john hawks weblog

paleoanthropology, genetics and evolution

population history

  • The North African Neandertal descendants

    Thu, 2012-10-18 16:25 -- John Hawks

    A new paper by Federico Sánchez-Quinto and colleagues reports on comparisons of North African population samples with the Neandertal DNA project data [1]. The paper shows that North African populations also carry a substantial trace of Neandertal ancestry, like living populations outside of Africa, much more than populations of sub-Saharan Africa.

    One of the main findings derived from the analysis of the Neandertal genome was the evidence for admixture between Neandertals and non-African modern humans. An alternative scenario is that the ancestral population of non-Africans was closer to Neandertals than to Africans because of ancient population substructure. Thus, the study of North African populations is crucial for testing both hypotheses. We analyzed a total of 780,000 SNPs in 125 individuals representing seven different North African locations and searched for their ancestral/derived state in comparison to different human populations and Neandertals. We found that North African populations have a significant excess of derived alleles shared with Neandertals, when compared to sub-Saharan Africans. This excess is similar to that found in non-African humans, a fact that can be interpreted as a sign of Neandertal admixture. Furthermore, the Neandertal's genetic signal is higher in populations with a local, pre-Neolithic North African ancestry. Therefore, the detected ancient admixture is not due to recent Near Eastern or European migrations. Sub-Saharan populations are the only ones not affected by the admixture event with Neandertals.

    The interesting aspect of the paper is that the authors attempted to separate the ancestry of North African samples into a pre-Neolithic indigenous African component, and a residual component that represents more recent gene flow into North Africa, from all sources. The historic movement into North Africa has been fairly cosmopolitan, involving sub-Saharan Africans, Arabs, Medieval Europeans, Romans, Carthaginians and many other peoples. Sánchez-Quinto and colleagues used the ADMIXTURE program to try to sort out a pre-Neolithic indigenous component and analyze that specifically for Neandertal similarity.

    Unsurprisingly, the fraction of estimated sub-Saharan African ancestry in each population sample was inversely correlated with the estimated Neandertal ancestry. That is, the more a population looks like sub-Saharan Africans, the less Neandertal it has.

    Here's what's surprising: When they sorted out parts of the genome in Tunisians that ADMIXTURE determines to be most likely from pre-Neolithic North Africans, they found these parts of the genome had more Neandertal ancestry than typical of the CEU sample of northern European ancestry. Is it possible that ancient North Africans had more Neandertal similarity than today's Europeans?

    Sánchez-Quinto and colleagues suggest that the Neandertal ancestry in this population came in Upper Paleolithic times from the Near East. That is possible, or some of the Neandertal similarity may reflect ancient African population structure. Really I think we will have to do a finer analysis of chromosome blocks to examine the subset of shared Neandertal derived alleles that reflect introgression versus incomplete sorting from the ancestral African population. It will be very interesting to examine more closely the mixture of population history within Egypt, through which most Near Eastern pre-Neolithic population movement must have come.

    The authors note that the distribution of Neandertal similarity outside Africa increases with distance from Africa.

    A previous study [26] observed that the similarity to Neandertals increases with distance from Africa and suggested this could be explained by SNP ascertainment bias plus a strong genetic drift in East Asian populations. Nonetheless more complex, population-biased, ascertainment schemes might have additional effects (i.e bottlenecks), but these are not expected to significantly increase the rate of false positives in admixture tests [31]. The Tunisian population has been reported to be a genetic isolate [17] so it is plausible that part of the signal detected is actually due to genetic drift. However, this should not affect the other North African groups in our study. Finally, given that SNP arrays are based on common alleles and probably the relevant admixture information is encoded within the rare and very rare alleles, the potential bias, if anything, will underestimate ancient hominid admixture signals, as shown in previous studies [2],[3].

    This pattern was also observed by Meyer and colleagues earlier this year [2], and I discussed it in my post on that paper ("Denisova at high coverage"). Both papers note that ascertainment bias may contribute to this pattern. I added that Meyer and colleagues had assumed that genes found in sub-Saharan African populations could not have come from Neandertals, which greatly biased their estimates against Europe and West Asia, considering historical and prehistoric gene flow across the Sahara and along the Indian Ocean coast. So I'm not yet accepting the relative numbers of Neandertal ancestry from different populations, as we don't know that they have all come from consistent assumptions. In particular, an elevated amount of Neandertal ancestry in China -- this paper puts it almost as double the amount of Neandertal ancestry in northern Europeans -- is unlikely. There is no pattern of bottlenecks that can give rise to that excess without additional population mixture, and hard to see where such population mixture would have happened without also affecting the ancestors of Europeans. Instead, we have some work to do in reducing the biases on these comparisons.

    References

    1. Sánchez-Quinto F, Botigué LR, Civit S, Arenas C, Ávila-Arcos MC, Bustamante CD, Comas D, Lalueza-Fox C. North African Populations Carry the Signature of Admixture with Neandertals Caramelli D. PLoS ONE. 2012;7(10):e47765.
    2. Meyer M, Kircher M, Gansauge M-T, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prüfer K, de Filippo C, et al. A High-Coverage Genome Sequence from an Archaic Denisovan Individual. Science. 2012;338(6104):222-226.
    Tags: 
    Neandertal DNA
    introgression
    admixture
    population history
    population structure
    North Africa
    Africa
    Synopsis: 
    A study of North African genetic variation shows that Neandertal genes were widespread in the area before the Neolithic.

  • New data on Ashkenazi population history

    Thu, 2010-08-26 19:37 -- John Hawks

    Bray and colleagues [1] report on genotyping of 471 people of Ashkenazi Jewish descent. This is one of the largest samples of a single human population, and is therefore very interesting for studies of population history and recent natural selection.

    There's a lot in the paper. One of the key findings in the paper is that the Ashkenazi population doesn't look bottlenecked -- in fact, it looks outbred compared to Europeans generally. The paper also documents a high amount of admixture with non-Ashkenazi Europeans, ranging from 35% to 55%. Figuring out the actual history of the population -- when and where its ancestors lived and how they interacted with other people -- is beyond the scope of this kind of analysis. But I expect that somebody can put together a really compelling historical account using these data.

    I turned quickly to the issue of selection. They are able to substantiate evidence of positive selection on several disease-causing alleles in the Ashkenazi population, including the Tay-Sachs allele. The lack of evidence for bottlenecks or founder effects pretty much takes away the alternative explanation. Yet they were unable to show statistical evidence of selection on some other disease-causing alleles in Ashkenazi populations:

    To explore whether regions of selection in the AJ population included any loci of known Ashkenazi diseases, we examined 21 disease- and cancer-susceptibility loci with known mutations found at higher frequency in the Ashkenazi population. Only 6 of the 21 genes fell in or near (within 500 kb) the top 5% of the AJ iHS windows (Table 2). Among these is the Tay-Sachs disease gene, HEXA, whose selection has been widely debated (4, 5, 14–16) and was found ~400 kb downstream of a window on chromosome 15 identified in the top 1% of the AJ iHS hits. Although none of the SNPs interrogated immediately adjacent to the HEXA locus showed elevated iHS signals, it is possible that the nearby region may contain regulatory elements under selection that affect HEXA expression. Cochran et al. (14) speculated that selection of many of the AJ- prevalent disease loci, especially the lysosomal diseases, conferred an increase in intelligence that was necessary historically for the AJ economic survival. Our data shows evidence of strong selection at or near only six disease loci, including only one out of the four AJ- prevalent lysosomal storage diseases, thus arguing that most AJ disease loci are not under strong positive selection, but rather rose to their current frequency through genetic drift after a bottleneck. However, we cannot exclude the possibility that selection of some AJ disease loci are outside the limits of detection by the extended haplotype tests, which are known to have less power to detect se- lection of lower frequency alleles (38, 41).

    It seems to me that this passage probably wasn't written by the same author who showed the lack of evidence for founder effects a few pages before. In this case, the confusion probably comes from the fact that the "detection of positive selection" is actually a refutation of the hypothesis of genetic drift. With a larger sample it will be possible to test the hypothesis with greater power.

    Ddisease-causing alleles are at low frequencies currently, making them unlikely to rise to the top percentages of the statistics. It would be interesting to control for current frequency, but I haven't seen a test that uses frequency information in this way.

    It's quite remarkable to reflect on the idea that positive selection has now been demonstrated on six disease-causing alleles in the Ashkenazi population. Every one of these is a case of overdominance -- where the heterozygote carrying an allele has some selective advantage, while the homozygote carrying two copies has a disorder. I was having a conversation with a very prominent geneticist a few months ago, who claimed that no case of overdominance in humans had ever been demonstrated except sickle cell. Now, that was obviously false even at the time -- as I pointed out, the many hemoglobinopathies are fairly clear examples. But we've come an awfully long way.

    From data like these, we're going to learn a huge amount about low-frequency selected alleles. The Tay-Sachs-causing allele is one of the most common recessive lethal genes in any human population, but like all genes subject to strong selection in homozygotes, it remains rare. Finding selection on these kinds of alleles is very hard unless sample sizes increase to several hundred individuals. Here we are seeing evidence of selection in historic populations -- within the last 2000 years. More will be coming.

    References

    1. Bray SM, Mulle JG, Dodd AF, Pulver AE, Wooding S, Warren ST. Signatures of founder effects, admixture, and selection in the Ashkenazi Jewish population. Proceedings of the National Academy of Sciences of the United States of America [Internet]. 2010;107:16222–16227. Available from: http://dx.doi.org/10.1073/pnas.1004381107
    Tags: 
    effective population size
    history
    recent selection
    bottlenecks
    Europe
    population history

  • French Neolithic discontinuities

    Sun, 2010-08-22 19:47 -- John Hawks

    Marie-France Deguilloux and colleagues [1] present a short analysis of ancient mtDNA recovered from a Neolithic burial at Prissé-la-Charrière, between the Loire and Garonne valleys of western France.

    The mtDNA sample in the end was only three individuals -- one haplogroup X2, one U5a and one N1a. Each is intriguing, as far as a single sequence can be, because all are rare or absent from France today. I think one shouldn't go far interpreting three samples, but they contribute to the view that Neolithic mitochondrial variation in Europe was very different from recent Europeans. The N1a and U5b sequences fit within the already-known Neolithic (and for U5a, Mesolithic) variation in central and northern Europe.

    It is from the U5a that Deguilloux and colleagues make a point about possible Mesolithic population continuity.

    Subhaplogroup U5b has also been encountered in German Neolithic remains from the Corded Ware Culture (Haak et al., 2008) and in the hunter-gatherers studied by Bramanti et al. (2009), although in both instances, the branches concerned were distinct from the U5b in the Prissé sample. It is, however, worth noting that haplogroup U5 has been encountered in surprising frequency in the hunter-gatherers studied by Bramanti et al. (2009) and could correspond to a Mesolithic heritage.

    The story of N1a is that it was very common in the central European Neolithic, even though it is very rare today. That was first noted by Wolfgang Haak and colleagues [2], and has in subsequent years been joined by the observation that the pre-Neolithic hunter-gatherers had yet other common haplogroups. The population history of Europe was a lot more interesting than we suspected 10 years ago.

    Deguilloux and colleagues attempt a conservative explanation for the frequencies of N1a in Neolithic samples:

    The widespread distribution of the N1a lineage in Early and Middle Neolithic northwestern Europe may indicate genetic continuity from Mesolithic populations. This scenario would support a Mesolithic contribution to the earliest Neolithic of Atlantic Europe. This would imply that the N1a lineage was already common in indigenous north European populations and that the spread of the Neolithic was principally the result of cultural diffusion. Although so far the N1a lineage has not been encountered among late European hunter-gatherers in central and north Europe (Bramanti et al., 2009; Malmström et al., 2009), it is worth noting that less than half of the hunter-gatherers' paleogenetic data come indeed from the pre-Neolithic period (predating LBK expansion). Finally, no paleogenetic data currently exist for the Mesolithic period in Western Europe. This prevents any conclusion being drawn about N1a occurrence during the Mesolithic period in those regions.

    I will note this -- the more that N1a is replicated across the Neolithic of Europe, the less and less likely that its subsequent vast reduction in frequency could result from genetic drift. When there was only one or two samples from Central Europe with high N1a, it was at least possible that this was a local founder population that did not spread its mtDNA diversity very far. If it were localized, even in the central Danube (a fairly big region) it might be possible to maintain that the later decline of N1a to its present low frequency had been due to population replacement.

    Now N1a seems like a real marker of the LBK, spread widely into Western Europe. It may be, as Deguilloux and colleagues suggest, that it will be found at substantial frequencies in earlier samples somewhere in Europe. We do want some explanation for how it got to be common in this culture area.

    Dienekes has written about the study. His point is a good one: If N1a were present somewhere in pre-Neolithic Europe, it would require some kind of "partition" of the pre-Neolithic population, along with its propagation -- presumably southeastward -- into the LBK of central Europe. Seems doubtful.

    The study includes an illuminating paragraph about the sources of contaminating sequence in these Neolithic extractions.

    Strict precautions were followed during all procedures (including precautions during excavation) and proved to be effective, because all researchers who directly participated in this study (from people working in the field to those working in the laboratory) were genotyped and their sequences were never observed during analyses. However, European sequences were randomly found in clones (28% of the sequences obtained). These specific sequences are regularly observed in the laboratory, whatever the project tackled (including samples from Polynesia or South America), in clones from samples or negative controls. They are not reproducible for a specific sample and are different from researchers' sequences. These facts lead us to suspect the contamination of PCR reagents (Leonard et al., 2007). It was relatively easy, however, to discard those contaminating sequences from our analyses because they were largely in the minority when compared with endogenous sequences.

    It would not be very difficult to compare the results from different labs and do a forensic-quality analysis of these reagent contamination events. Surely a good fraction of ancient DNA results prior to the last few years must represent such contamination. Nowadays people have the expectation that Neolithic-era remains may have rare or exotic haplogroups, but it hasn't been so long since people assumed that French equals French. I expressed some concern about this criterion before -- "strange" stands in for "non-contaminated" in too many studies.

    It might be very helpful to have a paper outlining the actual contamination pathways that have been found to affect multiple labs. Then the results could be compared against reports that have come out over the years. If people are reluctant to cull doubtful ancient DNA results, at the very least they can target a set for replication studies.

    References

    1. Deguilloux M-F, Soler L, Pemonge M-H, Scarre C, Joussaume R, Laporte L. News from the west: Ancient DNA from a French megalithic burial chamber. Am. J. Phys. Anthropol. [Internet]. 2011;144:108–118. Available from: http://dx.doi.org/10.1002/ajpa.21376
    2. Haak W, Forster P, Bramanti B, Matsumura S, Brandt G, Tänzer M, Villems R, Renfrew C, Gronenborn D, Alt KW, et al. Ancient DNA from the First European Farmers in 7500-Year-Old Neolithic Sites. Science [Internet]. 2005;310:1016–1018. Available from: http://dx.doi.org/10.1126/science.1118725
    Tags: 
    population history
    Upper Paleolithic
    France
    mtDNA
    Neolithic
    population structure
    Europe
    migration
    mtDNA migrations
    Synopsis: 
    Study of mtDNA from a Neolithic-era burial in France contributes to an overall picture of Neolithic population replacement in Europe

  • SNPtastic India

    Wed, 2009-09-23 14:49 -- John Hawks

    The cover story in Nature this week is a paper about the population history of India, from David Reich's lab. It's an important contribution to our knowledge of human genetic variation, and provides a very interesting set of data for further investigation of modern human origins, the dispersal of agriculture into the subcontinent, and the history of more recent Indian populations.

    Here's the abstract:

    India has been underrepresented in genome-wide surveys of human variation. We analyse 25 diverse groups in India to provide strong evidence for two ancient populations, genetically divergent, that are ancestral to most Indians today. One, the 'Ancestral North Indians' (ANI), is genetically close to Middle Easterners, Central Asians, and Europeans, whereas the other, the 'Ancestral South Indians' (ASI), is as distinct from ANI and East Asians as they are from each other. By introducing methods that can estimate ancestry without accurate ancestral populations, we show that ANI ancestry ranges from 39–71% in most Indian groups, and is higher in traditionally upper caste and Indo-European speakers. Groups with only ASI ancestry may no longer exist in mainland India. However, the indigenous Andaman Islanders are unique in being ASI-related groups without ANI ancestry. Allele frequency differences between groups in India are larger than in Europe, reflecting strong founder effects whose signatures have been maintained for thousands of years owing to endogamy. We therefore predict that there will be an excess of recessive diseases in India, which should be possible to screen and map genetically.

    The number of individuals is not huge for the purposes of population genetic analysis -- only 132 people from 25 groups -- but it is very significant in terms of recent samples. By comparison, it is around double the number of effective individuals in any of the HapMap v.1 populations, genotyped at more than 560,000 SNPs.

    The results of the study are basic population genetic issues, including the degree of endogamy, the pattern of regional differentiation, the likelihood of discovering new recessive genetic disorders by additional sampling. Some notes:

    Population mixture. The authors propose that today's groups descend in varying proportions from two ancient (and no longer existing) populations, which they call "ancestral North Indian" and "ancestral South Indian".

    I'm always skeptical of mixture models, especially when the putative source populations no longer exist. There are just too many ways that structured migration or dispersal can lead to the appearance of mixture. People once thought of "Alpines" as a mixture of pure Nordic and Mediterranean elements, after all-- and that was just because their heads were mesocephalic.

    Still, with a half-million SNPs, it's possible to do a better job testing the hypothesis of mixture versus structured migration. The authors in this paper didn't -- they applied a simplified "3 Population Test" that compares the empirical allele frequencies to proportions expected under only two scenarios: simple mixture or complete isolation. It seems to me that the null should be simple isolation by distance, which would give the same result as "mixture" according to their test. If you really want to look for population mixture, you need to involve the dimension of time, for example, by demonstrating the antiquity of haplotypes that have mixed together.

    So I don't accept this ancestral division, certainly not at face value. It does seem plausible that West Asian (and thereby European-related) genes have introgressed into India over time, perhaps in association with the growth of high-density agricultural populations. Maybe some of this gene flow occurred under the influence of positive selection, but processes of elite dominance and differential growth may have been sufficient.

    Regional differences. The results show a greater degree of regional genetic differentiation in India than has been found for continental Europe. Still, with an FST of only 0.01, we're not talking about major population splits here. With that number, the subcontinent is closer to panmixia than one might expect for a region its size. The authors suggest that founder effects explain the regional differentiation:

    We propose that the high FST among Indian groups could be explained if many groups were founded by a few individuals, followed by limited gene flow. This hypothesis predicts that within groups, pairs of individuals will tend to have substantial stretches of the genome in which they share at least one allele at each SNP. We find signals of excess allele sharing in many groups (Supplementary Fig. 2), which as expected tend to occur in the groups that have the highest FST values from all others (P = 0.002 for a correlation). To estimate the age of founder events, we measured the genetic distance scale over which allele-sharing decays, and verified the robustness of our procedure by simulation (Supplementary Fig. 3). Six Indo-European- and Dravidian-speaking groups have evidence of founder events dating to more than 30 generations ago (Supplementary Fig. 2), including the Vysya at more than 100 generations ago (Fig. 2). Strong endogamy must have applied since then (average gene flow less than 1 in 30 per generation) to prevent the genetic signatures of founder events from being erased by gene flow.

    I don't think that explanation works. With those times in generations, we're talking about events within the last 600-2000 years. Since all these calculations are done on the whole dataset assuming complete neutrality, I think we should look more closely at the distribution of LD across loci. It seems likely that some of the high-LD loci that appear to point to founder effects will actually be found to be selected.

    Relationships of Indian to non-Indian populations. One of the real problems of assuming a tree with no migration is that it leads to statements like this:

    [T]he ANI [ancestral North Indian] and CEU [HapMap European sample] form a clade, and further analysis shows that the Adygei, a Caucasian group, are an outgroup (Supplementary Note 4). Many Indian and European groups speak Indo-European languages, whereas the Adygei speak a Northwest Caucasian language. It is tempting to assume that the population ancestral to ANI and CEU spoke 'Proto-Indo-European', which has been reconstructed as ancestral to both Sanskrit and European languages, although we cannot be certain without a date for ANI–ASI mixture.

    Some of the common ancestors of some living Europeans and some Indians were probably speakers of proto-Indo-European speakers. But we can easily refute the hypothesis that all of the common ancestors did so -- some of those common ancestors lived more than 40,000 years ago, as is well-known from the mtDNA chronology. The tree model with complete isolation does not explain the data. So as simple as it is -- and as well-used by Cavalli-Sforza and others -- it would be better to use a more accurate model.

    UPDATE (2009-09-24): Gene Expression has a full review of the paper.

    UPDATE (2009-09-27): Very interesting angle by Suvrat Kher at Reporting on a Revolution:

    The Indian Press has made a hash of the finding....

    But I can't blame the press entirely. The scientists who gave interviews to the press didn't mention this. They wimped out on reporting this potential inflammatory and politically incorrect finding. This is just poor and irresponsible science outreach on part of the scientists. How can you ignore a finding that is staring out at you from the very paper you are talking about? The press may be guilty of not digging in but it was just reporting what the scientists told them.

    References:

    Reich D, Thangaraj K, Patterson N, Price AL, Singh L. 2009. Reconstructing Indian population history. Nature 461:489-494. doi:10.1038/nature08365

    Tags: 
    India
    population history
    admixture
    HapMap
    population growth
    genomics

  • Ceci n'est pas un pothole

    Thu, 2009-03-26 10:54 -- John Hawks

    In 2005 I wrote this:

    "Unusual compared to the rest of the genome" is a phrase you should expect to hear a lot of in the next few years.

    I was looking back at that old post today, as I'm writing new stuff about bottlenecks. It's about the ability to detect selection using the HapMap data -- written just as I was starting to think about recent selection:

    Suppose we wanted to use a detailed topographic survey of a road to find the potholes. But for everyday roads, there is a problem -- there are lots of bumps and grooves that aren't potholes. And different parts of the road are more or less bumpy. It would help a lot if we could use the empirical distribution of bumps to simulate a section of road -- then we could figure out whether anomalies in the real road were likely to be potholes or not.

    Now suppose that the road isn't just pocked with the occasional pothole -- it has a pothole every three or four feet. Remember why we're using simulations -- not only do we not know where the potholes are, we don't know how common they are. So our simulations based on the pothole-rich road will find that pothole-sized bumps are normal. If pothole-sized bumps are not unusual, then our simulation can have only one result: a pothole is not a pothole.

    So I've been writing about the same problem for over three years -- the problem of ignoring history and archaeology when applying models of population history, and how they skew simulations of genetic drift. Time to do something about it, I guess.

    Tags: 
    population growth
    recent selection
    HapMap
    population history

  • Plumbing for bottlenecks

    Fri, 2009-03-20 16:43 -- John Hawks

    My series on mutual information and tests of selection (which began with "Information theory: a short introduction") is at a branching point. One of the critical factors determining the power of such tests is the ancient rate of genetic drift. So it's important to come to some understanding of the archaeological record and our best estimates of ancient demography, so that we can independently test the hypothesis that genetic drift was very strong in recent human evolution. That's a long project, potentially the topic of several review papers. Since nobody else has put together these data in useful way for population genetics, I'm going to do it in one place. What you see in this series are my notes about this project. Being notes, they are not complete, but they may occasionally be better than any other sources. Where it's appropriate, I'll spin off the results for review and publication, and point to them here.

    Many geneticists believe that there were massive population bottlenecks within the last 30,000 years, citing both genetic and archaeological evidence in support of this proposition. Some claim that there have been significant population bottlenecks in the last 5000 years.

    Some archaeologists agree. However, I think this is one of those Inigo Montoya cases: "That word, I do not think it means what you think it means." Archaeology and genetics have completely different interpretations of the words, "bottleneck," "contraction," and "expansion." The result has been a lot of confusion about the relation of archaeological and genetic estimates of population size.

    A population bottleneck impacts genetics by increasing the rate of inbreeding. This takes time to change gene frequencies, and does so in inverse proportion to population size. It may seem surprising that a truly massive die-off, on the scale of the Black Death, will have no measurable genetic impact. But cutting a population of millions down by half just doesn't impact gene frequencies. That is, unless you are looking at genes that helped people to survive the plague, in which case you're looking at natural selection, not a bottleneck.

    A significant genetic bottleneck is not just any population contraction -- it's an event in which the population is cut by a large fraction for a long time. In paleontological terms, we're usually considering cases where the ratio of the number of individuals and the number of generations is near one. In other words, if you cut the population down to a thousand individuals, and keep it there for a thousand generations, you're going to have a large genetic impact. Likewise, you can have a significant bottleneck that's ten generations long, but you need to cut the population down to around ten people.

    You can do a bit better measuring inbreeding by looking at lots and lots of people to study very rare alleles, like a rare genetic disease in a founder population. There, you may spot changes that unfolded in ten generations, even in a relatively large population of a hundred people. Increasingly, as we develop larger and larger datasets of gene variations, we will add power to detect such events in human prehistory.

    In archaeology, a significant event is one in which fewer sites were occupied by ancient people in a well-studied region. The length of such a contraction depends on the sampling intensity and dating methods available -- it might be a hundred years or many thousands. Likewise, the magnitude of population contraction will be uncertain -- you can get an accurate estimate, but with substantial sampling error. As in genetics, there are other possible explanations for an apparent contraction. We might lack geological exposures of the right age, or people may simply have moved from formerly favored locations to new ones. Worse, it might just be that archaeologists haven't looked hard enough at a given time interval.

    Archaeology is necessarily imprecise about the census population that existed at any given time. So is genetics. Both have their strengths and weaknesses. We want these different areas of evidence to bear on the same prehistoric events.

    Too much, instead of testing hypotheses, people just line up chronologies and look for matches. A geologist may claim that African paleoclimate is important because it may explain ``modern human origins.'' An archaeologist may claim that a hiatus at a site is consistent with ``genetic bottlenecks.'' And the geneticist may claim that inbreeding in a modern-day genetic sample dates to a period of time corresponding to the replacement of one tool industry by another.

    Any might be a valid hypothesis, but we need to take it further, to actually provide some tests. I believe we can do better now, because of the growing amount of genetic information. But we're going to have to do away with the facile idea that we're looking for massive bottlenecks, we need to introduce a recognition of the role of selection in human genetic variation, and we need to start addressing the archaeological record as it really exists.

    That's a forward to what follows. I'm going through regions of the world at different time intervals, to discuss what we know about population size from the archaeological record.

    Next: No Late Pleistocene bottleneck in southern Africa

    Tags: 
    genetic drift
    population history
    recent selection
    demography
    bottlenecks

  • Gene-culture models and reductionism

    Sat, 2008-11-08 19:40 -- John Hawks

    In the random corners of Google, I was led to a short 2004 letter in American Anthropologist by Daniel Wildcat, Irena Sumi and Vine Deloria, Jr. I found this paragraph thought-provoking:

    No doubt one can find high correlations between genes, languages, and kinship systems in many places. However, the definition of social structure that is associated with such analyses is terribly simplistic and reified. Involving population genetics is particularly misleading: Population genetics employs a mathematical model whose crucial dynamic variable is “mutation” readable in genetic markers such as mtDNA and the Y-chromosome. The frequency of these mutations is matter of speculation: It is deemed accurate or credible when the computed spans of time between mutations fit a preset, hypothetical scenario of a “demic expansion.” Exciting as such speculative science may be, it nevertheless yields bland, linear, and unimaginative speculation on humankind’s past. Moreover, it seems to exploit the fact that few social scientists familiarize themselves with modern genetics, and likewise geneticists seem largely ignorant of what social scientists know about the way humans build their communities and imagine the past, as well as how social scientists in turn represent these notions. This mutual ignorance seems to increasingly produce unquestioned mutual belief (Wildcat et al. 2004:641).

    This is at its root an anti-reductionist argument, and since I think there is substantial promise for reductionist approaches to culture history, I don't subscribe to the motivating spirit of the remark.

    But there is much here with which I do agree. Attempts at connecting genetic variation with linguistic or cultural history have been "bland, linear, and unimaginative." They follow essentially nineteenth-century models of culture transmission, in which both culture and genes are inherited in a vertical direction, and horizontal transfer (of either) has little importance. Because selection has been assumed to be unimportant or insignificant, the genetic models must rely on bottlenecks and isolation to explain genetic differences. Cultural diffusion -- and its extreme manifestation, language and subsistence shifts -- are unwanted noise that only obscures efforts to reconstruct "deep history." Correlations between genes and cultural traits are accidents of history.

    I can't say that the current pattern of biocultural research is wrong. People have developed clever ways to test the usual models, and those models will -- after all -- be correct in some cases. At worst, they will be rejected, and that increases our knowledge as well.

    But there is much of interest that remains to be explained, that must involve different patterns of culture-gene interactions. Not just vertical transmission, but codiffusion, true coevolution of genes and culture traits, and historical constraints on both cultural and genetic changes. As we extend our data across the genome, we can study the interactions not of one or two genetic loci with culture history, but of thousands. Natural selection has been very common, not rare. This gives us an incredible opportunity to test hypotheses about the historical causes of genetic change.

    These efforts may also be criticized as overly reductionist. But I find them very compelling because they make us focus on the role of individuals in culture-historical processes. In the usual models, individuals are passive repositories of genes and culture traits as they are passed forward through time. In models with genetic and cultural selection, individuals become agents, making decisions about adopting traits horizontally or vertically transmitted, and succeeding or failing based on both those decisions and combinations of selected genes.

    References

    Wildcat D, Sumi I, Deloria V, Jr. 2004. A response to Doug Jones. Am Anthropol 106:641.

    Tags: 
    models
    biocultural evolution
    population history
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