How many generations did the experiment run for?
QUESTION 1
How many generations did the experiment run for?
10 points
QUESTION 2
Approximately how many samples from each population in each generation?
10 points
QUESTION 3
At approximately what generation was the movement among microcosms first allowed?
10 points
QUESTION 4
At approximately what generation was the temperature gradient first turned off?
10 points
QUESTION 5
At approximately what generation was the temperature gradient then turned on again?
10 points
QUESTION 6
For the next four questions, consider just generation 800
In how many of the ten populations (microcosms) was genetic marker 1 (gm1) fixed or lost?
10 points
QUESTION 7
In how many of the ten populations (microcosms) was genetic marker 20 (gm20) fixed or lost?
10 points
QUESTION 8
How many of the 20 markers had been fixed or lost in the first microcosm?
10 points
QUESTION 9
Genetic marker 19 was most frequent in which population/microcosm (just enter the number of the microcosm)?
10 points
QUESTION 10
For the next four questions, consider just generation 1500
In how many of the ten populations (microcosms) was genetic marker 1 (gm1) fixed or lost?
10 points
QUESTION 11
In how many of the ten populations (microcosms) was genetic marker 20 (gm20) fixed or lost?
10 points
QUESTION 12
How many of the 20 markers had been fixed or lost in the first microcosm?
10 points
QUESTION 13
Genetic marker 19 was most frequent in which population/microcosm (just enter the number of the microcosm)?
10 points
QUESTION 14
At which generation did gm1 first become fixed or lost in population 1?
10 points
QUESTION 15
At which generation did gm2 first become fixed or lost in population 1?
10 points
QUESTION 16
At which generation did gm2 first become fixed or lost in any of the populations?
10 points
QUESTION 17
And which population was it?
10 points
QUESTION 18
At which generation did any of the 20 genetic markers first become fixed or lost in population 1?
10 points
QUESTION 19
And which marker was it?
10 points
QUESTION 20
At which generation did any of the 20 genetic markers first become fixed or lost in any of the populations?
10 points
QUESTION 21
And which population was it?
10 points
QUESTION 22
And which marker was it?
10 points
QUESTION 23
For functional trait 1 (ft1)... (indicate all correct responses)
There is an overall trend of selection in this trait over time in the microcosms, towards a value greater than the initial value
There is an overall trend of selection in this trait over time in the microcosms, towards a value less than the initial value
There is no overall trend of selection in this trait over time in the microcosms
There is evidence that temperature is affecting the evolution of this trait
There is no evidence that temperature is affecting the evolution of this trait
The allowing of movement among microcosms affected the trait values
10 points
QUESTION 24
For functional trait 2 (ft2)... (indicate all correct responses)
There is an overall trend of selection in this trait over time in the microcosms, towards a value greater than the initial value
There is an overall trend of selection in this trait over time in the microcosms, towards a value less than the initial value
There is no overall trend of selection in this trait over time in the microcosms
There is evidence that temperature is affecting the evolution of this trait
There is no evidence that temperature is affecting the evolution of this trait
The allowing of movement among microcosms affected the trait values
10 points
QUESTION 25
For functional trait 3 (ft3)... (indicate all correct responses)
There is an overall trend of selection in this trait over time in the microcosms, towards a value greater than the initial value
There is an overall trend of selection in this trait over time in the microcosms, towards a value less than the initial value
There is no overall trend of selection in this trait over time in the microcosms
There is evidence that temperature is affecting the evolution of this trait
There is no evidence that temperature is affecting the evolution of this trait
The allowing of movement among microcosms affected the trait values
10 points
QUESTION 26
At the generation just before movement was allowed, in how many of the populations had genetic marker 1 (gm1) NOT been lost?
10 points
QUESTION 27
At the generation just before movement was allowed, in population 1, how many of the 20 genetic markers had NOT been lost?
10 points
QUESTION 28
At the generation just before movement was allowed, in population 1, how many of the 20 genetic markers had been fixed?
10 points
QUESTION 29
At the generation just before movement was allowed, in population 1, of the genetic markers that had NOT been lost, which was closest to being lost (ie had the lowest frequency)?
10 points
QUESTION 30
Which traits appear to be under general selection during the experiment, towards values different to their starting values?
ft1
ft2
ft3
ft4
ft5
mt1
mt2
mt3
mt4
mt5
sct1
sct2
sct3
40 points
QUESTION 31
Which traits appear to be under selection specifically due to temperature during the experiment?
ft1
ft2
ft3
ft4
ft5
mt1
mt2
mt3
mt4
mt5
sct1
sct2
sct3
40 points
QUESTION 32
The fancy equipment obviously needed to be used again. So the researchers ran the whole experiment again. The results are in the e2 data files. Have a look at these files in whatever way you wish and work out what the researchers did differently in this experiment in terms of allowing movement and applying the temperature gradient. (Select all that are correct)
Movement was allowed between generation 0 and 500
Movement was allowed between generation 500 and 1000
Movement was allowed between generation 1000 and 1500
Movement was allowed between generation 1500 and 2000
Movement was allowed between generation 2000 and 2500
Temperature gradient was imposed between generation 500 and 1000
Temperature gradient was imposed between generation 1000 and 1500
Temperature gradient was imposed between generation 1500 and 2000
Temperature gradient was imposed between generation 2000 and 2500
50 points
QUESTION 33
Which traits appear to be under selection specifically due to temperature during THIS experiment?
ft1
ft2
ft3
ft4
ft5
mt1
mt2
mt3
mt4
mt5
sct1
sct2
sct3
Microcosm Evolution
Some researchers design an experiment to investigate evolution in relatively small populations. They set up ten microcosms, each with a population of flies in it. The flies are initially randomly allocated to microcosms. The flies are then allowed to breed and the experiment is run for many generations. The microcosm equipment is designed so that some movement among microcosms can be allowed or closed off by the researchers. In this experiment, movement is initially closed off, but at some point during the experiment it is opened up and allowed. The equipment also allows a temperature gradient to be applied across the microcosms, so that microcosm 1 is a little hotter than microcosm 2, which is a little hotter than microcosm 3, which is a little hotter than microcosm 4, and so on, with microcosm 10 being the coolest. Alternatively, all microcosms can be set to the same intermediate temperature. In this experiment, temperature is first set to have a gradient across the microcosms, then at some point set to be equal across the microcosms, and then again set to have a gradient across the microcosms.
The researchers sample from the flies in each microcosm at each generation, and use some expensive new equipment to measure five functional traits, five morphological traits, and three semi-cryptic traits for each individual fly sampled. They also test 20 marker loci and measure the number of a specific test marker allele at each of the loci giving either 0, 1 or 2 of the test alleles at each of the marker 20 loci. The markers were specifically chosen to be neutral markers, ie the expectation is that they would not be under selective pressures. The trait and genetic data are recorded in a separate file for each generation. At the end of the experiment the researchers are faced with a large amount of data and not much idea how to deal with it. As a recent graduate with some skills and experience in big biological data, you are called in to help!
Work through the look at data.R script, checking that you understand what the code is doing. If you are unsure of anything, make sure you ask for clarification.
When you are ready, extend the code to look at different traits and different generations, following the suggestions in the script.
You will want to consider some of the following general questions
Do some of the genes become fixed or lost? Does this happen for only some genes or all genes? Only some populations or all populations? Some generations or all generations?
Are there trends of change over time in any of the traits and/or genetic frequencies? Are these consistent over time, or do they change at certain times? Do trait values and/or genetic frequencies in the populations diverge from each other, or remain close, or diverge and then become close again? Do any of these patterns indicate that any of the traits or genes are under selective pressures at any times? And/or that there is gene flow among populations at any time?
For the assignment, you will need to enter answers to some more specific questions about this data set through an LMS quiz.
