Mutation is the process whereby DNA becomes altered.
Genetic variation among individuals is ultimately down to mutation but they are not the same thing. Imagine a population of 1000 individuals all with a genotype AA at a gene. A mutant then arises causing a new version (allele) of the gene, lets call it "a" and one individual carries a copy of this new version
We now have 999 xAA and 1 xAa and no aa genotypes. So there is some variation at this gene, but not much since nearly all individuals we might sample from the population are genetically identical.
Now imagine that some (maybe 10's-100's of) generations later, we look at the population again. It is stable in size so still 1000 individuals - but now the two alleles are equal in frequency - so we might find we have 250xAA, 500xAa and 250x aa. Clearly there is now more variation among individuals in their genotypes, and - if this gene actually influences something we can measure (e.g. body size) we might see more variation in that trait now as well.
So mutation is the ultimate source of (genetic) variation, but the amount of variation present will depend on the allele frequencies. Most mutations are lost by chance (a process called genetic drift), but some may be fixed (go to 100% frequency). So if in the above example all individuals at some stage in the future have genotype aa - then the original allele A has been entirely (and been replaced by the mutation). A mutation is more likely to be lost if it is deleterious (selected against) than if it is advantageous (selected for), but important to bear in mind that chance can be much more important than selection in determining the fate of new mutations in anything but the largest populations.
Fixation is not speciation. Fixation refers to the relacement of an existing allele (or alleles) at a genetic locus by a mutant (i,e, new allele) so that individuals in a single population become genetically identical (at that locus). Speciation occurs when these population-specific genetic processes (selection, mutation, drift) result in so much differentiation between populations (e.g. some pops fixed for some alleles, others for different ones, selection favouring some genes in one population, different genes in another) that individuals from the populations can (or will) no longer succesfully reproduce with each other. This is not generally thought to be a consequence of a mutation being fixed at a single gene, but rather an accumulation of genetic differences between populations at lots of loci (although there are likely exceptions to this generalism). Importantly gene flow (movement and breeding of individuals) among populations acts to reduce among-population genetic differentiation (and hence reduce the likelihood of speciation). This is why isolation is so important - isolated populations will tend to diverge genetically, but gene flow among populations is often sufficient to limit (or even completely nullify) this - meaning speciation will not occur.
Hope that's useful. I realise I have not answered all your questions so will try and respond to more later if other's don't beat me to it!
>p.s. is there a way to respond to an expert's answer as a dialogue?
Nope. Many other sites are based on interactive conversation, ours is a deliberately different model (q+a)!
Last edited by Alistair Wilson (17th May 2016 18:55:47)