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I am working on phylogeography on one model species and I am a beginner. You can imagine one species that came on locality more than 5 mya (million years ago). It was a good environment, so the species expanded very quickly. After climatic changes this model species split in two refugiums (isolated locations for a once widespread species) and evolved into two species. This happened several times and now we have from that one ancestral species six valid species.

I have data from MrBayes and BEAST molecular clock. Can you recommend some phylogeographical program which can consider also expansion and contraction of model species?

My input data:

molecular identification (sequences) coordinates (lat, lon) for each species geographical data of a continent (altitude, precipitation etc.)

My goal:

Create a map where will be polygons (areas) of each species. These areas will expand and contract (step-by-step not like a do not want create video).

My problem:

I am able to make polygons by MCP, or kernel density, but unable to incorporate barriers into model. For example, polygons of species which lives in mountain region created by MCP include areas of lowland inside...

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You might want to consider asking this question on biostars.org as well. Just to be clear, it is completely on topic and welcome to stay here, but you could also ask it on biostars. –  terdon Mar 4 at 0:17
    
@terdon thanks for recommendation..I try it :) –  tatiana.aghova Mar 4 at 7:41
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