In our journal club from last Monday, we discussed an interesting paper by McGovern and co-workers: “Divergence genetics analysis reveal historical population processes leading to contrasting phylogeographic patterns in co-distributed species” (Molecular Ecology, 2010, 19, 5043–5060).
The paper emphasizes the importance of taking into consideration the historical perspective when studying any spatial genetic pattern. A phylogeographic break does not necessarily means that the gene flow is currently restricted (that’s what is happening in the bat star across QCS). The contrary is also true a more subtle differentiation at this break is not equals to a greater contemporaneous gene flow (instead it can be due to a more recent divergence time, this is what is happening in the snail).
Contrary to the extrapolation of gene flow from traditional Fst, the software IMa does not make assumptions of equilibrium (genetic drift/mutation/migration) and allows disentangling between ancestral polymorphism and ongoing gene flow. A good paper to read about this topic is the paper accessible in the September edition of TREE from Marko & Hart (The complex analytical landscape of gene flow inference, Trends in Ecology and Evolution September 2011, Vol. 26, No. 9).
We also discussed the extirpation of the snail and the recolonization range. Why was the snail extirpated if it is the cold species of the two? And when did it recolonize this entire range? Indeed, the date of divergence between north and south populations does not approximate the recolonization but just the population split. The recolonization of the north by the snails could have happened any time between 282000 and 11000-17000 years ago.
We discussed the possible causes explaining the fact that the older event in the bat star (282000) was visible by AMOVA but not the more recent one (100000). Maybe a difference in the duration of the separation is the explanation, given that gene flow seems homogeneous across the range of the bat star.
We also discussed the problems of using a single gene. We talked about selection and the difference of informativeness/variability between nuclear and mitochondrial markers.
We discussed about the choice of the markers, particularly tRNAs, and the importance of the calibration in the dating of divergence time.
Thanks Emilie. I really enjoyed Monday's journal club. And thanks for sending the Marko & Hart paper. I'm sure we will all be more careful now when it comes to directly inferring gene flow from Fst or other measures of differentiation.
ReplyDeleteThanks Emilie. What I really liked in this paper was that they clearly showed the weak power of F-statistic to contrast between historical factors (divergence, expansion) and ongoing gene flow. I think that this is particularly true when working on sequences rather than microsatellites. So we should keep that in mind when using such summary statistics
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