Allelic variants: Simple refutation of "Kinds" (and/or decreasing genetic diversity)

In the forum Does the Flood Add Up?, PaulK provided a brilliantly simple falsification of his opponent's points: Unfortunately this important (and to Faith's position, devastating) point appears to have been quickly lost amongst the usual mish-mash of Flood-related hand-waving, so I bring it up separately here:If the current species within a kind all derive from two ancestors and mutation does not contribute to genetic diversity, then the most alleles that would be found for a given gene across all of those species would be four.We know that four-alleles-or-less-per-gene is definitely not the case. Below is a table taken from the 2004 paper Molecular origins of rapid and continuous morphological evolution by Fondon & Garner. (I reproduce it directly from their work since the paper is freely available to the public in PubMed Central here.) As is easily seen, there are genes with many more than four alleles - the coyote Twist-1 gene alone has seventeen alleles. It is important to note that these are NOT detrimental mutations - they occur in coding sequence of genes that still produce functional proteins - so arguments of mutation producing deleterious alleles as a result of the Fall are not applicable. Thus, either modern coyotes did not all descend from two individuals of their ancestral kind, or mutation has contributed extensively to their genetic diversity. This is just the beginning of the problem with the ancestral kind pair position, since all varying alleles from all species within a kind would be added to get the total that would need to be present in the ancestral pair.Polyploidy of the ancestral kind pair was briefly mentioned as a way of providing more than four alleles. A few points refute this possibility:- Polyploidy is extremely rare in mammals; in fact, only one non-diploid mammal is known, the tetraploid (four sets of chromosomes) red viscacha rat, Tympanoctomys barrerae. Additionally, current understanding of the tetraploidy of the rat is that it resulted from a genome duplication, that is, its ancestors were diploid.- In order to provide for the coyote's alleles alone, their ancestral kind pair would have to be at least nonaploid (nine sets of chromosomes), which is beyond unheard-of for mammals. Sperm size is directly correlated to genome size, so that the tetraploid rat has sperm over three times the size of diploid mammals. Nonaploid sperm would be so enormous that the reproductive biology of a nonaploid mammal would be quite unlike that of any real mammal.- Comparative genomic analysis has been used to infer the ancestral vertebrate karyotype - diploid with twelve chromosomes. I feel Faith's position, which others hold as well, is refuted in a straightforward manner simply by counting alleles in existing populations. Either mutation has contributed significantly to evolution and genetic diversity, or there was no severe bottleneck resulting from pairs of animals rescued from the Flood. Alone these points could be argued, but in light of simple and obvious evidence - current allelic numbers within kinds - the two points directly contradict each other.If one accepts a literal reading of the Flood story, it follows that genetic diversity must be increasing to explain the allelic variants we can easily count today.
_____* While I repeatedly attack Faith's position in this post, I feel it is representative of a position held by others who have frequented EvC. The post is not meant as an attack on Faith, and I would happily engage in (hopefully constructive) one-on-one debate on the subject if Faith is interested.

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