I've been discussing pits here, here, and here, if you are interested, but so far without diagrams. There's a reason for that. I'm rubbish at diagrams. OK, I don’t have a decent graphics program, but that wouldn’t matter anyway. I'm still rubbish. That’s why I prefer my fossils in 2D! However, here is an attempt at a graphic representation of what I’m talking about.
The first diagram represents speciation via a concentration of alleles, adaptation, whatever.
A) This represents the current species as a morphospace topography. The shape doesn’t really matter, nor does the orientation, as in morphospace all three dimensions are equal, and there is no “up” or “down”. The shape is just to invoke some idea of 3D. If you want to get fancy, there may be gaps on close-up, but for now we are just giving an impression of the extent of the topography that defines this species. Basically the topography represents the extent of allele distribution that represents this species.
B) A beneficial allele appears at a location and its presence in the populations begins to increase preferentially. The circle represents the increasing occurrence of the allele.
C) Frame of view rotated to show what’s happening underneath. The allele increases in concentration at this location faster than it occurs elsewhere in the population, and so the topography warps in response, forming a pit. As the allele concentration increases, the local allele distribution departs from that of the surrounding ‘normal’ allele population and so the bottom of the pit continues to move away from the ‘normal’ topography. (This is pretty much the same as the Mt. Improbable version, but reversed.)
D) Speciation! Well incipient speciation anyway. The local allele distribution departs from the ‘normal' to the extent that further interaction with the original species ceases. The new population is now isolated and begins to change independently of the original species.
E) Speciation. The new daughter species is established. The new species clusters together with the old species in morphospace, since they share far more alleles that the new species shares with any other species out there. The topography of the new species is similar to the old species, which also to invokes a relationship. There is no connection between them, so no allele swapping, so a new species. The topography of the old species also changes slightly due to the change in allele frequency.
OK now lets see what happens what the daughter species starts the same speciation process.
A) A beneficial allele occurs and starts to become preferentially concentrated at one location in the population. The pit forms and continues to grow as the concentration of the beneficial allele continues to increase. This time the pit isn’t ‘downward’ because there is no ‘down’. The pit forms at 90 degrees to whatever the surface orientation is.
B) Incipient speciation as before, with the new population separated from the main population.
C) The new species is established, and again clusters close to the parent species as they share more alleles in common with each other than they share with any other species.
This group could also be classed as a Genus as we have a direct ancestor-descendant relationship. Also we can wind the tape back and show that relationship as the daughter species run back into original species.
This model is also internally consistent, because the topography can represent the origin of species, genera, families, even phyla. The same process, the same imagery. It's like a Mandelbrot set, with the same imagery showing species, families, or phyla, depending on the magnification.
For example, the first diagram could be used to represent the evolution of birds from dinosaurs (albeit very crudely - it'll need some work), with the original topography representing dinosaurs and the daughter "species" representing birds. In this instance, the next image in the sequence "F" would show the dinosaur topography shrinking, and eventually disappearing altogether as the as the dinosaurs moved towards, and finally became, extinct.
As a bonus, here's how genetic drift would look like.
A) The morphospace topography of the population.
B) A new allele occurs and starts to spread in the population.
C) Instead of being preferentially concentrated in one area as a beneficial allele would, the allele slowly increases by spreading out into the surrounding population. In other words it spreads out 'faster' than it concentrates in one location.
D) The new allele is fixed in the population, causing the topography to change somewhat as the new allele frequency is slightly different than the original one.
Johnny, I'll try and get around to your questions in the next couple of days.