Add most pertinent references for issue #57

JOSS/paper.bib

@@ -1,4 +1,6 @@
  @article{Barido-Sottani_Saupe_Smiley_Soul_Wright_Warnock_2020, title={Seven rules for simulations in paleobiology}, volume={46}, ISSN={0094-8373, 1938-5331}, DOI={10.1017/pab.2020.30}, abstractNote={Simulations are playing an increasingly important role in paleobiology. When designing a simulation study, many decisions have to be made and common challenges will be encountered along the way. Here, we outline seven rules for executing a good simulation study. We cover topics including the choice of study question, the empirical data used as a basis for the study, statistical and methodological concerns, how to validate the study, and how to ensure it can be reproduced and extended by others. We hope that these rules and the accompanying examples will guide paleobiologists when using simulation tools to address fundamental questions about the evolution of life.}, number={4}, journal={Paleobiology}, publisher={Cambridge University Press}, author={Barido-Sottani, Joëlle and Saupe, Erin E. and Smiley, Tara M. and Soul, Laura C. and Wright, April M. and Warnock, Rachel C. M.}, year={2020}, month=nov, pages={435–444}, language={en} }
+ @article{Butterfield_2011, title={Animals and the invention of the Phanerozoic Earth system.}, volume={26}, DOI={10.1016/j.tree.2010.11.012}, abstractNote={Animals do not just occupy the modern biosphere, they permeate its structure and define how it works. Their unique combination of organ-grade multicellularity, motility and heterotrophic habit makes them powerful geobiological agents, imposing myriad feedbacks on nutrient cycling, productivity and environment. Most significantly, animals have “engineered” the biosphere over evolutionary time, forcing the diversification of, for example, phytoplankton, land plants, trophic structure, large body size, bioturbation, biomineralization and indeed the evolutionary process itself. This review surveys how animals contribute to the modern world and provides a basis for reconstructing ancient ecosystems. Earlier, less animal-influenced biospheres worked quite differently from the one currently occupied, with the Ediacaran-Cambrian radiation of organ-grade animals marking a fundamental shift in macroecological and macroevolutionary expression.}, number={2}, journal={Trends in ecology & evolution}, author={Butterfield, Nicholas J}, year={2011}, month=feb, pages={81–7} }
+ @article{Condamine_Rolland_Morlon_2013, title={Macroevolutionary perspectives to environmental change}, volume={16}, ISSN={1461-0248}, DOI={10.1111/ele.12062}, abstractNote={Ecology Letters is a broad-scope ecology journal considering all taxa, in any biome and geographic area, and spanning community, microbial & evolutionary ecology.}, journal={Ecology Letters}, publisher={John Wiley & Sons, Ltd}, author={Condamine, Fabien L. and Rolland, Jonathan and Morlon, Hélène}, year={2013}, month=jan, pages={72–85}, language={en} }
  @article{Dolson_Ofria_2021, title={Digital Evolution for Ecology Research: A Review}, volume={9}, ISSN={2296-701X}, DOI={10.3389/fevo.2021.750779}, url={https://www.frontiersin.org/articles/10.3389/fevo.2021.750779}, abstractNote={In digital evolution, populations of computational organisms evolve via the same principles that govern natural selection in nature. These platforms have been used to great effect as a controlled system in which to conduct evolutionary experiments and develop novel evolutionary theory. In addition to their complex evolutionary dynamics, many digital evolution systems also produce rich ecological communities. As a result, digital evolution is also a powerful tool for research on eco-evolutionary dynamics. Here, we review the research to date in which digital evolution platforms have been used to address eco-evolutionary (and in some cases purely ecological) questions. This work has spanned a wide range of topics, including competition, facilitation, parasitism, predation, and macroecological scaling laws. We argue for the value of further ecological research in digital evolution systems and present some particularly promising directions for further research.}, journal={Frontiers in Ecology and Evolution}, author={Dolson, Emily and Ofria, Charles}, year={2021} }
  @article{Furness_Garwood_Sutton_2023, title={REvoSim v3: A fast evolutionary simulation tool with ecological processes}, volume={8}, rights={Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence (CC-BY-NC-ND)}, ISSN={2475-9066}, DOI={10.21105/joss.05284}, abstractNote={Furness et al., (2023). REvoSim v3: A fast evolutionary simulation tool with ecological processes. Journal of Open Source Software, 8(89), 5284, https://doi.org/10.21105/joss.05284}, number={89}, journal={Journal of Open Source Software}, author={Furness, Euan N. and Garwood, Russell J. and Sutton, Mark D.}, year={2023}, month=sep, pages={5284}, language={en} }
  @article{Garwood_Spencer_Sutton_2019, title={REvoSim: Organism-level simulation of macro and microevolution}, volume={62}, rights={© The Palaeontological Association}, ISSN={1475-4983}, DOI={10.1111/pala.12420}, abstractNote={Macroevolutionary processes dictate the generation and loss of biodiversity. Understanding them is a key challenge when interrogating the earth–life system in deep time. Model-based approaches can reveal important macroevolutionary patterns and generate hypotheses on the underlying processes. Here we present and document a novel model called REvoSim (Rapid Evolutionary Simulator) coupled with a software implementation of this model. The latter is available here as both source code (C++/Qt, GNU General Public License) and as distributables for a variety of operating systems. REvoSim is an individual-based model with a strong focus on computational efficiency. It can simulate populations of 105–107 digital organisms over geological timescales on a typical desktop computer, and incorporates spatial and temporal environmental variation, recombinant reproduction, mutation and dispersal. Whilst microevolutionary processes drive the model, macroevolutionary phenomena such as speciation and extinction emerge. We present results and analysis of the model focusing on validation, and note a number potential applications. REvoSim can serve as a multipurpose platform for studying both macro and microevolution, and bridges this divide. It will be continually developed by the authors to expand its capabilities and hence its utility.}, number={3}, journal={Palaeontology}, author={Garwood, Russell J. and Spencer, Alan R. T. and Sutton, Mark D.}, year={2019}, pages={339–355}, language={en} }

JOSS/paper.md

@@ -93,7 +93,7 @@ TREvoSim v3.0.0 includes a suite of new features that allow the investigation of
 
 ### Ecosystem engineering
 
-A new ecosystem engineering system allows organism-environment feedback to be investigated. When the ecosystem engineering option is enabled (it is disabled in default settings), a species is assigned ecosystem engineering status halfway through a run, and passes this status to descendents. When this occurs, the genome of that organism is either used to overwrite an environmental mask, or added to the environment as an additional mask. Overwriting a mask reduces the hamming distance between engineers and masks, and -- assuming a low fitness target -- thus directly improves their fitness relative to non-engineers. In contrast, adding a mask changes the fitness landscape changes the nature of the fitness landscape for all organisms, but with a weaker direct benefit to ecosystem engineers. Ecosystem engineering can occur just once (‘one-shot’ ecosystem engineering) or can be repeated after the first application (‘persistent’). When a mask is added in the first application, it is overwritten in subsequent applications when ecosystem engineers are persistent. A new facility to log the ecosystem-engineering status of individuals is provided. 
+A new ecosystem engineering system allows the impact of organism-environment feedback to be investigated [@Butterfield_2011]. When the ecosystem engineering option is enabled (it is disabled in default settings), a species is assigned ecosystem engineering status halfway through a run, and passes this status to descendents. When this occurs, the genome of that organism is either used to overwrite an environmental mask, or added to the environment as an additional mask. Overwriting a mask reduces the hamming distance between engineers and masks, and -- assuming a low fitness target -- thus directly improves their fitness relative to non-engineers. In contrast, adding a mask changes the fitness landscape changes the nature of the fitness landscape for all organisms, but with a weaker direct benefit to ecosystem engineers. Ecosystem engineering can occur just once (‘one-shot’ ecosystem engineering) or can be repeated after the first application (‘persistent’). When a mask is added in the first application, it is overwritten in subsequent applications when ecosystem engineers are persistent. A new facility to log the ecosystem-engineering status of individuals is provided. 
 
 ### Expanding playing field 
 
@@ -117,7 +117,7 @@ Provides a layer of abstraction between an organism’s genome and the bits used
 
 ### Perturbations
 
-This implements a limited period of increased rates of environmental change that occurs halfway through a run (when half the requested species have evolved, or at half the requested iteration number). This is intended for study of scenarios where evolutionary dynamics are driven by variations in the rate of environmental change. There is an option to also increase mixing between playing fields during a perturbation. 
+This implements a limited period of increased rates of environmental change that occurs halfway through a run (when half the requested species have evolved, or at half the requested iteration number). This is intended for study of scenarios where evolutionary dynamics are driven by variations in the rate of environmental change[@Condamine_Rolland_Morlon_2013]. There is an option to also increase mixing between playing fields during a perturbation. 
 
 ## Software modifications