Lesson 19

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This lesson is going to take all of the population genetics processes we have learned, and look at how they can produce differences between populations. We will have drift, mutation, selection, and importantly, migration. The key number to look at here is FST. This is our F statistic: the observed relative to expected heterozygotes, compared not within one individual, but between individuals within a subpopulation. FST is the level of inbreeding, F, in the subpopulation, S, relative to the inbreeding of the total population, T. You can think of this very directly as how different the 2 subpopulations are from one another. An FST of 1 means the 2 populations are perfectly different: you can tell readily which population an individual came from by its genes. An FST of 0 means that the populations are perfectly the same: you cannot tell genetically which population it came from.

We're going to use, as our example here, fish in ponds. Imagine 2 ponds; we'll call them orange and blue. There are fish in each pond. Fish can only move from one pond to the other pond when there's a flood. We're going to control how often a flood occurs, generations between floods, and how many fish move during each flood, the migration during flood. We will also control the number of fish in the pond, the mutation rate, which is going to be the same across ponds, and the recombination rate. For this first part, those are the only toggles we're going to have. Your goal is to reach the target FST using these toggles.

The two pondsOne population of fish splits into two ponds: orange on the left, blue on the right. Each fish: two chromosomes of 40 loci, drawn as beads.Grey: the alleles the population started with. A new allele takes its pond's colour, orange or blue.Run 1 of the 16 that Go plays.

TargetEach generation every fish is replaced by young of two parents from its own pond. Nothing here helps or harms a fish.A flood comes at generation 1, then every so many generations. Go plays 400 generations, 16 times; the last is just before a flood.FST across the genome: how different the two ponds are at each locus, as in Lesson 17. 0: the same mix of alleles in both.Bars: each of the 40 loci, the 16 runs averaged. Dots: run 1. A locus where both ponds carry the same one allele has no FST, and is left out.The line: the bars' average, FST over the whole genome. The red box: where the line should end.

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We're sticking with ponds and fish, and we're still monitoring FST. We're now going to base these fish a little more biologically on the stickleback. The stickleback is a little fish, and it can have multiple different forms. Some of them have pharyngeal teeth, teeth in their throat. The extent of these pharyngeal teeth is controlled by a locus called Bmp6. Having these pharyngeal teeth makes them very good at eating prey on the bottom, large prey, things like snails. There's another locus that controls their gill rakers. These are fine structures in their throat that help them filter food out of the water, like plankton. These genes are at separate loci. These are 2 different genes that increase the fish's ability to eat food.

      
Bmp6 causes pharyngeal teeth. Pharyngeal teeth cause you to eat snails. The gill-raker gene causes gill rakers. Gill rakers like plankton, and what we adjust is the number of plankton compared to the number of snails in the 2 populations.

      
There is a fitness surface shown, which shows the fitness of the Bmp6 and gill-raker locus genotypes as a little pair of boxes. They show the position of the fish at the beginning, and the color of the boxes shows you the relative fitness as a result of that. Your goal here is to, again, generate differences between the populations. Except this time, you're going to generate differences at specific loci. So what you're controlling here again is migration rate during a flood, the frequency of floods, the recombination rate, and now fitness.

    

  


  

    

      

        
The two pondsThreespine sticklebacks. The ponds have been apart a long time: every locus in the orange pond carries its own allele, every locus in the blue pond its own. At the food genes the orange pond's fish start benthic, the blue pond's limnetic.The square left of each fish: its food genes, light (limnetic) to dark (benthic). The two genes' loci are boxed. Run 1 of the 16 that Go plays.

        
      

      

        
FST across the genomeBars: FST between the ponds at each locus, the 16 runs averaged. Dots: run 1.Under them, the chromosome. Drag ▲ (Bmp6) and ■ (a gill-raker gene) along it to set where each gene sits.

        
      

      

        

        
      

    

    

      

        
Genes, Traits, & SurvivalBmp6: benthic sticklebacks carry an allele that about doubles their pharyngeal teeth (teeth in the throat), for crushing snails (Paxton Lake; Cleves et al. 2014). Its real home is chromosome 21.A gill-raker gene: limnetic alleles give more gill rakers, which sieve plankton; benthic alleles fewer. Real ones map to chromosomes 4 and 20 (Glazer et al. 2014).Teeth help a fish eat snails, gill rakers plankton, as much as its pond holds (set in the Target card).Teeth and rakers cost something to grow: each pays only where its food is plentiful. With few snails a fish does better without teeth; with little plankton, without many rakers.Grey arrows: fixed.

        

      

      

        
Fitness surfaceEach pond's, side by side, from its snails and plankton.Across: benthic alleles at Bmp6 (▲), ○ none, ◐ one, ● two. Up: the same at the gill-raker gene (■).Darker: a better chance to survive in that pond. Dots: run 1's fish, the bigger the more of them.

        
      

      

        
TargetFish a pond: 50. No new mutations. Go plays 200 generations, 16 times.The picture: FST across the genome as it should look at generation 200, with ▲ and ■ where they sit now. The red boxes: where those loci's bars should end.Under it, each pond's food: snails and plankton, none to plenty. Click or drag up and down a column to set it; the 0 under it clears it. 

        

        
        

          
          
          

          

          

          

          

            
            
          

        

        

      

      

        
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The individual loci we looked at above in part B were not the only loci. Every locus has a chance for mutations to occur. Sometimes a mutation can arise in one population, and a different mutation can arise in a different population. Isolated, these two mutations, each arisen in a different population, are fine. They have no fitness effect. But, due to epistasis, if I combine the new mutation from population orange with the new mutation from population blue, they may have an incompatibility: something that causes fish that have both of these new alleles to have lower fitness. We call that an incompatible pair.

      
For this, we're again going to control the same general patterns we did before, with mutation rate being particularly important, and the chance that a pair of mutations is incompatible. Using these dials, we're going to run and see what it does to things like hybrid survival rate and FST between the ponds.

    

  


  

    

      

        
The two pondsB's sticklebacks, just after one population split into the two ponds: grey alleles shared, Bmp6 (locus 10) and the gill-raker gene (locus 30) already benthic in the orange pond and limnetic in the blue. The orange pond holds plenty of snails and no plankton, the blue pond plenty of plankton and no snails.A new allele takes its pond's colour. Run 1 of the 16 that Go plays.

        
      

      

        

        
      

      

        
Fitness surfaceOne incompatible pair: a new orange allele and a new blue allele.Across: copies of the pair's orange allele; up: copies of its blue allele. Darker: a better chance to survive.The arrows: the path each pond took, one new allele at a time.

        
      

    

    

      

        
Genes, Traits, & SurvivalB's diagram. One more cause: a new allele from the orange pond and a new allele from the blue pond, at two different loci, are an incompatible pair with the chance set below. One copy of each in a young fish is enough.Inside one pond, the two never meet.Click the red arrow, then drag it: how much each incompatible pair lowers the chance to survive.

        

      

      

        
TargetFish a pond: 25. Go plays 400 generations, 16 times.The picture: a run that hits, as the plot over time draws it (the menu turns to that plot when a target opens). The red box: where the run should end. Over the last four floods: FST should hardly fall at each. 

        
        

          
          

          

          

          

          

          

            
            
          

        

        

      

      

        
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We're going to focus in only on Bmp6 again, and we're adding a new gene, this throat gene. This throat gene controls the color of the throat of a fish, the color of the skin. There will also be a gene for a preference. So there is the food allele, which controls survival in the 2 populations; a preference allele, which controls how strongly fish tend to mate with individuals of a particular color: AA prefers to mate with black-throated fish, BB prefers to mate with red-throated fish, and AB is non-selective; and then a throat color gene that controls the color of the throat. The location of the throat gene and the preference gene is the important bit, because that's what can be scrambled by recombination.

    

  


  

    

      

        
The two pondsBenthic sticklebacks in the orange pond, limnetic in the blue, long apart, now flooding together. Bmp6 (locus 20) is the food gene this time: the orange pond's food is all snails, the blue pond's all plankton.Left of each fish: its food genotype, light (limnetic) to dark (benthic), and its throat colour, red to black.The three genes' loci are boxed. At the preference gene, pale red: prefers red; grey: prefers black.Run 1 of the 16 that Go plays.

        
      

      

        
FST across the genomeBars: FST between the ponds at each locus, the 16 runs averaged. Dots: run 1.Under them, the chromosome: ▲ Bmp6, fixed at locus 20. Drag ♥, the throat-colour gene, and ◆, the preference gene, along it.Ticked, an inversion runs over the three genes on every chromosome that starts in the orange pond: in a fish with one inverted and one standard chromosome, no crossover falls inside it.

        
        

      

      

        

        
      

      

        
Fitness surfaceBmp6, the food gene. Across: benthic alleles at Bmp6, ○ none, ◐ one, ● two. Up: the chance to survive in each pond.Drag ◐ up or down: a hybrid's chance to survive, the same in both ponds. The faint line: halfway between its parents. Below it, a hybrid falls between two foods (Hatfield & Schluter 1999; Arnegard et al. 2014).Enos Lake, British Columbia: after signal crayfish arrived, its benthic and limnetic sticklebacks became one hybrid population (Taylor et al. 2006); in ponds with crayfish, hybrids grow better relative to the two species (Kinney et al. 2025).

        
      

    

    

      

        
Survival, mating frequency, offspringMale sticklebacks show a throat colour when they breed: red in limnetic fish, often black in benthic fish (Boughman 2001).The preference gene: a fish with two prefers-black alleles turns down a red-throated partner, one with two prefers-red alleles a black-throated one, with the chance on the choosiness arrow. One of each: it takes anyone. It looks up to 4 times, then takes the next it meets. A fish turned down mates less.throat gene → throat colour: where one red and one black allele look. Number of offspring is not set anywhere: it comes out of survival and mating frequency.

        

      

      

        
TargetFish a pond: 100. Go plays 300 generations, 16 times.The picture: FST at Bmp6 over time, in runs that hit. 1: the ponds wholly apart in food; 0: one food allele has taken both. The red box: where the thick line, the 16 runs' average, should end.Throat alleles arose in different ponds: black throats and prefers-black in the benthic (orange) pond, red throats and prefers-red in the limnetic (blue) pond. Present in both ponds: in each pond 3 in 10 throat alleles black and 3 in 10 preference alleles prefers-black. 

        

        
        

          
          
initial throat alleles

          

          

          

          

          

            
            
          

        

        

      

      

        
Fitness by Bmp6 genotypeOver the run's last 20 generations, each pond: survival, the share of young that survived; mating frequency (1 = the pond's average); number of offspring, the two multiplied (1 = the pond's average).

        
      

      

        
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