotundus [43–45], which perform cooperative breeding (i.e.,
reciprocal altruism) by sharing blood between themselves. Cooperative hunting, in which
the individuals of a given species cooperate to catch the prey, has been described in
lions (Panthera leo) [46], brown hyenas (Hyaena brunnea) [47], wild chimpanzees (Pan
troglodites) [48], or the fish species Caranx ignobilis [49]. Invertebrate species, such as
arthropods, can also hunt cooperatively: Golden-web spiders (Nephila clavipes) [50], the
Stegodyphid spider (Stegodyphus mimosarum) [51], or the heteroptera Microvelia douglasi
atrolineata [52]. Examples of inter-specific cooperation (cooperation between individuals of
different species) have been described in the deep-sea tube worm Lamellibranchia luymesi
and microbial symbionts [40], as well as in arbuscular-mycorrhizal fungi, which form an
obligate symbiosis with more than 80% of plant species in all terrestrial habitats [42].
Up to now, most of the research on hypercycles has focused on the dynamics arising
from the processes of cooperation between replicators, and some works have also included
competition for resources (e.g., available mononucleotides or available space) [3,53] and
mutation processes [54–56]. In this sense, different architectural changes in hypercycles
jeopardising their stability and persistence have been thoroughly investigated to date,
mainly considering the so-called catalytic parasites [15,57–60] and, to a lesser extent, cat-
alytic short-circuits [61,62]. Both catalytic parasites and short-circuits involve modifications
in the cyclic catalytic patterns. The former involves the emergence (e.g., via mutation) of
a replicator that receives catalysis but does not reciprocate the catalytic aid. The latter
involves an internal catalytic connection generating a smaller catalytic cycle within the
full system.
Some authors have recently been interested in possible shifts in cooperation among
species and have used the hypercycle equations to evaluate the dynamics arising from
such shifts [63]. For instance, molecular replicators are subject to mutational processes and
ecological species to behavioural shifts due to environmental or ecological changes, and one
 Mathematics 2021, 9, 1809 3 of 22

might expect such species to switch from cooperative to antagonistic interactions in what
we call a functional shift. The dynamics arising due to functional shifts in hypercycles are
still unexplored. The impact of a shift from catalytic cooperation to directed degradation
has recently been studied in small discrete-time hypercycles [63]. For this particular case, it
was assumed that one of the hypercycle replicators (ribozyme) became a degrading species
instead of being cooperative. To the extent of our knowledge, no works have investigated
how these shifts may affect the stability of small hypercycles in time-continuous systems.

(a) Obligate two-member hypercycle (a) Facultative two-member hypercycle

exponential replication
heterocatalysis
S1 ! S1 heterocatalysis
!

including opportunistic
! " # (especially on eggs and chicks). Here S
predation ! 2

(c) RNA hypercycle with directed degradation (d) Ecological hypercycle with predation

exponential replication intrinsic growth rate

S1 heterocatalysis cooperation
! S1 !
β β
$ $
! !
degradation predation
(1 − β ) (1 − β )
including
nistic predation (especially on eggs opportunistic
and chicks). Here S2 predation (especially on eggs and chicks). Here S2

Fraction β receives catalysis from S1 Fraction β receives aid from S1

Fraction (1 − β) degrades population S1 Fraction (1 − β) predates population S1

Figure 1. The different hypercycle architectures studied in this article: (a) obligate two-species
hypercycle with heterocatalysis; (b) facultative system with heterocatalysis and autonomous self-
replication; (c) hypercycle including directed degradation of S1 by S2 while still keeping some
fractions of the population receiving catalytic aid; (d) two-species ecological hypercycle (e.g., wader
and seagull) including opportunistic predation (especially on eggs and chicks). Here, S2 consumes
S1 , while some individuals still receive cooperation from S1 .

Examples of functional shifts between cooperating species are found in different

ecosystems. For instance, large fish and mammal pelagic predators (tuna, sharks, dolphins)
likely cooperate to locate and handle small pelagic shoals [64], and the predation of sharks
on dolphins and tuna has been recorded [65,66]. Seabirds form inter-specific flocks that
cooperate to locate food at sea, and the predation that occurs at land while breeding
in colonies. Body size drives the predatory matrix, which increases its values when
environmental conditions worsen [67,68]. Waterbirds form inter-specific mixed colonies to
protect against predators (they can contain several different species of waders, terns, and
gulls), but some species may predate opportunistically (especially on eggs and chicks) on
heterospecifics or may exert kleptoparasitism for food, especially when the environment
is harsher [69–75]. Although this may be anecdotal, and the cooperation may be subtle,
marine mammals may “cooperate” to locate and capture prey, and at the same time, larger
species may exert some predation, e.g., killer whales on elephant seals [76].
Mathematics 2021, 9, 1809 4 of 22

In this article, we analyse two-species (labeled as S1 and S2 ) hypercycles considering,

together with cooperation, directed degradation and predation (see Figure 1). The paper is
organised as follows. In Section 2, we introduce the general model that considers crossed
cooperation, competition, and decay of the species and includes the interactions due to
the functional shifts. Section 3 contains the results of four different systems that can be
studied from the general model by removing some of the interactions. This allows a
better comprehension of the dynamics only considering cooperation (plus competition
and decay) between species and the dynamical changes arising from directed degradation
or predation. First, an obligate two-member hypercycle (Figure 1a), which has been
thoroughly investigated in Ref. [53] (see also [77]), is briefly commented. The same system
including autonomous self-replication for the two species (see Figure 1b) is explored. Then
we explore a hypercycle with a functional shift in a given fraction of S2 population, which
is able to degrade S1 while still providing catalytic aid to the first species (Figure 1c). This
system is inspired in two populations of ribozymes in which some molecules of one of
the species (the rest still receive catalysis) acquires the capacity to degrade the other one,
still maintaining the catalytic aid. Finally, we explore a similar system in an ecological
context considering that a given fraction of S2 population predates on S1 (the other fraction
receiving aid from S1 ) while maintaining the crossed cooperation. Section 4 is devoted to
some conclusions.

2. General Mathematical Model

Let us consider a two-member hypercycle with species S1 and S2 , and let x1 and
x2 represent their respective concentrations (population numbers). The mathematical
model we investigate adds further interactions to a standard two-member hypercycle [53]
considering processes of directed degradation or predation between the two species while
keeping some degree of cooperation between the hypercycle members. This model is given
by the following dynamical system:
 !

 x1 + x2

 ẋ1 = (α1 x1 + kx1 x2 ) 1 − − εx1 − (1 − β)ε 12 x1 x2 ,
 c0
! (1)

 x1 + x2

 ẋ2 = (α2 x2 + βηk kx1 x2 ) 1 − c
 − ηε εx2 + γ(1 − β)ε 12 x1 x2 ,
0

where all parameters except ηk and ηε are assumed to be bound in I = [0, 1] (see below),
and ηk , ηε ≥ 0. That is, parameters have non-negativity constraints: αi , k, ε, β, ε ij , ηk,ε , γ ≥ 0,
and c0 > 0, with i, j = 1, 2 and i 6= j. Each of the model parameters corresponds to the
following biological processes (see also Figure 1):
• αi : autonomous self-replication rate (Malthusian growth) of species i = 1, 2. αi 6= 0
implies that species can replicate themselves without the catalytic aid of the other replicator.
• k: the cross-catalytic replication parameter between S1 and S2 . In the case of S2 , the
term ηk allows considering a non-symmetric case in which both species are kinetically
different. The case ηk = 1 involves symmetric catalytic replication.
• c0 : known as the carrying capacity, which limits the population of replicators due to
finite resources or (implicit) space. Due to the large number of parameters, we will set
c0 = 1.
• ε: density-independent spontaneous degradation or death of the species. Analogously
to the characteristics of ηk , ηε 6= 1 allows considering a non-symmetric decay scenario
for S1 and S2 .
• ε 12 : the density-dependent degradation rate due to the cleavage (or predation, see
below) of species S1 by S2 . We notice that the degradative and predatory dynamics are
exclusive. That is, we do not consider a case with directed degradation and predation
taking place at the same time (these two different cases will be considered with γ = 0
or γ 6= 0, respectively).
Mathematics 2021, 9, 1809 5 of 22

• β: the fraction of the S2 population still receiving cooperation from S1 replication. The
term 1 − β corresponds to the rest of the S2 population that exerts the degradation or
the predation of species S1 .
• γ: the energetic efficiency coefficient from predation. It can be understood as the
amount of energy species S2 can gain from predating S1 and investing it for repro-
duction (due to energetic constraints γ < 1). As mentioned, the investigation of the
degradative model will be performed by setting γ = 0, while the predatory system
will consider 0 < γ < 1.
As previously mentioned, we focus on parameter values restricted to the interval
I = [0, 1], except for ηk , ηε since we are interested in asymmetric cases. Since the qualitative
dynamics mainly depends upon the relative relations between replication/growth and de-
cay/predation parameters, with such an interval we expect to gather all possible dynamics.
As mentioned, parameters β and γ are naturally found within this interval in order to be
biologically meaningful. Moreover, the carrying capacity has been set to 1 for simplicity.
The choice of a different value for c0 does not change dynamics qualitatively.
It is clear that for the system to hold biological meaning, the phase space is bounded
only to the first quadrant of R2 . In general terms, the system Equation (1) is able to model
the directed degradation of S1 by S2 for values of 0 ≤ β < 1 and γ = 0 that becomes
fully predatory when γ > 0. The term 1 − ( x1 + x2 )/c0 in Equation (1) is a logistic-like
function that introduces competition between the two hypercycle species, also bounding
the dynamics.
To provide a general modeling framework and investigate the interplay between
cooperation (plus competition and decay) and the functional shifts, i.e., directed degrada-
tion or predation, we have kept the cross-catalytic terms. A simpler system considering
that species S2 receives aid from S1 and a given fraction (1 − β), with 0 ≤ β < 1, of the
S2 population only exerts directed degradation (or predation) on S1 and the rest of the
population catalyses S1 can be also investigated by changing kx1 x2 to βkx1 x2 in ẋ1 ; and
βηk kx1 x2 to µηk x1 x2 in ẋ2 , µ being the rate of replication due to the catalysis performed by
S1 on S2 .

3. Results and Discussion

In this Section, we will investigate the dynamics of Equation (1) considering four dif-
ferent systems. Section 3.1 summarises the results for the obligate two-member hypercycle
in which the two species can only replicate catalytically (Figure 1a, see [53,77] for a detailed
investigation of this system). Section 3.2 provides further results on this system, including
the exponential (non-catalytic) replication of each species. In Section 3.3, we investigate the
model considering directed degradation, while Section 3.4 provides further results on the
model with predation.

3.1. Obligate Two-Member Hypercycle

Before analysing the models of interest given by directed degradation and predation,
it is interesting to start the analysis at a much simpler level. Here, we briefly summarise the
dynamics of an obligate two-member hypercycle (Figure 1a). This system, which considers
that a species can only replicate due to catalytic (cooperative) processes, can be obtained
from Equation (1), setting α1 = α2 = γ = 0 and β = 1. This model is given by
(
ẋ1 = Φ1 ( x1 , x2 ) = kx1 x2 (1 − x1 − x2 ) − εx1 ,
(2)
ẋ2 = Φ2 ( x1 , x2 ) = ηk kx1 x2 (1 − x1 − x2 ) − ηε εx2 .

This dynamical system was thoroughly investigated in Ref. [53] (see also [77]). The
system has three fixed points: the origin (0, 0) and the pair ((ηε /ηk )Γ± , Γ± ), where
r !
1 4εξ
Γ± = 1± 1− , (3)
2ξ k
Mathematics 2021, 9, 1809 6 of 22

and ξ := 1 + ηε /ηk . Note, however, that the expression Γ± is well defined only for
ε ≤ k/4ξ =: ε c . Otherwise, Γ± ∈ C. The origin is a locally asymptotically stable equilib-
rium, while Γ− is a saddle point and Γ+ can be either a stable node [53] or a weak stable
focus (see Appendix A). The pair Γ± suffers a saddle-node bifurcation at the critical value
ε c . Above this threshold, the origin becomes globally asymptotically stable (see Ref. [53]
for further details and the study of this system using spatially-explicit models).

3.2. Facultative Two-Member Hypercycle

The obligate two-member hypercycle is a simple case in which species depend explic-
itly on the presence of the other to survive. For S1 to replicate, S2 must be present in the
system, and vice versa [53]. We shall extend the previous model to a system that considers
both exponential replication and cross-catalysis, i.e., facultative hypercycle, proposing a
setting that has not been analysed in detail so far (see Refs. [78–80] for two-species faculta-
tive hypercycles with mutation and error tail). The coupled system of ODEs now involves
a parameter of autonomous replication (Malthusian growth), which can be introduced
in (1) setting α1,2 > 0, while maintaining with β = 1 and γ = 0. We thus consider:
(
ẋ1 = Φ1 ( x1 , x2 ) = (α1 x1 + kx1 x2 )(1 − x1 − x2 ) − εx1 ,
(4)
ẋ2 = Φ2 ( x1 , x2 ) = (α2 x2 + ηk kx1 x2 )(1 − x1 − x2 ) − ηε εx2 .
To understand this system, we may differentiate three cases depending on the relative
value of αi and ε. We will consider αi > ε for i = 1, 2, αi < ε < α j for i 6= j, and αi < ε for
i = 1, 2.
Solving Equation (4) for ẋ1 = ẋ2 = 0 gives five critical, i.e., equilibrium, points:
! !
α2 − ηε ε α1 − ε
(0, 0), 0, , ,0 , ( Γ ± , Ω ± ),
α2 α1

where √
ηε ηk k + ηε ηk α1 − ηε α2 − 2ηk α2 ± ηε ∆
Γ± = , (5)
2kηk (ηε + ηk )
√
− 2ηε α1 + ηk k − ηk α1 + a2 ± ∆
Ω± = , (6)
2k(ηε + ηk )
and
∆ = (k2 + (−4ε + 2α1 )k + α21 )ηk2 + ((−4ηε ε + 2α2 )k + sα1 α2 )ηk + α22 . (7)
The nullclines of the system are the set of solutions of Φ1 ( x1 , x2 ) = 0 and Φ2 ( x1 , x2 ) = 0
and determine the direction of the flow in the phase space. Most of the results presented
below will be obtained from the nullclines, which are given by:

kx22 − kx2 + x2 α1 + ε − α1
x1 = 0, x1 = − = : g ( x2 ) (8)
kx2 + α1

for Φ1 , and

ηk kx12 − ηk kx1 + x1 α2 + ηε ε − α2
x2 = 0, x2 = − = : h ( x1 ) (9)
ηk kx1 + α2

for Φ2 . The intersection point of a curve in Equation (8) with another in Equation (9) is
an equilibrium point, here denoted by ( x1∗ , x2∗ ), where the flow vanishes. Hence, we are
interested in the existence of such equilibria in the phase space (x1 , x2 > 0), as well as in
their stability.
Let us consider α1 , α2 /ηε > ε. The nullclines from Equations (8) and (9) allow for three
possible configurations, which are shown in Figure 2 and will be shown in the following
construction. These can be analytically separated by studying the relative position of each
Mathematics 2021, 9, 1809 7 of 22

curve’s intersection with the axes. On one hand, g( x2 ) crosses the x1 axis at the critical
point ((α1 − ε)/α1 , 0) and intersects with the x2 axis at (0, Θ± ), where
q
k − α1 ± k2 + (−4ε + 2α1 )k + α21
Θ± = . (10)
2k
Note that Θ± is well defined since for its square root to be real, it is needed that
ε < (k + α1 )2 /4k, and this holds since ε < α1 ≤ (k + α1 )2 /4k, indeed

(k + α1 )2 − 4kα1 = k2 + α21 − 2kα1 = (k − α1 )2 ≥ 0

( k + α1 )2 (11)
⇒ α1 ≤ .
4k
Similarly, h( x1 ) intersects with the x1 axis at (Λ± , 0) with
q
kηk − α2 ± ηk2 k2 + (−4ηε ε + 2α2 )kηk + α22
Λ± = (12)
2ηk k

and at (0, (α2 − ηε ε)/α2 ) with the x2 axis. Again, Λ± is well defined since for its square
root to be real we need
(kηk + α2 )2
ε≤ (13)
4ηk kηε
and we have

α2
(kηk + α2 )2 − 4ηk kηε = k2 ηk2 + α22 − 2kηk α2 = (kηk − α2 )2 ≥ 0
ηε
(14)
α2 (hηk + α2 )2
⇒ ≤ .
ηε 4ηk kηε

Thus, as expected
α2 (kηk + α2 )2
ε< ≤ . (15)
ηε 4ηk kηε
In order for the case in Figure 2a to take place, the following conditions must be fulfilled:

α1 − ε − α1 ( ηε α1 − ηk k − α2 )
< Λ+ ⇒ ε < ε 1 := , (16)
α1 ηk k

and
α2 − ηε ε α2 (kηε + ηε α1 − α2 )
< Θ+ ⇒ ε < ε 2 := . (17)
α2 ηε2 k
Therefore, we will encounter Figure 2b if ε 1 < ε < ε 2 and Figure 2c when ε 2 < ε < ε 1 .
Given the nature of the considered parameters and the curves g( x2 ) and h( x1 ), ε can not be
greater than both ε 1 and ε 2 simultaneously: Let us assume ε > ε 1 . We can express ε 1 and
ε 2 as
!
α2 − ηε α1
ε 1 = α1 1 + ,
ηk k
! (18)
α2 α2 − ηε α1
ε2 = 1− ,
ηε ηε k

and since ε < α1 , we have α2 − ηε α1 < 0. This implies ε 2 > α2 /ηε , and since ε < α2 /ηε , the
proof is finished. The negation of this statement allows us to justify the impossibility of
ε < ε 1 , ε 2 . Therefore, only the three scenarios presented in Figure 2 will be considered.
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isoclines. deaths
Solutions vs.of kẋdeaths
1 =a0 ±are 2
+ a21 ra
317 In conclusion, parameters # 1 and # allow us
2 been set to 1 for to have a certain
1 k +control
( 4# + 2aon1 ) k the
of318
eachofspecies. Figure
As long
each species. Direction
8.Asas theyasare
long ofboth
they thearedynamical
plotted
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higher black
than system
and# in
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than vector
redattractive
for ẋ2 = 0.
< # 1 ,species.
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coexistence
attractive possible
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without
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=without < .
#1 < # <# #an 2 . attractive
318
318 of# each As long as they are both higher than 2k coexistence w
319 athem
0.28, #being
= 0.4.them able
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= 0.17, a
k1=, aable
to /h# to
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20.59, together
extinct.
abecome with
0.96, isoclines
aHowever,
extinct. gconsider
However,
0.27. (0.17,
as ) and
x2soon kas , ah
as soon
20.40,
plotted
#xi1#)<>as
(/h ##.1(i in
1,
<0.28,
=
#Plotting black
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j , jis6 =
Sallows
species i,j , will
Sthree j 6= Parameters
become
will
i, since become
2 319 1 = 2 =Let #us=319 them
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2Note extinct. ± However,
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soonfor itsas
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(c)# i <by# (i = 1, 2), species
297
that Q well square root to be real it is needed
extinct.extinct. used: (a) # = 0.16, k = in0.74,
Figurea
298 17 =
as 0.28,
will beashown
2 = 0.4;
in the (b)following
# 0.17, k =
construction. 0.59, These
a 1 =can 0.96,
be =
analytically
a 2 0.27;
2 /4k, separated
320 320 this holds since # < a  ( k + a ) indeed
Figure 2. Possible dynamical
# = 0.17, k = 0.40,Figure 7. Possible
scenarios
studying
a1 = 0.28,
according
a2 =
299 the320 extinct.
dynamical
relative
0.78
toposition
the shape scenarios
of eachof the according
nullclines.
curve’s intersection to with
the shape
Solutions the ofaxes.ẋ1of
1= the
0 areisoclines.
1plotted Solutions
in black and of ẋ1 = 0 are
in red for ẋ2 = 0. The symmetry coefficients
plotted in black and
300 η and
k in red η have been set to 1 for the
ε for ẋ2 = 0. The symmetry coefficients have three plots. (k + abeen
1)
2 set1to
4ka =1 k for
2
+ a1the2ka
2 three
1 = (plots.
k a1 )2
On the one hand, g( x2 ) crosses the x1 axis at the previously introduced critical point, ((a1
( k + a1
#)/a1 ,corresponding
0) and intersects with the x2 axis at (0, Q±of
) where
# = 0.17, k = 297
0.40, a1 = 0.28, Let2 us consider a1 , a2 /hphase
a = The
0.78. portraits the three presented cases can be obtained)by
# > #. Plotting these isoclines allows three possible situations show
a1 
4k
q
further extending the study in on
thethe nullclines and the sign Φ1 and
ofThese Φ in the phase space,
ionVersion
May 10,May Possible dynamical
Figuresubmitted
2021 10,7.2021 to Journal
submitted 298 NotinSpecified
toscenarios
JournalFigure
according 7toas
Not Specified the will ofbe
shape theshown
isoclines. Solutions offollowing
a10±are k2 +construction.
kẋ1 = ( 4# + 2a1 )k19 a21 ??
+ of 19 of ??can 2be analytically separated b
plotted in black and in red for ẋ2 = 0. Theas we show
symmetry in have
coefficients Figure 3.toIt1Qfor
been set is interesting
± the
= three plots. to2knote that the. origin is a repulsive (24) node for
299 studying the relative position of each curve’s intersection with the axes.
all three scenarios, as its associated Jacobian matrix has positive eigenvalues α − ε and
, #<2 .# 1 , #Let
< # 1#297 2 . us consider a1 , a2 /h300
# > #. Plotting these #1 < isoclines
Note ## 1< <#Q
that
allows
2#.±< is well. defined
# 2three possible situations shown
since for its square root to be# 2 <it##is2<
real needed # 1#. < (k + a1 )2 /4k and1
<# 1#. <that
7onclusion, parameters # 1 andin# #1theallow α us − η
tothis ε.
have This
εus toahave implies
certain that critical points located on each axis are attractive, i.e., there will
acontrol aon 2 the ratio
theof
In298 conclusion, 7 as parameters 2and # 2 allow Thesea can bybirths vs. deaths
# <certain +control on ratio of births vs. deaths
in Figure will be shown following2 construction. be analytically separated
holds since 1 ) /4k,the
1x )( kcrosses indeed
studying the relative position of each curve’s On the one
intersection hand,
with the g (
axes. x axis at the
never be a complete extinction of both species simultaneously as they can survive without
2 1 previously introduced critical point, ((a1
8achofspecies. As long
each species.
299
Asaslong theyasare both
they arehigher than # than
both higher an attractive
# an attractive coexistence will
coexistence take
willplacetake without
place2without
300 #)/a1the , 0) need
and intersects
of the other.withFigure (the
k + ax 1 )2 axis
2
4ka1at
=( k20,+Q a21± )2kawhere
1 = (k a1 ) 0
m
90.96,
being
them able
a2 being
= On0.27.to
#the 0.17,
become
=able
one to kbecome
hand, g(0.40,
=extinct. 1 =
x2 ) crosses the0.28,
aHowever,
extinct. as
xHowever,
a
axis 2
at =
the0.78.
soonas as
soon
#
previously
i < as# #(i =
<
introduced
i 1,
# 2),
(i = 8.
critical1,Direction
species
2), S
species
point, (( j
a , jof
6 =the
Si,
j , jdynamical
will
6 = become
i, system
will become vector field for all possible situat
1 1
( k + a1 )2 (25)
0nct.
extinct.
#)/a1 , 0) and intersects with the x2 axis at (0, Q± ) where q
a1 , a2 /h# together with isoclines ) a1 g( x2 ) and h( x1 ) plotted in black and red, respe
Figure 7.
#<Possible ,##<
# 1(a) . #
# <,
dynamical
2 1 21 2# # . , # . scenarios according to the
# shape
<
(b) # #< of<
# # .
the
# << ## < .
isoclines.# . Solutions
1 , # . 2(a) k#2 = a0.16, of ẋ
k2 0.74, = 0
+ 1( a14#(c) are #
4k < # #
2a21 )ak2# 1+=<< <
2#
# .
# <
< ## < . # .
q
1
# 1< 2#used:
1 2 1±k = =+0.28, 2a 12
0.4;
1# <(b)# 2 .#1 = 10.17, k = 0.59, a1 =
plotted in black and in red for ẋ2 = k0. The a1 ± symmetry
k + ( 4# +coefficients
2 2a1 )k + a1 have
2 Q±been = set to 1 for=the three plots. . (2
Q± = . # = 0.17, k = 0.40, a(24) 1 0.28, 2k a2 = 0.78
2k
Let usNote
consider a1 , adefined
2 /h# > #. Plotting these isoclines allows# three possible situations shown
and root to be real it is needed that # < ( k + a1 )2 /4k an
that Q± is well Note
since for its square Q±toisbewell
that root real itdefined since
is needed that < (for
k + aits 2
square
1 ) /4k
igure 7this
asholds
willsince
be #shown in the 2 following
< a1  (k + a1 ) /4k, indeed construction. These can be analytically separated by
this holds since # < a1  (k + a1 )2 /4k, indeed
ying the relative position(kof each curve’s intersection with the axes.
+ a )2 4ka = k2 + a2 2ka = (k a )2 0
1 1 1 1 1
2 a )2
(k +(ak1 )+ k2 + a21 2ka1 = (k
4ka1 = (25) a1 )2 0
8. Direction 1 possible
FigureFigure
8. Direction of the of the dynamical
dynamical systemsystem vector
vector)field field
a1  for allfor all
possible situations
situations regarding
regarding # < # <
On the one hand, g( x2 ) crosses the x1 axis at the previously 4k introduced critical point, ((a1 (2
a1 , a2 /ha , atogether
2 /h# together with isoclines
with isoclines g( x2 )h(and
g( x2 ) and h( x1 ) plotted
x1 ) plotted in black in and
blackred, andrespectively.
red, respectively. Parameters (k + a1 )2
Parameters
1 , 0) and1#intersects with the x2 axis at (0, Q± ) where ) a 1 
0.28,
used: = 0.78.
a2used:
(a) # =(a)0.16,
# =k0.16,= 0.74,k =a0.74,
1 = a 1 =a0.28,
0.28, 2 = a 0.4;
2 =(b) 0.4; # =(b)0.17,
# =k0.17, = 0.59,k =a0.59,
1 = a 1 =a0.96,
0.96, 2 = a0.27; 0.27; (c)
2 = (c) 4k
# = # =k 0.17,
0.17, = k =a0.40,
0.40, = Figure
0.28,
a =a9. =All
0.28, possible
0.78
a 2
1the isoclines.
2 = 0.78 q
phase portraits for the two-member hypercycle with exponential replication
s according to the 1
shape of Solutions of ẋ 0 are
< # 1 #, #<
2. #1, #2. parameter higher k athan # < #2#<
1 ±1 itskdecay 1+< #(12 #.rate
= <+
4# #in2 .2a + a21 In particular, the# 2plots
both)kspecies. < ##have
<
2 <# 1 #.been 1.
< #obtained for
The symmetry Figure 8. Direction
Figure
coefficients have of the
8.QDirection
been setdynamical
of
tothe
1 for thesystem
dynamical
three system vector 1vector
plots. field for all for
field
. possible situations
all possible regarding
situations regarding
(24) # < # <
± =
the values: (a) a1 = 0.39, a2 = 2k 0.94, # = 0.14,# < #
Figure,
1k =# .
2 1,8.hkDirection
= 3.6, h# of
= the
2.95;dynamical system
(b) a1 = 0.77, #
a21 =<vector
0.51, . for all possible situati
# < ##field
2=
a1 , a2 /h
a#1 ,together with isoclines
a2 /h# together g( x2 ) and
with isoclines g( x2h)( xand1 ) plotted in black
h( x1 ) plotted inand red,
black and respectively. Parameters
red, respectively. Parameters
0.14, k = 0.28, hk = 3.6, h# = 2.95; (c) a1 = 0.27, a1 , aa22 /h together
= #0.93, withk isoclines
# = 0.16, 2 ) and
g( x0.35, x1 ) plotted in black and red, respec
h(1.45.
otting these used: isoclines
(a)
used: # allows
=(a) # =three
0.16, = 0.74,
k 0.16, possible
k =a10.74, situations
= 0.28,
a 1 =a20.28, ashown
= 0.4; 2 = (b)0.4;
# =(b) 0.17,
# =k 0.17,
= 0.59, = 0.3,
=
k =a10.59, 0.96,
a =
hk =
= 0.27;
a20.96,
h =
a2 #=(c) 0.27; (c)
e that Q± is well defined since for its square root to be real it used:is needed
(a) # =that0.16,# k<= + a1a11)2=/4k
(k0.74, and
0.28, a2 = 0.4; (b) # = 0.17, k = 0.59, a1 =
lowing construction.# = 0.17,#= k= 0.40,
0.17,
These k= = 0.28,
0.40,
a1can be = 0.78
a20.28, a2 = 0.78
a1 analytically
= separated by
holds since # < a1  (k + a1 )2 /4k, indeed # = 0.17, k = 0.40, a1 = 0.28, a2 = 0.78
urve’s intersection with the axes.
(k + a1 )2 4ka1 = k2 + a21 2ka1 = (k a1 )2 0
he x1 axis at the previously introduced critical point, ((a1 (25)
( k + a1 )2
at (0, Q± ) where ) a1 
4k
.# 1 , # 2 .
< # 1#, #<2q # 1 < ## 1<<# 2#. < # 2 . # 2 < ## 2<<# 1#. < # 1 .
2
a1 ± k + ( 4# + 2a1 )k + a1 2
3.ofThe
thedirection of the dynamical
vectorsystem vector Figure
field All
9.all possible phase portraits
# < # for the
α1two-member hypercycle with expo
FigureFigure Figure
8. Direction8. Direction dynamical
of system
the .dynamical system field for
vector all
field for
(24) allfor
possible possible
situations
possible situations
regarding
situations regarding
regarding <ε < , α2 /ηε together with
a1 , a2 /h 2k
nullclines
a # , together
a /h# together g ( x
with isoclines
with
2 ) and h ( x
isoclines ) plotted
g( x12 ) and in black and
x1 ) plotted
g( x h)(and red,
in black
h( x ) plotted
parameter
respectively.
inand
blackred,
and
higher
Parameters than
respectively. its
used: decay
(a)
Parameters
red, respectively. ε =rate in
0.16,
Parameters kboth
= species.
0.74, α 1 = In particular,
0.28, α 2 = 0.4; the plots hav
1 2 2 1
# =(b) ε# ==k0.17, 0.59, the==values: (a) = 0.39,
a0.96, 2a ==
a0.27; 0.94, # = 0.14, k = 1, hk = 3.6,phase
h# = 2.95; (b) a1 =
used: (a)
used: (a)0.16, = 0.74,
0.16, k k== a10.74, a=1 0.96,
=α10.28, =2 =
α
=a20.28, a20.27;
0.4; = (c)
(b)0.4;
# = ε2(b) 0.17,
# =k k0.17,
=0.17, 0.40, = 0.28,
k =aα10.59,
0.59, 1= ==0.78.
a11 =αa220.96, 2
Below,
0.27;we
(c) (c)display all possible
ts square# root ,#to be
.
< # 1portraits
#< # real
, # . it is needed that # < ( k + a
# 1 )
< /4k
# #< and
<# .
0.14,
# < k# =. 0.28, = 3.6, = 2.95; (c) # =<0.27,
# #< <# .
#
= <
0.93,
# . = 0.16, k = 0.3, hk = 0.3
# = 0.17,
# =k = 0.40,
0.17, =for
k2 =a110.40, athe
20.28,
1 =atwo-member
= 0.78
20.28, a2 = 0.78hypercycle with 1 exponential
#1< 2# 1 , # 2replication
.2
h kparameter h a
# higher than1its 2 decay
#1 <
a
2 rate
2#1< in #
# 2both
. 1 species.
indeed In particular, the plots have been obtained for the values: (a) α1 = 0.39, α2 = 0.94, ε = 0.14, k = 1, ηk = 3.6, ηε = 2.95;
(b) α1 = 0.77, α2 = 0.51, ε = 0.14, k = 0.28, ηk = 3.6, ηε = 2.95; (c) α1 = 0.27, α2 = 0.93, ε = 0.16, k = 0.3, ηk = 0.35, ηε = 1.45.
a1 = k2 + a21 Stable 2kaequilibria
1 = ( k are
2
0 with red solid circles.
a1 )denoted
( k + a1 )2 (25)
) a1  In conclusion, parameters ε 1 and ε 2 allow us to have certain control on the ratio of
FigureFigure
9. All 9. All possible
possible phase phase4kportraits
portraits for thefor the two-member
two-member hypercycle
hypercycle with exponential
with exponential replication
replication
births versus deaths of each species. As long as they are both higher than ε, an attractive
parameter
parameter higherhigher
than itsthan its decay
decay rate inrate
both inspecies.
both species. In particular,
In particular, the have
the plots plotsbeen
haveobtained
been obtained
for for
the values:
the values: (a) a1 (a) a1 =a0.39,
= 0.39, 2 = 0.94,
a 2 =# 0.94,
= 0.14,
# =k 0.14,
= 1,kh =
k =1,3.6,
h =
k #h 3.6,
= 2.95;
h # = 2.95;
(b) a 1 (b)
= 0.77,
a 1 =a 0.77,
2 = 0.51,
a 2 = # 0.51,
= #=
0.14, k = 0.28,
0.14, k = 0.28, hk = 3.6,
h = 3.6,
k h# = 2.95;
h = 2.95; (c)
# (c) a1 = 0.27,
a = 0.27,
1 a2 = 0.93,
a = 0.93, # = 0.16, k = 0.3,
2 # = 0.16, k = 0.3, hk = 0.35, h 0.35,
k h# = 1.45.
= h # = 1.45.
9. All possible
Figure Figure phase portraits
9. All possible for the for
phase portraits two-member hypercycle
the two-member with exponential
hypercycle replication
with exponential replication
< # 1 #, #< Figure 9. All possible phase portraits
# 1for the two-member hypercycle with expo
2 . # 1 , # 2parameter
. higher higher
parameter than itsthan
decay
its < #in
# 1rate
decay#< <# 2 #. in<
1rate
both # 2 . species.
species.
both In particular, the plots
In particular, thehave
plots <
# 2been
have< < #. <
##obtained
2 been 1.
#for
obtained for
Mathematics 2021, 9, 1809 9 of 22

coexistence will take place without them being able to become extinct. However, as soon
as ε i < ε (i = 1, 2), species S j , j 6= i, will become extinct.
Let us now consider the case α1 > ε, α2 < ε/ηε . The nullclines allow the five qualitative
distributions represented in Figure 4. Since they cannot be all obtained only by variations of
ε, it is more adequate to use a different control parameter, specifically α1 . Since α1 > ε, there
will always be at least another critical point apart from the origin located at ((α1 − ε)/α1 , 0).
This is a result of the exponential self-replication rate for species S1 being higher than its
decay and not needing species S2 for replication.

Figure 4. The direction of the dynamical system vector field for all possible situations regarding α1 > ε and α2 < ηε ε.
Below, we display a phase portrait of the system in the five possible situations studied. Specifically, the plots have
been obtained using the following parameters: (a) α1 = 0.3, α2 = 0.18, ε = 0.23, k = 0.29, ηk = 5.5, ηε = 2.3; (b) α1 =
0.24, α2 = 0.05, ε = 0.21, k = 0.37, ηk = 4.3, ηε = 1.2; (c) α1 = 0.34, α2 = 0.13, ε = 0.32, k = 1, ηk = 7.5, ηε = 2.75;
(d) α1 = 0.56, α2 = 0.13, ε = 0.32, k = 1, ηk = 7.5, ηε = 2.75; (e) α1 = 0.86, α2 = 0.14, ε = 0.17, k = 0.29, ηk = 7.5, ηε = 2.75.

It has already been seen in Equation (13) that h( x1 ) (red nullcline) intersects with axis
x1 as long as ε < (kηk + α2 )2 /(4ηk ηε k). If ε is greater than or equal to this value then, as
long as α1 > ε, there will only be two equilibrium points: the origin and ((α1 − ε)/α1 , 0), as
shown in Figure 4a. In this case, the origin is a saddle since its eigenvalues are α1 − ε > 0
in the x1 direction, and α2 − ηε ε < 0 in the x2 direction. The other equilibrium corresponds
to an attractive node since its eigenvalues are λ1 = ε − α1 < 0 in the x1 direction and

ε(εηk k + ηε α21 − ηk kα1 − α1 α2 )

λ2 = − < 0, (19)
α21

given the restriction on ε from Equation (13), in another direction, we can leave unspecified.
If ε is lower than the value given in (13), there is a possibility that more critical points
appear. As seen below, for the scenario in Figure 4b to take place, potential critical points
(Γ± , Ω± ) must be undefined, i.e., ε > ε c , which is equivalent to
p
− kηk − α2 + 2 εηk k(ηε + ηε )
α1 < =: α1c . (20)
ηk

In order to characterise cases in Figure 4c–e, we need to find the value of α1 for which the
nullclines intersect right on top of the x1 axis. After solving the corresponding equation,
the intersection at (Λ− , 0) happens if

2εηk k
α1 = q =: α1− . (21)
kηk + α2 + ηk2 k2 − (4ηε ε − 2α2 )kηk + α22
Mathematics 2021, 9, 1809 10 of 22

and at (Λ+ , 0) if

2εηk k
α1 = q =: α1+ . (22)
kηk + α2 − ηk2 k2 − (4ηε ε − 2α2 )kηk + α22

Note α1± are well defined since ε < (kηk + α2 )2 /(4ηk ηε k ). Therefore, we will see a
nullcline distribution similar to the one presented in Figure 4c if a1c < a1 < a1− , in Figure 4d
if a1− < a1 < a1+ , and in Figure 4e if α1+ < α1 .
As already stated, the origin is a saddle with positive eigenvalue in the x1 direction and
negative in the x2 . As for the critical point on the x1 axis, ((α1 − ε)/α1 , 0), its eigenvalues
are λ1 = ε − α1 < 0 in the x1 direction and λ2 from Equation (19) in another unspecified
direction. This last expression is positive for α1 ∈ (α1− , α1+ ) and negative elsewhere. By
Hartman’s theorem, we can conclude that it is a saddle in the case Figure 4d and an
attractive node in the rest. Note the degenerate situation for α1 = α1− , α1+ with a null
eigenvalue, while the other is still negative, thus being two stable equilibria. Representing
the vector field together with the nullclines allows us to see, as expected, that the critical
point (Γ− , Ω− ) present when α1c < α1 < α1− is a saddle and (Γ+ , Ω+ ) a stable node.
Figure 4 shows the corresponding phase portraits for all five possible scenarios commented.
In Figure 5, we present the bifurcation diagram in which all cases are probed using α1 as
the control parameter. First of all, the only stable critical point is the one located at the
x1 axis, as both nullclines do not intersect at (Γ± , Ω± ). After this region, there is a range,
(α1c , α1− ) = (0.3242, 0.3345), in which two equilibria are found. Indeed, one of them has
x2∗ = 0 corresponding to ((α1 − ε)/α1 , 0), while the other is (Γ+ , Ω+ ). Finally, the higher
equilibrium is lowered until it reaches the axis again and x2∗ becomes zero.

Figure 5. (Left) A bifurcation diagram when ε > (kηk + α2 )2 /(4ηk ηε k) using α1 ∈ (ε, 1) as control parameter for a set of
parameters such that the four cases in Figure 4b–e are present. Specifically, α2 = 0.14, ε = 0.26, k = 1, ηk = 2.75, ηε = 2.25.
Stable equilibria are represented in blue for x1∗ and in red for x2∗ coordinates. (Right) Close up of the diagram for α1 ∈ (α1c , α1− )
showing the coexistence of two stable equilibria; one of which implies the extinction of x2 .

A study regarding α1 < ε and α2 > ηε ε would bring us to a set of results analogous to
the ones exposed in the previous paragraphs because the symmetry of the problem allows
us to use the arguments already presented.
The last case we need to look into is when α1 < ε and α2 < ηε ε. Apart from the origin,
the other critical points there can be are (Γ± , Ω± ). These will be present as long as ε ≤ ε c
where the higher is an attractive node and the lower a saddle. At ε = ε c , the bifurcation
point, the critical point becomes a saddle-node, just as studied in Section 3.1.

3.3. Directed Degradation and Cooperation in Ribozymes

The next step towards the generalisation of the dynamical system to describe all
considered interactions is the addition of density-dependent degradation, describing the
Mathematics 2021, 9, 1809 11 of 22

process by which some replicators (ribozymes) can degrade the other hypercycle member
due to trans-cleaving activity. In order to do so, a new parameter must be introduced, β,
which may be regarded as the fraction of species S2 that receives catalysis from species
S1 , while (1 − β) does exactly the opposite with S2 degrading S1 at a rate ε 12 . In this case,
the cross-catalytic replication for species S2 is affected by the presence of this parameter as
only a fraction β of this species will receive catalysis.
For the sake of length and simplicity, this section is studied under the assumption that
α1 = α2 = ηε = k = c0 = 1, while ε, ε 12 , ηk and β are allowed to move freely. This lets us
focus strictly on the effect of the degradation behaviour led by S2 without over-complicating
the whole model. Furthermore, such restrictions have not been chosen arbitrarily but, in
fact, hold specific biological meaning and build the cases we are most interested in when
considering ribozyme interactions. Hence, the system we will focus on along this section is:
(
ẋ1 = ( x1 + x1 x2 )(1 − ( x1 + x2 )) − εx1 − (1 − β)ε 12 x1 x2 ,
(23)
ẋ2 = ( x2 + βηk x1 x2 )(1 − ( x1 + x2 )) − εx2 .

An analytical study, as has been carried out in the previous sections, shows that up to
three critical points in the first quadrant apart from the origin exist. As previously stated,
given α1 = α2 = 1 > ε = ηε ε, global extinction is impossible since the origin is a repulsive
node. As for the other equilibria, one is located on each axis representing the potential
survival of a single species without the need of the other. The third equilibrium is only
present for a set of values such that ηk > 0 and

ε
β > β bif = 1 − > 0, (24)
ε 12

stating that a certain amount of S2 higher than this specific threshold must collaborate with
S1 in order to achieve coexistence. Interestingly, for ε > ε 12 , both species evolve towards
their coexistence regardless of the initial conditions, as long as they are non-zero.
To prove the attractive behaviour of the critical point located outside the axes, we can
once again focus on the nullcline distribution. It is quite straightforward to see that bounded
to the x-axis, g( x ) > max{ h(0)}, where g( x1 ) and h( x2 ) have been defined analogously
to the previous sections. This describes the same scenario presented in Figure 3a, which
allows us to conclude this equilibrium is stable. The fact that g( x ) > max{h(0)} on the
abscissa tells us that shifting β to lower values results in the middle equilibrium to move
towards the critical point on the y-axis as long as ε ≤ ε 12 , i.e., β bif ≥ 0, until the critical
point leaves the phase space and a transcritical bifurcation takes place (β ≤ β bif ). See
Figure 6a,b. On the other hand, if ε > ε 12 , lowering β results in the approach of the critical
point present on the x-axis until β = 0, where they collide and a transcritical bifurcation
takes place as well. See Figure 6c,d.
Finally, a different behaviour is seen for ηk = 0, i.e., when S2 is unable to catalytically
replicate with the help of S1 . In this case, there are only three critical points in the region
of interest: the origin, which remains a repulsive node, and each individual survival.
If β > β bif , then the previous critical point approaches the equilibrium on the x −axis
as ηk is reduced until it reaches zero and is absorbed by it. However, for β < β bif , it
is the other equilibrium that becomes the ω −limit of the system. See Figure 6e and
Figure 6f, respectively.
Mathematics 2021, 9, 1809 12 of 22

Figure 6. Phase portraits of the system in the qualitatively different identified situations. Specifically, we have used: (a)
ε = 0.13, ε 12 = 0.72, β = 0.9, ηk = 1.7; (b) ε = 0.13, ε 12 = 0.72, β = 0.25, ηk = 1.7; (c) ε = 0.52, ε 12 = 0.22, β = 0.55, ηk = 0.8;
(d) ε = 0.52, ε 12 = 0.22, β = 0, ηk = 0.8; (e) ε = 0.25, ε 12 = 0.49, β = 0.8, ηk = 0; (f) ε = 0.25, ε 12 = 0.49, β = 0.14, ηk = 0.
Again, a red dot indicates the ω −limit of each orbit and a blue dot its initial condition.

The behaviour described above can be very well visualised by plotting three-dimensional
and heatmap bifurcation diagrams where the x1∗ or x2∗ equilibrium component is computed
for given parameters. This is possible given the fact that all orbits outside the axes will
evolve to the same equilibrium point and because the origin acts as a repulsive node at
all times. Thus, if we choose to plot x1∗ , i.e., the abscissa component of the equilibrium,
and it falls on 0, we can read that S1 has been extinguished, while S2 has survived. The
annihilation of S2 when ηk > 0 is only possible for ε > ε 12 and β = 0; therefore, it is more
adequate to represent x1∗ instead of x2∗ as the coexistence will be present as long as x1∗ > 0
and β 6= 0.
Keeping this argument in mind, Figure 7 collects all information presented in Figure 6a–c.
Indeed, we can see how the coexistence is present for β > β bif , while S1 ceases to exist
if β ≤ β bif . For ηk = 0, Figure 8 shows how x1∗ becomes zero if β < β bif , indicating that
S1 vanishes while S2 remains, and vice versa for β > β bif . In order to demonstrate that
coexistence is not possible in these scenarios, both x1∗ and x2∗ have been represented in
separate plots (Figure 8a,c and Figure 8b,d, respectively). Note that the coexistence that
can be observed on the curve β = β bif is not a mere casualty and is thoroughly explained
below.
As presented in Figure 8, the case β = β bif under ηk = 0 is quite interesting as well.
Here, both equilibria located on the axes are present; hence, the nullclines become the exact
same curves in the phase space. This translates to a continuum of fixed points filling the
attractive linear manifold x2 = 1 − ε − x1 . The dynamical system under these conditions
and the adequate simplification becomes:
(
ẋ1 = − x1 ( x2 + 1)( x1 + x2 + ε − 1),
(25)
ẋ2 = − x2 ( x1 + x2 + ε − 1).
Mathematics 2021, 9, 1809 13 of 22

(a) (b)
Figure 7. Two-parameter bifurcation diagram representing x1∗ as a function of ε 12 and β plotted as a surface (a) and as a
heat map (b) for a more intuitive understanding. Parameters used: ε = 0.2, ηk = 2.

Assuming ( x1 + x2 + ε − 1) 6= 0, we can compute the quotient ẋ1 / ẋ2 , allowing us to

find a first integral of the problem:
!
ẋ1 x1 ( x2 + 1) ẋ1 1
= ⇒ = 1+ ẋ2 , (26)
ẋ2 x2 x1 x2

integrating on both sides, we obtain

ln( x1 ) = x2 + ln( x2 ) + C, (27)

such that if initial conditions x1 (0), x2 (0) are the species initial conditions, Equation (27)
can be rewritten as
x1 (0)
x1 = x 2 e x2 − x2 (0) . (28)
x2 (0)
Taking H = ln( x1 ) − x2 − ln( x2 ) = 0 and X the system’s field, we have
 
x˙ 1
H 0 = h∇ H, X i = 1 − 1 + ẋ2 = 0 (29)
x1 x2

which confirms that the expression is a first integral. This result tells us that all orbits
outside the axes follow Equation (27) until they reach the stable line x2 = 1 − ε − x1 . This
is of course attractive since ẋ1 , ẋ2 > 0 for x1 + x2 < 1 − ε and ẋ1 , ẋ2 < 0 for x1 + x2 > 1 − ε.
The corresponding phase portrait for this setting is shown in Figure 9, where the solutions
can be seen to follow exactly the level curves of the first integral.
Interestingly enough, we are in front of a case of extreme equilibrium in which the
degrading species, S2 , is unable to cross-catalytically replicate with S1 , while S1 benefits
from this interaction with a fraction β of S2 but is degraded by a fraction 1 − β.
 Mathematics 2021, 9, 1809 14 of 22

Version May 10, 2021 submitted to Journal Not Specified 15 of 22

linear manifold x2 = 1 # x1 . The dynamical system under these conditions and the adequate
simplification becomes:
(
ẋ1 = x1 ( x2 + 1)( x1 + x2 + # 1)
(23)
ẋ2 = x2 ( x1 + x2 + # 1Version
). May 10, 2021 submitted to Journal Not Specified 16 o

Assuming ( x1 + x2 + # 1) 6= 0 we can compute the quotient ẋ1 / ẋ2 , allowing us to find a first integral
of the problem: Another
! case worth considering is that in which # = 0 and # 12 ⌧ 1, meaning that natu
ẋ1 x1 ( x2 + 1) ẋ1 1
degradation
= ) = 1+ ẋ2 , no longer present. This leaves
is (24) us with a system in which both species will only decre
ẋ2 x2 x1 x2 (a) x ∗
as a consequence Forx2∗# 12 = 0 the ODE system (1) becom
of the coupling term as long as x1 + x2 > 1.(b)
1
integrating on both sides we obtain (
ẋ1 = ( x1 + x1 x2 )(1 ( x1 + x2 ))
(
ln( x1 ) = x2 + ln( x2 ) + C, 2 + bhk x1 x2 )(1
ẋ2 = ( x(25) ( x1 + x2 )).

such that if initial conditions x1 (0) = A, x2 (0) = B, A, B 2These equations

(0, 1] are can beequation
considered, solved assuming
(25) can be1 ( x1 + x2 ) 6= 0, dividing ẋ1 over ẋ2 and organising b
rewritten as sides of the expression to find:
A
x 1 = x 2 e x2 B . (26) ! !
B 1 1
bhk + ẋ1 = 1 + ẋ2 , (
Of course, taking H = ln( x1 ) x2 ln( x2 ) = 0 and X the system’s field, we have x2 x2
✓ ◆
x˙1 1
which can be integrated resulting in
H 0 = hr H, X i = 1+ ẋ2 = 0 (27)
x1 x2
bhk x1 + ln( x1 ) = x2 + ln( x2 ) + C, (
proving again that the expression is a first integral. This result tells us that all orbits outside the axes
follow equation (25) until they reach the stable line x2313= 1where # C . This
x1= x1 (0is)+ oflncourse
( x1 (0))attractive
x2 (0) since
ln( x2 (0)). This curve describes the orbits followed by an ini
ẋ1 , ẋ2 > 0 for x1 + x2 < 1 # and ẋ1 , ẋ2 < 0 for x1 + > 1 (c)
314x2 condition#. This
(xx∗1 (0scenario’s
), x2 (0)) inphase portrait
the phase spaceis such that 1 ( x1(d) + xx2∗) 6= 0. Note that 1 ( x1 + x2 ) =
1 2
shown in Figure 12, where the solutions canFigure
be seen8.toTwo-parameter
follow
315 exactly the
a continuum offirst integral.
bifurcation diagram representing x1 (a,c) and xas
attractive equilibria and that the ∗origin acts a repulsive
∗ (b,d) node. Figure
as a function of ε 12 13 explic
2
Interestingly enough, we are in front of a case of extreme 316 equilibrium
shows this in which the Finally,
behaviour. degrading species,
as long as b > 0, a small variation in # 12 brings us straight to
and β plotted as a surface (a,b) and a heat map (c,d) for a more intuitive understanding. Parameters
S2 , is unable to cross-catalytically replicate with S1 , 317
while benefitsinfrom
S1 studied
case Figurethis??interaction
implying the with a
extinction of S1 , and a minor variation in # recovers Figure
used: ε = 0.13, ηk = 0.
fraction b of S2 but is degraded by a fraction 1 b. showing coexistence.
(a) (b)

Figure 12. Phase portrait showing a continuum of equilibrium points following

Figure x1 +
13. Phase x2 = 1 showing
portrait #. Initiala continuum of equilibrium points following x1 + x2 = 1. Initial
Figure 9. Phase portraits showing a continuum of equilibrium points following x1 + x2 = 1 − ε (line of quasi-neutral
conditions are represented with a blue dot and their w limit withconditions
a red dot. are
Specific parameters
represented withused:
a blue dot and their w limit with a red dot. Specific parameters used:
# = 0.25, # 12equilibria).
= 0.49, hk =Initial
0, andconditions are represented with
b = b bif = 0.8194. a blue dot and their ω −limit with a red dot. Specific parameters used are:
# = 0, # 12 = 0, hk = 0.8, and b = 0.5.
(a) ε = 0.25, ε 12 = 0.49, ηk = 0, and β =
318β bif = 0.8194; and (b) ε = 0, ε 12 = 0, ηk = 0.8, and β = 0.5.

3.3. Interplay between predation and cooperation in ecology

Another
319
case worth considering is that in which ε = 0 and ε 12  1, meaning that
natural degradation is no longer
All systems studiedpresent.
above have This
beenleaves us in
analysed with a system
order in awhich
to build up both hypercy
very general
model that allows us to consider all interactions presented in subsection 3.2 while S2 behaves a
predator. To summarise, our species are now under the influence of self-replication (ai > 0 for i = 1
and cross-catalytic replication (k, hk > 0), they are also degraded by natural causes (#, h# > 0), a fract
b of S2 cooperates with S1 , the rest of S2 (1 b) consumes S1 at a rate # 12 , and for the first time
benefits from this consumption, acting as a predator (with an efficiency g 2 (0, 1)). Indeed, we ha
Mathematics 2021, 9, 1809 15 of 22

species will only decrease as a consequence of the coupling term as long as x1 + x2 > 1.
For ε 12 = 0, the ODE system (1) becomes:
(
ẋ1 = ( x1 + x1 x2 )(1 − ( x1 + x2 )),
(30)
ẋ2 = ( x2 + βηk x1 x2 )(1 − ( x1 + x2 )).

These equations can be solved assuming 1 − ( x1 + x2 ) 6= 0, dividing ẋ1 over ẋ2 , and
organising both sides of the expression to find:
! !
1 1
βηk + ẋ = 1 + ẋ2 , (31)
x1 1 x2

which can be integrated resulting in

βηk x1 + ln( x1 ) = x2 + ln( x2 ) + C, (32)

where C = βηk x1 (0) + ln( x1 (0)) − x2 (0) − ln( x2 (0)). This curve describes the orbits
followed by an initial condition ( x1 (0), x2 (0)) in the phase space such that 1 − ( x1 (0) +
x2 (0)) 6= 0. Note that 1 − ( x1 + x2 ) = 0 is a continuum of attractive equilibria and that the
origin acts as a repulsive node. Figure 9b explicitly shows this behaviour. Finally, as long as
β > 0, a small variation in ε 12 brings us straight to the case studied in Figure 6b, implying
the extinction of S1 , and a minor variation in ε recovers Figure 6c, showing coexistence.

3.4. Interplay between Predation and Cooperation in Ecology

All systems studied above have been analysed in order to build up a general hyper-
cycle model that allows us to consider all interactions presented in Section 3.3 while S2
also behaves as a predator. Both species are now under the influence of self-replication
(αi > 0 for i = 1, 2) and cross-catalytic replication (k, ηk > 0), they are also degraded by
natural causes (ε, ηε > 0), a fraction β of S2 receives cooperation from S1 , the rest of S2
(1 − β) consumes S1 at a rate ε 12 , and for the first time, S2 benefits from this consumption
with an efficiency of γ ∈ (0, 1), acting as a predator. We now reached the system presented
in Equation (1), Section 2, with all parameters playing their corresponding biological roles:
(
ẋ1 = (α1 x1 + kx1 x2 )(1 − ( x1 + x2 )) − εx1 − (1 − β)ε 12 x1 x2 ,
(33)
ẋ2 = (α2 x2 + βηk kx1 x2 )(1 − ( x1 + x2 )) − ηε εx2 + γ(1 − β)ε 12 x1 x2 .

As we did above, we shall consider a simple scenario setting α1 = α2 = k = ηε = c0 = 1

to be able to analyse it mathematically and to obtain clearer results arising from predation.
Even though a new process is being considered in this case, surprisingly, the dynamics of
the predatory scenario behave exactly as those described in Section 3.3. Curiously enough,
although species S2 now grows at the expense of S1 , studying the relative positions of the
nullclines shows that for β > β bif = 1 − ε/ε 12 , there is coexistence while S1 vanishes for
β ≤ β bif (see Figures 10 and 11). As previously explained, the existence of the coexistence
equilibrium is given by the position of all four positive axis crossings of the nullclines.
∗ and claim that
We shall refer to the intersection of the x j nullcline with the xi −axis as xi,j
∗ < x ∗ and x ∗ > x ∗ for β > β , which implies the desired coexistence. Let us
x1,1 1,2 2,1 2,2 bif
compute these values explicitly. On the x1 axis, the intersections of interest happen at
∗
x1,1 = 1 − ε,
 q 
∗ 1 (34)
x1,2 = − βγε 12 + βηk + ε 12 γ − 1 + (− βγε 12 + βηk + ε 12 γ − 1)2 + 4βηk (1 − ε) ,
2βηk
Mathematics 2021, 9, 1809 16 of 22

for ẋ1 = 0 and ẋ2 , respectively. These values will coincide if

ε 12 γ
β= , (35)
ε 12 γ − εηk

which is greater than 1, positive for ε 12 γ > εηk , and negative for ε 12 γ < εηk . Notice that
the change of sign implies a change in the inequality such that for the considered range of
∗ < x ∗ . This is precisely the reason behind the non-alteration of
β, it can only be that x1,1 1,2
the dynamics under predatory behaviour. On the vertical axis, the crossings are given by
 q 
∗ 1 2 2
x2,1 = −ε 12 (1 − β) + ε 12 (1 − β) + 4(1 − ε) ,
2 (36)
∗
x2,2 = 1 − ε.
∗ = x ∗ occurs at the critical value
In this case, x2,1 2,2

ε
β = 1− = β bif , (37)
ε 12
∗ > x ∗ for β > β , a value that can very well be assumed by β. Thus, the claim
and x2,1 2,2 bif
follows, and we conclude that a dual behaviour within S2 concerning its interaction with
S1 does not modify the overall dynamics of the system. As expected, all equilibria are
found at values of S2 just above those studied in the preceding section since S2 is now
replicating from the extinction of S1 . Moreover, the results found for β = β bif are now
independent of ηk as the influence of γ on the system makes coexistence impossible under
such assumptions (see Figure 11a). Of course, since γ multiplies ε 12 in ẋ2 , considering
ε = ε 12 = 0 brings us to the same results shown in Equation (32) and small perturbation of
ε 12 will also result in the S1 to extinction given γε 12 > 0 (see Figure 11b).

(a) (b)
Figure 10. Two-parameter bifurcation diagram representing x1∗ as a function of ε 12 and β plotted as a surface (a) and a heat
map (b) for a more intuitive understanding. Parameters used: ε = 0.13, ηk = 1.4, γ = 0.5.
 Mathematics 2021, 9, 1809 17 of 22

2. Bifurcation diagram representing x1⇤ as a function of # 12 and b plotted as a surface (a) and a
p (b) for a more intuitive understanding. Parameters used: # = 0.13, hk = 1.4, g = 0.5.
hk = 0, b = b bif e = 0, e12 >
(a) (b)

hk = 0, b = b bif e = 0, e12 > 0

Figure
Figure 11. Phase portraits for different cases: k =Phase
(a) η13. 0, β = portraits forεspecial
β bif = 0.375, = 0.3, ε cases: (a)γhk==0.7;
12 = 0.48, 0, and b bifηk== 0.375,
b =(b) 3, β = # = 0.3, # 12 =
and
0.6, ε = 0, ε 12 = 0.48, γ = 0.2. As done in all (b) hk =
previous 3, b the
plots, = 0.6, = 0,circles
red #solid 0.48, g the
# 12 = denote = 0.2. As done
ω −limits in all
while theprevious plots, the red d
small blue
dots mark the initial condition for each orbit.
w limit while the blue one marks the initial condition for each orbit.

4. Conclusions
303 and editing, B.B. - E.F. - D.O - D.A. - J.S.; supervision, B.B. - E.F. - D.O - D.A. - J.S.; project adm
304Research on hypercycles
J.S; funding acquisition, has
J.S.. focused
All authors on have
the dynamics arisingtofrom
read and agreed the processes
the published version of th
of cooperation (e.g., catalysis) between replicators [3,53–56]. The cyclic architecture of
305 Funding: E.F. has been funded by Spanish Government grant PID2019-104851GB-I00 (MIC
cooperative
306 and the interactions is known to grant
Catalan Government provide stability and survival
2017-SGR-1374. D.O wasoffunded
all the byspecies.
the Spanish
However,
307 other different architectures
CGL2017-85210-P (MICIN/FEDER, able toUE) impair
D.O. such
D.A. stability
has beenhave been thoroughly
partially funded by the Span
investigated.
308 Ciencia, These include ythe
Innovación so-called catalytic
Universidades" underparasites [15,57–60]
the project CRISISand the catalytic
(PGC2018-096577-B-I00)
Regional
short-circuits
309 Development
[61,62]. Fund. J.S.
Recent research hashas been partially
combined fundedinteractions
cooperative by the CERCA withProgramme
other of
Catalunya",
antagonistic
310 processes by "Agencia
betweenEstatal
speciesde[63].
Investigacíon"
This is based grant
onRTI2018-098322-B-I00 and the "Ramó
the rationale that molecu-
3. Phase portraits for special cases: (a) lar =
hk 311 0,RYC-2017-22243.
b = b bifare
replicators 0.375, # to
=subject 0.3, # 12 = 0.48,
= mutational g = 0.7;
processes and ecological species to behavioural
hk = 3, b = 0.6, # = 0, # 12 = 0.48, g = 0.2.shifts
As312done
due in all
Conflicts previous
to environmental plots,
of Interest: The the red dot
or ecological denotes
changes.
authors declare the These changes
no conflict could
of interest. Themake
fundersspecies
had no role i
while the blue one marks the initial condition
switch
313 for
fromeach
study; inorbit.
the collection,
cooperative analyses, or interactions,
to antagonistic interpretationin, of data;
what inwethehave
writing of the
called manuscript,
here, a o
functional
314 publish
shift. the results.
These functional shifts could arise in ribozymes due to mutational pro-
cesses
.B. - E.F. - D.O - D.A. - J.S.; supervision, B.B. and- could
- E.F. involve
D.O - D.A. a shift
- J.S.; from
project cooperation (hetero-catalysis)
administration, E.F. and to directed degradation
(trans-cleavage) [63]. In the context
cquisition, J.S.. All authors have read and agreed to the published version of the manuscript. of complex ecosystems, several species undergoing
inter-specific cooperation are known to switch to predation (see for example Refs. [65–68]).
has been funded by Spanish Government grant PID2019-104851GB-I00 (MICINN/FEDER, UE)
Even though the drivers of such functional shifts may not be trivial and respond to com-
lan Government grant 2017-SGR-1374. D.O was funded by the Spanish Government grant
10-P (MICIN/FEDER, UE) D.O. D.A. has been plex behavioural
partiallypatterns
fundedamong by the species
Spanishor"Ministerio
both biotic deand abiotic changes, the dynamics
vación y Universidades" under the project arisingCRISIS
due to(PGC2018-096577-B-I00)
such functional shifts areand stillthe
an European
unexplored subject. As mentioned, some
elopment Fund. J.S. has been partially authorsfunded have by the used the hypercycle
CERCA Programme theory
of theto"Generalitat
investigate the de impact of these functional shifts
y "Agencia Estatal de Investigacíon" grant RTI2018-098322-B-I00
in ecosystems dynamics and [63].the "Ramón ythe
Specifically, Cajal" contract
impact of a shift from catalytic cooperation
43. to directed degradation was studied in small (one to four species) discrete-time hypercy-
nterest: The authors declare no conflictcles [63]. As far
of interest. Theasfunders
we know, hadno noworks
role inhave investigated
the design of the how these shifts may affect the
collection, analyses, or interpretation of stability
data; in the of small
writinghypercycles in time-continuous
of the manuscript, systems.
or in the decision to
sults. In this article, we have analysed two-species hypercycles considering, together with
cooperation, directed degradation or predation (see Figure 1). The changes due to func-
tional shifts have been studied using a general hypercycle model that allows for different
architectures by changing different parameter conditions. To understand the changes due
to these functional shifts, we have summarised and extended previous results on obligate
two-member hypercycles [53] while also analysing a facultative case.
The model considering directed degradation shows no full extinction when both
autocatalytic replication rates are higher than their natural decays. We have found a critical
value for β, β bif , below which only the dominant species S2 survives, while coexistence
is present for β > β bif . We have also identified parametric scenarios (i.e., considering no
catalytic support of the degrader species by the other one (ηk = 0) or no decay rate of any
of the two species (e = 0)), giving place to a continuum of fixed critical points following
a straight line at β = β bif . For these two scenarios, the complete analytical expressions
describing all orbits have been found. Finally, we considered a cooperative system with
Mathematics 2021, 9, 1809 18 of 22

predation. Interestingly, bifurcation parameters found for the directed degradation system
re-appeared in the same form, stating that no natural benefit towards S2 is enough to
change the dynamics of the system as long as ηk ε > 0. However, these extreme cases with
ηk = 0 or e = 0 stopped presenting a continuum of critical points and turned into the
extinction of S1 as a consequence of the predatory term.
Future research directions may consider functional shifts in non-autonomous systems,
considering that changes among cooperative and antagonistic interactions may vary in
time due to seasonality or external perturbations.

Author Contributions: Conceptualization, B.B., E.F., D.O., D.A. and J.S.; methodology, B.B., E.F. and
J.S.; software, B.B.; validation, B.B., E.F. and J.S; formal analysis, B.B., E.F. and J.S.; investigation, B.B.,
E.F. and J.S.; resources, J.S.; data curation, B.B.; writing–original draft preparation, B.B., E.F., D.O.,
D.A. and J.S.; writing—review and editing, B.B., E.F., D.O., D.A. and J.S.; supervision, B.B., E.F., D.O.,
D.A. and J.S.; project administration, E.F. and J.S; funding acquisition, J.S. All authors have read and
agreed to the published version of the manuscript.
Funding: E.F. has been funded by the Spanish Government grant PID2019-104851GB-I00 (MICINN/FEDER,
UE) and the Catalan Government grant 2017-SGR-1374. D.O. was funded by the Spanish Government
grant CGL2017-85210-P (MICIN/FEDER, UE). D.A. has been partially funded by the Spanish “Minis-
terio de Ciencia, Innovación y Universidades” under the project CRISIS (PGC2018-096577-B-I00) and
the European Regional Development Fund. J.S. has been partially funded by the CERCA Programme
of the “Generalitat de Catalunya”, by “Agencia Estatal de Investigacíon” grant RTI2018-098322-B-I00,
and the “Ramón y Cajal” contract RYC-2017-22243.
Institutional Review Board Statement: Not applicable.
Informed Consent Statement: Not Applicable.
Data Availability Statement: Not Applicable.
Conflicts of Interest: The authors declare no conflict of interest. The funders had no role in the design
of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or
in the decision to publish the results.

Appendix A. Obligate Two-Member Hypercycle: Coexistence Equilibrium

Here, we extend previous research for the obligate two-member hypercycle reported
in Ref. [53], where numerical results suggested species coexistence via an internal stable
node. Here, we show that such a coexistence is also possible through a weak stable focus.
Specifically, we compute the stability of the coexistence equilibrium for the asymmetric
case of system (2), given by ((ηε /ηk )Γ+ , Γ+ ). We pay attention to the system’s Jacobian
Matrix eigenvalues evaluated at such equilibria. Assuming that these two equilibria exist,
i.e., ε ≤ ε c = k/(4(1 + ηε /ηk )) (see Section 3.1), the eigenvalues are given by:

1
λ +,± = ( A ± B) (A1)
4( ηε + ηk )2

for ((ηε /ηk )Γ+ , Γ+ ) and

1
λ −,± = ( C ± D ), (A2)
4( ηε + ηk )2
for ((ηε /ηk )Γ− , Γ− ), where
Mathematics 2021, 9, 1809 19 of 22

 q 
A = − ηε (k − 2ε)ηk − 2ηε ε + ((k − 4ε)ηk − 4ηε ε)ηk k (ηk + 1),
√     
B = 2 ηε −4 (ηε /2 + 1)ηk2 + 3ηε ηk + ηε2 + ηε /2 (ηε + ηk )ε + ηk kηε (ηk + 1)2
q  
× ((k − 4ε)ηk − 4ηε ε)ηk k + 16 (ηε /8 + 1)ηk2 + 9ηε ηk /4 + ηε2 + ηε /8 (ηε + ηk )2 ε2
1/2
− 4ηk (ηε + ηk )((ηε + 1)ηk2 + 4ηε ηk + ηε2 + ηε )kε + ηε ηk2 k2 (ηk + 1)2 ,
 q  (A3)
C = − (k − 2ε)ηk − 2ηε ε − ((k − 4ε)ηk − 4ηε ε)ηk k ηε (ηk + 1),
√     
D = 2 ηε 4 (ηε /2 + 1)ηk2 + 3ηε ηk + ηε2 + ηε /2 (ηε + ηk )ε − ηk kηε (ηk + 1)2
q  
× ((k − 4ε)ηk − 4ηε ε)ηk k + 16 (ηε /8 + 1)ηk2 + 9ηε ηk /4 + ηε2 + ηε /8 (ηε + ηk )2 ε2
1/2
− 4ηk (ηε + ηk )((ηε + 1)ηk2 + 4ηε ηk + ηε2 + ηε )kε + ηε ηk2 k2 (ηk + 1)2 .

Note that, although A and B may look very similar to C and D, respectively, these are
not the same expression. To establish in which cases these eigenvalues become imaginary,
we shall use the fact that the Jacobian Matrix is 2 × 2 and real, implying that, for example,
if λ−,+ = a + ib, then λ−,− = a − ib. Therefore, we can consider the potential real, a, and
imaginary times, i, ib, of these eigenvalues such that:

λ ±,− + λ ±,+
a± = (A4)
2
λ ±,− − λ ±,+
ib± = . (A5)
2
where λ±,± = a± ± ib± . We are most interested in the values that the imaginary
p part
of λ±,± can take. To simplify the problem, note that the term 4(ηε + ηk )2 / 2ηε can be
factored out, leaving a potential imaginary part squared of the form:

!2
4( ηε + ηk )2
p ib+ =16((ηε /8 + 1)ηk2 + (9ηε ηk )/4 + ηε2 + ηε /8)(ηε + ηk )2 ε2
2ηε
− 2(ηε + ηk )(2k(ηε + 1)ηk3
q
+ (8kηε + ((k − 4ε)ηk − 4ηε ε)ηk k)(ηε + 2))ηk2
q (A6)
+ 2ηε (k(ηε + 1) + 3 ((k − 4ε)ηk − 4ηε ε)ηk k)ηk
q
+ ((k − 4ε)ηk − 4ηε ε)ηk kηε (2ηε + 1))ε
q
+ kηε ηk (ηk + 1)2 (ηk k + ((k − 4ε)ηk − 4ηε ε)ηk k),
Mathematics 2021, 9, 1809 20 of 22

and
!2
4( ηε + ηk )2
p ib− =16((ηε /8 + 1)ηk2 + (9ηε ηk )/4 + ηε2 + ηε /8)(ηε + ηk )2 ε2
2ηε
+ 2(ηε + ηk )(−2k(ηε + 1)ηk3
q
+ (−8kηε + ((k − 4ε)ηk − 4ηε ε)ηk k)(ηε + 2))ηk2
q (A7)
+ 2ηε (−k(ηε + 1) + 3 ((k − 4ε)ηk − 4ηε ε)ηk k)ηk
q
+ ((k − 4ε)ηk − 4ηε ε)ηk kηε (2ηε + 1))ε
q
− kηε ηk (ηk + 1)2 (−ηk k + ((k − 4ε)ηk − 4ηε ε)ηk k).

Equalling these two expressions to zero shows that there exist two solutions for ib+ = 0
and none for ib− = 0, stating that for ib+ , there is a change in its sign, while ib− stays
always with the same one. Notice that omputations to show such zeros are non-double are
not included for the sake of length. After plugging any set of acceptable parameters in the
second expression, we can see that ib− is, in fact, not an imaginary value. Therefore, it is
only necessary to study the eigenvalue sign, which easily shows that the critical point under
inspection is a saddle. As for the other equilibrium, we have found two solutions for ε such
that the imaginary part changes sign. These are ξ ± = ( R ± S)/T, where
   
5 2 9 5
R = 8ηk k (ηε + ηk ) ηε2 + ηk + ηk + ηε + ηk2 , (A8)
4 2 4
q
S = 8ηk k (ηε − 1)(−ηk2 + ηε )(4ηε2 + (−ηk2 + 6ηk − 1)ηε + 4ηk2 ), (A9)
T = (ηk2 ηε + 8ηε2 + 18ηε ηk + 8ηk2 + ηε )2 . (A10)

For ε ∈ (ξ − , ξ + ), (ib+ )2 is a negative expression, indicating that the eigenvalue is

indeed imaginary and that, in this region, the analysed equilibrium behaves as a focus.
Note that ξ + ≤ ε c , thus always defining a region below the critical value of ε in which the
stable point is a focus. This result holds for all values of ηε and ηk as long as S is real, i.e.,
(ηε − 1)(−ηk2 + ηε ) ≥ 0.

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