Our aim is to determine whether C. gariepinus specimens sampled from two different locations belong to the same or separate populations. One site is a surface water system and the second a subterranean (cave) river system. The two systems are interlinked via conduits, cracks and fissures.
Hi Gerhard, difficult to answer! I would say a trivial "you have to try!". Also, it depends on your available resources (money, lab equipment, chemicals, etc.). I usually carry out preliminary population genetics screening with "simple" genetic markers such as RAPDs or ISSRs; however, if you have the possibility to use microsats or sequences is better. The important thing to consider is that; if you use 1 genetic marker and you do not find genetic differences between your 2 local samples, you cannot say they are not differntiated. If that is the case, you need multiple evidence from different (not necessarily genetic) markers.
Last consideration: have you checked if genetic work has been carried out on the same species or other congeneric species? If so, you could get important information from there.
From when has the population from the surface water system been existent? It is less likely to find genetic differences between populations of the same species if the habitat divergence is "recent". Look for reliable markers; sequences which are both common in these kind of species and, at the same time, evolve at reasonable rate. After DNA extraction & purification, carry out the PCR with these markers. Samples showing successful hybridization are to be sequenced and analyzed using bioinformatics tools. Who knows, you may get two branches in your tree :)
Hi Gerhard,
I would say that it depends on the level of divergence you might encounter. There is lots of historical diversity of Cg in Southern Africa that can be assessed with mitochondrial (preferentially cyt b) and nuclear markers (rhodopsin, ...). However, if populations are closely related and network analysis doesn't help you, try the microsatellites available on GenBank. With 10 markers you might obain a satisfying answer. Good luck.
Filip
Thank you for all the responses! Will consider the options and obtain some relevant literature, regards
Dear Gerhard,
You might want to test the power (to find differences) of the markers before you actually apply them. To do so, the ConGRESS website (http://www.congressgenetics.eu/simulatorhome.aspx) contains a simulation module called the "Sample planning tool". You are probably interested in the "connectivity module"!
The tutorials/publications coming with the tools are well written but if you need more assistance you can ask me or Sean Hoban (the developper of the tools).
Success,
Peter
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