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Tired of hearing of these urban legends and popular opinions, I ask this question here to see if there really is scientific merit to this belief. My questions is, is it really "harmful" for a person to reproduce with his/her own first cousin? Everyone, at least in America, seems to think that this is incest which I completely dismiss because incest is purely a religious concept. The next argument I get is that we want more genetic diversity and having offspring with a first cousin is detrimental to our survival as a species. If you have any genetic weaknesses then your cousin is likely to be carrying them as well and then the chances of your offspring carrying them increase and so on.

I don't really believe any of this. It is rather well known (or may be not so well known) that only a very small percentage of a human individual is different from another human individual's genome. Differences due to skin color, race, ethnicity, and such are literally skin deep. So one reproducing with her cousin or someone half way across the globe is only negligibly different.

Forgetting about religion, has this been scientifically systematically tested and/or proven? Has any research been done on this? Is it true one way or the other? I don't mean to spark any debates here. Opinions are of course welcome. But if anyone can point me to any reputable sources or published results/references, that would be ideal.

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Inbreeding depression, "the reduced survival and fertility of offspring of related individuals" (quoting the linked article), is a well-known and well-understood biological effect. It does, indeed, affect humans.

The problem is that recessive mutations become more likely to affect the survival of the offspring of relatives. Imagine that you have a mutation affecting, say, some gene that's critical to your metabolism, which is entirely possible. But, since you have two copies of the gene and only one of them is faulty, you are not affected by this. Nevertheless, you, by chance, pass the non-functional one on to a couple of your kids, who are also not affected due to only having one copy as well. They, in turn, pass it on to one or more of their kids. Now, two of them, cousins, have a kid. The kid gets both copies and can no longer properly metabolize something due to having two faulty copies of the gene. This can prove to be fatal or at least severely debilitating.

Now, lest you think this is improbable, there are on average 70-something mutations per generation. Some of those will be neutral in effect, others will be detrimental. Once an offspring gets two copies of those detrimental alleles, then there could be serious health effects. The likelihood of an offspring getting two copies decreases as the relatedness of its parents decreases. So, sibling or parent/child pairings would be the most likely to produce offspring with the problems. Pairing between 3rd generation (First-cousins) or any pairings between them and their siblings, parents, aunts/uncles or grand-parents would be the next most likely.

So yes, first-cousins marrying and having kids is a bad idea for very basic scientific reasons.

I missed the "as a species" part of your question. Inbreeding will only likely have an effect within small, closed populations, though it will continue to have a lasting effect even as those populations grow and open up. Two textbook examples are French Canadians and Ashkenazi Jews. Even now, there is continued elevated risk of certain rare genetic diseases in these populations. As for the species as a whole, it is likely to be really detrimental only if the effective population size of the species becomes really low: a general rule of thumb used by conservation biologists is that the effective population size should be at least 50 to avoid the effects of inbreeding (and 500 to avoid the effects of genetic drift) (50/500 rule).

Sorry about the confusion.

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    $\begingroup$ This is a good explanation of the mechanics, but maybe you could add a bit about the rates here. Inbreeding certainly can have an effect, but is it a big one? Somehow, cousin-cousin marriages are permitted in many cultures and even encouraged in some; likewise, at points in history, effective population size in many human populations has been very small, without any lasting negative effects. It takes a seriously concentrated effort of sustained intermarriage within families over hundreds of years (European Royals and pituitary hormone deficiency or haemophilia) to actually produce an effect. $\endgroup$
    – Oreotrephes
    Jul 23, 2013 at 10:36
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    $\begingroup$ Just because cousin-cousin marriages are permitted or encouraged does not mean that they're wise. On the other hand, there are many examples of elevated genetic disease rates originating from small, closed populations: French Canadians, for example, or the textbook example of Tay-Sachs disease in Ashkenazi Jews. And it only takes one or two generations to see an effect, unless you're looking for a population-wide elevated frequency. Of course it's possibly harmful for the 1st gen offspring... $\endgroup$
    – user3934
    Jul 23, 2013 at 10:45
  • $\begingroup$ I can't edit my comment anymore: but it only potentially takes one generation (not "one or two") to see an effect, and I mean one generation after the cousin-cousin mating. I read the question as "Is it detrimental for cousins to marry" and the answer is "Yes, for the offspring it is likely to be detrimental". I missed the "as a species" part. $\endgroup$
    – user3934
    Jul 23, 2013 at 11:03
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    $\begingroup$ Good points, good examples, and good answer: +1. $\endgroup$
    – Oreotrephes
    Jul 23, 2013 at 11:40
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    $\begingroup$ Technically.. it just reduces diversity in the population and moves the it towards homozygosity. It may increase the likelihood of a disease but it may also select for a good trait. So the societies which promote consanguineous marriages are perhaps thinking that they are selecting for a trait that they think is good. But what happens most times is that we don't really have an idea of all the traits and their combinations and inbreeding leads to amplification of deleterious mutations. $\endgroup$
    – WYSIWYG
    Jul 23, 2013 at 17:32

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