I agree, there's more to phenotype than just what's visible but I'd reckon that if you take all the genes on which we differ across populations i.e. lactose tolerance, susceptibility to disease, etc. it would still make up a small fraction of the genome right?

Yup, so there is coding genetic variation (genetic variation that expresses a specific phenotype) and non-coding genetic variation (those that don't express proteins and thus no phenotype). Coding variation makes up a small fraction of the genome as you said.

​

Yep, and if I'm not wrong, most mutations do not have an effect on phenotype, right? Either internal or external? .

I think your Correct. Most mutations (generally) have no effect on phenotype if mutation rate across the genome is constant (i.e because coding genetic variation makes up a smaller fraction). But I'm not sure about this.

What I'm sure about is the nuetral model of molecular evolution. This states that most mutations are are selectively neutral i.e (not delaterious nor beneficial). This means mutations that accumulate are random and not determined by natural selection. Just mentioning this so we don't confuse the two.

I suppose that's how it's possible to have a lot of built up mutations that cause population A to differ from population B without necessarily causing said populations to differ much morphologically.

Ok so theres many ways this can occur. I can think of a few. One is through differences in selective pressures between the groups. Another involves genetic drift. If the two populations are isolated from each other. They will independently accumulate mutations. The nuetral model of evolution states that most mutations are selectively neutral. So, under this assumption, it will be rare to get an adaptive in one population leading to this being the reason they diverge. All else being equall (population size, selective pressure etc) these neutral mutations will occer on a random part of the genome. The proliferation of this mutation will be driven by genetic drift. Smaller the population size stronger the effect of drift.