[Population Modeling] eVOLUTUS: the simulator of multiscale evolutionary processes tested on Foraminifera

[Pawel Topa]

Dear members of Population Modeling Working Group,

let me introduce our project named "eVOLUTUS: the simulator of 
multiscale evolutionary processes tested on Foraminifera":


Our goal is to design a new algorithmic framework for testing and 
simulating evolutionary principles and their consequences in defined 
environments at various spatiotemporal scales. Due to biological 
complexity of organisms and their interactions with the environment, it 
has never been attempted to design such a numerical framework for the 
simulation of evolutionary patterns derived from the fossil record of 
real organisms. As a model organism we will implement Foraminifera, 
single-celled eukaryotes that occupy marine benthic and pelagic zones 
throughout the world andhave an extraordinary fossil record throughout 
the Phanerozoic. This makes them an ideal model often used for testing 
general evolutionary hypotheses.  Recent studies have shown that shell 
architecture and most prominent morphogenetic trends in shell 
development distinctly follow molecular phylogenetic patterns.

We use approach named Individual Based Modelling in which modeler tries 
to present population of living organisms as being composed of discrete 
individual organisms. The model that uses IBM in natural way can be 
implemented using Agent-based Modeling computational paradigm. In order 
to model evolutionary processes we use the well known genetic operators: 
mutation and crossing over which are applied to the virtual genome 
consisted of parameters that govern agent (foraminifers) behavior. 
Selection is simply made by adaptation to environmental conditions in 
virtual habitat.

References:
1) Paweł Topa, Łukasz Faber, Jarosław Tyszka, Maciej Komosinski, 
Modelling ecology and evolution of Foraminifera in the agent-oriented 
distributed platform, Journal of Computational Science, Volume 18, 
January 2017, Pages 69-84, ISSN 1877-7503, 
http://dx.doi.org/10.1016/j.jocs.2016.07.009.
(//www.sciencedirect.com/science/article/pii/S1877750316301168)
Abstract: Abstract
We present a new software platform called eVolutus for simulating 
evolution of living organisms. We choose Foraminifera as model organisms 
that represent a group of single-cellular, mainly marine, organisms that 
construct well fossilisable protective shells. They have lived on Earth 
for more than 540 million years and have left an extraordinary fossil 
record that is excellent for testing palaeoecological and evolutionary 
hypotheses. We use the AgE platform, which is a lightweight 
agent-oriented platform supporting distributed computation. The paper 
presents the general architecture of this modelling environment as well 
as more detailed descriptions of the implemented rules and applied 
solutions. The utility of this software is demonstrated by presenting 
the configuration and results of sample experiments.
Keywords: Agent-based modelling; Artificial Life; Multi-agent systems; 
Foraminifera

2) Maciej Komosinski, Agnieszka Mensfelt, Jarosław Tyszka, Jan Goleń, 
Multi-agent simulation of benthic foraminifera response to annual 
variability of feeding fluxes, Journal of Computational Science, 
Available online 3 October 2016, ISSN 1877-7503, 
http://dx.doi.org/10.1016/j.jocs.2016.09.009.
(//www.sciencedirect.com/science/article/pii/S1877750316301715)
Abstract: Abstract
In this work we describe a novel simulation model of foraminifera and 
their microhabitat. The simulations reported here are focused on the 
response of foraminiferal populations to environmental feeding fluxes. 
The experiments allowed to calibrate the model and to simulate realistic 
population patterns known from culture experiments, as well as from 
oceanographic and paleoecologic studies. Variability of annual food flux 
has a direct impact on productivity of foraminifera: population sizes 
closely follow the intensity of constant and seasonal food fluxes in 
both scenarios. This correlation between the food influx and population 
size is interpreted as the consequence of changing the carrying capacity 
of the system. Seasonal pulses of particulate organic matter enhance the 
population size which is represented by a higher number of fossilized 
shells. Our model offers a flexible experimental design to run 
sophisticated in silico experiments. This approach reveals a novel 
methodology for testing sensitivity of fossil and recent foraminiferal 
assemblages to environmental changes. Furthermore, it facilitates 
predictive applications for monitoring studies based on simulation of 
various scenarios.
Keywords: Foraminifera; Simulation; Population dynamics; Life cycles; 
Seasonality

> 2. Categorize your modeling approach by research area. Keywords we 
> used in the past are:
> Managing disease spread
> Resource planning and allocation
> Predicting drug effects
> Risk assessment
> Ecosystem management
> Testing theory
> Epidemiology and public health
Individual based modeling.


>
> 3. Add keywords for computational methods you used. Examples include 
> Agent Based Models, differential equations, Monte-Carlo simulation, 
> yet there are many more options that you can find in: Table 1 in: 
> https://simtk.org/docman/view.php/962/1963/SummerSim_2016_PopMod_Submit_2016_05_15_Robert_Smith.pdf
* Agent Based Modeling
* Evolutionary Computations


Kind regards

Paweł Topa
Jarek Tyszka
Maciek Komosinski
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