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Thread: Introgression - Solution to Neanderthal-Sapiens Interbreeding?

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    Introgression - Solution to Neanderthal-Sapiens Interbreeding?

    Introgression is a new concept in anthropology. It allows for genetic interchange between taxons. This avoids all the "species" implications of genetic isolation by simply not mentioning them. It seems that in the real world species do exchange genes on a limited basis if and only if there is positive selection for the new gene(s).

    Genes without a positive selective basis (genes resulting from genetic drift) are quickly eleminated in the receiving species. Genetic linkage is broken down over the course of generations. This all may sound confusing and it was confusing to me until I read several explanations of introgression.

    Here is a blog site of Anthropologist John Hawks which deals with Neanderthal inheritance and introgression and a couple of his blogs specifically on the subject:


    -----------------

    Introgression and Microcephalin FAQ


    Considering the paper by Evans and colleagues, I've come up with a list of questions and answers:


    What is introgression?

    Introgression is the transfer of alleles across species or subspecies boundaries. In other words, it describes gene flow between populations that are partially isolated. For archaic humans, there is no test of the strength or permeability of boundaries between populations; it is common to use the term "introgression" to describe gene flow in such situations, even if such gene flow is fairly common. The paper by Evans and colleagues describes a scenario of adaptive introgression. In such cases, an allele with a selective advantage moves from one population to another.


    Adaptive introgression must be a very unusual event, right? I mean, I've never heard of it before!

    If you haven't heard of adaptive introgression, you haven't been reading the literature. Adaptive introgression across species boundaries is very common in mammals, and is almost ubiquitous where closely related species are sympatric. It has long been known to happen on the basis of morphological characters that spread through hybrid zones into adjacent populations. But now that molecular surveys have become common, introgressive genes have been found moving out of current hybrid zones, and also in the areas where hybrid zones likely occurred long in the past.

    Hybrid zones themselves are often quite obvious. But introgression is not about hybrids. It occurs when backcrosses spread alleles into the other parental species. Hybrids may have a mixture of many genes and characters. Introgression involves a small number of genes, which are much more likely to spread if alleles are adaptive. Where different populations are in reproductive contact, adaptive introgression may often be the most important source of adaptive alleles -- it provides a way for a species or population to benefit from the adaptive evolution of neighboring species.

    There is one thing that impedes introgression: linkage to deleterious alleles. Species separated for longer times are more likely to have alleles that are bad on the genetic background of related species, and so potential adaptive alleles must have advantages outweighing all the deleterious alleles they are linked to. In these situations, adaptive introgression may only occur after enough recombination has broken the adaptive allele apart from some or all of its linked deleterious neighbors.


    But I thought that "species" means "no interbreeding!"

    Get with the times, man! Mammal species just don't establish reproductive barriers very quickly. Comparing mammals, postzygotic isolating mechanisms take between 2 and 10 million years to evolve. No primate species pairs have evolved postzygotic isolation on the timescale represented by the evolution of Homo. When archaic and modern humans were in contact, they certainly interbred.


    OK, but why is this gene introgression? Why couldn't it just have originated in ancient Africans?

    The current evidence for introgression comes from the mismatch between the ancient coalescence time for all haplogroups of the microcephalin gene, compared to the very recent selection on the D haplogroup. Now recent selection on an ancient variant could occur within a single population, for example, if the allele was formerly neutral and gained a new advantage with some difference in the genetic background. And an ancient coalescence date would not be unusual in a single population -- several other loci match the 1.7 million years estimated for the microcephalin genealogy.

    Two things make this case especially persuasive. First, there is almost no evidence of recombination between the D and non-D haplogroups. If they existed within the same population for 1.7 million years, they should have recombined a lot with each other, and we should see some of those recombinants today. We don't. The best explanation is that the alleles were in different ancient populations, somewhat isolated from each other so that recombination was very rare.

    Second, the D haplogroup is common in Europe and Asia, but is very rare in Africa. If it increased under selection from its origin in some ancient African population, then it ought to be most common in Africa now. We might also expect a deeper origin for the D haplogroup in Africa, similar to the structure of many other genetic loci. We observe neither.


    Hey, why should this gene be so unique? There's never been any evidence for archaic genes before!

    Now, this is clearly where I have let you down, by not blogging about these papers as they have been coming out. What can I say, I have to make a living somehow! If I give away all my research, how can I stay a step ahead?

    The most similar locus to microcephalin is the region around MAPT on chromosome 17. Hardy and colleagues (2005) suggested that this locus is a Neandertal introgression. Like microcephalin, the locus has an ancient coalescence (>2 million years), and like microcephalin, an allele is under selection, with its highest current frequency in Europe. Like microcephalin, MAPT is brain-active, with most research centered on its possible role in Alzheimer's and Parkinson's disease. Unlike microcephalin, there are no recombinants between the major (H1 and H2) haplogroups; this is due to a chromosomal inversion between them. Evans and colleagues (2006) note that balancing selection might not be statistically ruled out when there is such an inversion preventing recombination. Still, balancing selection doesn't easily explain the recent positive selection, nor the geographic distribution of variation.

    Garrigan et al. (2005b) found evidence for an ancient Asian allele being retained in living Asians. This allele was from a non-coding locus, so it seems unlikely that adaptive introgression is the cause, which might suggest even more widespread genetic survival of archaic DNA. Some loci suggest the survival of archaic lineages within Africa, including another X chromosome noncoding region (Garrigan et al. 2005a) and the dystrophin gene (Zietkiewicz et al. 2003). These would presumably be attributable to partial isolation of Middle Pleistocene African populations, with introgressive gene flow among them.

    The widest survey for introgression thus far was by Plagnol and Wall (2006), who conclude that around five percent of human genes show some evidence for introgression from archaic humans. Their statistical test was looking for loci with ancient divergence times and in particular divergent alleles centered in Eurasian (non-African) populations. So this is a kind of estimate under the assumption of relatively great genetic differentiation among archaic human populations.

    I'll end with Templeton (e.g., 2005), who found that human autosomal variation supports a broad ancestry of living humans among Eurasian and African archaics, with evidence of genetic dispersals from Africa several times during the Pleistocene. Under this model, intermixture among archaic populations would have been fairly common, at least intermittently. This is the argument that I made with Milford Wolpoff several years ago (Hawks and Wolpoff 2001) -- we just don't see a lot of evidence for genetic differentiation among archaic humans.

    This kind of model would imply that genes like microcephalin -- with strong evidence for some isolation of populations -- might be fairly rare. The fact that several of them have now cropped up (the 5 percent estimate from Plagnol and Wall, 2006, being the most informative on this score) means that we have a lot about archaic human population structure yet to discover.

    But notice the nature of this uncertainty. We have a difference between substantial introgression among populations structured like hominoid subspecies on one side, and ubiquitous genetic exchanges among populations structured like human races on the other side. Complete replacement is completely out. "Mostly" replacement, or "assimilation" is still in, but with the observation that archaic human genes had substantial evolutionary importance in the adaptation of modern humans.

    In other words, we have moved the ball down the field. Time to line up for the next play.


    What is all this about microcephalin possibly not being from Neandertals?

    Well, the D haplogroup is common in many areas outside of Africa in addition to Europe. So it isn't possible to really specify in what archaic population it may have originated. There is some chance that it may be found in the Neandertal genome sequence, when that becomes available. In fact, that would be the ultimate test for many candidate introgressive alleles.

    But there is a good chance that it won't be found in the Neandertal sequence. After all, Neandertals were probably pretty thin on the ground -- especially in Europe. A sampling of their genes would be sort of unlikely to yield a high proportion of archaic alleles that may have survived to the present day. So there is hope that we will find and document such alleles, but the best evidence for many of them may remain their current pattern of variation in living people.


    Now, bear with me here. Neandertals were stupid, right? So why would one of their brain genes be advantageous in modern humans? There are so many possibilities here.

    1. Late Neandertals certainly weren't stupid. Consider the Châtelperronian. And the European Mousterian includes basically all the elements that are thought to represent cognitive sophistication in MSA Africans.

    2. Neandertal brains were big, and their heat generation requirements means that energetic constraints were very different from other archaic populations. The brain doesn't function in isolation -- its development, growth, and ongoing maintenance depend on metabolic constraints. So Neandertals might easily have had brain development alleles that had different responses to their high-energy lifestyles. Considering that early Upper Paleolithic people had much more effective foraging strategies than Neandertals, high-energy brain development may have had an even greater advantage than it had previously enjoyed.

    3. Modern humans are variable in brain morphology and cognition. That variability certainly includes alternative strategies (for example, personality types) that may be maintained by frequency-dependent selection. An archaic population that had particular constraints on its behavioral strategies might have given rise to strategies that worked within the modern human mix. In that context, Neandertals are fairly unique in having a very strong dietary dependence on meat, and their means of hunting was both risky and required cooperation. That adaptation may have led to behavioral strategies that succeeded in modern humans, even as Neandertal anatomies disappeared.

    Those are some possibilities we are working on. There are probably many others. The key is that we are looking at the function of some genes that survived, through our reconstruction of the total phenome of a population that no longer survives. We are limited by the evidence, but there are many suggestive hypotheses.


    Neandertals went extinct! Their features disappeared in later humans! How can any of their genes have survived?

    This is my favorite one to answer, because it invokes the true paradox of introgression. The features that we recognize as Neandertal features, were defined as Neandertal features by virtue of the fact that they are mostly gone! That means that any alleles correlated with Neandertal morphological features were almost certainly selected against, or were at best neutral. That means that those recognizably Neandertal genes are gone!

    But here we have a gene that looks to have come from some archaic population. Adaptive introgression occurs when adaptive alleles are selected, and broken apart from their genetic background. So even as many (perhaps most) Neandertal alleles disappeared, some of their alleles began to increase in frequency -- slowly at first, then very rapidly.

    Some adaptive introgressions may already have been fixed, particularly in Europe (from Neandertals). Others, like microcephalin, are still growing in frequency. The key is to remember Mendel -- this is not blending inheritance of Neandertal traits, it is the extinction of many alleles and the proliferation of some others.

    The reduction in frequency of Neandertal-like morphological traits over time is entirely consistent with this scenario. In fact, it shows the widespread importance of Neandertal-modern matings, which led to the emergence of a modern population with many Neandertal traits. The widespread genetic contact is documented by the distribution of the traits -- with different Neandertal-like traits in different specimens. That kind of contact is most likely to enable adaptive introgression to proceed.


    References:

    Evans PD, Mekel-Bobrov N, Vallender EJ, Hudson RR, Lahn BT. 2006. Evidence that the adaptive allele of the brain size gene microcephalin introgressed into Homo sapiens from an archaic Homo lineage. Proc Nat Acad Sci (early edition) DOI link

    Garrigan, D., Mobasher, Z., Kingan, S. B., Wilder, J. A., Hammer, M. F. 2005a. Deep haplotype divergence and long-range linkage disequilibrium at Xp21.1 provides evidence that humans descend from a structured ancestral population. Genetics 170:1849-1856.

    Garrigan, D., Mobasher, Z., Severson, T., Wilder, J. A., Hammer, M. F. 2005b. Evidence for archaic Asian ancestry on the human X chromosome. Mol. Biol. Evol. 22:189-192. DOI link.

    Hardy, J., Pittman, A., Myers, A., Gwinn-Hardy, K., Fung, H. C., de Silva, R., Hutton, M. and Duckworth, J. 2005. Evidence suggesting that Homo neanderthalensis contributed the H2 MAPT haplotype to Homo sapiens. Biochemical Society Transactions 33:582-585.

    Hawks, J., Wolpoff, M. H. 2001. The accretion model of Neandertal evolution. Evolution 55:1474-1485.

    Plagnol, V., Wall, J. D. 2006. Possible ancestral structure in human populations. PLoS Genet. 2:e105. DOI link.

    Templeton AR. 2005. Haplotype trees and modern human origins. Yrbk Phys Anthropol 48:33-59. DOI link

    Zietkiewicz, E., Yotova, V., Gehl, D., Wambach, T., Arrieta, I., Batzer, M., Cole, D. E., Hechtman, P., Kaplan, F., Modiano, D., Moisan, J. P., Michalski, R., Labuda, D. 2003. Haplotypes in the dystrophin DNA segment point to a mosaic origin of modern human diversity. Am. J. hum. Genet. 73:994-1015.



    -------------------

    Why introgression?

    I heard from a long-time correspondent this morning concerning introgression of microcephalin from archaic humans. I'm not sharing the whole message, but I thought it would be worth paraphrasing a key point for some thought.


    The basic point is this: Why are we talking about "introgression"? Why isn't this just gene flow?

    Let me start by saying this: "Introgression" is a useful term because it conveys a genetic reality, regardless of the taxonomic rank we are talking about. The literal meaning is "moving into", and what we are talking about is an allele moving into a new population. But more than that (and what distinguishes the term from gene flow) we are talking about an allele moving onto a new genetic background. The "genetic background" implies that there might be constraints on the movement of such an allele coming from epistasis or negative effects of linked alleles.

    I think it is especially useful in the case of MCPH1 because we are interested in the clear positive selection of this allele as a contrast to the clear decline in frequency of most archaic morphologies. The differential fates of different genes seem like a good example of some genes introgressing into a new genetic background.

    Now, one may object that "genetic background" isn't really a meaningful term. At the very least, it isn't very specific -- it might be better to have a list of genes that interact with each other and exert epistasis on potential introgressions. But it has the virtue of being empirically quantifiable. The overall genetic differences between archaic humans will eventually be measured, including their differentiation from the later modern population. As I mentioned in the FAQ, we can't narrow these values down right now, but more knowledge of genomics is going to make it quite possible. I think that the idea of archaic genes moving into a modern genetic background is going to describe the some of the evolution of early modern humans -- and I think these are important because they are selected. In other words, it is their dynamics that makes them important, not the other way around.


    UPDATE (11/9/2006): Razib gets into the introgression-defining act:

    Gene flow is a generic term, and can correctly characterize a whole host of dynamics, while introgression is very specific and precise, a subset of gene flow rather than a synonym.
    The description that follows is worthwhile, but it is a little problematic. For instance, there is the introduction of a hybrid zone as a mediator through which introgressive genes move in the process of transfer from one population to another. From some points of view this seems to work. For example, cottonwoods in Utah have well-defined hybrid zones (determined by altitude), through which introgressive alleles are thought to have passed, although now they are distributed widely into the range of the opposite parental population.

    But lots of other populations don't have hybrid zones at all. Wolves and coyotes (and dogs) mate fairly extensively wherever they are sympatric. Bison had a time in history when they received lots of genes from cattle, and introgression has continued here and there. There was never any well-defined hybrid zone, unless we consider the entire surviving population of bison to have been the zone. Introgression from mountain hare into European hare in Spain seems to have been structured around ancient Pleistocene contact zones rather than current distributions.


    Source:John Hawks

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    I found this post to be extremely interesting and I enjoyed it considerably. As a biologist, however, I would like to make just a few comments as I think that John Hawks is probably not as good at biology as he is with anthroplogy.


    Quote Originally Posted by Dr. Solar Wolff View Post
    Introgression is a new concept in anthropology. It allows for genetic interchange between taxons. This avoids all the "species" implications of genetic isolation by simply not mentioning them. It seems that in the real world species do exchange genes on a limited basis if and only if there is positive selection for the new gene(s). Genes without a positive selective basis (genes resulting from genetic drift) are quickly eleminated in the receiving species. Genetic linkage is broken down over the course of generations. This all may sound confusing and it was confusing to me until I read several explanations of introgression. Here is a blog site of Anthropologist John Hawks which deals with Neanderthal inheritance and introgression and a couple of his blogs specifically on the subject:


    http://johnhawks.net/weblog/reviews/neandertals/index.html
    The application of introgression may be new to anthropology, but systematic biologists and population geneticists have been using it for some time. Introgression can result from either interspecific hybridization (hybridization between two species) or infraspecific hybridization (hybridization between members belonging to the same species, but of different populations, subspecies, varieties, etc.).

    Quote Originally Posted by Dr. Solar Wolff View Post
    Considering the paper by Evans and colleagues, I've come up with a list of questions and answers:

    What is introgression?
    Introgression is the transfer of alleles across species or subspecies boundaries. In other words, it describes gene flow between populations that are partially isolated. For archaic humans, there is no test of the strength or permeability of boundaries between populations; it is common to use the term "introgression" to describe gene flow in such situations, even if such gene flow is fairly common.

    Not only is Hawks’ definition vague, it really doesn’t define introgression. Now remember, introgression results from hybridization (whether interspecific or infraspecific) between two different taxa (whether species, subspecies, or whatever). For it to be introgression, the resulting hybrids and their descendents will mate with members of one parental taxon only, and not the other.

    What happens is this: Individuals from two distinct taxa (let’s call them Species 1 & Species 2) interbreed and produce hybrids. Under introgression, the hybrid organisms mate with members of Species 1, but not with Species 2. Likewise, the resulting offspring will mate with members of Species 1, but not with Species 2. This process continues on for each subsequent generation. With each new generation, the amount of genetic material from Species 2 is decreased as the hybrid lineage becomes genetically more similar to Species 1.

    Quote Originally Posted by Dr. Solar Wolff View Post
    Hybrid zones themselves are often quite obvious. But introgression is not about hybrids. It occurs when backcrosses spread alleles into the other parental species.
    Again, I do not think that Hawks is very clear. It is true that there can be hybridization without introgression, but there is no introgression without some type of hybridization (even if it is infraspecific). Introgression is not mere backcrossing (backcrossing can occur without introgression), but repeated and generational backcrossing of a hybrid lineage with only one parental taxon.


    Quote Originally Posted by Dr. Solar Wolff View Post
    But I thought that "species" means "no interbreeding!"
    Get with the times, man! Mammal species just don't establish reproductive barriers very quickly. Comparing mammals, postzygotic isolating mechanisms take between 2 and 10 million years to evolve. No primate species pairs have evolved postzygotic isolation on the timescale represented by the evolution of Homo. When archaic and modern humans were in contact, they certainly interbred.
    First, what is a species? Most biologists acknowledge that the species has an actual reality in nature. The problem is that there is no precise agreement as to what a species is. There are numerous species concepts. Some taxa are species under some species concepts, but not species under other species concepts. By the way, the above talk about interbreeding and reproductive isolation is a reference to Ernst Mayr’s Biological (or Isolation) Species Concept, which is the most widely known species concept and the one usually used in college biology courses.

    Second, not all taxonomists/systematists use the same classification system (because there is no one agreed upon system). So what one taxonomist calls a species might be considered either a genus or a subspecies by another taxonomist. That is why Neanderthals are sometimes called Homo neanderthalensis (a species distinct from Homo sapiens) and other times as Homo sapiens neanderthalensis (a subspecies within Homo sapiens). While it is true that Neanderthals are usually considered to be a distinct human species (i.e., Homo neanderthalensis), the debate is far from settled. It mainly depends on how you interpret the mtDNA evidence (and not everyone interprets it the same way). If Neanderthals are Homo sapiens neanderthalensis, then we may be dealing with infraspecific introgression.

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    Thanks Northerner for your great comments and insight. Actually, I feel like someone who has just found company after a long trip in space. There was another website on introgression which had a more biological orientation but for some reason it is now lost to me. As far as I know, Hawks is a bone anthropologist but he uses archaeology in his website to further the concept of introgression.

    You are right about hybrid populations, demes or clines as they do not exist in introgression. In fact, they point out that the introgression can take place once per generation, each generation in a given population so there is no need of a hybrid population, or cline or deme (names given by various diciplines). The big difference between gene flow and introgression is that in introgression, genetic drift plays no role--it is all selection. Normally, the chances of any new allele becoming fixed through drift in the population is exactly the same as the frequency of that allele. But, as they point out, a new allele entering the population at .10 (10%) increases its chances to almost 90% of becoming fixed if its positive selective value is only 10%. And, it does not matter if the allele enters once through several individuals or over generations at one individual at a time.

    Introgression, with its focuss of selection, also says that linked traits to that one useful allele (assuming Neanderthals had many different alleles) would break down over the generations through independent assortment. Since only alleles with positive selective value would be retained, the other alleles would fall away but their linkages would be more apparent at first. This is why some Neanderthal characteristics were retained in sapiens in Europe. This is also why different archaic characteristics manifested themselves in different early sapiens populations in Europe. Since only positively selected alleles were retained in the new population, we today have almost no archaic alleles but do have some few Neanderthals alleles, like the microcephilin allele, but no heavy brow ridges, etc. of the Neanderthals.

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