Examining Community Stability in the Face of Mass Extinction in Communities of Digital Organisms

Digital evolution is a computer-based instantiation of Darwinian evolution in which short self-replicating computer programs compete, mutate, and evolve. It is an excellent platform for addressing topics in long-term evolution and paleobiology, such as mass extinction and recovery, with experimental evolutionary approaches. We evolved model communities with ecological interdependence among community members, which were subjected to two principal types of mass extinction: a pulse extinction that killed randomly, and a selective press extinction involving an alteration of the abiotic environment to which the communities had to adapt. These treatments were applied at two different strengths, along with unperturbed control experiments. We examined how stability in the digital communities was affected from the perspectives of division of labor, relative shift in rank abundance, and genealogical connectedness of the community's component ecotypes. Mass extinction that was due to a Strong Press treatment was most effective in producing reshaped communities that differed from the pre-treatment ones in all of the measured perspectives; weaker versions of the treatments did not generally produce significant departures from a Control treatment; and results for the Strong Pulse treatment generally fell between those extremes. The Strong Pulse treatment differed from others in that it produced a slight but detectable shift towards more generalized communities. Compared to Press treatments, Pulse treatments also showed a greater contribution from re-evolved ecological doppelgangers rather than new ecotypes. However, relatively few Control communities showed stability in any of these metrics over the whole course of the experiment, and most did not represent stable states (by some measure of stability) that were disrupted by the extinction treatments. Our results have interesting, broad qualitative parallels with findings from the paleontological record, and show the potential of digital evolution studies to illuminate many aspects of mass extinction and recovery by addressing them in a truly experimental manner

Data from: Examining community stability in the face of mass extinction in communities of digital organisms

Digital evolution is a computer-based instantiation of Darwinian evolution in which short self-replicating computer programs compete, mutate, and evolve. It is an excellent platform for addressing topics in long-term evolution and paleobiology, such as mass extinction and recovery, with experimental evolutionary approaches. We evolved model communities with ecological interdependence among community members, which were subjected to two principal types of mass extinction: a pulse extinction that killed randomly, and a selective press extinction involving an alteration of the abiotic environment to which the communities had to adapt. These treatments were applied at two different strengths, along with unperturbed control experiments. We examined how stability in the digital communities was affected from the perspectives of division of labor, relative shift in rank abundance, and genealogical connectedness of the community's component ecotypes. Mass extinction that was due to a Strong Press treatment was most effective in producing reshaped communities that differed from the pre-treatment ones in all of the measured perspectives; weaker versions of the treatments did not generally produce significant departures from a Control treatment; and results for the Strong Pulse treatment generally fell between those extremes. The Strong Pulse treatment differed from others in that it produced a slight but detectable shift towards more generalized communities. Compared to Press treatments, Pulse treatments also showed a greater contribution from re-evolved ecological doppelgangers rather than new ecotypes. However, relatively few Control communities showed stability in any of these metrics over the whole course of the experiment, and most did not represent stable states (by some measure of stability) that were disrupted by the extinction treatments. Our results have interesting, broad qualitative parallels with findings from the paleontological record, and show the potential of digital evolution studies to illuminate many aspects of mass extinction and recovery by addressing them in a truly experimental manner

Spéciation guidée par l'environnement‎ : interactions sur des périodes évolutionnaires de communautés de plantes artificielles

Depuis des décades, les chercheurs en Vie Artificielle on créé une pléthore de créatures en utilisant de multiples schémas d’encodage, capacités motrices et aptitudes cognitives. Un motif récurrent, cependant, est que la focalisation est centrée sur les individus à évoluer, ne laissant que peu de place aux variations environnementales. Dans ce travail, nous argumentons que des contraintes abiotiques plus complexes pourraient diriger un processus évolutionnaire vers des régions de l’espace génétique plus robustes and diverses. Nous avons conçu un modèle morphologique complexe, basé sur les graphes orientés de K. Sims, qui repose sur le moteur physique Bullet pour la précision et utilise des contraintes à 6 Degrés de Liberté pour connecter les paires d’organes. Nous avons ainsi évolué un panel de plantes à l’aspect naturel qui devaient survivre malgré des niveaux de ressources variables induits par une source de lumière mobile et des motifs de pluies saisonnières. En plus de cette expérience, nous avons aussi obtenu une meilleure croissance verticale en ajoutant une contrainte biotique artificielle sous la forme de brins d’herbe statiques. La complexité de ce modèle, cependant, ne permettait pas la mise a l’échelle d’une évolution de populations et a donc été réduit dans l’expérience suivante, notamment en supprimant le moteur physique. Cela nous a amené à l’exploration de la co-évolution de populations composées d’une unique espèce et ayant la capacité de se reproduire de manière autonome grâce à notre Bail-Out Crossover (Croisement avec Désistement). Bien que les populations résultantes n’ont pas démontré un grand intérêt pour cette aptitude, elles ont néanmoins fourni d’importantes informations sur les mécanismes d’auto-reproduction. Ceux-ci ont été mis en action dans un second modèle inspiré des travaux de Bornhofen. Grâce à sa légèreté, cela nous a permis de traiter non seulement de plus grandes populations (de l’ordre de milliers d’individus) mais aussi de plus longues périodes évolutionnaires (100 années, approximativement 5000 générations). Notre première expérience avec ce modèle s’est concentrée sur la possibilité de reproduire des cas d’école de spéciation (allopatrique, parapatrique, péripatrique) sur cette plate-forme. Grâce à APOGet, une nouvelle procédure de regroupement pour l’extraction en parallèle d’espèces à partir d’un arbre généalogique, nous avons pu affirmer que le système était effectivement capable de spéciation spontanée. Cela nous a conduit à une dernière expérience dans laquelle l’environnement était contrôlé par de la Programmation Génétique Cartésienne (CGP), permettant ainsi une évolution automatique d’une population et des contraintes abiotiques auxquelles elle était confrontée. Par une variation du traditionnel algorithme 1 + λ nous avons obtenu 10 populations finales qui ont survécu à de brutales et imprévisibles variations environnementales. En les comparant à un groupe contrôle c pour lequel les contraintes ont été maintenues faibles et constantes, le groupe évolué e a montré des performances mitigées: dans les deux types de tests, une moitié de e surpassait c qui, à son tour, surpassait la moitié restante de e. Nous avons aussi trouvé une très forte corrélation entre les chutes catastrophiques de population et la performance des évolutions correspondantes. Il en résulte que l’évolution de population dans des environnements hostiles et dynamiques n’est pas une panacée bien que ces expériences en démontrent le potentiel et souligne le besoin d’études ultérieures plus approfondies.Artificial Life researchers have, for decades, created a plethora of creatures using numerous encoding schemes, motile capabilities and cognitive capacities. One recurring pattern, however, is that focus is solely put on the evolved individuals, with very limited environmental variations. In this work, we argue that more complex abiotic constraints could drive an evolutionary process towards more robust and diverse regions of the genetic space. We started with a complex morphogenetic model, based on K. Sims’ directed graphs, which relied on the Bullet physics engine for accuracy and used 6Degrees of Freedom constraints to connect pairs of organs. We evolved a panel of natural-looking plants which had to cope with varying resource levels thanks to a mobile light source and seasonal rain patterns. In addition to this experiment, we also obtained improved vertical growth by adding an artificialbiotic constraint in the form of static grass blades. However, the computational cost of this model precluded scaling to a population-level evolution and was reduced in the successive experiment, notably by removing the physical engine. This led to the exploration of co-evolution on single-species populations which, thanks to our Bail-Out Crossover (BOC) algorithm, were able to self-reproduce. The resulting populations provided valuable insight into the mechanisms of self-sustainability. These were put to action in an even more straightforward morphogenetic model inspired by the work of Bornhofen. Due to its light weightness, this allowed for both larger populations (up to thousands of individuals) and longer evolutionary periods (100 years, roughly 5K generations). Our first experiment on this model tested whether text-book cases of speciation could be reproduced in our framework. Such positive results were observed thanks to the species monitoring capacities of APOGeT, a novel clustering procedure we designed for online extraction of species from a genealogic tree. This drove us to a final experiment in which the environment was controlled through Cartesian Genetic Programming thus allowing the automated evolution of both the population and abiotic constraints it is subjected to. Through a variation of the traditional1 + λ algorithm, we obtained 10 populations (evolved group e) which had endured in harsh and unpredictable environments. These were confronted to a control group c, in which the constraints were kept mild and constant, on two types of colonization evaluation. Results showed that the evolved group was heterogeneous with half of e consistently outperforming members of c and the other half exhibiting worse performances than the baseline. We also found a very strong positive correlation between catastrophic drops in population level during evolution with the robustness of their final representatives. From this work, two conclusions can be drawn. First, though the need to fight on both the abiotic and biotic fronts can lead to worse performances, more robust individuals can be found in reasonable time-frames. Second, the automated co-evolution of populations and their environments is essential in exploring counter-intuitive, yet fundamental, dynamics both in biological and artificial life