john hawks weblog

paleoanthropology, genetics and evolution

Colin Renfrew

  • 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

    Synopsis: 
    A new paper places the origin of Indo-European in Anatolia, but the story may be more complex.
  • Genes and archaeology

    Tue, 2010-02-23 21:33 -- John Hawks

    Current Biology has released a special issue titled "Global genetic history of Homo sapiens". There is much of interest in this issue, with seven papers, mostly regionally focused in different parts of the world, but one paper by Jonathan Pritchard and colleagues discussing recent adaptive evolution.

    The geneticists to varying extents in this volume depend on archaeological observations, but in many cases read the archaeology very selectively. Speaking as someone who takes archaeology seriously, I find this very frustrating. With more genetic data, we need to demand

    An editorial by archaeologist Colin Renfrew leads off the special issue ("Archaeogenetics -- towards a 'new synthesis'?").

    Today, we have an abundance of data about the genetic variation of living people that we did not have ten years ago. In addition to our samples from living populations, we are beginning to find a trove of information about ancient people, from DNA extracted directly from skeletal material. But despite the attempts of geneticists and (rather pitifully few) archaeologists, I don't see a "new synthesis" emerging.

    Reading the first paragraph of his editorial, it seems to me that Colin Renfrew agrees:

    It seems a timely moment to review human population history of the five continents as it emerges from recent archaeogenetic studies, as summarised in the reviews of this special issue of Current Biology. Has the ‘new synthesis’ — between genetics, archaeology and linguistics — arrived which I, perhaps incautiously, heralded a few years ago [1]? These highly informative reviews document, it seems to me, both achievement and uncertainty: the achievement relates to the remarkably consistent picture which has now emerged about the out-of-Africa emergence of our own species Homo sapiens and the initial peopling of the Earth. The uncertainty involves the application of archaeogenetics to the more recent, Holocene period, when most of the planet was already peopled — except much of Oceania — and sedentary, farming-based communities emerged. Here, it appears that much of our current understanding still depends on archaeological or, sometimes, linguistic evidence. And, with a few exceptions, the archaeogenetic evidence has not yet been assimilated into a genuine synthesis; but, let us begin with the good news.

    I find it a markedly bad sign that Renfrew thinks the best of "archaeogenetics" is the part with the least archaeological evidence. If the genetics doesn't seem to work where there is abundant archaeology, why should we believe the genetics in cases where the archaeology is poor?

    I write that quite seriously, as someone engaged directly with the genetics. It's too easy to make stuff up. How can you test a hypothesis that seems consistent with genetic data? The obvious approach is to try to falsify the hypothesis with archaeological observations -- but sadly, archaeology is often pitifully silent on the subject of demography and gene flow, or there are many scenarios equally consistent with the same archaeological record.

    In the Holocene, archaeology has a lot of power to rule out hypotheses about demography and population movement. So this is where I want to see serious attempts to falsify archaeological models using genetics. And that's what we're starting to get! The finding from ancient DNA that early European farmers were neither closely related to earlier hunter-gatherers nor to later agriculturalists has been very surprising. It seems to reject the hypothesis that today's gene distributions come from an initial dispersal of farmers with their Indo-European languages -- the European component of the so-called "language-farming hypothesis".

    Why? Well, because a later massive genetic change suggests that the language transition may well have happened a lot later (as suggested by much of the linguistic evidence itself), and the mtDNA haplotypes carried by the early European farmers have no clear relationship to Near Eastern or central Asian populations.

    It's no surprise that Colin Renfrew would find disagreements with this genetic work; he's the biggest supporter of the "language-farming hypothesis".

    But I think that the current situation is very healthy. Geneticists are testing hypotheses and showing them to be false. At the same time, they're proposing models that archaeology can easily show to be false. For example, many recent evaluations of adaptive evolution have looked for genetic outliers against a "neutral" population model that involves very small Holocene population size. From the genetic perspective, this small population size assumption is conservative -- it means that some genuine cases of adaptive evolution will look less statistically significant. But archaeology can actually inform us about these cases. Any scenario in which the Holocene population was smaller than millions of individuals must be false. In many cases, a less conservative model is in order.

    I think there are tremendous opportunities for integrating adaptive evolution remains to be integrated with our understanding of demography. I don't put a lot of faith in the current storyline about genetics and the earlier part of prehistory. That story will continue to develop as we deepen our understanding of the demographic and adaptive factors that have shaped human genetic variation within the last 50,000 years.

    References:

    Renfrew C. 2010. Archaeogenetics -- towards a 'New Synthesis'? Curr Biol 20:R162-R165. doi:10.1016/j.cub.2009.11.056

  • Colin Renfrew on recent human evolution

    Wed, 2009-03-25 21:41 -- John Hawks

    Colin Renfrew is an archaeologist, in recent years well-known for his work on Neolithic Europeans and Indo-European origins. Last week, someone pointed me to his recent book, Prehistory: The Making of the Human Mind. I read a short review somewhere, but I've lost the link!

    The book was first published in 2007, so its writing would have predated the publication of recent scans of the genome for selection. Renfrew of course has his own distinctive point of view, and he is not himself a geneticist. However, he has worked to integrate his work with genetic insights, interacts closely with many geneticists, and even coined the term, archaeogenetics, to describe a certain kind of gene-driven investigation of population history. So he's no neophyte when it comes to how geneticists describe the evolution of recent human populations.

    A number of passages of the book are very interesting, from the perspective of the conventional wisdom about recent human evolution. I wanted to cite these paragraphs from page 92:

    The genetic composition of living humans at birth (the human genotype) is closely similar from individual to individual today. That was an underlying assumption of the Human Genome Project and it is being further researched in studies of human genetic diversity. We are all truly born much the same. Moreover a child born today, in the twenty-first century of the Common Era, would be very little different in its DNA -- i.e., in the genotype, and hence in innate capacities -- from one born 60,000 years ago.

    Then on page 93, after some additional discussion of Neandertal genetic results:

    The implication here must be that the changes in human behaviour and life that have taken place since that time [between 60,000 and 100,000 years ago], and all the behavoural diversity that has emerged -- sedentism, cities, writing, warfare -- are not in any way determined by the very limited genetic changes which, as we understand the matter, distinguish us from our ancestors of 60,000 years ago. So the differences in human behaviour that we see now, when contrasted with the more limited range of behaviours then, are not to be explained by any inherent or emerging genetic differences. Modern molecular genetics suggests that, apart from the normal distribution range present in all populations in matters such as IQ, all humans are born equal.

    This represents a widespread point of view, one with a long pedigree in archaeology and human genetics (refer also to my post on Ashley Montagu). Renfrew quite clearly claimed that human evolution stopped once humans became "modern". He emphasizes this point as the basis of a "paradox" -- the observation that no large anatomical changes correlate with the increase in archaeological complexity of the last 30,000 years.

    I believe there is no paradox: rapid archaeological change certainly is no proof of evolutionary stasis!

Subscribe to Colin Renfrew

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.

Denisova

From a finger bone of an ancient human came the record of a completely unexpected population. My lab is working on the science of the Denisova genome.

Acceleration

The advent of agriculture caused natural selection to speed up greatly in humans. We're uncovering some of the ways that populations have rapidly changed during the last 10,000 years.

Malapa

Just outside Johannesburg, the Malapa site is producing some of the most exciting finds in human evolution. This site is the headquarters of the Malapa Soft Tissue Project.