john hawks weblog

paleoanthropology, genetics and evolution

Neolithic

  • Tracing teeth troubles with fossil bacteria

    Sun, 2013-02-17 19:36 -- John Hawks

    Ed Yong has a great account today of some research from Alan Cooper's lab on the oral microbiome in pre-agricultural and post-agricultural Europeans: "Prehistoric Plaque and the Gentrification of Europe’s Mouth".

    The hunter-gatherers had a diverse array of bacteria including several groups that are associated with good health. That fits with the relative absence of tooth decay or gum disease among modern or prehistoric hunter-gatherers. “They were at the end of a long period of happy co-evolution between us and oral bacteria,” says Cooper.

    The advent of farming disrupted that tango. After the Agricultural Revolution, as humans began to chow down upon barley, wheat and other domesticated crops, the diversity of the mouth microbes fell, and species associated with oral diseases became more common. “Eating all this soft squishy carbohydrate and leaving it lying around the base of your teeth is effectively inviting in a whole new range of bugs to take up permanent residence in your mouth,” says Cooper.

    I'll have some more comments on this new research when I can sit down to write them up. I've been waiting for this to come out for quite a long time -- I first heard about the research almost three years ago. The potential to characterize oral ecology across time is immense, and we have some excellent data on dental pathologies across the entire timespan. Caries and other dental pathologies are very new in human populations, and although starchy diets have been blamed, very little has been known about how oral bacteria themselves may have become more pathogenic over time. This study is really great because it opens a new door to looking at this evolution across time. We will need to compare this record with the evidence for morphological change in teeth across the same time span. Smaller teeth may have been a consequence of selection associated with dental pathology in agricultural peoples.

    Next we will need to compare across space -- including greater sampling of oral microbiome variation among living humans. This is another new area in which we know more about prehistoric people than we do about living human variation!

    Tags: 
    microbiome
    teeth
    pathology
    health
    Neolithic
    recent selection

  • Cheesy evidence

    Wed, 2012-12-12 14:40 -- John Hawks

    I'm totally socked in with work this week, but this new paper in Nature is an interesting piece of archaeological chemistry relevant to diet change in the European Neolithic: "Earliest evidence for cheese making in the sixth millennium bc in northern Europe" [1].

    The finding of abundant milk residues in pottery vessels from seventh millennium sites from north-western Anatolia provided the earliest evidence of milk processing, although the exact practice could not be explicitly defined1. Notably, the discovery of potsherds pierced with small holes appear at early Neolithic sites in temperate Europe in the sixth millennium BC and have been interpreted typologically as ‘cheese-strainers’10, although a direct association with milk processing has not yet been demonstrated. Organic residues preserved in pottery vessels have provided direct evidence for early milk use in the Neolithic period in the Near East and south-eastern Europe, north Africa, Denmark and the British Isles, based on the δ13C and Δ13C values of the major fatty acids in milk1, 2, 3, 4. Here we apply the same approach to investigate the function of sieves/strainer vessels, providing direct chemical evidence for their use in milk processing. The presence of abundant milk fat in these specialized vessels, comparable in form to modern cheese strainers11, provides compelling evidence for the vessels having being used to separate fat-rich milk curds from the lactose-containing whey. This new evidence emphasizes the importance of pottery vessels in processing dairy products, particularly in the manufacture of reduced-lactose milk products among lactose-intolerant prehistoric farming communities.

    Nice job of narrowing down the function of pots from fragments, following the processing steps that are evidenced in known cases of milk and cheese production. The early presence of cheese making may also be relevant to the selection pressure for lactase persistence -- one argument being that cheese and yogurt production make lactase persistence less advantageous relative to non-persistence. If cheese making was there from nearly the start of the Neolithic, that implies that the fitness advantage of lactase persistence was strong even in its presence.

    References

    1. Salque M, Bogucki PI, Pyzel J, Sobkowiak-Tabaka I, Grygiel R, Szmyt M, Evershed RP. Earliest evidence for cheese making in the sixth millennium bc in northern Europe. Nature. 2012.
    Tags: 
    lactase
    diet
    Europe
    Neolithic

  • Serbian Neolithic on display

    Tue, 2012-11-06 15:29 -- John Hawks

    Here's an interesting story for today:

    A hoard of jewelry, figurines and other objects crafted by early farmers in Serbia nearly 8,000 years ago is set to go on public display for the first time at a German museum. Archaeologists dug up the largely undisturbed stash of artifacts during excavations this summer at the site of a Neolithic settlement in Belica, Serbia, about 90 miles (140 kilometers) south of Belgrade.

    Tags: 
    Neolithic
    Serbia
    Europe

  • When and where was proto-Indo-European?

    Sat, 2012-08-25 00:51 -- John Hawks

    A new study by Remco Bouckaert and colleagues attempts to place the origin of Indo-European languages by using an epidemiological population model, essentially plotting the "spread" of languages from a common source [1].

    To test these two hypotheses, we adapted and extended a Bayesian phylogeographic inference framework developed to investigate the origin of virus outbreaks from molecular sequence data (13, 14). We used this approach to analyze a data set of basic vocabulary terms and geographic range assignments for 103 ancient and contemporary Indo-European languages (15–17). Following previous work that applied Bayesian phylogenetic methods to linguistic data (1–3), we modeled language evolution as the gain and loss of “cognates” (homologous words) through time (18–20). We combined phylogenetic inference with a relaxed random walk (RRW) (14) model of continuous spatial diffusion along the branches of an unknown, yet estimable, phylogeny to jointly infer the Indo-European language phylogeny and the most probable geographic ranges at the root and internal nodes. This phylogeographic approach treats language location as a continuous vector (longitude and latitude) that evolves through time along the branches of a tree and seeks to infer ancestral locations at internal nodes on the tree while simultaneously accounting for uncertainty in the tree.

    Diffusion models applied to spatial data tend to place the origin at the center of the present geographic distribution. That's just the simplest way to explain any geographic distribution under the diffusion model, which assumes that people act like random particles.

    By contrast, Phylogeographic models tend to place the origin near the point with maximal clade distance. One ancient Anatolian language, Hittite, is attested in written records and according to the phylogenetic analysis is an outgroup to other, more recent Indo-European languages. Armenian, Greek, and Albanian also belong to relatively deep clades, and they geographically flank Anatolia in different directions.

    So in this case, both diffusion and phylogenetic approaches point toward Anatolia as the most parsimonious origin.

    Additionally, when the centers of diversification of the major Indo-European families are considered (e.g., Celtic, Romance, and Indo-Aryan), the geographic center of their distribution is Anatolia. Figure 2 of the paper illustrates the geographic ranges estimated as origins for the different clades within Indo-European:

    Figure 2 from Bouckaert et al. 2012

    Looking at the picture, Anatolia looks like ground zero for the viral spread of Indo-European languages.

    OK, so the logic of the model pretty much inevitably leads to the conclusion. Anatolia is at the geographic center of the early Indo-European families, and is geographically central to the earliest branches of the language tree. But should we believe it? Languages, after all, don't spread exactly like viruses. And viruses don't spread by diffusion much of the time -- if they did, the movie Contagion would have had a lot more boring plot.

    I have no strong reason to be skeptical of the main conclusion, that the first Indo-European language may have originated in Anatolia. But I do note that it's strongly influenced by the evidence we happen to have about ancient languages. If we had a stronger record of the ancient languages of Central Asia, who knows what we might find? Tocharian, in the Tarim Basin of western China, was also a relatively deep clade in the Indo-European phylogeny, spoken within the last 2000 years. Could there have been others?

    Also, Razib Khan points out some issues with the dates that the model attributes to branch points in the tree: "There are more things in prehistory than are dreamt of in our urheimat".

    Bouckaert and colleagues set up an opposition between two hypotheses for the origin of the Indo-European. The first derives the family from Anatolia more than 8000 years ago, possibly shortly after the origin of agriculture in the Fertile Crescent. This is more or less the Colin Renfrew model of Indo-European, which posits that the language family was able to spread due to the population expansion of agriculturalists. In this model, the first Neolithic peoples of Europe should have been Indo-European speakers.

    The alternate hypothesis is that Indo-European originated on the steppes of Central Asia and Eastern Europe. This is more or less the Marija Birute Gimbutas model, where early steppe peoples spread westward carrying Indo-European with them. Some linguists and archaeologists have strongly favored this model because of the words reconstructed as part of the proto-Indo-European language, which include many technological and ecological elements that would have been familiar to steppe pastoralists of 4500-6000 years ago.

    This seems like a clear dichotomy -- either Indo-European was early and spread with agriculture, or it was later and spread into regions already agricultural. In the first case, the language spread was mostly caused by demographic growth, in the latter case, other mechanisms such as elite dominance and conquest may have played more important roles. So it is interesting that this paper, after concluding an early Anatolian origin was supported by the data, actually argues for a much softer, intermediate position:

    Despite support for an Anatolian Indo-European origin, we think it unlikely that agriculture serves as the sole driver of language expansion on the continent. The five major Indo-European subfamilies—Celtic, Germanic, Italic, Balto-Slavic, and Indo-Iranian—all emerged as distinct lineages between 4000 and 6000 years ago (Fig. 2 and fig. S1), contemporaneous with a number of later cultural expansions evident in the archaeological record, including the Kurgan expansion (5–7). Our inferred tree also shows that within each subfamily, the languages we sampled began to diversify between 2000 and 4500 years ago, well after the agricultural expansion had run its course.

    I think this is the most important passage of the paper. Reading between the lines, it says that the origination point for Indo-European languages simply may not address the archaeological record. What if Indo-European got its start in Anatolia 10,000 years ago, but many of the modern branches of Indo-European within Europe -- Celtic, Italic, Germanic -- all moved into Europe in several separate waves, starting less than 6000 years ago from the Pontic Steppe? We have pretty good genetic evidence now that the first farmers in Europe were not very much like recent Europeans. We need later migrations into Europe from elsewhere to explain the genetic record, and the archaeology (and later, history) provides plenty of reasons to think that later migrations were important.

    So, there we are. Even though the present study supports an early, Anatolian origin for Indo-European, other evidence rejects the simple Colin Renfrew model. The present Indo-European families did not reach their present geographic distributions with the first agriculturalists. That means we need to look at more complex intermediate steps to explain how current and historic Indo-European languages got to their attested locations. The steppic model might well explain the spread of languages between 6000 and 4000 years ago, even if they shared earlier ancestors that fit the Anatolian model.

    References

    1. Bouckaert R, Lemey P, Dunn M, Greenhill SJ, Alekseyenko AV, Drummond AJ, Gray RD, Suchard MA, Atkinson QD. Mapping the Origins and Expansion of the Indo-European Language Family. Science. 2012;337(6097):957 - 960.
    Tags: 
    Indo-European
    Neolithic
    Bronze Age
    pastoralism
    Altai
    Anatolia
    Colin Renfrew
    Synopsis: 
    A new paper places the origin of Indo-European in Anatolia, but the story may be more complex.

  • Neandertal ancestry "Iced"

    Wed, 2012-08-15 15:24 -- John Hawks

    I've been mobbed with e-mails from readers asking about my reaction to the new paper by Anders Eriksson and Andrea Manica in PNAS, titled "Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins" [1]. The paper asserts that Neandertal similarity in the genomes of living people outside Africa can be explained only in terms of incomplete lineage sorting from the shared human-Neandertal common ancestral population in Africa. If the paper's assertions were accurate, we could go back to thinking that all the genetic heritage of people today traces back to Africa, although we would still need to abandon the idea that the African population had undergone a small bottleneck.

    I have not been posting as frequently the last month or two because I have been out of the country doing science.

    The new paper's press release has given rise to quite a lot of media attention, much of which unfortunately misrepresents our current knowledge of human and Neandertal genomes. Razib Khan summarized the situation on Monday, in a post titled, "Why you shouldn't publish in PNAS". I agree with his criticism, although I have a perspective coming out soon in PNAS. In fact, I suppose this episode shows why everyone should publish in PNAS, because so many journalists will just parrot press releases instead of asking relevant experts. Ewen Callaway did a great job on this story by putting it into the broader context ("Neandertal sex debate highlights benefits of pre-publication"). You will notice how no other science writers with any Neandertal knowledge picked up this press release...

    Paleoanthropology is a field where data are rare and precious, and we do a lot of arguing about the validity of models. I love arguing about the validity of models (Cliff Notes version: All models are wrong).

    Genomics is not such a field. We have abundant data today to compare with Neandertal genomes. Yet puzzlingly, the idea of Neandertal ancestry has been challenged by several papers that haven't performed any new empirical comparisons at all. I'm struggling to figure this out. We have an unparalleled ability to explore the genomes of humans and Neandertals, and we should believe a computer model with no empirical data?

    I've been assessing the Neandertal similarity of 1000 Genomes Project samples here on my blog (e.g., "Which population in the 1000 Genomes Project samples has the most Neandertal similarity?"). This is ongoing research here in my group, but we've been making it open because it tells us immediately that some hypotheses about Neandertal similarity must be wrong. Modeling is a lot of work. We're trying to avoid putting a lot of investment into modeling that will be easily refuted by the next piece of genomic data. Data are flowing now so rapidly that we can afford to be naive empiricists.

    For example, our comparisons quickly refute the hypothesis that Neandertal similarity comes only from ancient population structure in Africa. That hypothesis predicts much more heterogeneity within Africans in Neandertal similarity than exists today. We've shown that the heterogeneity in Africans is basically the same as within Europeans or Asians, and that the variance among African populations so far is quite small. Those are very simple observations, which are consistent with what Yang and colleagues [2] concluded on the basis of the frequency spectrum of Neandertal alleles in large samples of living people. Even though many Neandertal-shared SNP alleles came from incomplete lineage sorting, the signature of excess Neandertal sharing outside Africa must come mostly from recent introgression. In Ewen Callaway's article about this research, David Reich dismissed the new paper by Eriksson and Manica as "obsolete". I agree. The paper describes a model without carrying out any new empirical comparisons, and so has fallen behind where the science has gone.

    Another example is the proportion of Neandertal ancestry. Initially, the proportion of ancestry from Neandertals in living people was argued to be between 1 and 4 percent [3]. That was a model-based estimate that was the best possible under the assumption that Africans have no Neandertal ancestry. We now have a lot more human comparisons, which would make possible a more precise estimate of the mean. I hesitate to provide a new estimate, because we have shown that some Africans have substantial evidence of Neandertal similarity, which throws the baseline for any estimate into question. How much Neandertal ancestry is present in living people must depend on a more complex model of mixture among later populations. The result will still be small (probably less than 6 percent) but understanding this proportion will help us to evaluate when and where Neandertal genes flowed into our populations.

    Here's a third example. I haven't written about here yet, but I have been lecturing about it quite widely over the past few months. Earlier this year, the genome of Ötzi the Tyrolean Iceman was reported by Andreas Keller and colleagues [4]. Aaron Sams and I downloaded the data and have been carrying out several different kinds of comparisons. A picture:

    Otzi 1000 Genomes Neandertal comparison

    I'd like to see the model of African population structure that could explain this result...

    If you'll remember my earlier posts on the 1000 Genomes Project samples, this chart is a histogram of the number of shared Neandertal derived SNP alleles in different samples. The European and Asian samples are substantially greater than either African sample (here, Luhya and Yoruba colored differently). If we took as a baseline that Europeans have an average of 3.5 percent Neandertal, Ötzi would have around 5.5 percent (again, the actual percentage would be highly model-dependent). He has substantially greater sharing with Neandertals than any other recent person we have ever examined.

    You can imagine, we have carried out just about every comparison we can think that could explain this result as anything other than greater Neandertal ancestry. Aaron and I will be putting our manuscript on the arXiv as soon as we've both signed off on all the text and figures, hopefully this week. This is simple stuff, and I see no reason not to be open about it -- anybody with the Ötzi data can immediately do the same thing.

    We think that showing and sharing these comparisons will save people a lot of useless effort. Personally, I can't believe that these people spending effort on population models for Neandertals aren't talking to those of us who have already carried out these comparisons and have already presented them in public. I guess we'll find out if secrecy or openness leads to better science.

    Meanwhile, I can share the abstract of the conference paper I'll be presenting in September at the meeting of the European Society of Human Evolution in Bordeaux:

    Evaluating recent evolution, migration and Neandertal ancestry in the Tyrolean Iceman

    Paleogenetic evidence from Neandertals, the Neolithic and other eras has the potential to transform our knowledge of human population dynamics. Previous work has established the level of contribution of Neandertals to living human populations. Here, I consider data from the Tyrolean Iceman. The genome of this Neolithic-era individual shows a substantially higher degree of Ne- andertal ancestry than living Europeans. This comparison suggests that early Upper Paleolithic Europeans may have mixed with Neandertals to a greater degree than other modern human populations. I also use this genome to evaluate the pattern of selection in post-Neolithic Europeans. In large part, the evidence of selection from living people’s genetic data is confirmed by this specimen, but in some cases selection may be disproved by the Iceman’s genotypes. Neolithic-living human comparisons provide information about migration and diffusion of genes into Europe. I compare these data to the situation within Neandertals, and the transition of Neandertals to Upper Paleolithic populations – three demographic transitions in Europe that generated strong genetic disequi- libria in successive populations.

    References

    1. Eriksson A, Manica A. Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins. Proceedings of the National Academy of Sciences. 2012.
    2. Yang MA, Malaspinas A-S, Durand EY, Slatkin M. Ancient structure in Africa unlikely to explain Neanderthal and non-African genetic similarity. Molecular biology and evolution. 2012.
    3. Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, et al. A Draft Sequence of the Neandertal Genome. Science [Internet]. 2010;328:710–722. Available from: http://dx.doi.org/10.1126/science.1188021
    4. Keller A, Graefen A, Ball M, Matzas M, Boisguerin V, Maixner F, Leidinger P, Backes C, Khairat R, Forster M, et al. New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing. Nature communications. 2012;3:698.
    Tags: 
    Neandertal DNA
    Otzi
    ancient DNA
    Neolithic
    Europe
    introgression
    gene flow
    population structure
    modeling
    metascience

  • Spurring the growth of cities

    Fri, 2012-02-17 11:34 -- John Hawks

    Science this week has a news feature by Andrew Lawler on excavations in southern Mesopotamia looking into what may be the earliest urban developments: "Uncovering Civilization's Roots" (paywall).

    The riddle confronting University of Warsaw scientist Bielinski is part of an ambitious attempt to explain how humans made the momentous leap from village life to urban sprawl. That transformation first happened in Mesopotamia sometime during the 4th millennium B.C.E. in what archaeologists call the Uruk phase, named after a southern Iraq metropolis some 300 kilometers north of Bahra. But recent excavations in Kuwait, Syria, Iran, and Saudi Arabia provide mounting evidence that the origin of the urban revolution is to be found in the prior era, called the Ubaid, which began around 5500 B.C.E and lasted until about 4000 B.C.E. (see timeline, p. 792). Piecing together how and where that mysterious culture began, spread, and evolved “is a particularly hot topic right now,” says Harvard University archaeologist Jason Ur. Adds University of Chicago archaeologist Gil Stein: “This is the earliest complex society in the world. If you want to understand the roots of the urban revolution, you have to look at the Ubaid.”

    There is much discussion in the article about migration versus in situ cultural intensification as triggers for urbanization. I think today it is misleading to present these mechanisms as opposed to each other. Interactions among populations were likely necessary for intensification of settlements, at the same time we know from genetics that large-scale migrations were happening in early agricultural populations.

    It will be fruitful to consider how migration both introduces external change into a society but also how it spurs internal changes. I don't think that early civilizations are unique in this regard and so we should turn to a diversity of models to understand the dynamics.

    Tags: 
    social dynamics
    urbanization
    Mesopotamia
    Neolithic
    agriculture
    cities

  • Denisovan DNA in the islands, and an Australian genome

    Thu, 2011-09-22 18:09 -- John Hawks

    David Reich and colleagues today report on the persistence of Denisova-like ancestry in island Southeast Asia and Australia (citation not yet available). Meanwhile, Morten Rasmussen and colleagues (citation not yet available) report on the whole-genome sequencing of hair from an Aboriginal Australian who lived some 100 years ago.

    The most obvious story: These data utterly destroy the hypothesis of a single out-of-Africa colonization of Southeast Asia by modern humans. Many human geneticists have argued our present pattern of diversity originated in a wave of successive founder effects coming from a single recent African origin. They were wrong.

    Instead, we can turn to a complex model with successive dispersals and episodes of population mixture. This is not a static model of isolation-by-distance; it is a dynamic model in which populations grow and spread across large spans of the Old World, again and again and again. By my count, at least three massive episodes of population dispersal and mixture are necessary in Reich and colleagues' model. A picture of their admixture hypothesis:

    Denisova admixture model from Reich et al. 2011

    This model depicts (a) an early divergence of an African (represented by Yoruba) and Asian/Australasian populations. These mix with first Neandertals and then (for the Australian/New Guinea/Mamanwa populations) with Denisova-like people. Later (b), after the initial habitation of the Philippines by the ancestors of Mamanwa, a population like Andamanese Onge pushes into the islands, mixing with the ancestors of New Guinea and Australian populations. Later still (c), a population ancestral to today's Chinese people mixes with Philippines and other Southeast Asian people.

    As complicated as it looks, even this model must be a vast oversimplification. I don't like or attribute much belief to mixture models like this, as they assume too much about relative population sizes and the timing of mixture. Many recent hunting and gathering populations of Southeast Asia are not included in the current samples, and the Chinese sample is itself the result of very recent demographic events, covering what once may have been a wider diversity of peoples. Depicting Australian and New Guinean populations as monolithic is an artifact of the small sample; these places themselves housed a tremendous diversity of peoples. Nevertheless, the true model won't be simpler than this one; it will involve many more events that the data cannot yet resolve.

    Hints of that complexity emerge from the Aboriginal Australian whole genome. Rasmussen and colleagues show that this individual shares some ancestry with East Asian peoples, but on the whole populations in Europe and East Asia are much more genetically similar to each other than to this genome. The picture from the whole genome is essentially the same as that drawn by the SNP comparisons by Reich and colleagues, but with the potential (in the long run) to actually trace the histories of individual genes. And I think the gene-by-gene account of history will be important, because we already have some evidence that a few Denisovan genes do persist in mainland Asia, even though most are gone.

    To explain why, we can look at the proportion of Denisovan ancestry in different populations as depicted in a map by Reich and colleagues. The pie charts are confusing here, because they report the fraction of ancestry from Denisovans in each population relative to the 5% estimate for New Guinea. So Australians also have 5% in this figure, Timorese have around 2.5%, and Bougainville has more than 4%.

    Notice the apparent lack of Denisovan ancestry in anyone who lives anywhere that was once connected by land with mainland Asia. I say "apparent" deliberately: Abi-Rached and colleagues reported last month on the widespread distribution of Denisovan HLA types among today's Asian populations, and those may well be products of Denisovan genes that were later selected. I've already identified a handful of other loci that seem to reflect Denisovan ancestry in mainland Asian people. According to the comparisons by Reich and colleagues, such loci must be exceptions.

    At the same time, the mixture model presents an important idea: Once there were people in Southeast Asia who had much more Denisovan ancestry than any populations still remaining today. Both Australian/New Guinea populations and Philippine populations like the Mamanwa have subsequently mixed with new immigrants who lacked any sign of Denisovan ancestry. Prior to this later mixture, the ancestors of those populations must have been more Denisovan -- Reich and colleagues estimate 7%. This is the first evidence that ancestry from archaic people of Eurasia was diluted to a lower value by later population movements. If the population mixture originally happened somewhere in mainland Asia, any traces of Denisovan ancestry in those areas has been diluted almost to nonexistence. But the persistence of some genes would be predicted if natural selection were maintaining them in the face of demographic pressure from elsewhere.

    About the Australian genome, there will be much more interesting analyses to come, I expect. As whole-genome data come to represent more of the variation within human populations, we get a larger store of information about how we came to be variable. Variation traces not only to population movements and demography, but also to natural selection. Australia's population history has been very different from many populations of the Old World, and this genome should give us new perspective on the effects of that demographic history.

    Tags: 
    Australia
    Denisova
    New Guinea
    Philippines
    Asia
    East Asia
    China
    gene flow
    population expansion
    founder effect
    introgression
    Neolithic
    migrations
    Synopsis: 
    The hypothesis of a single out-of-Africa dispersal is rejected by new data about Denisovan mixture and whole-genome sequencing of an Aboriginal Australian.

  • Neolithic discontinuity in Hungary

    Thu, 2011-09-22 16:53 -- John Hawks

    Dienekes comments on a new paper finding another strange mixture of haplotypes in Neolithic-era sample of mtDNA from central Europe ("Unexpected ancient mtDNA from Neolithic Hungary").

    I don't think even a science fiction writer could have predicted the kinds of ancient DNA results we are getting from Europe. We have genetic discontinuity between Paleolithic and Neolithic, and between Neolithic and present, and, apparently, discontinuity between Neolithic cultures themselves, and wholly unexpected links to East Asia all the way to Central Europe.

    The paper is by Zsuzsanna Guba and colleagues [1]. The final phrase of the abstract:

    Our investigation is the first to study mutations form Neolithic of Hungary, resulting in an outcome of Far Eastern haplogroups in the Carpathian Basin. It is worth further investigation as a non-descendant theory, instead of a continuous population history, supporting genetic gaps between ancient and recent human populations.

    Past populations had incredible dynamism across Eurasia. Of course, as shown later, we need not maintain that the haplogroups presently common in East Asia have necessarily been there all that long.

    References

    1. Guba Z, Hadadi É, Major Á, Furka T, Juhász E, Koós J, Nagy K, Zeke T. HVS-I polymorphism screening of ancient human mitochondrial DNA provides evidence for N9a discontinuity and East Asian haplogroups in the Neolithic Hungary. Journal of Human Genetics. 2011.
    Tags: 
    Neolithic
    Europe
    population dynamics
    Hungary
    migration
    mtDNA migrations

  • Y chronology awry

    Wed, 2011-08-24 09:57 -- John Hawks

    Dienekes links to and discusses a current paper by George Busby and colleagues [1] on the Y chromosome chronology for the settlement of Europe: "Back to the drawing board for R-M269 (Busby et al. 2011)." The main idea is that microsatellite loci on the Y chromosome have made up the majority of our information about biogeography using this marker, but the rate of mutational changes of these loci has been badly misapplied:

    A bad clock is not useless: it gives you some information about time. Moreover, you can often use several to iron out the inaccuracy of any single one of them.

    Unfortunately, better estimation through averaging of bad estimators works only in one case: when the estimators are unbiased.

    The inclusion of some fast-mutating STR loci tends to make all estimates too young. The paper finds that this problem is general, affecting most commonly-used datasets.

    Our analysis confirms that this phenomenon is not specific to the R-M269 haplogroup nor to methods using ASD. Figure 4b shows that STRs with high D produce larger estimates of T. What is clear is that estimates of T implicitly depend on the STRs that are selected to make this inference. Using BATWING on an HGDP population for which 65 Y-STRs are available, we have shown that the median estimate of TMRCA can differ by over five times when STRs are selected on the basis of the expected duration of linearity (electronic supplementary material, figure S4). While researchers take into account STR mutation rates when estimating divergence time with ASD, commonly used STRs do not have the specific attributes that allow linearity to be assumed further into the past. The majority of haplogroup dates based on such sets of STRs may therefore have been systematically underestimated.

    One weakness of the study is that its reliance on geographic patterns of the haplotypes depends on the assumption that they have evolved neutrally relative to each other. Selection might radically affect this pattern.

    References

    1. Busby GBJ, Brisighelli F, Sanchez-Diz P, Ramos-Luis E, Martinez-Cadenas C, Thomas MG, Bradley DG, Gusmao L, Winney B, Bodmer W, et al. The peopling of Europe and the cautionary tale of Y chromosome lineage R-M269. Proceedings of the Royal Society B: Biological Sciences. 2011.
    Tags: 
    Y chromosome
    Neolithic
    Europe
    migration
    dispersal
    population structure
    recent

  • Agriculture, population expansion and mtDNA variation

    Mon, 2011-05-23 11:50 -- John Hawks

    Earlier this spring, I wrote about a paper by Brenna Henn and colleagues that presented new data on SNP variation in recent African hunter-gatherer populations [1] ("Population structure within Africa: has 'modern human origins' become a non sequitur?").

    Another paper that came out this spring from the same research group is also very interesting. Christopher Gignoux, Henn and Joanna Mountain [2] examined the evidence for Holocene population growth in Europe, Africa and Southeast Asia, from within-haplogroup variability of mtDNA haplogroups. The idea is that earlier samples were not finely resolved enough to examine events of the last few thousand years, either because they included only small sequences (e.g., control region) with limited variation, or because they included whole mtDNA genomes with too few individuals to look at within-haplogroup coalescents. So here they add more individuals. It is still a small number (425 total) and so I expect that we will see better ones in the next few years.

    The results are nonetheless useful because they provide some nice matches for the archaeology of early agriculture. For example, in Africa:

    We find two periods of population expansion within our sample of lineages originating during the Holocene in western Africa. Although the majority of coalescent events occur during the Holocene, a number of lineages from this sample also coalesce during the Upper Paleolithic. The earliest growth begins at ≈38,000 ya (CI: 33,500–45,000 ya) (Table 1 and Fig. S1) and the second period begins at ≈4,600 ya (CI: 3,000–10,000 ya) (Table 1 and Fig. 1B). The correspondence between the timing of genetic evidence for a sharp increase in population size at 4,600 ya in our Holocene sample of sub-Saharan Africans and the archaeological evidence for origins of agriculture in western Africa is quite close (Fig. 1B and Table 1). In contrast, our southern African Upper Paleolithic sample representative of hunter-gatherers shows no growth over the past 20,000 y. We suggest Bantu-speaking farmers and other pastoralist groups migrated throughout southern Africa 2,000 ya (27) without impacting southern African mtDNA lineages (Fig. 1B).

    We can't really understand the pattern of genetic variation within Africa without understanding when the population grew. In Africa, Middle Stone Age genetic variation must have been more extensive than that in other regions of the world. But the survival of that MSA variation to the present day depends on the demography of populations over the past 50,000 years. In a growing population, fewer lineages will be lost by random genetic drift. So if Gignoux, Henn and Mountain are right about the growth of West African populations by 35,000 years ago, we might expect that region to preserve some extensive variation from MSA times. That might explain why that population preserves very deep Y chromosome lineages [3]. Regarding only mtDNA, one might conclude that a historical paucity of migration between hunter-gatherer and agricultural groups would be the most important reason why MSA variation remains in the present-day African population. This has been the explanation for survival of deep mtDNA lineages in southern Africa, for example. The Y chromosome result and the current paper remind us that population growth can also preserve variation from earlier time periods.

    I think this proposal of African population history matches very well the model that we assumed in our acceleration paper [4], which we based on the archaeological record. We suggested early population growth in Africa by 35,000 years ago followed by an agricultural expansion after 5000 years ago. The evidence for relatively late agricultural intensification, within the last 4000-5000 years in sub-Saharan Africa, is very clear archaeologically. Less clear: How big was the earlier, pre-agricultural human population? The LSA might correspond to a demographic intensification, generally after 45,000 years ago. Genetics has certainly seemed to support such a view, and we found it consistent with the evidence that positive selection had increased in rate much earlier in Africa than in other regions. Still, the more detailed study by Gignoux and colleagues helps to clarify this picture.

    The results also show agricultural population growth to have been late in Southeast Asia.

    Direct archaeological evidence for rice agriculture in southeastern Asia dates to only ≈4,400 ya in Thailand (28). Agriculture spread throughout Island Southeast Asia, with evidence of rice in Taiwan again dating to ≈4,400 ya. Our Southeastern Asian Holocene population size curve indicates expansion beginning ≈4,700 ya (CI: 3,000–5,700 ya) (Fig. 1C and Table 1).

    Again, useful. I think we need to exert some effort making sure that the initial dispersal of people into South/Southeast Asia can be differentiated from the post-agricultural history. But assuming that Gignoux and colleagues are correct, it makes sense in an overall picture of slowly adapting early crops to tropical climate regimes, or replacing early domesticates with different ones in those areas.

    I am less sanguine about their results for Europe. They show a gradual period of growth associated in time with the Younger Dryas (around 12,000 years ago), which could make sense in the archaeology. But I am not convinced that the "European" haplogroups here are really European to that time depth. We know that the Neolithic and post-Neolithic saw some large-scale shifts in the frequencies of mtDNA haplogroups in Central and Western Europe. Some Upper Paleolithic Europeans probably contributed mtDNA to this later population, but I have no confidence that the proportion was great enough to accurately infer the demography of that pre-Neolithic population. (This is also a problem with the current paper in Current Anthropology by Peter Rowley-Conwy. I'll discuss this sometime soon.)

    The next frontier in reconstructing the population history of Europe will be ancient DNA. A good sample of Neolithic and pre-Neolithic whole mtDNA genomes would settle this question and allow inferences about the kind of demographic recovery Europe underwent after the Last Glacial Maximum.

    An open question is to what extent the other populations have similar problems. The European population of today reflects West Asian population dynamics 10,000 years ago. The East African population today reflects West African population dynamics from before the Bantu expansion, possibly to a similar extent. The population of Southeast Asia reflects the population dynamics of early rice agriculturalists in South China. And so on.

    Adding large-scale migration and partial population replacement to this kind of demographic analysis is not easy, but it will be essential if we want a better picture of how agriculture affected human populations. Considering these problems, I think it's easy to see why I started working on Holocene population dynamics. Evidence about Late Pleistocene populations, like MSA Africans and Neandertals, still lies within our genomes. But we see it through a lens. Holocene population dynamics -- movements and population growth -- distort that lens. If we don't account for those Holocene dynamics, we will conclude wrongly about the earlier dynamics.

    I like this a lot, because this is what anthropology is really good for. We can bring a lot of archaeological and historical knowledge to bear on the question of post-agricultural population dynamics. But it's a deep, deep field with a lot of specialized literature.

    References

    1. Henn BM, Gignoux CR, Jobin M, Granka JM, Macpherson JM, Kidd JM, Rodr\'ıguez-Botigué L, Ramachandran S, Hon L, Brisbin A, et al. Hunter-gatherer genomic diversity suggests a southern African origin for modern humans. Proceedings of the National Academy of Sciences [Internet]. 2011;108:5154–5162. Available from: http://dx.doi.org/10.1073/pnas.1017511108
    2. Gignoux CR, Henn BM, Mountain JL. Rapid, global demographic expansions after the origins of agriculture. Proceedings of the National Academy of Sciences [Internet]. 2011;108:6044–6049. Available from: http://dx.doi.org/10.1073/pnas.0914274108
    3. Cruciani F, Trombetta B, Massaia A, Destro-Bisol G, Sellitto D, Scozzari R. A Revised Root for the Human Y Chromosomal Phylogenetic Tree: The Origin of Patrilineal Diversity in Africa. American journal of human genetics [Internet]. 2011. Available from: http://dx.doi.org/10.1016/j.ajhg.2011.05.002
    4. Hawks J, Wang ET, Cochran G, Harpending HC, Moyzis RK. Recent acceleration of human adaptive evolution. Proceedings of the National Academy of Sciences, U. S. A. [Internet]. 2007;104:20753–20758. Available from: http://dx.doi.org/10.1073/pnas.0707650104
    Tags: 
    mtDNA migrations
    population growth
    agriculture
    demography
    mtDNA
    Neolithic
    Africa
    population structure
    Asia
    Europe
    Synopsis: 
    A study of mtDNA variation attempts to find the times and magnitudes of population expansions in early agriculturalists.

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Neandertals

For years, I've worked on their bones. Now I'm working on their genes. Read more about the science studying these ancient people.

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