[Mesquitelist] Testing phylogeographical hypotheses using coalescent simulations
wmaddisn at interchange.ubc.ca
Mon Sep 12 10:12:43 PDT 2011
Could you send me the file saved so that it is doing the analysis? I think I'll need to see it to understand what is going wrong.
On 14 Jun 2011, at 4:49 AM, Mark Ravinet wrote:
> Dear Mesquite users,
> I am somewhat new to Mesquite and I would very much appreciate your
> input regarding my issues with attempting to follow the hypothesis
> testing methodology of Knowles (2001, Mol Ecol) and Knowles & Maddison
> (2002, Mol Ecol). I understand the theory behind the approach but
> unfortunately, no one else in my department has used Mesquite for this
> purpose and I am unsure of whether I am conducting the analysis correctly.
> Essentially I am attempting to infer the number of refugia involved in
> colonization of Northern Europe by three-spine stickleback using my
> mitochondrial dataset for the British Isles and additionally, previously
> published sequences for the rest of Europe.
> For a simple case, I have three hypotheses - i.e. one refugia
> (fragmentation, the null hypothesis), two refugia and three refugia.
> After Knowles, I have attempted to model 1000 genealogies constrained
> within the null hypothesis and then I have attempted to constrain this
> to one of the alternative hypothesis models to generate an expected
> distribution of discordance.
> To do this, I have one file with a taxa block for each hypothesis and
> one main taxa block for the mtDNA haplotypes. Then I have set up
> associations between each hypothesis and the haplotypes before using
> coalescent simulations to make a new tree block of 1000 genealogies
> constrained within the displayed hypothesis tree.
> The issue comes when I try to use Mesquite to calculate the discordance
> between the simulated gene trees from the null hypothesis and the
> alternative hypothesis. To do this, I have been using the Analysis >
> charts > trees commands, selecting the haplotypes taxa block for the
> tree values and then choosing stored trees > null hypothesis to generate
> a distribution of Slatkin's S. In order to generate the distribution, I
> use the association for the displayed hypothesis tree.
> My problem is that whenever I do this, I seem to get exactly the same
> distribution of discordance for when the genealogies are constrained
> under the null tree - i.e. there is no difference between genealogical
> discordance within the null tree and between it and the alternative
> hypothesis tree. At first I thought this might be a problem with my
> data, but it also occurs when I use a 'model' dataset I concocted to
> test the problem.
> I must apologise for the long email, but this is becoming a really very
> frustrating situation. If anyone could shed any light on what I might be
> doing wrong, or even if anyone has a simple protocol for running these
> type of analyses I might be able to follow I would very much appreciate it.
> Many thanks in advance
> Mark Ravinet
> Mark Ravinet
> PhD Student
> School of Biological Sciences
> Queen's University Belfast
> Medical Biology Centre
> Lisburn Road
> BT9 7BL
> Mob: 07841675863
> Email: mravinet01 at qub.ac.uk
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