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Defining The Migration Matrix

(Note: it is recommended that you be familiar with the material in the data file conversion section before reading this section.)

The Migration Matrix defines how populations mix. Each cell displays the parameters for migration from one population to another. The populations may mix randomly, symmetrically, at a constant rate, or not at all. If they mix, various parameters including the rate can be defined. The values in the cells can be edited to match the user's current model. This same format is used for displaying and defining Divergence which is discussed later.

Smart modeling of how your populations mix will yield much better results from LAMARC's analysis. Think about how your populations relate to each other geographically or temporally. For example, if you are looking at populations in a series of valleys separated by mountains, symmetrical migration makes sense. But if you are looking at barnicle populations along an island chain that has a strong prevailing current, migration downstream is easy but migration upstream isn't. You should not infer symmetrical rates here, and perhaps should consider setting the upstream rates to zero.

Of course, if you are not sure what model to use, try an ensemble of runs testing each model and compare the results. Each will give you different insights into your data. Coalescence analysis is a tool to investigate your data not an oracle.

This is the Migration Matrix tab of the LAMARC Converter interface which displays the currently defined Migration Matrix.

Migration Matrix for chrom1.mig

There are several things you should note:

By default LAMARC allows unconstrained migration between all populations in your data set and sets the rates all equal. If you wish to change any of the values, double click on an editable cell and the following dialog will appear:

Edit Migration Matrix Cell

You can edit four settings here:

Generally you will want to make your migration rates Unconstrained unless that is leading to inferring too many parameters, which it easily can. For cases in which there is no reason to expect asymmetry, Symmetrical rates greatly reduce the number of parameters. If your populations are laid out in such a way that only a few migration routes are feasible, you should set all other routes to Invalid. Finally, setting rates to Constant is relatively seldom used, but is useful when you already have a Migration rate estimate in hand and want to concentrate your statistical efforts on some other parameter.

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