meta-Ne

[Ishihama Fumiko]

Hi, Ivan and all,

Thank you so much for sending the very useful reference (Table 2 in https://onlinelibrary.wiley.com/doi/full/10.1002/ece3.485).

The concept of meta-Ne looks very relevant to the Ne fragmentation index and it is important to know the backgrounds.

Meanwhile, the meta-Ne generally results in a larger value than the simple sum of Nes of subpopulations, considering the genetic differentiation among subpopulations. Assuming isolation by distance, it means that contribution of distant populations is larger than closer populations.
It is in contrast to the concept of habitat fragmentation or connectivity (please see the example of Hanski 2000 in my presentation), for which a more distant population contributes less. The Ne fragmentation index assumes a similar pattern as connectivity (limiting dispersal range is a kind of distance decay).

I think the incongruence comes from the difference in viewpoint.
The meta-Ne evaluates “genetic diversity” of “the whole metapopulation”, but the connectivity evaluates total volume of “migration” between subpopulations.
From the viewpoint of genetic diversity of “a subpopulation”, frequent migration from genetically different sources would be most effective to enhance it.

Thus, both contrasting effects of distance are true; frequency of migration decreases by distance, but the effect of a migration event would increase due to the genetic differentiation (a distant individual will provide more divergent gene than a closer individual).
In combination, the contribution from a distant subpopulation to a focal subpopulation would decay depending on distance, but the decay would be slower than expected from the frequency of migration due to the increased effect of a migration event by genetic differentiation.

Best,

Fumiko

[Joachim Mergeay]

Good discussion!

If you take Table 2 at face value and calculate values for several metapopulations, you'll see that it rarely exceeds the sum of the subpopulation Ne values by much, if you consider a functional metapopulation as demes which exchange more than 1 migrant per generation. 

For example, we have a metapopulation of a butterfly, Hipparchia semele. Overall FST is circa 0.06, and the maximum pairwise FST never exceeds 0.11. This corresponds to (global FST) 4 MPG, or 2 MPG at worst (assuming the island model). 

For the 19 subpopulations we sampled (all known sites where reproduction occurs), the sum of the subpopulation Ne values is 592.    

If we take the Nunney (1999) approach, and use the FIT values (average 0.2), we get a meta-Ne = 592/1.2= 493

If we take Wright's formula (1943) and correct for FST (0.06), we get Meta-Ne=630

Taking the spatiotemporal formula and assume Nm=4, we get Meta-Ne= 630 (which is just another way to calculate Wright's 1943 formula)

Given the errors on the estimates, these values are all within the same ballpark as the sum of the subpopulations. So as long as you can assume that you're dealing with a functionally connected metapopulation, just taking the sums of the different subpopulations will give you a decent estimate of the Meta-Ne. 

Since we're aiming for simplicity while still being robust, I wouldn't bother going into the nitty gritty difference between Meta-Ne and the sum of the subpopulation Ne-values. 

My 2ct on this matter.

Joachim 

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Joachim Mergeay (he/him)

Research Institute for Nature and Forest - Belgium                                  

Associate Professor KULeuven Ecology Evolution and Biodiversity Conservation

Tel: +32 499 942 942

Meldpunt wolven Vlaamse overheid : wo...@inbo.be

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[Ishihama Fumiko]

Hi Joachim,

Thank you for showing a clear example. It was very helpful for me to understand the effect of considering differentiation among subpopulations on Ne.

>Given the errors on the estimates, these values are all within the same ballpark as the sum of the subpopulations. 

I totally agree, especially when we are estimating Ne based on Nc (the error due to the variance of Ne/Nc ratio would be much larger than the metapopulation effect) and we are aiming for simplicity, as you say.

So, if we were going to write a paper about the fragmentation index, we could mention meta-Ne and the theoretical studies as the background and that the effect of differentiation among subpopulations would not be serious in our situation.

Best,

Fumiko

2023年5月2日火曜日 17:38:20 UTC+9 joachim...@inbo.be: