Faith writes:
I think speciation is a somewhat artificial concept myself, the point being that all the processes that tend toward speciation all reduce genetic diversity along the way as new phenotypes are developed.
A new phenotype does not necessarily mean that the alleles for a previous phenotype are lost. There are mechanisms which help to preserve genetic diversity within a gene pool such as diploidy, balancing selection and neutral variation. I'm sure that these mechanisms would have been discussed on this board before, but I can go into detail if you like.
Population bottlenecks do reduce alleles but the above mechanisms help to stabilise those left in the pool, with mutation increasing the diversity.
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