No, that's not what you have.
You have one species, delivered to a geographically isolated area 500 years ago. That species still exists on the mainland.
In the isolated area, you have 5 or 6 new species showing exactly the kind of chromosomal variations you asked for, all on the island. They are all, on the island. They are mixed, hence the dispute about how many species are actually represented. This is ongoing.
Examples, made to order, don't get any better than that.
You specifically asked about chromosomal changes, to show you one ongoing specifically requires a species with instability in this area. Like mice. A perfect natural laboratory of mice. Madeira.
If you want other types of genetic speciation, look at Ensatina salamanders, or pizzly bears. (yes, Pizzly.)
If you want a behaviorally generated genetic speciation event, look at apple maggot flies, or American Meadowlarks and their separation into Eastern and Western species.
But, I suspect you don't want anything actually going on in the natural world. Let me know.
I do appreciate your providing this list of examples. As you suspected, I was actually looking for data collected outside of nature; in a laboratory to be specific. These samples taken from nature, have no control imposed on them, and can therefore be explained by a vast array of diverse hypotheses, none of which can be succinctly proven. In order to keep this discussion focused, I will stick to the example of the madeira mice, reported in 2000. Since the discovery of these mice, there has been a great amount of research conducted, and I will use this to illustrate my point, which is not that I can
prove Darwin's theory of evolution to be false, but that it
cannot be proven to be true, using evidence such as what you've provided.
The original report of chromosomal races speculated that the differentiation had arisen from drift in isolates in the steep valleys radiating from the old volcanoes, which rise to a height of 1862 m (Britton-Davidian et al. 1990, elaborated in Britton-Davidian et al. 2005) – a suggestion reminiscent of that made by Henry Crampton to account for differentiation in Partula populations, which he studied for almost 50 years on the Society Island of Moorea, a hypothesis comprehensively demolished by Johnson et al. (1993). More detailed studies of the Madeiran mice, extending to allozyme and mtDNA analyses, indicated no lack of diversity, implying that the colonization was by a large number of founders or that there had been more than one colonizing event (Gündüz et al. 2001; Britton-Davidian et al. 2007). The authors favoured the latter explanation, not least because the island mice allozyme comparisons showed them to be more closely related to animals from their likely source on mainland Portugal, while their mtDNA haplotypes suggested immigrants from northern Europe.
This conclusion is strengthened by a paper in this issue (Förster et al. 2009). Previous comparisons largely lacked information about variation in the genomes of Portuguese mainland mice; they were based on only nine mice from central Portugal. This new study fills this gap with 76 animals caught at 14 sites in Portugal, mainly from ports which had historical links with Madeira (Fig. 1), allowing more precise comparisons with samples from Madeira and its neighbouring island of Porto Santo. The authors found four mitochondrial (D-loop) lineages in the mainland animals, one of which dominates. The diversity of the samples in Portugal was similar to that found elsewhere (in Italy, Greece and Turkey). They concluded that there were probably multiple colonizations into Portugal, with a most likely common ancestor from the eastern Mediterranean area. Estimates of expansion time concur with zooarchaeological findings that mice reached the Iberian Peninsula at least 2500 years ago.
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Figure 1.  Portuguese house mice, such as this one caught and photographed in Vila Franca de Xira, Portugal, have apparently contributed substantial nuclear, but not mitochondrial variation to house mouse populations in Madeira. Photo credit: Sofia Gabriel.
The island mice are very different. Only one animal had a haplotype of the dominant Portuguese clade; 99% of the mice had sequences common in Denmark, Sweden and Germany, more than half having haplotypes identical with those found in northern Europe. Estimates of the time of expansion of the Madeiran population are imprecise, but suggest a date more than 900 years ago, much earlier than 1419 ad, the traditional date of discovery of Madeira by Portuguese voyagers. However, the previous finding that the nuclear genome of the island mice is much more like the Portuguese variation than north European complicates this picture (Britton-Davidian et al. 2007). Förster et al. suggest that it might be explained by the asymmetric spread of nuclear genes following introduction of mice from Portugal into an already established ‘north European’ population, along the lines of the situation uncovered by Jones et al. (1995) in an introduction experiment on the Isle of May (Scotland).
So what you have here, originally presumed to have been a single migration event of a homogeneous group of mice, has been demonstrably shown to have been multiple migrations spanning from 500 BC until the present. One of those migrations included mice from portugal, and you now have a genetic mixed bag of mice, which are all related to the mice from Portugal, and the mice from Italy, Greece, Turkey, Denmark, Sweden, and Germany. Meanwhile, the original hypothesis of a single migration event of mice, self differentiating and changing their number of chromosomes over the course of the past 500 years has probably been printed and reprinted in biology textbooks, as proof of speciation, and most likely still remains in those textbooks, without being tempered by the most recent research, which
proves that this was a vast array of species, which came here, over the course of multiple migrations, from various parts of Europe.
This is why we can't put blind faith in scientists who have no Faith in God. I agree with you that there is no reason for Catholics to put issues like this on the front burner. Prayer, study, and penance are what we do. By the same token, we are under no obligation to blindly accept the "findings" of scientists with clear bias against a supernatural explanation of our world.