We'll start with one population of fish in a pond, but eventually the population will split. Explore what happens to the genes over time in this system with periodic floods (like in our prior lessons).
Population size sets how many fish live in each pond.
Generations sets how long the run lasts.
Split at generation sets when the pond divides.
Mutation rate sets how often a new allele appears.
Click a locus to trace its ancestors and descendants, and tick lock to keep several traces on screen.
One pond splits in twoEach row is a generation, the first at the top. Each fish has two chromosomes, one from each parent, drawn as two rows of loci (the eight traced ones).Dashed line: the split. Orange pond left, blue right; they never mix again.Grey loci: alleles the three founding fish carried. A new allele (a mutation) is coloured by where it arose: green with a dark dot before the split, orange or blue after.Click a locus: red lines trace up to its ancestral copies, blue lines down to every copy descended from it.
QuestionFour questions on the pedigree and four targets, in any order; click a circle to move between them.A question: click a copy in the pedigree, then Lock in. A target: Go runs sixteen pedigrees with your settings and shows the first. The picture: a run that hits; red boxes: where most of each line should sit.
To finish
Complete eight questions and targets 0 of 8
Stage B is open.
R code
B
Finish Stage A to unlock this section.
We'll have our two ponds from before, and have periodic floods that allow for migration. But now mutations can produce incompatibilities! See how that changes things in this activity.
Generations apart sets how long the ponds evolve separately before the floods.
Mutation rate sets how fast new alleles, and so incompatible pairs, build up.
Migration sets how many fish switch ponds each generation of floods.
The two pondsStage A's ponds, run longer: one population splits into an orange and a blue pond of 40 fish each, kept apart for the generations you set. Each fish: two chromosomes of 40 loci, in A's colours (grey, the founders' alleles; orange or blue, new alleles from that pond).Then floods: each generation, some fish switch ponds.Square left of each fish: the share of its new alleles from each pond, orange to blue. Shown: run 1 of the 16 that Go plays.
Incompatible pairs and survivalA new allele from the orange pond and one from the blue, at different loci, form an incompatible pair with chance 0.05 (Lesson 19 C: 0.02). One copy of each in an offspring is enough. Until the floods they cannot meet, since each arose in a different pond.Red arrow: how much each incompatible pair lowers survival, held fixed during the targets; once they are done, click and drag it.
TargetGo plays the generations apart and then 150 generations of floods, 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 thick line, the 16 runs' average, should be.
To finish
Complete two targets 0 of 2
Stage C is open.
R code
C
Finish Stage B to unlock this section.
Phylogenies show patterns of species divergence over time. They're just like the coalescence plots of individual loci (Part A) or pedigrees of individuals...just reflecting full sunderings of lineages. Below you'll answer some random, regenerating phylogeny-reading questions. When it says "the" nearest relative--any of several equally near relatives is fine. Be able to draw a phylogeny if I tell you what the relatedness patterns are, too!
Click a letter or an ancestor (node), then Lock in, and use Another tree to try again on a new tree.
A treeLiving species (letters, right), drawn back to where their lineages meet; time runs left to right, the oldest ancestor (node) on the left. Each circle is a node, a common ancestor.Swapping an ancestor's two branches, up for down, gives the same tree.Click a letter or a circle to pick it, then Lock in.
QuestionSix questions, in any order; click a circle to move between them. A wrong answer shows the right one; Another tree asks again on a new tree.
To finish
Complete six questions 0 of 6
Stage D is open.
R code
Good job!
That is all that is required of Lesson 20. Your completion code is below — copy it and hand it in. Parts D and E are optional: you can skip them, or do them for practice. Anything you get in them is added to your code, which is regenerated each time, so copy it again afterward if you want those results counted.
D
Finish Stage C to unlock this section.
Simulate a population and click on the population to cause a split. Repeat that for different populations over time & examine what patterns emerge.
Click a population's bar to split it, and use Pause to stop the clock while you decide.
Population size sets how many fish each population holds.
Mutation rate sets how often a new allele appears.
Crossovers per chromosome sets whether loci on a chromosome are inherited together or separately.
The populationsOne population of A's and B's fish runs for 400 generations. Click a population's bar while it runs to split it: its fish are shuffled into two halves that never meet again, each growing back to about the population size you set. Up to 16 populations.Each bar: a population, from its start to its split or the present. Letters name the populations living at the end.At the end, black: the populations' tree, drawn back past generation 0 (the population was already old then). Thin, over it: each locus's tree, traced from one chromosome per living population back through its ancestors, as in A. Blue ✓: same branching as the populations, each ancestor (node) in the population just before the matching split. Orange ↶: same branching, but an ancestor (node) older than that. Red ✗: different branching.
Your runsOne dot per run that ended with three or more populations. Across: the average generations between successive splits, divided by population size. Right: splits far apart in small populations. Left: splits close together, or large populations. Up: how many of the eight loci's trees match the populations' tree (blue ✓).
TargetGo runs one population for 400 generations while you split it. Pause to think; clicks still split while paused.The picture: a tree that hits, with its eight loci as squares. Red boxes: how many of the eight may be of the kind drawn; filled ones: how many must. =: all eight loci share one tree.
To finish
Complete four targets 0 of 4
Stage E is open.
R code
E
Finish Stage D to unlock this section.
Wing length in birds helps them overcome barriers. This means wing length can influence their gene flow and population sizes...which means it can influence how likely a population is to speciate or go extinct. Explore that here.
Drag the wing-length curve to set the first species' average.
Drag the VA and VE arrows to set how much wing length varies through genes and through environment.
Drag the ends of the gene-flow and range-size lines to set how each depends on wing length.
Drag the arrows into speciation and extinction to set how strongly gene flow and range size act on each.
Clade 1One bird species at time 0 and all its descendants: one line per species, back to the speciation event that split it from its parent. Coloured: species living now and their ancestors. Grey with a ×: species that went extinct and left no descendants.Shade: the species' average wing length, light (short) to dark (long).Shown: clade 1 of the 64 that Go plays.
Wing length among the speciesBars: the living species of all 64 clades, by average wing length. Dashed curve: the birds of the first species, as set in the diagram's wing-length box.
From wing length to speciation and extinctionA bird's wing length is its genetic value plus an environmental effect. Within a species, wing length varies by the additive genetic variance (VA) and the environmental variance (VE): the arrows into wing length; thicker, larger. In the wing-length box: dark, the birds' genetic values; light, their wing lengths. Drag the curve sideways to set the first species' average.Gene flow: the chance a bird disperses to another population of its species. Range size: the share of the largest possible range that a species with such wings holds, which sets its census size. Each depends on wing length: drag either end of a line; the number on the arrow from wing length is the line's slope, the change per cm. Dots: clade 1's living species.Gene flow holds a species' populations together, leaving fewer fragments to become new species. A larger range holds more birds, so the species is less likely to go extinct. Click an arrow, then drag it.At each speciation event, a fragment cut off from the rest becomes the new species. It starts from one bird that did not disperse, whose genetic value becomes the new species' average. So a new species differs from its parent by about the square root of VA in cm (VA is in cm²), and leans toward the wing lengths of birds that stay.
TargetGo runs 64 clades for 200 million years.The picture: a run that hits, as the plot over time draws it. The red box: where the thick line, the 64 clades' average, should end.