[Mesquitelist] about error warnings

[Jeffrey C. Oliver]

Hi Xiao Chen,

The problem arises because you have a single haplotype assigned to multiple
populations in your Mesquite file.  For example, in the Chlaenius file, in
the TaxaAssociation, there are two haplotypes (T5 and T8) which are present
in both the GDB population and the GLD population:

<snip>
    GDB /  T5 T8 T11 T25 T26 T28 T29 T30 T58 T59 ,
    GZQ /  T21 T27 ,
    GLD /  T5 T8 T25 T47 T64 ,
</snip>

For the Neutral Coalescence simulations to work, haplotypes can be assigned
to only *one* population.  Presumably, these identical haplotypes were
found in different individuals, so a taxa block of all the individuals
(which may have identical haplotypes) might be more appropriate for this
analysis.

-Jeff


2011/10/28 生物系 李晓晨 <xiaochen at snnu.edu.cn>

> Dear colleagues,**
>
> I intended to test the model of population fragmentation using my mtDNA
> data. I met some warnings when I ran ****Mesquite**** with my data from
> two species of ground beetles: *Pheropsophus jessoensis* & *Chlaenius
> pallipes*. Of course each running deals with data only from one species.
> The warnings are listed as below:**
>
> There has been an error in the Neutral Coalescence simulation. It may be
> due to a contained taxon (e.g., haplotyoe) occurring in more than one
> containing taxon (e.g., species), which is not allowed in the current
> version of the simulation. Details are written in the Mesquite Log file.
> This error message will not be repeated during this calculation.**
>
> However, the running continued after I clicked the ‘OK’ option in the
> warning window. The warnings appeared the second time. I kept clicking
> ‘Ok’, the program gave the s-value distribution result at last (see the log
> file). I am not sure that the results are correct.**
>
> Above error should not happen since there is only one taxa association in
> the running.**
>
> Haplotype T48 has a gap at site **935 in***Pheropsophus jessoensis* (*Ne*= 1046130, 300000 generations from past to present), haplotypes T56 and T57
> have an insert at site **943 in** *Chlaenius pallipes* (*Ne* = 580000,
> 254400 generations from past to present). At first I thought these warnings
> are caused by the gaps or inserts in the sequences. However, when I deleted
> the haplotypes containing gaps or inserts, the warnings still popped up
> during the running. I send the log files for both species as attachments. I
> would appreciate very much your helping me find out the errors with my
> data. Thank you.**
>
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>
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