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How to quantify effects of Muller's ratchet

Evolution@home has compiled the largest existing database of Muller's ratchet simulation results. This allows quantifications of the threat of extinction and other aspects of Muller's ratchet with unprecedented accuracy. Depending on what you know about your favorite organism, evolution@home results might help to work out what the ratchet does there.

Quantifying the absolute rate of mutation accumulation from Muller's ratchet requires the knowledge of a number of parameters, but not all are of equal importance. Thus it can be perfectly acceptable to have only very rough upper and lower limits for some parameters - depending on other known details of the system this may still be enough to infer something useful about the effects of Muller's ratchet. Please note that valuable estimates can often be obtained from closely related species.

The following list of questions tries to be as general as possible and may thus ask some questions that are not appropriate for your study organism. If you think you might know enough answers to the following questions or if you are simply curious about an attempt to quantify Muller's ratchet, then please contact Laurence Loewe with more details.

 

Population size and life history


1. What is the total number of individuals?
      min=                      mid=                            max=

2. Are there estimates of effective population size?
      min=                      mid=                            max=

3. What is the generation time (give typical and most extreme limits known)?
      min=                      mid=                            max=

4. What is the maximal number of offspring that survive to reproductive maturity

    a.  in the lab?
      min=                      mid=                            max=

    b. in the wild?
      min=                      mid=                            max=

Mutation rates and effects


5. How large is the neutral (synonymous/silent) point mutation rate /site/generation?
    Please do not give long term averages to avoid a 'slowdown' due to multiple hits.
    Several estimates from independent methods are welcome.
      min=                      mid=                            max=

6. How many insertions and deletions occur /site/generation in neutral DNA?
    Please do not give long term averages to avoid a 'slowdown' due to multiple hits.
    Several estimates from independent methods are welcome.
      min=                      mid=                            max=

7. How often do transposable elements move /site/generation in neutral DNA?
    Please do not give long term averages to avoid a 'slowdown' due to multiple hits.
    Several estimates from independent methods are welcome.
      min=                      mid=                            max=

8. What substitution rates are assumed for molecular clocks in related species?
    Such estimates may help to establish the lowest possible mutation rate.
      min=                      mid=                            max=

9. How large is the effective genome size ?
    a. all protein coding sequences (exons)
      min=                      mid=                            max=

    b. all non-coding functional sequences
      min=                      mid=                            max=

10. Are there close relatives that can be used to infer data for mutational parameters?
     (How do differences between the two species affect mutation rate estimates?)

11. Are there estimates about the strength of selection ?
      Probably the least is known about this, but that may not matter too much,
      as the current method to estimate Muller's ratchet
      does not make many assumptions here and
      the distribution of mutational effects is probably very wide
      in most organisms. Just check, if more details are known from ...

    a. Mutation accumulation experiments

    b. Population genetic estimates of the distribution of mutational effects

    c. Related species that could be used to infer mutational effects?

12. How many copies of a genome are usually present in a cell?

 

Recombination


13. How many years did this species presumably live without recombination?
      min=                      mid=                            max=

14. Asexuality: Is there good evidence for obligate parthenogenesis / vegetative reproduction?

15. How many mitotic recombination events occur /genome/generation?

16. Selfing: Is there regular meiotic recombination between sister chromosomes?

17. How rare is outcrossing? How many years since the last outcrossing event?

 

Evolutionary history


18. Is the species an ecological specialist or generalist?
      Compare it to its sexual sister species?      

19. Does this species have a compact or inflated genome?
      Have all unnecessary genes probably been removed?

20. Are there known bottlenecks or population expansions in the species' history?

 

 

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