What is inbreeding?

By Razib Khan | July 22, 2012 10:23 pm

I’ve put up a bunch of posts relating to inbreeding recently (1, 2, 3, 4). But I haven’t really defined it. First, let’s stipulate what inbreeding is not: it is not the same as incest. Acts of incest can include individuals who have no blood relationship to each other (e.g., Hamlet). Additionally, there are instances of inbreeding which are not necessarily incestuous. If a population is highly inbred, then individuals who are not relations by social custom may still be so genetically similar to a point where the pairing can not credibly be stated as an outcross. But still, what do I mean? To refresh myself I re-read the section on inbreeding in Hartl & Clark. And I think that helped clarify one implicit assumption which I have which may not be clear to everyone, and I’ll get to that.

In any case, first, what’s the deal with inbreeding? The short answer is that inbreeding is a measure of the probability of identity by descent of two alleles at a given locus in a given individual. This concise definition itself is the problem. These are all abstract concepts, close to being human categorical fictions useful in an instrumental sense. Locus is the most concrete one, as it is basically a gene (though not necessarily a gene, and you are probably aware that gene itself is a term which is the subject of contention). It just refers to a position on the genetic map. An allele is a genetic variant. If there is variation in genetic type at a locus, then you have at least two alleles. But note that alleles are a pre-DNA abstraction. They’re not specific changes in base pairs, or variations in genomic architecture. They’re just variants in a generic sense.

Identity by descent is both straightforward and almost mystical. It simply means that the two alleles are the same because they derive from the same common ancestor, as if they share a Platonic essence through the meiotic replication process. Note that if two alleles are the same in state they are not necessarily identical by descent. This is easy to understand. There are four base pair states, and one can imagine a circumstance where two alleles exhibit the same state because one of them has mutated from the ancestral state to a derived one.

And so there you have it, inbreeding isn’t like adenine or the human heart, it’s not a concrete material object, but an abstract conceptual phenomenon at some remove from everyday experience in a process sense.  Of course the concrete outcomes of inbreeding (e.g., recessive diseases) are well known to us from “folk genetics.” But knowing the result or outcome of a process does not equip someone to properly model it.

Above I implied one aspect of the inbreeding phenomenon which I don’t think I discussed earlier: the dimension of time. I referred to “ancestral” and “derived” states. And obviously identity by descent refers to descent from a common ancestor across generations. Inbreeding can not be understood without its proper historical-demographic context, which shapes the genetic state of a given population at a given time.

Obviously if you go far back enough in time all allelic lineages coalesce back to a common ancestor. On a deep level all alleles are identical by descent at a given locus (granting the confusions which occur due to orthology, etc.). Therefore when you ascertain identity by descent you have to set a cut-off date at which all alleles are not identical by descent. From this point, time = 0, some alleles will go extinct and some will increase in frequency, due to random genetic drift. In a purely stochastic system eventually all alleles will become identical by descent in reference to time = 0 as one allele fixes in the population at frequency ~100%.

What does all this have to do with inbreeding? Let’s make this concrete. Let’s set time = 0 at 2,000 years before the present. Every individual in the world alive today has a specific genealogy which stretches back to that point, and their genes have genealogies which go back to 2,000 years ago. Some ancestors show up many times in our genealogies, while others show up rarely. In other words we are all somewhat inbred when compared to an idealized Hardy-Weinberg equilibrium. That’s because there is structure in human populations. But there is inbreeding, and then there is inbreeding. Inbreeding basically is a measure of the tangled reticulation of your genealogy. Populations which have gone through bottlenecks, and have lower long term effective populations, exhibit more of this collapse in number of distinct ancestors. It doesn’t take a rocket scientist to intuit that fewer ancestors often means more alleles identical by descent (any given individual is going to show up a lot more prominently in a person’s genealogy, and so likely to donate an allele which is passed on from both mother and father). Compared to Africans non-Africans are inbred. People who are not African have fewer distinct ancestors at time = 50,000 years before the present, and this shows in their genomes. Populations which have gone through bottlenecks, and have been isolated (e.g., on islands) tend toward more inbreeding.

But as I said above, there is inbreeding, and there is inbreeding. People whose parents are siblings or first cousins are genuinely inbred in a way that Amerindians, who went through a bottleneck, are not. Though inbreeding coefficients apply across the whole genome, giving a measure of the genetic contribution of recent the same ancestors from both parents, one of the primary negative outcomes are the fitness hits due to relatively rare problematic alleles. All humans come with a complement of very bad allelic variants, but most of them have strongly recessive expression. But if you have many loci where the alleles are identical by descent, that is, you’re homozygous, then the problematic alleles will be unmasked.

In other words, the primary genetic reason that inbreeding is not optimal is the exposure of these rare large effect deleterious alleles. If you had two siblings who mated who were totally purged of mutational, load then the progeny would be far less problematic. In fact with plants selfing lineages achieve just this state of mutational perfection by exposing their recessive alleles and purging their genetic load (this seems less attainable with complex animals).*

With genomic methods a lot of this has become more concrete. As I note above ascertaining identity by descent at a base pair to a high degree of certainty is difficult because there are only four base pair variants. But if you look at long tracts of DNA then you see very specific independent sequences of genetic variations, which serve to tag specific ancestors. That’s why looking at “runs of homozygosity” is probably one of the better ways to get at inbreeding. If you still have a lot of runs of homozygosity that means that the common ancestry was recent enough that mutation and recombination was not able to eliminate blocks of visible descent. It is also probable that rare deleterious mutations are still shared across these blocks (i.e., selection hasn’t purged them from the population, or they haven’t mutated back to a functional form).

And there you have it, bringing inbreeding back to intelligibility. Distinctive genomic patterns which span loci have a particular shelf-life because of recombination. That gives you a extreme upper bound in terms of how far back in time you want to go in considering a population inbred due to common ancestry. Second, these methods are comparative. The load imposed by rare deleterious alleles can be assessed by comparing with similar populations. Comparing Ashkenazi Jews with Africans is not useful. Rather, compare them with other West Eurasians.

Readers with clarifications in English welcome!

* Evolutionarily selfing lineages seem to be a dead end though. They become clonal types without ay genetic variation to adapt to suboptimal conditions.

CATEGORIZED UNDER: Population Genetics
MORE ABOUT: Inbreeding

Comments (25)

  1. JJ

    Wow! Inbreeding for me is very simple, ’cause I’m microbiologist. I’ll explain what I used to think about inbreeding before I have read your comment:

    Inbreeding for me and Yeast genetists is mating between relatives (sibling x sibling, parent x sibling and any relative which has similar genetic origin). What can you obtain doing inbreeding? You can find alleles which modify a fenotype in a positive way (e. g. Glucose and Nitrogen compounds uptake) or in a negative way. Homozygous individuals are what we look for.
    If we talk about higher eukaryotes, an Inbred population is one which individuals have mated among distant or close relatives and as a matter of fact, the allele diversity is lower. If you analise a tribe you can find inbreeding, but if you analise south american population you will find so little inbreeding, because our population have been generated from different cultures and “genetic backgrounds”.

    Have I resolved your problem? 😀 Simple ideas (diversity) could help you.

  2. Miley Cyrax

    Yes, people tend to think of incest of as a binary thing, but it’s really more of a gradient.

    A fun pub discussion at the bar is taking a poll of what the closest hypothetical blood relative that your friends would guiltlessly take to pound town–err I mean, with whom your friends would copulate without reservation if he/she were attractive.

    Third cousin is the closest relative I’d do (share a pair of great-great-grandparents).

  3. “The short answer is that inbreeding is a measure of the probability of identity by descent of two alleles at a given locus in a given individual.”
    Surely the level of inbreeding in an individual cannot be a “probability” but must be a measure of the degree to which his/her parents are related. The degree of relatedness is real but may be unknown.
    Without invoking the arcane mysteries (for me) of genetics I recall conversations many years ago with my grandmother where she used to quantify the degree of relatedness of a couple quite easily as just tw0 numbers:
    1. the number of generations to the earliest common maternal ancestor, and
    2. the number of generations to the earliest common paternal ancestor.
    It is the numbers themselves which are the inverse measure of the level of inbreeding. Is it not so that where these numbers are unknown then genetics can provide an estimate – with a probability of error – of what these unknown but real numbers are?

  4. A while back I searched for a comprehensive definition of inbreeding because I felt that it wasn’t being adequately explained in lectures or in any texts that I was assigned. Most of the time, this concept is simplified down to the point that it’s either (a) too simple to mean anything or (b) to concise to be enlightening with regard to the effects of inbreeding (e.g., the definition stated above).

    The best definition I’ve found comes from Gillespie’s Population Genetics: A Concise Guide:

    Inbreeding occurs when an individual mates with a relative. The progeny of such matings are more likely to be homozygous than are progeny produced by random mating…

    The book further goes on to explain inbreeding coefficient as above, but what I like most about this definition is that it states in no uncertain terms what the effect of inbreeding can be on a population. That said, this post will make an excellent bookmark for the future as it’s a far greater explanation of the concept than I’ve found in any one book.

  5. Markk

    It is somewhat confusing because it seems like two different things are being called inbreeding by the commenters and essay here. #3 above is describing a trait of an individuls and the essay is describing a trait of a population.

    So it seems like an inbreeding at the individual level is a historical trait for that individual – a measure of how many ancestors they have back a few generations. For the population one could use the same definition – how many ancestors the population has back a given reporductive distance, but reading this, one today has to look at sets of alleles or genetic populations for similarity. Not just any similarity, rather similarity in “chunks” as given in the essay.

    The individual level is straightforward for sexual reproducing things, the second is a little more abstract and fuzzier in some sense, but I think perhaps more “parameter free” in definition, that is, one could come up with some absolute measure where you just feed in a set of genomes, or pieces of genomes and get a scalar value.

  6. So it’s a safe bet that Barack Obama is our least inbred President, given that it’s unlikely any common ancestor could be found between his father’s Kenyan Luo ancestry and his mother’s mixed European ancestry. Any consanguinity between his sets of grandparents would be rendered nil by that great genetic distance. He’s quite possibly an outcross tens of thousands of years in the making.

    If I had to venture a guess on the Presidents most likely to be inbred, I’d suggest the first 10 or so Presidents would be the most fruitful given the demographics of the colonies and the isolation of money and power.

  7. Interesting discussion…indeed inbreeding is slippery as it can be calculated using individuals, for example by quantifying the inbreeding coefficient using Path analysis (counting up the number of lines of descent that an allele has from ancestor to descendant)–this is akin to what Krishna’s grandmother has suggested (in the comment above), and one can calculate the average inbreeding coefficient in a population, where we keep track of different individual inbreeding coefficients and take their average–this value, usually denoted as F, is what is then plugged into equations to calculate expected genotype frequencies under inbreeding (assuming H-W conditions). As Razib noted, inbreeding doesn’t much change allele frequencies, only rearranges the probability of getting homozygotes. There is also the idea of random versus nonrandom inbreeding, since in a small, closed populations there is likely to be some amount of random inbreeding simply by chance (e.g., if every potential mate in this small population was a 3rd cousin). Nonrandom inbreeding is the amount of inbreeding above this random (or chance) level; for example in the population of 3rd cousins, some folks explicitly seek out 1st cousins as mates. In this sense, inbreeding is a microevolutionary phenomenon, in that most researchers are only concerned with the properties of the population a few generations back, and the degree to which the background population is related as well as the degree to any two individuals in the population choose mates who are more (or less) related than the background relatedness. Too much inbreeding (choosing mates who are more related than the background relatedness) can lead to inbreeding depression, which is the term for the negative consequences of inbreeding. This distinction–inbreeding versus inbreeding depression–arises since not all inbreeding is generally bad (at least theoretically). Fisher suggested that a sister can gain a benefit by mating with her brother and also mating with a random male. Her direct fitness gain would be N (# of offspring) if she mated with the random male and she would also gain indirect fitness gains (r*N) by improving her brother’s mating success by mating with him. So her total fitness is (1+r)*N, whereas it would only be N if she mated with the random male.

    A nice introduction to inbreeding is given in John Relethford’s new book “Human Population Genetics.” This book is basically a gentle introduction to pop-gen, with some human examples thrown in.

  8. In this sense

    that’s the problem right. we have to say “in this sense….”

    #6, yes, obama surely has the fewest runs of homozygosity. as for the converse, there are many examples of ethnically homogeneous presidents. i would bet john adams or van buren. anyone know if a president was the product of cousin marriage?

  9. Chad

    FDR was the product of 6th cousin marriages, otherwise I don’t know of any.

  10. Hassan

    Another example is John Adams who married his third cousin Abigail.

    John Quincy Adams, the 6th President, was the product of this marriage.

  11. interesting post on inbreeding. Here is a practical definition, at least for mice. Jackson Labs, which sells inbred mice defines inbreeding as
    An inbred strain is one that:

    is produced using at least 20 consecutive generations of sister x brother or parent x offspring matings, or;
    is traceable to a single ancestral pair in the 20th or subsequent generation.

  12. John Emerson

    What is the Icelandic situation? As I understand, almost all Icelanders are descended from a few thousand early settlers up to about 950 AD. (435 are named, but presumably the list had a big bias toward males, freemen, and landowners). All or almost all were Norse or Irish. But I don’t know how much replenishment there has been since then, and I know that there’s been more than one bottleneck since. After 950 AD Iceland was never so rich as to attract immigrants, but presumably there was replenishment after the die-offs.

  13. John Emerson

    To me it’s peculiar because in Iceland it seems quite likely that some people have exactly the same ancestors 10 or 20 generations back even though their more recent ancestors don’t overlap at all. This could be mathematically presented as though it were serious inbreeding (identical gene pools), even though I think that that would be erroneous.

  14. @ 12 and 13


    a search engine called Íslendingabók (the Book of Icelanders) allows users to plug in their own name alongside that of a prospective mate, determining any familial overlap. The site claims to track 1,200 years of genealogical information about the island’s inhabitants.

    The database may be found here :


    The database is in Icelandic and is unfortunately not available in other languages.

    Access to the genealogical database Íslendingabók is currently limited to Icelandic citizens and legal residents of Iceland who have been issued an Icelandic ID number (kennitala).

  15. #12 & #13, they are like jews, but even more so. everyone in iceland is related on the order of 2nd or 3rd cousins i think:


    the medieval population bottleneck was a major issue. i don’t think they’re that troubled in regards to recessive diseases, so it goes to show that the real problem is 1st cousin marriage, and repeated instances. though i guess i could do some simulations to see….

  16. I’ve put up a bunch of posts relating to inbreeding recently

    And failed to mention in my opinion, one of the best articles I have ever come across on the subject, even from just a historical and human interest perspective:

    Inbreeding & the downfall of the Spanish Hapsburgs

  17. John Emerson

    I went through an Austrian Habsburg line once and found that one Emperor has 16 different ancestors at the 64-ancestor level.

    That’s some pretty determined inbreeding.

    Some inlaws of mine fear a family curse based on an uncle-niece marriage 2 or 3 generations back. There’s insanity in the family but I think that it’s more likely the result of several generations of concentrated meanness, nastiness, suspicion, and grudges.

    / inlaw-bashing.

    Some of the fear of inbreeding is more like a leftover from old traditional superstitions and old wives tales, without much connection to actual genetics.

  18. Tom Bri

    Modern Icelandics benefit from the rough climate and the poverty of their ancestors. If in a family of six or ten children all but two die, selection clears away the poorer variants very quickly.

  19. selection clears away the poorer variants very quickly.

    i don’t think there’s evidence of a lower number of deleterious in icelanders, but i could be wrong (this is a well studied population).

  20. Isabel

    “the medieval population bottleneck was a major issue. i don’t think they’re that troubled in regards to recessive diseases, so it goes to show that the real problem is 1st cousin marriage, and repeated instances. though i guess i could do some simulations to see….”

    Some ancestors are overly represented in Quebec’s current population, resulting in modern occurrences of recessive disease, including several forms of ataxia, even though the Catholic church required dispensations for marriages closer than 4th cousin. They did give out a few, but as far as I understand it, the appearances of the particular diseases in some French Canadien populations is due to the alleles spreading through drift as the population grew rapidly after the original bottleneck. Eventually the recessive, mutated allele was so widespread that people carrying it would marry and have affected children even if they were not knowingly related.

  21. Grey

    “Some of the fear of inbreeding is more like a leftover from old traditional superstitions and old wives tales, without much connection to actual genetics.”

    I wonder. I think it might depend on how quickly things like IQ inbreeding depression could lift. Say you had a bunch of inbred villages in a valley and a new settlement is created in virgin forest and settled by individuals from each of the local inbred villages who then inter-marry. Would the grand-children of the settlers already have changed enough to see their relatives in the inbred villages as some kind of mutant?

    (I mean mutant in comic book terms as inbred people are always portrayed that way in western or at least Anglo western culture. I wonder how old that portrayal is?)

  22. Ed


    Sorry if this is late, and forgive any misunderstandings I might have.

    So basically hybrid vigor vs. inbreeding yeah?

    How deleterious are the effects of inbreeding caused by population bottlenecks?
    Would you consider this study evidence of hybrid vigor like some other posters were in the comments?

  23. Solis

    William Henry Harrison was the product of 2nd cousin marriage.

  24. Grey

    “William Henry Harrison was the product of 2nd cousin marriage.”

    I think the question will turn out to be more one of either
    a) consciously repeated close-kin marriages among the same group of families for alliance or inheritance reasons
    b) unconsciously repeated close-kin marriages among the same group of families simply due to a *very* low total breeding population.

    I doubt one-offs among an otherwise outbred population are likely to matter much unless particularly unlucky.

    If so the Icelandic situation where you have a small population breeding exogamously where that small population is just large enough to avoid the second case may turn out to work very well.

  25. Gary

    Sorry if this has already been covered, but it appears that Willard Mitt Romney is pretty well inbred, given that his grandfather was with the Mormons in exile in Mexico for practicing polygomy. My understanding is that he had 5 wives.
    The actual history of this religion turns my stomach, and it’s no wonder they were driven out of Ohio, then Missouri, then Illinois, then Utah into Mexico. Considering how cruel they were to their own women and girls, not to mention everyone who was not of their cultish ‘faith’, it it truly amazing that anyone would associate themselves with present-day Mormons.
    My 5th grandparents were wiped out in the 1850’s by the Mormons in the Mountain Meadow Massacre, along with more than 120 other men, women, and children. Google this piece of history for another look at Mormon history. Romney as president makes my skin crawl.


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About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at http://www.razib.com


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