I have a friend who teaches at the University of Montana and was involved in the first set of research into this, funded by the US Army (not sure why). I'll take a crack at those questions from what I know talking to him...
First, the numbers of bees dead or alive are being counted by whom?
My friend and his colleagues weren't counting bees, they were counting domesticated colonies and mapping the CCD hives versus the non-CCD hives, then taking an average to determine bee count.
Second, are only domesticated bees being counted dead and alive?
As far as I know, yepp.
Third, are only certain types of domesticated bees being counted dead or alive?
No. The research I learned about was being done in California, Alabama, Kansas, Szechuan province, Lithuania & Latvia, South Africa and Brazil, and seemed to be a fairly good cross-section of (again) domesticated bees from many different bee-farms and permanently sited apiaries.
Forth, how have the numbers and ratio of both domesticated and non-domesticated bees changed in the last 20 years; year by year?
Good question. The people I know about, again, weren't dealing with non-domesticated.
Fifth, how can one count the numbers of non-domesticated bees?
Exactly the problem. Trying to capture a sample of non-domesticated bees is like trying to determine the number of dolphins in the world's oceans by sampling 10 cubic metres of water in the Adriatic. Where do you start?
Good questions, and it points out some problems with this research. The worst example I was told of was a university in California who had published a study generalising CCD by looking at a single bee provider's hives. That's the sort of science most researchers in this area are (I hope) trying to avoid.
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