1) Coevolution between hosts and parasites in a computational simulation drove the emergence of more complex traits in hosts. Hosts evolved to perform more complex logic functions when coevolving with parasites than when evolving alone. 2) Parasites promoted host complexity by maintaining genetic "memory" of past host phenotypes and continually deforming the hosts' adaptive landscape to favor more complex traits. 3) Breaking the coevolutionary feedback loop by freezing or replaying parasite populations prevented hosts from evolving the same level of complexity as with full coevolution.

1. Co­Evolution
Drives the Emergence of Complex Traits and Promotes Evolvability
Part A : Problem Statement
Through the evolution, life has evolved into the extremely diverse organisms with varyingly
complex traits that populate the Earth today. Considering the evolution (by means of natural
selection) often leads to increasing complexity, it is no garantuee that such complex traits will
necessarily increase the organisms fitness OR hold it constant.
So it quenches the mind with thoughts like “What actually drives to greater complecity ? when and
why is greater complexity favored?”
My research has long focused on understanding how simple processes can produce the amazing
levels of complexity and diversity we see in nature.
Part B : Background & Abstract
Researchers have long understood that coevolution produces rapid evolutionary changes: parasites
race to find new mechanisms to infect hosts and in turn those hosts are pressed to keep
evolving new defenses, just to survive. This effect was dubbed the red-queen hypothesis.
The “Red Queen” hypothesis in evolution is related to the coevolution of species. It states that
species must constantly adapt and evolve to pass on genes to the next generation and also to
keep from going extinct when other species within a symbiotic relationship are evolving.
In precise, it proposes that organisms must constantly adapt, evolve, and proliferate not merely to
gain reproductive advantage, but also simply to survive while pitted against ever-evolving opposing
organisms in an ever-changing environment, and intends to explain two different phenomena: the
constant extinction rates as observed in the paleontological record caused by co-evolution between
competing species and the advantage of sexual reproduction (as opposed to asexual reproduction) at
the level of individuals.
Evolutionary algorithms frequently use the Red Queen effect to promote rapid exploration and
increase the probability that better solutions will be discovered. In such cases, it’s not surprising
when complexity rises in association with new traits that provide a big fitness boost.
More surprising is the fact that coevolution can still produce complex traits even when they come
at a fitness cost. Normally, coevolution is thought to be helpful since it produces more diverse
populations (we’ve also seen such diversity increases in Avida#
).
#Avida is an artificial life software platform to study the evolutionary biology of self-replicating and evolving computer
programs (digital organisms).
Ranjith Raj Vasam 1 @ranjithrajvasam

2. Co­Evolution
Drives the Emergence of Complex Traits and Promotes Evolvability
More diversity means that the populations try out more possible solutions at a time, any one of
which might be more beneficial than anything discovered before. However, in the experiments
described in the paper, the only advantage of a more complex trait is that it forces a parasite to
evolve the same trait in order to infect this host; therefore it is harder for a parasite to evolve the
infection mechanism when hosts rely exclusively on more complex traits.
It's exciting enough to explore the interesting implications of this result on evolutionary
computation systems. When coevolutionary dynamics are introduced into a system, the selective
pressures on organisms change beyond simply forcing hosts to continually move around on the
fitness landscape. If some portions of the landscape are trickier for parasites to access, they
inherently have more of an advantage than their direct fitness might suggest. Such effects may
either help or hurt the hunt for the best solutions depending on the system’s details, but more
study is certainly warranted.
The other interesting result that we present in this paper is that the genetic architecture of the
organisms evolved in conjunction with parasites resulted in a different distribution of
mutational effects. Specifically, coevolved organisms were substantially more likely to gain
mutations that replace an old task with a new one, without changing the total number tasks that an
organism does. This new distribution of mutational effects are far more likely to aid an organism in
escaping from parasites – organisms need to perform at least one task to obtain resources, but doing
multiple tasks creates more opportunities for parasites to infect them. The evolution of this new
genetic architecture is surprising because the value of a certain distribution of mutational effects
takes several generations to be felt; that is, the real benefits are only realized once mutations
actually occur.
Such delayed benefits are why so many types of evolvability are difficult to see. In this paper,
they’ve previously used changing environments to try to encourage organisms to raise their
mutations rates or evolve sexual recombination, but in both cases they've failed to show any strong
improvement in evolutionary potential. As such, they were excited to see that parasites can produce
an increase in the evolvability of hosts. We currently have studies underway to see if parasites can
similarly push asexual populations to become sexual. Our initial results are already intriguing and
it's a hope to have something exciting to report in the near future.
Ranjith Raj Vasam 2 @ranjithrajvasam

3. Co­Evolution
Drives the Emergence of Complex Traits and Promotes Evolvability
Part C : Supporting Computational/Bioinformatics Approach to Problem Solving
One hypothesis is that antagonistic coevolution between hosts and parasites can drive the evolution
of more complex traits by promoting arms races with increased defenses and counter-defenses.
So by means of taking help of computaional biology, generating populations of self-replicating host
computer programs and parasitic programs, which steal processing power from their hosts, let's
see can it be demonstrated that coevolution promotes complexity of traits and promotes
evolvability.
Following experiments were performed using the Avida 2.13.0. Host and parasite populations lived
in a well-mixed chemostat-like environment, with a single type of resource entering at a constant
rate. Hosts obtained resources required for replication by performing any of nine distinct one- and
two-input logic functions, provided there were resources available in the environment.
Figure 1 : Hosts, parasites, functions, and resources in
Avida*
(A) A circular genome with pointers used to execute its
code and three functions— NOT , AND , and OR —
shown in different colors used to store binary values in a
host organism with stacks. Functions vary in complexity
as measured by the number of NAND gates required to
perform them.
(B) Organisms to take up resources from their
environment, by enabling respective functions.
(C) By performing the corresponding function, Parasites
uptake mechanisms of the hosts in this system by targeting
the resource.
#Note that some parasites can perform multiple functions
(shown by multiple colors) and thus infect hosts via
multiple uptake systems.
#When a parasite infects a host, it acquires a portion of the
host’s CPU cycles. Executing a single operation costs an
organism a single CPU cycle.
#Time in these experiments is measured in ‘‘updates,’’
which corresponds to a per capita average of 30 executed
CPU cycles.
*Avida is an artificial life software platform to study the
evolutionary biology of self-replicating and evolving
computer programs (digital organisms).
In this designed system, “coevolution occurs when hosts and parasites acquire and lose
functions.”
Ranjith Raj Vasam 3 @ranjithrajvasam

4. Co­Evolution
Drives the Emergence of Complex Traits and Promotes Evolvability
Evolution Experiments : Parasites Drive Greater Host Complexity
We initially monitored evolution under two main treatments, each with 50-fold replica-
tion: host organisms evolved alone in one treatment, and they coevolved with parasites in the
other. Each replicate started with a different numerical seed, and the resulting sequence of pseudo-
random numbers influenced mutations, parasite-host encounters, and other probabilistic events.
Figure 2 : Parasites promote the evolution of host complexity.
• The blue trajectory shows the grand mean complexity across 50 replicate populations (i.e.,
runs) that evolved in the absence of parasites.
• The red trajectory shows the corresponding values for 50 host populations that coevolved
with parasites.
• The green trajectory shows mean values for the same 50 parasite populations, except here
they were ‘‘cured’’.
The coevolutionary process clearly produced greater functional complexity in the hosts.
Per-site mutation rates were constant, so total genomic rates varied with changes in genome length.
Mutations occurred at random w.r.t genome position.
Ranjith Raj Vasam 4 @ranjithrajvasam

5. Co­Evolution
Drives the Emergence of Complex Traits and Promotes Evolvability
Challenging Experiment : Parasites Retain ‘‘Memory’’ of Previous Hosts
To eliminate all population-level interactions in both species, it's screened individual hosts and
parasites for defenses and counter defenses, rather than using evolving populations. Starting from
the same ancestral host, generated thousands of individuals using the same mutation regime as in
the evolution experiments, and randomly chose a single host mutant that was resistant to the
ancestral parasite. Then repeated this process for parasites, again using the same mutation regime
as in the evolution experiments, and we isolated a host-range mutant able to infect that
resistant host mutant. We continued the pairwise challenges using the derived host and parasite
genotypes for 50 rounds. A challenge experiment was stopped if we failed to isolate a relevant
mutant after screening 500,000 individuals. In the comparisons with the evolution and coevolution
treatments, we used 56 challenge experiments (out of 100 started) that achieved the full 50 rounds
of reciprocal defenses and counter-defenses. However, the truncated runs appeared to be
indistinguishable from those that went the full duration.
Figure 3 : Parasites evolve generalist
strategies while hosts remain specialists.
• The purple trajectory shows the average
number of different functions performed
by individual parasites across 50
replicates of the coevolution treatment.
• The black trajectory shows the
corresponding average for individual
hosts*;
*host populations were excluded from the
average after the corresponding parasite
populations had gone extinct..
Ranjith Raj Vasam 5 @ranjithrajvasam

6. Co­Evolution
Drives the Emergence of Complex Traits and Promotes Evolvability
Figure 4 : Effects of parasites on the host’s adaptive landscape.
(A) Assuming that unnecessary complexity is costly in the absence of any direct benefit, the fitness
peak corresponds to the simplest host phenotype.
(B) Once parasites are introduced, the landscape is deformed and selection favors a more complex
host phenotype.
(C, D) As coevolution continues, the parasites maintain a population-genetic memory of host
phenotypes, which pushes the fitness peak toward higher and higher levels of complexity.
(E–H) In the coevolution runs, they quantified the effect of parasites on the host adaptive
landscape as the proportion of parasites that were unable to infect hosts performing each of the
nine logic functions.
Freeze and Replay Experiments : Effects of Breaking the Coevolutionary Feedback
In these experiments, we allowed host populations to evolve with either ‘‘frozen’’ or ‘‘replayed’’
parasites. During the original coevolution experiments, we saved each replicate’s entire set of
host and parasite genotypes every 1,000 updates. We modified the Avida source code such that
this record of genotypes can be loaded into an on-going run at any point by adding an option to
override the normal replication process with one that samples from a genotype list. When
organisms reproduce, instead of inheriting their parent’s genome, the offspring is assigned a
random genotype from the list. This procedure can be implemented for hosts, parasites, or both;
however, in the freeze and replay experiments presented here, we manipulated only the parasite
populations using this new procedure. The genetic composition of the parasite population was
frozen throughout the run, although the total number of parasites could rise or fall in accord
with the dynamics of infections. Under the replay treatment, the frequencies of parasite
genotypes changed over time, but those changes were based on parasite evolution that had taken
place in an earlier coevolution run, rather than on the dynamics that were occurring in the
replay itself. That is, the list of parasite genotypes from which new parasites were drawn was
Ranjith Raj Vasam 6 @ranjithrajvasam

7. Co­Evolution
Drives the Emergence of Complex Traits and Promotes Evolvability
changed every 1,000 updates to reflect what had happened in the earlier run. As a consequence,
the host could evolve in response to the changing frequencies of the various parasite genotypes,
but not vice versa—the coevolutionary feedback was broken, although parasite diversity and the
temporal changes in that diversity were preserved.
Frozen and replayed parasite genotypes fail
to recapitulate the level of complexity seen in
the coevolution treatment.
Host complexity was measured as in Figure 2,
and the coevolved (red) and evolved-without-
parasites (blue) treatments are shown as before.
• The grey trajectory indicates the mean
level of host complexity that evolved
when parasite genotype frequencies were
frozen.
• The orange trajectory shows the level of
complexity that hosts evolved in the
replay treatment, where they faced
changing, but not coevolving, parasite
populations.
Higher levels of host complexity are also
maintained with coevolving parasites when
starting from complex ancestors.
As in figure 2, complexity was measured as
the minimum number of NAND instructions
that must be executed by a host to perform its
most complex logic function, averaged over
all individuals in a population.
• The blue trajectory shows the grand
mean complexity across 50 replicate
populations that evolved in the
absence of parasites.
• The red trajectory shows the
corresponding values for 50 host
populations that coevolved with
parasites.
Ranjith Raj Vasam 7 @ranjithrajvasam

8. Co­Evolution
Drives the Emergence of Complex Traits and Promotes Evolvability
Effects of Coevolving Parasites on Host Evolvability
Phylogenetic Analysis :
In Avida, the genealogy of organisms is known perfectly and, when coupled with the asexual
lineages studied here, allows construction of the exact phylogenetic history for a population. Used
python ete2.1 module to represent (Figure B) all of the genotypes present in two host populations
along with their ancestries through the various coalescences, the most recent common ancestor for
the entire population, and the founding genotype.
Figure B : Effect of coevolving parasites on host phylogenies.
Representative phylogenies for hosts that
evolved in the (A) presence and (B) absence of parasites.
The branch leading to the original ancestor is too short to be seen in (A).
The phylogenies show all of the host genotypes present at the end of the run,
and the phylogenies are known exactly in this system.
Evolvability Analysis :
They tested every possible one-step point mutation in the genetic background of the most abundant
host genotype at the end of all 50 evolution and coevolution runs. Each mutant was placed into one
of the following categories based on the phenotypic changes relative to its parent: (i) the mutant
cannot perform any functions or is otherwise nonviable; or (ii) the mutant is viable and (a) there is
no difference in the number or identity of functions performed; (b) the mutant performs more
functions; (c) the mutant performs fewer functions; or (d) the identity of functions performed has
changed, but the number has not. The last category, which we call ‘‘switching,’’ was the focus of
our analysis.
They also modified this analysis to take into account possible effects of differences in the number
and complexity of tasks performed by pairing host genotypes isolated from the evolved and
coevolved populations that performed identical sets of tasks. Genotypes were pooled across the
replicate runs based on what tasks they could perform. All of the coevolved populations were
compared with all of the evolved populations to identify paired host phenotypes that performed
identical sets of tasks. For each pair of phenotypes thus identified, a genotype from the evolved and
coevolved populations that performed the appropriate set of tasks was chosen at random, and all
possible one-step mutations were then generated for both genotypes.
Ranjith Raj Vasam 8 @ranjithrajvasam

9. Co­Evolution
Drives the Emergence of Complex Traits and Promotes Evolvability
The data are shown as box plots and smoothed frequency distributions for the times of origin of the
MRCA in 38 host populations that coevolved with parasites (excluding the 12 runs where the
parasites went extinct) and 50 populations that evolved without parasites.
Effect of coevolution on
coalescence times in host
phylogenies. The MRCAs
arose significantly earlier in the
coevolution treatment. The tail
of the distribution for the
coevolution treatment is more
pronounced if we include the
host populations where the
parasites went extinct, but the
difference remains highly
significant.
Proportion of point mutations in
host genomes that switch
functions without changing the
number of functions performed.
The data are shown as box plots
and smoothed frequency
distributions. Proportions were
obtained by testing all possible
one-step point mutations in the
genetic background of the most
abundant host genotype at the
end of all 50 runs with and
without parasites.
Proportion of point mutations
that switch functions without
changing the number of tasks
performed in paired genotypes,
where each pair includes hosts
from the coevolution and
evolution treatments that
perform identical sets of tasks.
Proportions were obtained by
testing all possible one-step
point mutations in each genetic
background.
Box hinges depict first and third quartiles and whiskers extend 1.5 6 interquartile range (IQR) out from their
corresponding hinge.
References :
Coevolution Drives the Emergence of Complex Traits and Promotes Evolvability (PLoS Biology
12(12):e1002023·December 2014)
Ranjith Raj Vasam 9 @ranjithrajvasam

10. Co­Evolution
Drives the Emergence of Complex Traits and Promotes Evolvability
Background Study :
1. 'Survival of the Sickest: The Surprising Connections Between Disease and Longevity' by Dr.
Sharon Maolem. (In this groundbreaking and absorbing book Dr. Sharon Moalem, delves back into the evolution of
man to offer a radical perspective on survival, the human body, and our understanding of disease. Survival of the
Sickest will change the way you think about your body.)
2. 'The Art of Being a Parasite' by Claude Combes.(is an extensive collection of wonderful and weird
stories that illuminate the ecology and evolution of interactions between species. Claude Combes illustrates what it
means to be a parasite by considering every stage of its interactions, from invading to reproducing and leaving the host.
An accessible and engaging follow-up to Combes's Parasitism, this book will be of interest to both scholars and
nonspecialists in the fields of biodiversity, natural history, ecology, public health, and evolution.)
Ranjith Raj Vasam 10 @ranjithrajvasam