@reasoning logic,
There are two bases for alleging that animals are different species, and one is two-part. The first is that they cannot interbreed (well, Du-uh), and the second part of that is that two animals might successfully breed, but their offspring will not be reproductively viable--they will be sterile.
The second is sexual isolation. Two members of a species will become sufficiently separated in distance over time so that they become, for all practical purposes, different species. A recent example of this was a bear which was discovered which was apparently the offspring of a mating of a grizzly and a polar bear. Unfortunately, the idiot who found the bear shot him, so we don't know if he were reproductively viable or not. If he had been, then the difference between the two species would be the product of sexual isolation. They would be reproductively viable, but would not reproduce because they do not live in the same range. With the climate warming, we may soon find out about grizzly bears and polar bears.
Based on the sequencing of the h. neanderthalensis genome which was done last year, contemporary h. sapiens whose ancestors left Africa more than 30,000 years ago do have DNA from h. neanderthalensis. What impact that has i don't think anyone can say, at least for the present. It is important to keep in mind that more than 90% of the genetic code of h. sapiens and h. neanderthalensis are identical, so that it would be difficult to say how much of that portion of our genetic make-up came from h. neanderthalensis--although it certainly wouldn't matter, since we'd have it no matter what the source.
We all have mitochondria in our cells (that's plural, the singular is mitochondrion). These organelles serve some crucial functions in our cells, acting like a power plant to produce the chemical which is used to provide energy for the cell, and are probably crucial in cell differentiation and cell death, and other crucial functions.
Genetically, mitochondria are important as markers to show the descent of animals. That's because MtDNA (the DNA of the mitochondrion) is passed on without recombination--it's a mirror of the mother's mitochondria. This is important in human genetics and the study of human pre-history because MtDNA markers can tell who were the ancestors of those who now possess it (MtDNA from the father does recombine). So, for example, there is now almost indisputable evidence that all modern humans are descended from a single woman who lived in Africa about 200,000 ybp--
Mitochondrial Eve.
MtDNA has also confirmed many theses of human migration in pre-historic times which had previously questioned or even dismissed out of hand. Because of recombination, the approximate age of the source MtDNA can be reasonably inferred. This tells us, for example, that 3% of all aboriginal Americans possess ancient European MtDNA--in eastern Canada, that rises to 25% of aboriginal populations. It also tells us that Madagascar (a large island off the east coast of Africa) was indeed colonized from what we think of as Indonesia, and not from the African mainland. Africans from the mainland did end up there, but only after the Australasians from, probably, Sumatra of Java, had already colonized the island. This was first suggested by linguistic evidence in the 19th century, but many scholars dismissed because they thought it too improbable. But the evidence from MtDNA is that the oldest male MtDNA on Madagascar come from Australasian sources.
