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.

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

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