First of all, let me say that the theory of evolution is widely accepted throughout the scientific establishment, and the taxonomic relationship between species is accepted, not only based on morphological data, or structure and appearance, but based on DNA sequence data. Considering the amount of DNA that we have, a few "motifs" or sequece structures are used over, and that seems to reafirm the universal relatedness of life.
That is not to say there are no flaws in Darwin's theory as he presented it. As presented, Darwins theory relies on the concept of "incrementalism", or the proposal that small incremental changes could, over time, lead to large differences in species. Much of his observations are indisputable, Darwin himself is reported to have been a breeder of a number of domesticated animals, such as carrier pidgeons, and he could see through his own breeding exparements, that different appearances could be obtained. Likewise, the dog may take on a large number of appearances, and yet all dogs are the same species.
The flaw in incrementalism lies in the discovery of chromosomes as a fundamental unit of DNA packaging and replication management within the cell. For example the DNA of the donkey is packaged in 62 chromosomes, where as the DNA of the horse is packaged in 64 chromosomes. When the two are crossed, the mismatch between the chromosomes produces a viable but sterile offspring called a mule or hinney, depending on the choice of sire and dam. Though threre have been some reports of nonsterile mules, they are rare.
Although we see that the mule and the horse are closely related, there is no "incremental" or small step way for a horse for example, with 64 chromosomes to change into a creature with 63 chromosomes. If there were a 63 chromosome horse, which is quite possible, at least at the cellular level, there is little chance that it would thrive, and almost no chance that it would live to produce offspring in it's natural environment. For that to happen, there would have to be a large number of the same chromosomal mutation in the population, and they would all have to be viable to reproduce. Of course, they would also have to be in the same location, and adapted to the environment. I am quite confident this has never happened.
So the argument here is that a chromosome num ber change cannot be explained in incremental terms. A chromosome number change could be expalined if two different species lived in proximity to each other and began to interbreed. Are there examples of this? Actually, they are quite hard to find at the mammalian level. If one would walk through remote forest and survey a large number, quite large, of white oak trees, one might find a tree that appeared to be a hybrid of, for example a white oak and a burr oak, or possibly willow oak. The leaves might for example be intermediate between two white oak family members, and not be quite identifyable. If under certain conditions, that hybrid was not only viable, but better adapted to the environment, it might over the course of time thrive, and even pollenate some similar hybrids. This would be a non-incremental form of species creation.
It is easier to visualize and find examples of cross species hybrids among external spawners. The coral reef is a good place to look for hybrids. The snapper family, or lutjanids are pelagic spawners, they spread their gametes into the current. When fishing on reefs in the Caribbean was at it's peak, it was not uncommon to report hybrids, or individual fish that were the result of natural cross hybridization. More commonly, a commercially cultured product, hybrid striped bass, is a cultured cross between a white bass and a striped bass. It has the characteristic stripe, which makes it marketable in the fish market, and yet it can be cultured in freshwater lakes and quarries.
As to a common underlying question, " are humans evolving ? " , we can safely say, from what we know about human genetics and the result of chromosome number changing mutations, that humans will never change their chromsome number. In the sense of becoming a vastly different form one day, the answere is no. In the incremental, or small yet ultimatelimited ways that Darwin proposed, the answer would be a definite "maybe".