Wesley R. Elsberry
Posts: 4991
Joined: May 2002
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I just ran Zachriel's modified parameter set under v1.2.1 and v.1.4.1. Both used exactly the same "mendel.in" configuration file. Only one each, but the v1.4.1 run does go to completion and shows the accumulation and fixation of favorable mutations. The v1.2.1 run, by contrast, shows a declining population that only lasts to generation 31. The value for "before sel: geno fitness" looks particularly strange; in the final generation, the value was -90.5. In the v1.4.1 run, that value was never less than 1.0, and at generation 500 had reached a little over 20. I'm assuming at the moment that the "fitness" value is always with respect to the original absolute value at the start of the run.
Whatever else may be going on, it does seem that MA treatment of favorable mutations changed rather radically between those versions. I wouldn't want to validate v1.4.1 on this basis, but it comparatively is doing a much better job than v1.2.1, and I think my earlier comment stands: outcomes of experiments performed with MA v1.2.1 (and perhaps earlier versions) should be treated with skepticism until independently confirmed, preferably with a package that can be validated against actual popgen results.
ETA: Using Mendel's Accountant v.1.2.1 is like using a bank that inexplicably only records your withdrawals and fails to record your deposits.
Edited by Wesley R. Elsberry on June 11 2009,13:57
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"You can't teach an old dogma new tricks." - Dorothy Parker
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