john hawks weblog

paleoanthropology, genetics and evolution

hybridization

  • No Neandertal safe sex

    Wed, 2011-09-14 09:39 -- John Hawks

    Laurent Excoffier and colleagues' work has investigated how range expansions may have affected human genetic diversity. I've commented on this work several times ("One model, hold the extra parameters", "The Neandertal mtDNA story, 2004 edition, "Surfing and recent selection). They have applied a "geographically explicit" model to questions of human population history, modeling how populations expand and interact in the face of a simulated model of the Old World.

    In the past, I've found some things I like in this work, and other points where I disagree with the models' assumptions. Personally, I like to examine analytical models first, because the assumptions are often much more explicit, so we can see more easily how the results follow from them.

    This week, a new paper by Mathias Currat and Excoffier in PNAS claims to find evidence for some degree of reproductive incompatibility between Neandertals and modern humans. This is another case where I think the approach is very clever but I disagree with the model's assumptions. I just don't believe that today's distribution of genetic variation can tell us about "reproductive incompatibility" with Neandertals or other archaic people.

    Today, if you take a large random sample of people within the continental U.S. and look for a DNA legacy from Precolumbian American people, you will find it in your sample at a level somewhat under 2 percent. This percentage results from the differential growth of European and African-derived peoples during the last 500 years of American history. Whatever else it may be, the current percentage is notevidence for hybrid incompatibility of the world's populations before 500 years ago.

    It's not a perfect analogy. Today, Native American ancestry is heterogeneous in the continental U.S., with some people carrying very high fractions. After 30,000 years, such heterogeneity would likely have balanced out. With the Neandertals, we are looking at a much longer history, and different events.

    I would contend that the events that have affected today's representation of Neandertal-derived genes were demographically larger than those leading to the European colonization of the Americas. The contraction of the European population during the Last Glacial Maximum, the subsequent movements of Late Upper Paleolithic and settlement of Mesolithic peoples, followed by the introduction of agriculture and waves of population growth and invasions, have partially erased the genetic patterns of the initial Upper Paleolithic. We know that the mtDNA complement of Europe changed markedly both before and after the Neolithic. Today's Europeans are not the people who encountered the Neandertals 35,000 years ago. The genes of those initial Upper Paleolithic people may be almost as rare today as Neandertal genes.

    Range expansions and surfing

    Nevertheless, I think the analysis in this paper gives us some valuable information about how populations may have interacted at that final stage of population mixture among archaic populations.

    A range expansion occurs when a population that is initially limited to some small area begins to expand outward across a larger area. The expansion may include interbreeding with other populations who already occupy those areas, for example, the movement of Neolithic agriculturalists into Europe. Or the range expansion may go into territory where nobody lives, like the initial habitation of the Americas some 14,000 years ago.

    Range expansions can distort allele frequencies beyond the pattern expected in a random-mating population. As the population pushes its boundary outward, individuals at the frontier carry with them a slightly skewed sample of the alleles in the population as a whole. Pushing further and further along, this skewed sample gives rise to a founder effect. This phenomenon has been called "allele surfing", by analogy with a spreading wave of population expansion.

    When a population expands its range into that of another population, the invaders usually mate with the natives. As the "wave" of migration continues to spread, more and more of the natives' genes are picked up into the expanding population. As a result, you expect to see a gradient of genetic contribution from the original native population, higher and higher as you look farther from the invaders' point of origin.

    Currat and Excoffier [1] assume that a group of 50 people originated in Northeast Africa 50,000 years ago and then began to spread throughout the Old World. This population (moderns) expands into the range of another human population (Neandertals) by virtue of a higher carrying capacity: in fact they assume that modern humans existed at four times the density of Neandertal populations. The modern human value is set at 1 person per 10 square kilometers, which is very low compared to ethnographically described hunter-gatherers. The population as a whole is made up of demes that occupy an area 100 km on a side (in some trials, four times as many demes 50 km on a side). The outcome is inevitable: the higher carrying capacity leads modern humans to replace Neandertals, while incorporating some amount of Neandertal ancestry.

    Any model is unrealistic to some extent. An unrealistic model generally leads to results that are very different from reality. In modeling, there's a common strategy to deal with this problem: Leave one free parameter and change it until the results fit reality. In this case, the free parameter is migration rate, the probability that an individual will move to an adjoining deme. Currat and Excoffier used values for this parameter that caused their "modern" population to displace Neandertals in Europe over a span of 6000 years. The value that made this dispersal speed was 20 percent per generation for the dispersing modern human population.

    I'm a little concerned that a whole literature of geographically explicit population models has emerged in human genetics without any apparent reference to the anthropological literature on human demography. If you know ethnography, a migration rate of 20 percent per generation over 100 km distances seems very high. It's more than double the observed rate of intertribe marriages among precontact Aboriginal Australian people, for example. The value of one person per 10 square kilometers for population density is near the low end ever observed for hunter-gatherers. If it's a stretch to make a model fit with parameters found in known hunter-gatherers, that's when I go back to the drawing board. But then, my philosophy about this is different from most human geneticists. I'm an anthropologist.

    Anyway, with these values the result is foreordained: modern humans will replace Neandertals, and fast. What Currat and Excoffier observe in their simulated populations is that the modern humans tend to pick up a larger fraction of Neandertal genes, especially in Europe. How can we explain why our population today has a relatively small fraction of Neandertal genes? In particular, how can we explain why Europeans have no more Neandertal genes than any other population? They conclude that some kind of reproductive incompatibility must have existed.

    Where I think the method falls short

    I think this paper would be perfectly reasonable if I was willing to assume that the range expansion of modern humans was the last major event in our evolution. If this were true, then echoes of this range expansion would be the most highly visible today — just as astronomers can still find echoes of the Big Bang in the cosmic microwave background.

    But I would offer that our genetic diversity today is not the result of a single Big Bang of movement out of Africa. Many population movements of comparable or even larger scale have happened during the last 30,000 years.

    The paper presents the hypothesis of reproductive incompatibility as an attempt to solve two problems: First, Chinese, New World peoples, Southeast Asians and Europeans today have approximately the same amount of Neandertal ancestry. Second, the amount of Neandertal ancestry in Europe is only around 2-4 percent. A 6000-year wave of population growth and mixture as modern humans entered Europe might have left more Neandertal genes, and a higher proportion in this Neandertal-rich area of the world than in East Asia.

    Here's how I currently see those problems. Europeans today are not the Europeans of the past. They have undergone massive population movements and replacements since the initial Upper Paleolithic people encountered Neandertals. That's not only the result of archaeology, it's also clear from the paleogenetics. If we recognize this subsequent history, then we will find it easy to explain why the rest of the population outside Africa has basically the same small amount of Neandertal ancestry: they received a massive influx of genes from some West Asian population with Neandertal mixture. Europe also got these genes, mostly long after the initial Upper Paleolithic.

    So I don't think the present fraction of Neandertal genes tells us anything about sex between Neandertals and humans, except that it happened. Many times. Hooba-hooba.

    There is some irony in the timing of this publication, since only last week PNAS published a paper claiming that today's African populations derive some of their DNA from a population fully twice as different from non-Africans as Neandertals were.

    I don't fully believe that, either.


    References

    Synopsis: 
    A new paper claims humans and Neandertals were reproductively incompatible. I don't think so.
  • A problem of fuzzy mammoths

    Sat, 2011-06-04 03:56 -- John Hawks

    Paleogenomics is changing the way we study evolution. In a number of cases, it now allows us to study extinct organisms with the same methods as we study living ones. A study last year in PLoS Biology[1] used genetic evidence from living elephants, extinct mammoths and mastodons, to reconstruct the times that these species diverged.

    Woolly and Columbian mammoths

    Mammoths are back in the news this week because of a paper by Jacob Enk and colleagues [2]. I think this paper represents a very nice collaboration of paleontologists (Dan Fisher, Ross MacPhee) and paleogeneticists (led by Hendrik Poinar's lab). It's refreshing to read a paper that describes not only the way that the DNA was sampled but also the age and morphological attributes of the sampled mammoths. For example:

    This 60+ year old bull is exceptionally well preserved, and exhibits the classic character suite of his species, including low molar lamellar frequency (Figure S1 in Additional file 3), broadly divergent tusk alveoli, a markedly downturned mandibular symphysis, and tremendous body size. We used tusk fragments for the shotgun sequencing, and both tusk and bone samples for PCR and Sanger sequencing.

    Every genetics paper should have descriptions like that. Very nicely done.

    As an anthropologist, I pay a lot of attention to studies of elephants, because they are another long-lived social mammal, in some ways closer to us in population structure and dynamics than most primates. As in the case of hominins, some taxonomists have argued that we should recognize lots of fossil elephants, others question that distinctiveness. And just as we are discovering for hominins, the elephants are showing evidence for population mixture among groups once considered to be different species.

    Enk and colleagues sampled the mtDNA from two Columbian mammoths and one woolly mammoth from North America. The Columbian mammoth is seen by pretty much everybody as a separate species (Mammuthus columbi) from woolly mammoths (Mammuthus primigenius), and paleontologists have thought that they diverged 1-2 million years ago. Woolly mammoths were Holarctic animals, with a range that extended from Europe to North America, while Columbian mammoths were limited to the Americas south of the U.S.-Canada border, roughly. Already other researchers have recovered dozens of woolly mammoth sequences, and their phylogenetic relations are well characterized (as shown in the paper). What Enk and colleagues show is that the two Columbian mammoths both have mtDNA sequences that belong to a single, relatively young clade that is present in woolly mammoths in Alaska and Yukon.

    The simplest explanation is that the Columbian and woolly mammoths of North America were exchanging genes.

    The authors also suggest the possibility of incomplete lineage sorting (ILS) -- the retention of a single ancestral clade in two isolated species. This seems unlikely given the topology of the clade within woolly mammoths, but the authors omitted the crucial test: the date of the most recent common ancestor of the mtDNA within the clade. If it's truly younger than a million years, we might easily rule out ILS.

    Forest and savanna elephants

    A lot more information about the variation within living elephantids has appeared within the past year. Looking at them compared to the fossil species, it's pretty clear that taxonomists haven't done well matching taxonomic levels in these groups. Here is a quote from the paper by Rohland and colleagues, who considered the genetic relationships of forest and savanna elephants in Africa.

    We also find that savanna and forest elephants, which some have argued are the same species, are as or more divergent in the nuclear genome as mammoths and Asian elephants, which are considered to be distinct genera, thus resolving a long-standing debate about the appropriate taxonomic classification of the African elephants.

    Forest and savanna elephants may deserve a species rank, but we might equally say that the mammoth-Asian elephant divergence doesn't merit the genus rank it has historically been given. As reconstructed in the paper, the forest-savanna elephant and Asian elephant-mammoth divergences both fall within ranges from 2.5 to 5.5 million years. Some widely-recognized mammalian genera (e.g., Homo) are younger, but most mammalian divergences in this range of times are recognized below the genus rank. Should mammoths be put into Elephas? That would probably be a better recognition of the adaptive radiation of Eurasian elephants.

    One way to consider the question is by examining the pattern of speciation. With a large number of sampled loci, a far more detailed consideration of speciation can be achieved. This brings us back to a more careful examination of ILS.

    We find a higher rate of inferred [Incomplete Lineage Sorting (ILS)] in forest and savanna elephants than in Asian elephants and mammoths: (FE+SE)/(AL+ML) = 3.1 (P = 4×10−8 for exceeding unity; Table 2), indicating that there are more lineages where savanna and forest elephants are unrelated back to the African-Eurasian speciation than is the case for Asian elephants and mammoths (Table 2). This could reflect a history in which the savanna-forest population divergence time TFS is older than the Asian-mammoth divergence time TAM, a larger population size ancestral to the African than to the Eurasian elephants, or a long period of gene flow between two incipient taxa. (We use upper case “T” to indicate population divergence time and lower case “t” to indicate average genetic divergence time (t≥T)).

    "A long period of gene flow" would reflect a very gradual speciation event, which might argue that the two resultant species should be classified in the same genus. Or...it might suggest that the ecological differentiation actually commenced much earlier in time than the modal estimate, with later hybridization. Mammoths and Asian elephants, by contrast, seem to have a cleaner separation even though the genetic relationships are almost equally close.

    We're not quite able to test these alternatives, yet, because only a single individual has been sampled from most of these species. Testing for gene flow really will require larger samples of individuals. In particular, the longer geographic distance between Asian and mammoth samples compared to forest-savanna samples may mean that population structure is hiding within this comparison. I just find it remarkable that genetics has arrived at a point where the pattern of speciation of extinct species is within reach.

    The paper uses the extinct mammoth and mastodon comparisons as a frame for discussing the diversity and distinctiveness of African forest elephants. This is in a way unfortunate, because the mammoth-centric questions are probably more interesting to most readers. There's still a lot of productive biology to do there. But the status of forest elephants is a useful hook to hang a paper upon. Whether forest elephants should be given the status of a species has been a hot topic in proboscidean evolutionary biology during the past 10 years. Debruyne [3] gave a good historical review of the issues:

    Indeed, when discovered by Matschie in 1900, [forest elephants] were described as either a potential species, or a regional race of Cameroon (Matschie, 1900). Matschie advocated the usefulness of hydrographical basins in order to subdivide African elephants into distinct units. He thus contributed to the profusion of new taxa to be defined by the turn of the 20th century, so that the taxonomy of the African elephant quickly became extravagant, the most meagre morphological evidence being used to acknowledge a new form (Lyddeker, 1907). Up to 22 forms of Loxodonta were described that were finally assigned either to the savannah or the forest elephant—see Laursen and Bekoff (1978) for a review. Morphologists have addressed this question for decades according to their personal taxonomic perspectives. Some have considered that, although displaying a smaller size, smaller round ears—responsible for their designation as “cyclotis”—more toenail structures on both feet, thin down-pointing tusks and a flatter back and forehead, forest elephants belong to the same species—i.e., Loxodonta africana—as savannah elephants with whom they assumed were reproductively compatible (Backhaus, 1958; Carroll, 1988; Cousins, 1996). Many cases of intermediate morphology have supported this view, which had become prevalent (Laursen and Bekoff, 1978). Conversely, the “splitter” attitude led other authors to put forest elephants apart on the basis of the same anatomical distinctiveness (Frade, 1931; Frade, 1933; Allen, 1936; Petter, 1958). More doubtful morphological characters—extent of hair-covering, color of the skin, carriage of head—have been put forward to support this division.

    The problem became complicated upon recovery of genetic information. Most early phylogeography has been done using mtDNA. The deepest mtDNA clade in the African elephants defines two haplogroups, both of which are shared by the forest and savanna populations. Based on large samples of mtDNA alone, the two populations have been recently exchanging genes.

    Early analyses of nuclear microsatellites indicated the opposite pattern, with relatively little allele sharing between the two elephant varieties. I became interested in the question after a paper by Régis Debruyne (a coauthor on the current paper by Enk and colleagues as well). Debruyne emphasized the great gaps in our sampling of geographic variation in African savanna elephants. Providing some additional data, he showed a very deep mtDNA clade in many forest elephants that was also in many savanna elephants. He argued that the widespread evidence of gene flow refutes the hypothesis of different biological species of elephants.

    Rohland and colleagues also addressed the discordance between mtDNA and nuclear genetic variation.

    Our study also infers a strikingly deep population divergence time between forest and savanna elephant, supporting morphological and genetic studies that have classified forest and savanna elephants as distinct species [13],[16]–. The finding of deep nuclear divergence is important in light of findings from mtDNA, which indicate that the F-haplogroup is shared between some forest and savanna elephants, implying a common maternal ancestor within the last half million years [21]. The incongruent patterns between the nuclear genome and mtDNA (“cytonuclear dissociation”) have been hypothesized to be related to the matrilocal behavior of elephantids, whereby males disperse from core social groups (“herds”) but females do not [13],[38]. If forest elephant female herds experienced repeated waves of migration from dominant savanna bulls, displacing more and more of the nuclear gene pool in each wave, this could explain why today there are some savanna herds that have mtDNA that is characteristic of forest elephants but little or no trace of forest DNA in the nuclear genome [13],[14],[39],[40].

    The scenario may fit with the facts. It was proposed first by Roca and colleagues [4], who proposed it as a "genomic record of ancient habitat changes", which had brought the forest and savanna populations into contact across shifting hybrid zones. They reiterated the hypothesis in a later paper [5] supported with larger samples.

    Further progress will require larger samples and better models. I was interested in Debruyn's account of the geographic holes in genetic sampling across the African range of forest elephants. A highly-resolved test of recent gene flow demands finding and sampling potential contact zones between two populations. Some hypotheses can be tested surprisingly strongly using only a single individual from each population. But the power of such tests depends on the pattern of inbreeding in the past. We can imagine that the ancestry of a single individual stretches through the genealogical network of a species like a cone, widening into the past. Recent events are poorly tested by single individuals.

    If geographic structure is strong enough, distant populations will approximate different species in their recent genealogical connections. So the single individuals in the more recent study by Rohland and colleagues [1] carry a lot of weight.

    There are many parallels here between hominin population dynamics and the elephants. Also, as I pointed out in 2006, the elephant situation helps to clarify how we should consider genetic samples from living great apes.

    The past year has seen a real reversal in the race between data and analysis. For a long time, sequencing has been a bottleneck in serious analysis of population history. The genealogical connections among individuals ramify by double in every generation, so that the inheritance of a single gene reflects one possibility among countless trillions. If we can only afford to sequence a single gene, we are limited to a single sample of the genealogical links among individuals. Whole genomes give enormous samples of the genealogical history among samples. But they create their own challenges of analysis.


    References

    Synopsis: 
    Mammoth paleogenomics and African elephant population structure pose similar problems of sampling.
  • "Neandertal stimulation": Weckler and biogeography

    Sat, 2010-09-25 14:27 -- John Hawks

    I'm reviewing some old viewpoints about the relationships of Neandertals and other peoples. These include mainstream opinions that persisted over decades as well as more idiosyncratic ideas. This is mostly pre-1960 stuff for the time being.

    To the extent that old ideas are wrong it is no surprise: Science progresses by rejecting wrong ideas, and paleoanthropologists of the past lacked the luxury of today's data. To the extent that the ideas look familiar, they remind us that our current hypotheses in many instances echo ideas that were advanced fifty years ago or more.

    Weckler's model

    A bit off the mainstream was a paper published by Joseph E. Weckler [1], titled "The relationships between Neanderthal Man and Homo sapiens." Weckler was a cultural anthropologist who had done fieldwork in the American Southwest and the South Pacific [2]. He wrote only one paper on Neandertals but this received substantial attention, first published in the American Anthropologist and later revised in a simplified version for Scientific American. Weckler was very interested in the migration and dispersal of ancient populations, maybe because of his work on the ethnography of the South Pacific. He brought that perspective to the Neandertals and other ancient groups.

    Weckler saw Pleistocene human population dynamics as having been directed by glaciations and geographic barriers. In general, Weckler thought that the pre-modern population had been divided into allopatric species or subspecies. These groups would have been isolated from each other much of the time, but occasionally thrust back into contact by shifts in the climate. During glacial phases, Weckler posited that Europe and Asia north of the Caucusus-Himalaya axis would have been uninhabitable. During warmer interglacials humans moved into these northern areas, where water and mountainous barriers tended to isolate them. The overall pattern was evolutionary differentiation punctuated by occasional hybridization and cultural contact between long-separated groups.

    Weckler was not the first to propose that Neanderthal and modern lineages had been relatively isolated and later hybridized. The idea was widespread after the description of the Mount Carmel remains by McCown and Keith [3]. McCown and Keith themselves had favored a different explanation -- that the Skhul and Tabun remains represented a transient between a less specialized and more specialized (Neandertal-like) extreme. Others, including Carleton Coon [4] and Theodosius Dobzhansky [5], immediately favored the idea that the Mt. Carmel sample represented a hybrid population.

    Weckler broadened the idea of hybridization into a general theme. He supposed that we might expect recurrent contact during second (Mindel-Riss) interglacial times in Central Asia, and repeated dispersal from India into Southeast Asia throughout the Pleistocene. Thus, hybridization between divergent groups was not a one-time affair but instead was a fundamental aspect of Pleistocene human evolution.

    Interglacial population contact

    This scenario faced an obvious problem: There were essentially no data to test the hypothesis of population contact at any of these earlier times. Only the third interglacial, already treated by other authors, gave the appearance of sufficient information for a test. To illustrate the plausibility of recurrent exchanges, Weckler fleshed out a third interglacial model of population contact in some detail:

    Some of these pre-Neanderthal men wandered inland into Asia north of 40° during a period of warm climate. Part of this population may subsequently have been trapped north of the barrier in the general vicinity of Inner Mongolia or Sinkiang at the onset of the next glacial period. Primitive man caught in this area would have been unable to retreat directly southward because the great mountain mass that lay in that direction became frigid sooner than the lower lands to the north. Having lived where he was for hundreds of generations, primitive man might not have known he could escape the increasingly rigorous climate by moving east several hundred miles before turning south. Howell (1951:409) suggested that some of the physical characteristics of classic Neanderthal man may represent biological adaptation to a glacial climate. Coon stated in a letter to me (1953) that he has long been of that opinion. If this is so, I suggest the evolution occurred, not in Europe during the fourth glaciation, but in eastern Asia during an earlier one (Weckler 1954:1010).

    This is an early exposition of the idea that Neandertals repeatedly invaded the west from a homeland somewhere in central Asia or further east. Weckler discussed the idea that these populations originated in northwestern China, but he had no good examples (as indeed there are still no such examples).

    Weckler's discussion may seem confused because he accepted Zhoukoudian as an eastern "Neanderthaloid" population. His division of humanity can best be aligned along a "paleanthropic/neanthropic" distinction. Today, we might more simply state his biogeographic model as a shifting border between the paleanthropic "Neanderthaloids" and neanthropic "Homo sapiens" along a shifting Movius line somewhere in India or the Middle East, stretching to northwestern China.

    A central Asian source

    Teshik Tash bears much importance to Weckler's ideas, as it did to Movius, Howell, Weidenreich, and many others. To those unfamiliar with the site, an interesting place to start is my interview with Mica Glantz. Teshik-Tash is once again central to our ideas of Neandertal biogeography, with the addition of genetic evidence from the juvenile specimen from the site and others in Central Asia.

    In the early 1950s, Teshik-Tash raised many of the same issues that it does today. Today, of course, Teshik-Tash is far from alone, with several sites in Central Asia bearing evidence of a local Mousterian, physical remains with Neandertal-like mtDNA sequences. There was great uncertainty about the date represented by the Teshik-Tash specimen. Teshik-Tash had a classic "Western" archaeological industry (in this case, Mousterian) and therefore evidenced long-range population contact with Europe. The East Asian fossil record was known to be very different from the west, raising the question of boundaries. Where did the Western sphere of biological influence end, and the Eastern begin?

    Today Denisova Cave, embedding a highly divergent mtDNA clade in an initial Upper Paleolithic assemblage [6], presents the same issues with even greater relief.

    Probably the most common interpretation of the Central Asian "Neandertal" sites is that they represent an eastward migration from the Neandertals' center of evolution in Europe. But the opposite hypothesis is an obvious alternative: that the center of Neandertal evolution was somewhere in Central Asia, and that they invaded Europe from outside. Some may see parallels for a Neandertal invasion of Europe from outside, by looking both earlier in evolution (the first Europeans obviously came from somewhere) and later (the Upper Paleolithic, the Neolithic).

    Why posit Central Asia in particular as a source area, above and beyond the general idea of invasion? I thought the idea might have originated with Henry Fairfield Osborn because of his long interest in Central Asia as a center of human evolution. For Osborn, Central Asia was a source of humanity, but his "Dawn Man" idea supposed that the modern human form had long resided in Central Asia, with more primitive humans at the periphery. The idea that a Neandertal center of evolution existed in Asia is quite different from Osborn's idea, which was itself a sketch supported by little evidence. I'll have more on Osborn later.

    Weckler presented his idea to address a classic problem: To many paleoanthropologists, early Neandertals appeared to be more like later human than were the later, "classic" Neandertals. Howell [7] summed up this observation as follows:

    Many features of early Neanderthal morphology, both cranial and postcranial, are incipiently classic Neanderthal. However, the general morphological pattern of these early Neanderthal peoples bore a close resemblance to that of anatomically modern man, a fact which indicates again the special character of classic Neanderthal morphology (Howell 1957:332-333).

    The early Neandertals were those from the third interglacial, which during the 1950's would have included those from Krapina, Ehringsdorf, and Saccopastore. Howell's description highlights the most common hypothesis: classic Neanderthals had evolved toward greater and greater specialization over time.

    Weckler took a different approach: for him, the fourth glaciation Neandertals descended from already-specialized ancestors, who had existed in Central Asia:

    The Asiatic migrants, probably already mixed with Homo sapiens in central Asia in the Middle East, pushed on to central Europe during the third interglacial. They may have moved northwestward from Palestine or directly westward along the north face of the barrier. In the zone of contact in western Asia and eastern Europe further miscegenation and cultural exchange probably occurred. Then, when the climate deteriorated with the onset of the fourth glaciation, the bulk of the Homo sapiens population retreated south as was its wont. This left Europe open to further Neanderthal invasion and set the stage for the modern misconception that classic Neanderthals evolved rapidly (and in a curiously regressive fashion) in western Europe during Würm I. Probably all that actually happened was that additional Neanderthals of more classic type, adjusted by previous experience to life in a cold climate, kept pushing in behind the advance guard and, by weight of numbers, blotted out the neanthropic traits the earlier migrants had acquired along the way.

    Weckler proposed this scenario not long after F. Clark Howell's 1952 paper [8], in which Howell had proposed that climate isolated Neandertals within Europe during the last glaciation, leading to their increasing specialization. According to Weckler, the glaciations had not isolated Europe so much as they had wiped clean the evolutionary slate within Europe. After the last interglacial, migration from a central Asian source brought back a purer strain of Neandertal.

    Out of this welter of fact and interpretation emerge the few concepts necessary to the hypothesis supported in this paper. By the end of third glacial times Neanderthal had probably developed in eastern Asia to something approximating the classic form. His numbers had probably always been small compared to developing Homo sapiens: his range was incomparably smaller, and in part of this range he had no easy retreat from glacial conditions such as Homo sapiens enjoyed. His restricted range (and possibly his sometimes severe habitat) had militated against the racial diversification that characterized the development of Homo sapiens. In spite of his cultural advances his range and numbers were probably sharply reduced during every glacial episode he had to endure. This may be why, although he stood athwart the entrance to the New World, he never expanded his range sufficiently to explore that territory. But as the climate ameliorated after the rigors of the third glaciation, his numbers increased and he did finally expand his range. For reasons not as yet ascertained he looked westward, and the lowlands north of the barrier afforded him a route to Europe.

    Several strains of contemporary thought emerge in Weckler's formulation. Neandertals were always on the edge of extinction, being repeatedly driven to low numbers by deteriorating climate. Their tenuous existence did not allow them to disperse more broadly.

    That old Neandertal magic

    Where Weckler differed from the received view is in the way he accentuated the Neandertal positives. He wrote that the diversification of humans and Neandertals presented an opportunity to the evolution of our species. From their central Asian source, the Neandertals had acquired innovations necessary for existence in the cold north. Human colonization of these regions might be impossible without the adoption of Neandertal cultural and behavioral innovations:

    The Homo sapiens groups that retreated south from Europe and perhaps from central Asia [during the glaciation] had been touched by Neanderthal magic. They may have acquired some Neanderthal physical traits, but, more important, they had achieved a new cultural outlook. They had perhaps learned the use of fire, clothing and specialized hunting techniques, and possibly of cave dwelling -- accomplishments that freed man from dependence on a mild climate and from a grubbing existence (emphasis added).

    I find myself reading this on two levels. On the concrete, empirical side, Weckler would soon be proven wrong. Neandertals didn't invent fire; that was much older and more broadly shared by Middle and Late Pleistocene humans. They may have had better clothes for cold weather than contemporaries who lived further south, but the innovations of woven cloth, sewn garments, and shoes happened later. They certainly had specialized hunting techniques, but these were linked to a particular kind of social organization and technology. Later developments in both would have required new hunting (and gathering) methods. None of them lived in caves very often; their experience must have been fairly "grubbing" in either event.

    But on the abstract, Weckler presents a scenario where Neandertals had something of value, cultural or physical, without which later humans would have been as successful. He had already posited biological hybridization; here he suggests a kind of "cultural hybridization" as well.

    The essential idea I am suggesting is that the contact of Homo sapiens groups with "Neanderthal culture" in Asia and in Europe during the third interglacial resulted in an efflorescence of "Homo sapiens cultures" that gave rise to the Upper Paleolithic. There is general agreement, I think, that a sudden enrichment of culture is evident at the beginning of the Upper Paleolithic in Europe and that these richer and more varied cultures seem to have originated, for the most part, outside of Europe. Movius, discussing the European Upper Paleolithic (1953:171ff.), follows M. Denis Peyrony, Dorothy Garrod, and others in suggesting that different European cultures of that time may have originated in Palestine, Iran, the plains of southern Russia, and possibly Africa. All but the latter are areas where indigenous Homo sapiens was probably directly stimulated during the third interglacial by invading Neanderthal man (Weckler 1954:1016).

    So why has this idea been largely forgotten? The failure of the particulars was almost complete:

    Leakey claimed in the 1930's that Lower Aurignacian techniques of stone chipping were older in Africa than in Europe (1931:237-39; 1936:54-60, 161). Movius seems ready to dismiss Africa as a source of European Aurignacian (1953:171), but he doesn't dispose of Africa's claim to temporal priority. The sudden new competence Leakey claims for African Aurignacian cultures early in the fourth glaciation (1936:161) may have been the consequence of contact with Neanderthal. The stimulation may have come secondhand from Homo sapiens wanderers returning from Europe or may have resulted directly via diffusion or migration from the Middle East.

    He was overreaching here. He didn't overestimate the cultural sophistication of Neandertals, although he did accentuate behaviors, like fire, that would turn out to be less special than he assumed -- older than Neandertals and more broadly shared. More critically, Weckler rested his argument on the absence of evidence for cultural sophistication in the African contemporaries of the Neandertals. But Louis Leakey's earlier claims about an "African Aurignacian" also overreached, supported by a mistaken chronology. A better understanding of the Late Pleistocene African cultural sequence would emerge only later.

    When Homo sapiens had thoroughly assimilated and improved on the ideas he got from Neanderthal, he took advantage of the first interstadial of the Würm glaciation to launch forth on his initial conquest of the world. He overran Europe and pushed around the barrier into eastern Asia.... One might even hazard the guess that the reason Africa south of the Mediterranean littoral remained so backward during the Upper Paleolithic was because the Homo sapiens groups there had not had the full benefit of Neanderthal stimulation. In the new dynamics of cultural enrichment and sapiens migrations the hinterlands of Africa had become a dead end, far removed from the centers of rapid development.

    I find myself wondering about the nature of "Neanderthal stimulation"....

    This passage is worth examination. Most of the details have changed radically since 1954. We now know that MSA Africans had most of the tricks that Neandertals did, and vice-versa. Many MSA industrial innovations predate Mousterian or Middle Paleolithic occurrences. The complexity within Africa may itself represent a vastness of population history that we now can only guess at.

    Yet the development of Upper Paleolithic cultural complexity still wants some explanation. The biological innovation of "anatomical modernity" is not sufficient to explain the cultural evolution of the Late Pleistocene -- it does not match the pattern of cultural innovation in time or space.

    Bottom line

    I think there was some "Neandertal magic." Middle Pleistocene humans were more isolated than present-day populations, for a longer period of time. Less gene flow made it less likely for adaptive traits to spread beyond the population where they originated. Not impossible, just less likely. So any surge of population contact caused by migration would have been accompanied by a surge of introgression of adaptive genes. The evidence for Neandertal contribution to the later gene pool of non-Africans documents one such surge of population contact, but there may well have been others.

    Where genes are concerned, this is a simple matter of mathematics, discussed more fully by Greg Cochran and I in our 2006 paper [9]. Simply put, Neandertals and modern humans had comparable selection pressures for many aspects of their biology, similar adaptive responses, and the same time to adapt. Adaptive mutations are chance events, governed by demography and time. If the evolving African MSA population got many new adaptive mutations, Neandertals would have gotten nearly as many (possibly constrained by smaller population size). In a few cases, the same variants would occur in both populations by chance, but in most they would be different. These alleles should still be with us, as the extent of Neandertal contribution to our population was great enough to pick up almost all of them.

    But what about Neandertal cultural traits? These were the real focus of Weckler's argument, and here I think the question is very difficult to resolve today. Cultures are ephemeral. As we know from history, if we choose a beginning and end point a few hundred years apart, it can be difficult to show the continuity of cultural information even within a single place.

    With the transition from Mousterian, through Châtelperronian into Aurignacian in France and northern Spain -- a place where we have relatively dense archaeological documentation -- we are nevertheless talking about time gaps of hundreds of years. I'm skeptical that we're in a position to test the hypothesis of cultural exchanges across these time periods.

    We're in a better position to test the hypothesis of stasis. If genetic exchanges happened in the absence of culture change, that would tell us something very relevant to the relation between gene flow and demographic contact. Likewise, persistent stasis of different cultures in adjacent areas tells us something about the absence of information flow. A kind of regional stasis, over thousands of years, seems to have been the norm in MSA and Middle Paleolithic contexts, and it's not a pattern that we are well-placed to understand without a better understanding of the limits on information exchange. Some of those limits may, in these ancient populations, have been biological constraints. So I'm less confident that we will be able to understand the cultural consequences of Neandertal contact.


    References

  • Mailbag: Zorse pigmentation

    Wed, 2010-09-15 20:59 -- John Hawks

    Re: Horse-zebra hybrids

    I know you saw the picture of the zebra horse in the NYT this morning. Are we SURE that hasn't been photoshopped? I mean, I know it is the NYT, but it makes me thinkk that I don't understand ANYTHING about genetics at all!

    Yeah, apparently this particular one is unique.

    The stripes come from patterning genes that activate the melanin pathway; the pattern gradient inhibits expression of a gene that synthesizes melanin. White spots occur when a different gene is turned off, on the same pathway. So the two combine -- it's like a palomino that has stripes instead of splotches, I guess.

    I have a slide that shows a cattle-bison hybrid with similar spots, like a cow.

  • Babi yaga

    Wed, 2010-02-17 07:30 -- John Hawks

    Tetrapod Zoology writes about the mysterious babirusa:

    Despite the ancient divergence of babyrousines from other suids, a male babirusa hybridised with a female domestic pig at Copenhagen Zoo in 2006. Of the five resulting piglets, one died but the others survived. As you can see from the photo here, they look surprisingly normal.

    Timeframe of divergence not entirely clear; certainly Miocene and possibly Early Miocene. Babirusas are number 2 on my list of why we won't find hobbits on Sulawesi.

  • Mailbag: More on coywolves

    Thu, 2009-09-24 21:14 -- John Hawks

    Regarding coywolves:

    Hi John. This coy-wolf paper is the iceberg tip a a huge, complex, and controversial literature. You describe some correct aspects of it, but here are a couple of rejoinders.

    Since wolves existed around the Great Lakes "originally" and coyotes moved in from the south only after white human settlement drove the wolves back, it is probably more correct to say that the local wolves have acquired coyote genes, or at least equally correct. Many indisputably ecologically wolf individuals around the Great Lakes also have coyote mtDNA, including most (perhaps all?) of those on Isle Royale. There have also been critters called the Algonquin wolf and the Tweed wolf, believed initially and controversially to have been good species but more likely rather small wolves with rather fewer coyote genes, rather than "coy-wolves" (coyotes bulked up by wolf genes). Of course it's likely a continuum.

    Still controversial is whether all such introgression post-dates white contact.

    Several wildlife genetics labs have also had papers about this in the last year. Mike Schwartz did a good invited review of the sampling partialness of much of the evidence to date:

    Schwartz MK, Vucetich JA. Molecules and beyond: assessing the distinctness of the Great Lakes wolf. Mol Ecol. 2009 Jun;18(11):2307-9. Epub 2009 Apr 7. PubMed PMID: 19389174.

    In another life a student in my bailiwick looked for such introgression in the Rockies as a side-project to other things. The result was negative.

    I couldn't readily find a link to the original paper in the the MSNBC page. A bit frustrating.

    Ah, very interesting. Thanks! I reviewed the literature on this in 2006 but I can see that much has changed. It's such an encouraging sign that phylogeography is actually going somewhere.

  • Coywolves

    Thu, 2009-09-24 16:30 -- John Hawks

    Another case of large mammal evolution by introgressive hybridization:

    Coyote + wolf = new breed of predator

    New DNA evidence reveals that coyotes have bred with wolves in the the northeastern United States, turning mice-eating coyotes into much larger animals with a hunger for big prey, such as deer.

    The linked article describes a study by Roland Kays and others, who went looking at the mtDNA of nearly 700 museum coyotes and donated specimens, looking for wolf. When they found it, they were able to correlate skeletal measurements with wolf ancestry and trace the progress of the wolf introgression from somewhere "north of the Great Lakes".

    They hit on some essential points:

    "This is an evolutionary mechanism to generate new variation that can work faster than genetic mutation," added Kays, curator of mammals at the New York State Museum.

    If there's a niche for a more solitary canid predator, larger and more aggressive than coyotes, bringing in wolf genes may be the fastest way to get there.

    This is a dynamic system, caught in mid-transition. The coywolves have not reached any stable equilibrium distribution with coyotes, and the wolf chromosomes have not broken up within the coywolf descendants to allow the dissociation of adaptive from maladaptive wolf genes in the hybrid population. Over the long term, the wolf mtDNA might be lost entirely, if there are any negative epistases between wolf mitochondrial genes and the mostly nuclear coyote genes that interact with them. Assessment of hybridity by mtDNA is conservative (misses hybrids with paternal instead of maternal origin) and temporary (the purely maternal lineage may disappear over evolutionary time due to slightly negative epistasis).

    Other: "Adaptive introgression of coat color in wolves"

    UPDATE (2009-09-24): See also in the mailbag.

  • Independent hybridization of lager yeast

    Thu, 2008-09-18 17:44 -- John Hawks

    New Scientist reports on the parallel evolution of Budweiser and Heineken:

    Forced to produce their beer in the winter, brewers accidentally created conditions favouring the emergence of a hybrid yeast better suited to the cold. Researchers already knew that Saccharomyces pastorianus, now used to brew lager, is a hybrid produced through marriage between two yeast strains.

    One was S. cerevisiae, the "brewer's yeast" on which the brewing industry is founded because it ferments sugars into alcohol so efficiently. The other was S. bayanus, a yeast strain seldom used alone in brewing because it ferments sugar into alcohol far less efficiently.

    Now an analysis of the forensic ancestry of lager yeast has established that this same marriage happened independently at least twice, not once as previously thought, giving rise to two broad families of lager beer.

    So, now you know. Oh, and this should be especially interesting if you've been following the Heineken storyline on Mad Men...

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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.

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.