[This is a review of the original version. See Text S1 for the version history. The authors’ responses are included in line and are reflected in the published version.]

This is an interesting topic page, highlighting a new usage of digital evolution: the evolution of antagonistic and/or mutualistic interactions between digital organisms. While there are Wiki pages for both Avida and Tierra (http://en.wikipedia.org/w...), it is nice to see some of the history of digital life research covered here. The piece is perhaps a little heavy-handed in dealing with experimental evolution work (as noted by the first reviewer), but this is easily amended. It is difficult for me to assess how accessible this piece is to life scientists (perhaps because I'm too familiar with Avida), but in my experience readers fill in missing details by reading the literature.

‘’’Response:’’’ We appreciate very much the general assessment made by the reviewer. He has synthesized in one line the main goal of this topic page: "... highlighting a new usage of digital evolution: the evolution of antagonistic and/or mutualistic interaction between digital organisms". This is certainly the key message and we would like to add that this new usage aims at help us understand how coevolution shapes the structure of species interaction networks. Inspired by the clarity and simplicity of this one-sentence summary, we have reworded the following paragraph of the introductory section: "This topic page highlights new research avenues enabled by the inclusion of ecological interactions in digital systems. Research using self-replicating computer programs complements laboratory efforts by broadening the breadth of viable experiments focused on the emergence and diversification of coevolving interactions in complex communities. This cross-disciplinary research program provides fertile grounds for new collaborations between computer scientists and evolutionary biologists".
We are aware that we have been overly critical of the literature on experimental biological evolution (see our reply to the first reviewer) due to our enthusiasm for emphasizing the incorporation of ecology into evolutionary studies dealing with communities of interacting organisms. We have clarified our motivation and removed unnecessary criticisms as a justification for our arguments.
In addition, in response to this review we have tried to improve the readability of the topic for biologists/ecologists and we honestly think, since the first author of this topic page is an ecologist, that life scientists will fill in missing details by reading the literature (as the reviewer also pointed out).

I think that the section "Adding ecology" should be expanded to make it clearer. Also, I am unsure about whether limited resources are used in the host-parasite interactions, and what the impact of those are. Finally, mutualistic interactions are barely explained. How do parasites interact mutualistically with the host? Or are mutualistic interactions only possible for non-parasitic interactions between avidian hosts?

‘’’Response:’’’ We have reorganized the topic page by moving the content of the previous "Adding ecology" subsection to a more detailed section of "Digital interactions" in which antagonistic and mutualistic digital interactions have been better explained under three different subsections: host-parasite, mutualistic, and predator-prey interactions. We think the ms has improved in terms of clarity regarding the implementation of the interactions between digital organisms.
In the case of the host-parasite interactions, there is no necessary reason limited resources have to be used. Several ongoing projects with host-parasite interactions use limited resources and several do not. Instead, we opted to expand the mutualistic interaction example as requested by the reviewer. In doing so, we also included one example implementation that explain a bit about how resources may be used. We hope this new expanded section answers any further questions about mutualistic interactions in Avida.

The section "Research" should probably be entitled "Research Questions", because that's really what is presented there. Perhaps another question that can be addressed here is the stability of the networks that form. This is a very controversial topic, and there is a recent paper in Science http://www.sciencemag.org... that discusses the stability of ecological networks with mixed interaction types (antagonistic and mutualistic). The formation and evolution of these networks is not well-studied, and perhaps digital organism are a way to address the stability issue from an "experimental" point of view.

‘’’Response:’’’ We agree. This was also a point stressed by the first reviewer. It is now entitled "Research directions" because that is really what is presented there. We have to remind ourselves that this is not a research paper but a topic page in which the goal is to introduce a new computational tool for studying the evolution of species interaction networks in artificial evolving systems. It is a very good point to incorporate the potential of this approach to shed light on the diversity-stability debate (i.e., whether or not more diverse communities enhance the stability of ecological networks). But species diversity if just half of the story. The recent paper published in Science by Mougi and Kondoh (Diversity of interaction types and ecological community stability) pointed out by the reviewer, focuses on the other half of the story: diversity in interaction types. We have added the following text to the "Research directions" section: "The stability-diversity debate is a long-standing debate about whether more diverse ecological networks are also more stable. Until recently, this debate has focused on one component of biodiversity: species diversity. However, newer research has begun dealing with another component of biodiversity: diversity in species interactions. Mathematical models show that a mixture of antagonistic and mutualistic interactions can stabilize population dynamics and that the loss of one interaction type may critically destabilize ecosystems. Studies with digital organisms can shed light on this debate from an empirical perspective because the types of interactions included can be manipulated and the stability of the resulting evolving digital ecological network can be measured".

Minor comment: in the Acknowledgements, perhaps the word "largely" should be replaced, because it implies that the comments of those that are thanked improved the manuscript "for the most part" only. Unless this is precisely what the authors intend to imply.

‘’’Response:’’’ We have reworded the Acknowledgements section, which now reads: "We thank Simon A. Levin, Jordi Bascompte, Justin Meyer and other members of the BEACON Center, for useful discussions, comments and suggestions that have contributed to the initial development of the manuscript".