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Researcher Daniel Wilks claims:

Blood type O is a universal blood type. Blood types are further broken down into two groups, negative and positive. This is called the RH factor. The RH factor is the Rhesus (rhesus as in monkey) blood factor. The RH- type contains no rhesus (monkey) blood

No solid scientific explanation exists as to how or why Rh- blood came about.

Is there a scientific explanation for how or why Rh- blood came about?

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The Rhesus factor is due to a particular mutation and is a gene which derives from our common ancestors with chimpanzees and gorillas:

The human RH locus is responsible for the expression of the Rh blood group antigens. It consists of two closely linked genes, RHD and RHCE, that exhibit 92% similarity between coding regions. These observations suggest that they are derived from a relatively recent duplication event. Previously a study of nonhuman primate RH-like genes demonstrated that ancestral RH gene duplication occurred in the common ancestor of man, chimpanzees and gorillas.1

However, not all people have the same genetic code or carry this mutation. Like lactose intolerance, which has a similar origin, only some people carry it.

The scientific explanation for this is natural selection related to toxoplasmosis: there is a big difference in the distribution of Rh- persons in Europe versus Africa, and this has a similar distribution to the prevalence of this disease.

The observed effects of RhD phenotype could provide not only a clue to the long-standing evolutionary enigma of the origin of RhD polymorphism in humans (the effect of balancing selection), differences in the RhD+ allele frequencies in geographically distinct populations (resulting from geographic variation in the prevalence of Toxoplasma gondii), but might also be the missing piece in the puzzle of the physiological function of the RhD molecule.2

So, in Africa we have almost no Rh- and our closest co-descendants (chimpanzees) are also located in Africa. Is it surprising that they also have a similar distribution of Rh factor?

Also, keep in mind the human version of the Rh genes has strong similarities with the chimpanzee mutation, but it's not exactly the same. This is strong proof of a common ancestor and of evolution.

The Rh, factors of chimpanzee blood are different from the Rh,, factors of human blood, as proved by the absorption experiments described in the present paper … Therefore, according to the degree of resemblance of the Rh-Hr reactions to those of man, the apes could be arranged in the order: chimpanzee, gibbon, gorilla, and orangutan.3

A big nod to this Biology.SE question which I used to put together this answer.

References

1 J Hered. 2000 May-Jun;91(3):205-10. Evolution of RH genes in hominoids: characterization of a gorilla RHCE-like gene. Blancher A, Apoil PA.

2 Neuro Endocrinol Lett. 2008 Aug;29(4):475-81. Neurophysiological effect of the Rh factor. Protective role of the RhD molecule against Toxoplasma-induced impairment of reaction times in women. Flegr J, Novotná M, Lindová J, Havlícek J.

3 Am J Hum Genet. 1964 June; 16(2): 246–253. Blood Groups of Apes and Monkeys. IV. The Rh-Hr Blood Types of Anthropoid Apes A. S. Wiener, J. Moor-Jankowski, and E. B. Gordon

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Sklivvz
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    This answer unfortunately answers nothing and is based on speculative hearsay: "RH-like genes" - Really!? Come on now-that really is a non statement. There is no explanation here why 40% of the population of Europe have no monkey gene or blood when we are ALL supposed to share a recent ancestor with apes. For a proper and thorough evaluation we need to return to Lloyd Pye again: http://www.youtube.com/watch?v=fzuLlDEB2sg –  Feb 04 '14 at 23:57
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    @Morgan "The observed effects of RhD phenotype could provide not only a clue to the long-standing evolutionary enigma of the origin of RhD polymorphism in humans (the effect of balancing selection), differences in the RhD+ allele frequencies in geographically distinct populations (resulting from geographic variation in the prevalence of Toxoplasma gondii)" is not guesswork in the least. It's the scientific explanation you wanted. – Sklivvz Feb 05 '14 at 00:00
  • @Skliwz I believe the 'could' and the 'might' in the paragraph you allude to would suggest otherwise –  May 19 '14 at 11:39
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    @Morgan There's a difference between a scientific hypothesis based on facts and guesswork: namely the same difference that there is between a realistic, possible explanation (this) and some ridiculous childish fantasy (biblical creationism). – Sklivvz May 19 '14 at 11:55
  • Ad hominem comments doesn't strengthen an argument, it sadly diminishes it. Incidentally, at no point have I mentioned biblical creationism - I would suggest such polarized ways of looking at subjects is not very conducive to a healthy open discussion. –  May 19 '14 at 12:21
  • @Morgan there are no ad hominems in my comment. An ad-hominem is name calling the other person in order to invalidate their argument, but I did not name call you, nor a person in general. I called a philosophical position (biblical creationism) a childish fantasy. It is, because it is an unscientific explanation -- therefore a fantasy -- which has been disproven by facts -- thus, asserting it as true is childish. – Sklivvz May 19 '14 at 12:29
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    You asked "Is there a scientific explanation for how or why Rh- blood came about?" and I've given you the current scientific explanation. The fact you don't find it convincing doesn't make it guesswork, nor it means that there is no answer. Not all in science is black and white, perfectly proven or perfectly disproven... like anything else in life besides religious arguments. – Sklivvz May 19 '14 at 12:32
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    @Skliwz I think you'll find an ad hominem reply or comment is 'a general category of fallacies in which a claim or argument is rejected on the basis of some irrelevant fact about the author of or the person presenting the claim or argument' Only you know why you've brought in biblical creationism when it hasn't been previously mentioned. I would also suggest that dismissing other points of view as being based on "ridiculous childish fantasy" is not befitting of impartial unbiased moderation work –  May 19 '14 at 12:43
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    Comments are for discussing answers, but so far I've only seen unsubstantiated criticism -- it's fine if it's all you got, but I can't really fix my answer through it. If you want to debate what constitutes an ad-hominem attack, the right place is [chat], once you have access. If you think I'm moderating unfairly, contact our community team in the [form](http://skeptics.stackexchange.com/contact) below. If there is some major aspect of creationism you think is accurate in the face of science, ask another question about it. Let's stop using the comments for frivolous conversation. – Sklivvz May 19 '14 at 13:03
  • I've removed another off topic comment. Stop promoting videos and sites in comments. – Sklivvz May 19 '14 at 14:22
  • Minor nitpick in a great answer: Isn't the mutation lactose persistence, rather than lactose intolerance? – octern Aug 10 '15 at 00:07