This is a general response to what I understand Faith and MJ's argument to be in regards to speciation generally causing a reduction in allelic diversity that mutation cannot/has not been shown to make up for and that the new phenotypes seen after speciation are only a result of "rare" alleles coming to the fore.
I propose a scenario showing that despite initial loss of diversity, previously "neutral" mutations or rare phenotypes/alleles can be affected by further mutation and selection, precipitating a speciation event, but conferring enough of a benefit to make the loss moot. This is a wholly speculative and over-simplified scenario, but I believe it "logically" shows the possibility that a single mutation can more than make up for a severe loss in diversity after a bottleneck/speciation event. Here goes.
We begin with a population of rodent-like creatures about the size of a rat that dwell in treeholes. They are largely insectivores, preying on the insects that fly about and those that crawl on the trees, but they also often risk ground dwelling predators to go down out of the trees to eat fallen fruit (the fruit on these trees are very hard to reach) and ground dwelling insects. The population of about 5000 consists of one dominant color (Black) and one rare recessive color (brown). The Black (BB/Bb) phenotype has a fairly short tail, while the brown (bb) phenotype usually has a longer tail (sometimes just a bit longer, but it varies). They both have very good grasping claws to climb the tree trunks with ease and without the threat of falling.
Now, the brown allele carries on it an immunity to a lethal disease (when homozygous) that has not yet presented itself to the population, so it is, as of yet, neutral. One day, the disease to which the bb are immune sweeps over the creatures and wipes out all of the BB and Bb. We are left with about 500 bb. This is a severe population and diversity loss. Slowly, the population rebuilds itself (with some genetic defects from some inbreeding popping up at first, but with population growth nipping them in the bud eventually). The new population again stabilizes at about 5000 with a similar diversity as before (due to allelic shuffling and mutation). Some previously rare traits emerge over time as dominant in the population (as Faith proposes occurs), but the species remains generally the same in behavior and basic phenotype (although the differences may be enough to allow them to be called a separate species from the original population before the disease and, therefore, speciation).
Fast forward many years (hundreds, thousands, milions...doesn't matter) and a dominant mutation occurs that allows for the prehensility of the tail and it slowly spreads through the population. This is only beneficial to some of the bb because, remember, the tail length varied (the tails of the Black phenotype were all too short for it to be any good and it would have merely been a neutral mutation for them). Also, this mutation only confers a benefit once it is realized that those with long, prehensile tails can reach the fruit on the trees by hanging from certain branches. Sexual selection comes into play, as those with the mutation begin selecting mates with longer and longer tails.
Eventually, those with the mutation start to outnumber those that don't (and those still with short tails as well) as they have a new, easy food supply and they don't have to risk predators on the ground anymore. They even learn to swing from branch to branch and sometimes tree to tree combining their tails and their grasping claws, even more greatly increasing their range and food supply. As their numbers increase, diversity, through both allele shuffling and mutation, also increases. They start spreading out to other areas (due to population size and availability of food) through the benefit of their increased mobility and mostly leave behind the other group. This probably causes more allele loss, but the gained advantage from this highly beneficial new mutation, plus the ever growing population from which new allele combinations and mutations come forth, far outweighs the comparatively small loss in diversity. Eventually, the two populations do not or cannot interbreed anymore due to either location and/or drift and/or incompatible mutations.
And the process begins again.
This mutation and the speciation that followed could have occured without the loss of the Bb and have had a similar effect, but it illustrates that such a huge loss can be overcome with one single beneficial mutation (and one which was only beneficial when combined with a neutral pre-existing trait/previous mutation) which confers enough of an advantage to allow for great population growth and, therefore, increased diversity.
PS I know I didn't think of everything necessary for this particular scenario to play out, but, like I said, it is pure speculation.
Edited by Jaderis, : No reason given.
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