Wide ranging species- examples and discussion

[shoban]

Several have come across wide ranging species with no clear population divisions.  Should population structure be assumed/ added to a wide range?  This is discussed already to some degree in the guidance doc (e.g. use ecoregions), but we can discuss more here.

Please provide in this thread details about examples.

An obvious one is tree populations which are often present over hundreds to even thousands of kilometers in a continuous fashion and have high population size and gene flow.

However, should the Quercus petraea of Europe be one population https://commons.wikimedia.org/wiki/File:Quercus_petraea_range.svg?  Arguably you should divide the range by ecoregions (e.g. https://www.eea.europa.eu/data-and-maps/figures/dmeer-digital-map-of-european-ecological-regions) to reflect populations which are adapted to different conditions (genetically distinct populations).

In my view the way to do this is to make your best effort using either ecoregions or some other boundaries and record this in the box under how populations were defined.  In the future after this pilot project we will need to create a much more rigorous methodology.

I paste below comments from emails, which diverge somewhat from each other, Linda and Joachim.  I mostly side with Linda in her interpretation.  Please continue the discussion

Joachim

No we shouldn’t: the effective size we need to consider is at the level of the metapopulation, because interconnected patches show correlated allele frequency changes over time as a result of gene flow. The threshold for this correlation is 1 migrant per generation. So if you have a continuously distributed population, there is essentially a single gene pool. When Nm>1, genetic drift at the local scale is mitigated sufficiently by gene flow from within the metapopulation. Also, considering Ne>500 assumes that the unit you are evaluating is closed to immigration (and will remain so “forever”).

As an easy illustration, consider the below simulation (attached pics) of a metapopulation of 10 pops of Ne=100 with 20 migrants per generation. It's not panmictic, but well connected. They show concerted drift, and you get fixation in approx 3000 generations (starting with p=0.5 as allele frequency). Which is what you expect for a single population of Ne=1000. There the expected time to fixation is 2777 generations (according to the formula 𝑇_𝑓𝑖𝑥=−(4𝑁(1−𝑝)* ln⁡(1−𝑝))/𝑝 )

So the well-connected subpopulations (Nm>>1) behave in terms of genetic drift (and therefore Ne) like a single large population that is the sum of the local effective sizes of the subpopulations.

As long as Nm>1, you find concerted genetic drift. Really, Nm=1 is the turning point. Below you rapidly lose this correlation in allele frequencies.

Linda

I see problems with assuming that a continuously distributed species over a very large area is one (meta)population and Ne>500 is applied to all of this distribution. I am concerned that:

1. Allele frequencies will not be as well correlated if migration is small.
2. Realized local Ne can be much lower and thus the rate of inbreeding too high.
3. In cases where CBD partners only use headline indicator A.4 and not our complementary indicator 2 also, extensive reductions can occur without being noticed.

[Joachim Mergeay]

Linda and I indeed diverge on this particular question. 

A lot will depend, I think, on variables that we have too limited information on. The problem we are facing here is akin to a two-dimensional stepping stone model, where you get isolation-by-distance in two dimensions, and we can consider genetic neighbourhoods (as defined by Wright 1943) as discrete demes of size N, exchanging a fraction m of migrants with adjacent neighbourhoods. This was discussed in great theoretical length by Maruyama 1971 and frankly it's too complex for me to understand entirely. 

As I understand it, it goes more or less like this

Depending on N and m, you can get very low to very high FST across the matrix. If the population-specific FST (HSi/HT for the ith population) is low (<0.2), there is little inbreeding in the local population relative to the total population, and I wouldn't worry about local Ne. What Linda refers to, I think, is local Ne, which reflects the number of breeders of a subpopulation (or neighbourhood or deme). but this local Ne is not the same as the inbreeding Ne. 

My assumption may be wrong, but I was under the impression that (at migration-drift equilibrium) the inbreeding Ne of a subpopulation relates to the Ne of the metapopulation like HS to HT   

I cannot recollect any study where FST values across continuously distributed populations are larger than 0.2, which means that each time, the local deme has (on average) more than 80% of the gene diversity of the total population. 

I even have a hard time finding studies showing FST>0.1 in continuously distributed populations. 

The weakness of thinking in terms of FST in relation to gene flow is that it assumes migration-drift equilibrium. But at least it's a framework I understand. 

If we are to give guidelines on how to consider substructure in continuously distributed populations, it needs to be firmly embedded in population genetic theory. As far as I know, we have no clear cut framework to say that we should evaluate continuous populations in chunks (how large?), where each chunk should have Ne>500. 

If Linda or anyone else has a better explanation, I'd be happy to try to get to the bottom of it. 

cheers

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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