4 Bug hunt camouflage (Netlogo)

4.1 Background

Adaptive evolution via natural selection is a fundamental concept in evolutionary biology and is one of the central mechanisms driving the diversity of life on Earth. This process is shaped by the interplay between variation in heritable traits within a population, differential survival and reproduction rates, and the environmental challenges faced by organisms. One illustrative example of natural selection is the phenomenon of camouflage in predator-prey systems.

In an environment where predators rely on visual cues to locate their prey, individuals with better camouflage that matches their surroundings are more likely to avoid detection and capture, leading to higher survival rates. Over generations, the frequency of camouflage traits increases in the prey population due to higher survival and increased reproduction of well-camouflaged individuals.

On the other hand, predators with better detection skills, like keen eyesight, are more successful at capturing prey, leading to increased survival and reproduction of these individuals. Consequently, traits associated with effective predation also become more prevalent in the predator population. This dynamic interplay between camouflage in prey and predator detection abilities exemplifies the power of natural selection in driving the adaptation and evolution of species to their ecological niches.

Learning outcomes:

• Understanding adaptive evolution via natural selection.
• Understanding how fitness depends on the environment.
• Understanding the terms adaptation, selection, selection pressure, heritability.

4.2 Your task

In this exercise, you will use an individual-based simulation to examine adaptive evolution and natural selection, exploring how living organisms can undergo transformations to better survive and thrive in their environments. You step into the role of a predatory bird and hunt bugs living in a virtual landscape. You will see how the colours of the bugs (“traits”) influence their survival. The bugs that blend into their surroundings have a higher chance of avoiding detection, leading to greater survival and more opportunities to pass on their advantageous traits to future generations.

The exercise is done using one of the built-in models in a computer program called NetLogo (https://ccl.northwestern.edu/netlogo/).

There are two ways to use NetLogo: (1) You can log in to our SDU Ucloud computing system at https://cloud.sdu.dk/, and use it there; (2) You can download and install NetLogo from the site above.

I recommend the UCloud option: Please follow these steps: (i) search for NetLogo in the search bar at the top of the screen; (ii) click on Applications and then on the NetLogo icon; (iii) click on “Run Application”; (iv) Give your job a name (e.g., “BB512”) and under “Hours” enter 1 hour; (v) under Machine Type, select “u1-standard-1”; (vi) click on Submit. After a few moments while Ucloud is preparing your job, an new screen appears. Click on Open Interface to open a virtual desktop. There, you can open NetLogo and use it as if it was on your own computer by clicking on its icon.

Open NetLogo and click File > Models Library. You can then use the search box at the bottom of the screen to find the model called “Bug Hunt Camouflage”.

This is a model of natural/artificial selection that shows how a population hunted by a predator can develop camouflaging. For example, in a forest with green leaves, green bugs may emerge as the predominant bug color.

In the simulation you assume the role of a predatory bird that feeds on insects, which can be different colours. You will see what effect your hunting has on the colour traits/genetics of these simulated insects, and also how this evolution affects your hunting efficiency.

4.2.1 Getting started

1. When you open the model, you will see a screen with various purple and green “sliders”, buttons and menus that control parts of the model.
2. Start with 30 bugs, by moving the “carrying-capacity” slider until it reads 30.
3. Now click “setup”. You should see the environment appear on the right hand side, and you should see a few “bugs” on the environment. Start the simulaton by clicking “go”.
4. After you click go, you need to click on bugs as fast as you can using your mouse/track pad. You can also keep the mouse button depressed, and move the cursor around the world to catch the bugs. Try to consume bugs as fast as possible to remove any “deliberation” on your part as a predator. The camouflaging effect will emerge more clearly if you aren’t taking your time trying to find bugs that typically would be more difficult to find.

You can track your progress by looking at the graphs on the left. The most important of these are the two at the top, which show (1) the number of bugs caught through time and (2) the average colour values of the bugs.

In the “Bugs Caught vs. Time” plot the slope of the curve gives a good idea of your hunting efficiency – the faster you can catch bugs, the steeper the slope. If you didn’t catch any bugs for a while, the slope would be horizontal.

You should notice that bugs with contrasting colours (e.g. black on white) are easier to catch. Keep hunting for 2 mins or until you can’t find any more bugs then pause the simulation by clicking “go” again. Now take a look at the graphs and see what effect your hunting has had on the phenotype distribution in the population.

To understand what’s going on, you need to understand how the simulation works.

4.2.1.1 How the simulation works.

Simple version: The simulation starts with bugs with random colours.

Each time you kill a bug, one of the remaining bugs produces an offspring so that the population size stays constant. The colour of the offspring is inherited from its parent, though it can change slightly due to mutation (determined by the “max-mutation-step” slider). Therefore, the offspring of a red parent will be reddish, the offspring of a blue parent will be blueish and so on. Therefore, if you consistently kill off (e.g.) non-reddish bugs, the reddish bugs that remain will have offspring that are also red and the average colour of the population will then shift towards being redder.

Colour here is indicated by “hue”, “saturation” and “brightness” which range from 0 to 255. Basically, hue describes colour value (red/green/blue), saturation describes how “washed out” or vivid the colour is (a low value for saturation would look white), and brightness describes how bright the colour is (a low value for brightness would look black). See below for more details.

Evolution can be defined as: “change in the heritable characteristics [colour traits] of biological populations [bugs] over successive generations [time].”

4.3 Questions

Answer the following questions, then make sure you confirm your understanding and have the right answers with an instructor.

• What happens to the average colour of the bug population with time as you hunt?
• What happens to your hunting efficiency?
• Would you say that the bug population becomes worse or better adapted to their environment?
• Can you explain how this happens?
• After simulating in one environment (e.g. poppy field) for a few minutes, pause then switch to another environment. Are the bugs now well- or poorly-adapted to their environment?
• Do the genotypes of individuals change (e.g. with individual age)?
• Increasing the “max-mutation-step” makes bug offspring less like their parents. How do you think this will influence the speed of adaptation of the bugs?

Some useful keywords:

• Selection
• Adaptation
• Selection pressure
• Heritability

4.4 Details about colours (optional)

The primary colours red, green and blue (RGB) can be mixed to produce any colour (this is how the pixels of TVs and computer monitors work if you look closely). Mixtures of these colours are also used to control the colour of the bugs. Each bug has three pigment “genes” (R, G and B) that determine their colour phenotype. The more frequently the gene for a pigment is coded for, the stronger that presence of color is in the overall blend of pigments that results in a single phenotype for coloration. For example, a bug that had lots of R, but little G or B would appear as red. In this simulation RGB can vary from 0 to 100. The mixture of these primary colours results in a colour which has a particular hue, brightness and saturation (Fig 4.1).

Hue ranges from 0 to 255 with both ends of that spectrum being red, and as you move from 0 to 255 you pass through all the colours of the rainbow.

The other two elements of colour are brightness and saturation. If a colour is bright it is very vibrant, if it is not bright, it is dark: a brightness value of 0, would be black, no matter what the hue was. Similarly, a low saturation values give “washed out” colours and a valeue of 0 would be white.

Figure 4.1: Hue, brightness and saturation

Read more about the model here: http://ccl.northwestern.edu/netlogo/models/BugHuntCamouflage