First, I assume that in the original creation, organisms were created for a variety of different environments. Since there is a continuum of environments, we should also expect to see a continuum of organisms. However, since there were only a finite number of different kinds of organisms at the creation, this continuum should be composed of a finite set of discrete organisms.
So we should expect to find reptiles and amphibians, each adapted for a different environment. Since there are environments in between, we should also expect to find organisms having some characteristics of reptiles and some characteristics of amphibians. Thus we should expect to find sequences of organisms A,B,C,D,E,F,G,H where A is a reptile and H is an amphibian, and the characteristics of the organisms gradually become more amphibian-like and less reptile-like. However, there will not be any links between A and B, or between B and C, et cetera, because these are a finite set of discrete organisms.
In addition, since these organisms were all created at about the same time, and did not evolve from one another, we should not expect to find any clear ancestor-descendent relationship between different organisms in the fossil record. In fact, it should be very difficult to construct reasonable and convincing phylogenies of organisms. Furthermore, we should not expect living creatures to have a clear hierarchical relationship, in most respects, since they were created for a continuum of environments.
Now, since the basic organisms were created recently, we should expect all of the descendents of a created kind to be very similar. They should generally have the same number of chromosomes, and the same genes at the same locations on corresponding chromosomes. They also should often be able to interbreed, which should make tracing their evolutionary relationships fairly complex. In addition, their nuclear and mitochondrial DNA should be fairly similar. However, between different created kinds, we should generally expect to find greater differences in the nuclear and mitochondrial DNA.
In fact, we should be able to quantify how much genetic diversity there is within a species. The genetic diversity measures the probability that a corresponding base pair of DNA will differ between two randomly chosen individuals. If the genetic diversity is 1/100, this means that two randomly chosen individuals will differ in about 1/100 of their DNA. We predict that the amount of genetic diversity should be consistent with the theory of neutral evolution and an origin about 6,000 years ago. We choose the theory of neutral evolution because one would expect created beings to be optimal in some sense, so that very few mutations would be beneficial. Thus the great majority of mutations should be neutral or slightly harmful.
Thus if we know the rate r of mutation per generation, which is the percent change in DNA per generation, and the generation time g in years, then the genetic (nucleotide) diversity should be about 2(6000/g)r, since there will be 6000/g generations since the creation and each one will tend to contribute 2r to the genetic diversity. Or it could be less, for species originating more recently. This means that for organisms with similar rates of mutation, we should expect the genetic diversity to be inversely proportional to the generation time. It is reasonable to assume, for example, that most of the mammals have similar rates of mutation, since many of the mammals are very similar genetically. This implies that the genetic diversity of mammal species should generally be inversely proportional to their generation times. Similar comments apply to the amount of genetic difference between species that have diverged from a created kind since the creation.
The hypervariable parts of the mitochondrial DNA control regions appear to mutate at a rate of about one percent every 200 to 300 generations in humans, and this seems to be a reasonable figure for any organism having about the same number of cell divisions in the female germ line (24) as man. So for this part of the mitochondrial DNA, we can let r be about 1/20,000, and our above formula gives a genetic diversity of 2(6000/g)(1/20,000) or 0.6/g. Thus with a generation time of 20 years for humans we should expect a diversity of 0.6/20 or 0.03 in the hypervariable regions of the mitochondrial DNA. For organisms with a one year generation time, and about 20 cell divisions in the female germ line, we should expect a diversity of about 60 percent. Of course, as one approaches the limit of 75 percent, these estimates of genetic diversity have to be reduced to some extent, because there will be many repeated mutations at the same base pair.
A similar calculation can be done on the nuclear DNA, assuming that most of it is non-functional. However, this calculation should be based on mutation rates that are directly observed as differences in DNA sequences from one generation to the next, and not based on evolutionary assumptions.
We refer the reader to the article How Old is Humanity?, where we see that for a few organisms, these predictions about DNA diversity appear largely to be borne out.