Evolution of genetic organization in digital organisms

We examine the evolution of expression patterns and the organization of genetic information in populations of self-replicating digital organisms. Seeding the experiments with a linearly expressed ancestor, we witness the development of complex, parallel secondary expression patterns. Using principles from information theory, we demonstrate an evolutionary pressure towards overlapping expressions causing variation (and hence further evolution) to sharply drop. Finally, we compare the overlapping sections of dominant genomes to those portions which are singly expressed and observe a significant difference in the entropy of their encoding.Comment: 18 pages with 5 embedded figures. Proc. of DIMACS workshop on "Evolution as Computation", Jan. 11-12, Princeton, NJ. L. Landweber and E. Winfree, eds. (Springer, 1999

Bifurcation into functional niches in adaptation

One of the central questions in evolutionary biology concerns the dynamics of adaptation and diversification. This issue can be addressed experimentally if replicate populations adapting to identical environments Call be investigated in detail. We have studied 501 such replicas Using digital organisms adapting to at least two fundamentally different functional niches (survival strategies) present in the same environment: one in which fast replication is the way to live, and another where exploitation of the environment's complexity leads to complex organisms with longer life spans and smaller replication rates. While these two modes of survival are closely analogous to those expected to emerge in so-called r and K selection scenarios respectively, the bifurcation of evolutionary histories according to these functional niches occurs in identical environments, under identical selective pressures. We find that the branching occurs early, and leads to drastic phenotypic differences (in fitness, sequence length, and gestation time) that are permanent and irreversible. This study confirms an earlier experimental effort using microorganisms, in that diversification can be understood at least in part in terms of bifurcations on saddle points leading to peak shifts, as in the picture drawn by Sewall Wright

A Simple Explanation for Taxon Abundance Patterns

For taxonomic levels higher than species, the abundance distributions of number of subtaxa per taxon tend to approximate power laws, but often show strong deviationns from such a law. Previously, these deviations were attributed to finite-time effects in a continuous time branching process at the generic level. Instead, we describe here a simple discrete branching process which generates the observed distributions and find that the distribution's deviation from power-law form is not caused by disequilibration, but rather that it is time-independent and determined by the evolutionary properties of the taxa of interest. Our model predicts-with no free parameters-the rank-frequency distribution of number of families in fossil marine animal orders obtained from the fossil record. We find that near power-law distributions are statistically almost inevitable for taxa higher than species. The branching model also sheds light on species abundance patterns, as well as on links between evolutionary processes, self-organized criticality and fractals.Comment: 10 pages, 4 Fig

Influence of chance, history, and adaptation on digital evolution

We evolved multiple clones of populations of digital organisms to study the effects of chance, history, and adaptation in evolution. We show that clones adapted to a specific environment can adapt to new environments quickly and efficiently, although their history remains a significant factor in their fitness. Adaptation is most significant (and the effects of history less so) if the old and new environments are dissimilar. For more similar environments, adaptation is slower while history is more prominent. For both similar and dissimilar transfer environments, populations quickly lose the ability to perform computations (the analogue of beneficial chemical reactions) that are no longer rewarded in the new environment. Populations that developed few computational "genes" in their original environment were unable to acquire them in the new environment

Does self-replication imply evolvability?

The most prominent property of life on Earth is its ability to evolve. It is often taken for granted that self-replication--the characteristic that makes life possible--implies evolvability, but many examples such as the lack of evolvability in computer viruses seem to challenge this view. Is evolvability itself a property that needs to evolve, or is it automatically present within any chemistry that supports sequences that can evolve in principle? Here, we study evolvability in the digital life system Avida, where self-replicating sequences written by hand are used to seed evolutionary experiments. We use 170 self-replicators that we found in a search through 3 billion randomly generated sequences (at three different sequence lengths) to study the evolvability of generic rather than hand-designed self-replicators. We find that most can evolve but some are evolutionarily sterile. From this limited data set we are led to conclude that evolvability is a likely--but not a guaranteed-- property of random replicators in a digital chemistry.Comment: 8 pages, 5 figures. To appear in "Advances in Artificial Life": Proceedings of the 13th European Conference on Artificial Life (ECAL 2015