john hawks weblog

paleoanthropology, genetics and evolution

Neandertal DNA

  • Fusing chromosomes

    Thu, 2012-07-19 15:20 -- John Hawks

    Carl Zimmer recounts recent research by Evan Eichler's group on the evolution of human chromosome 2, which represents a fusion of two separate chromosomes in ancient apes, which still remain separate in the living great apes: "The Mystery of the Missing Chromosome (With A Special Guest Appearance from Facebook Creationists)". The research paper is by Mario Ventura and colleagues [1].

    The two chromosomes fused, and the cap was deleted, inclusing StSat. It could no longer spread around our genome, the way it did in chimpanzees and gorillas.

    This study is an important advance in our understanding of how human chromosomes evolved–a subject of medical significance, too, since the duplication of the DNA at the end of chromosomes can cause dangerous mutations that can cause genetic disorders. Plus, it is very cool to see how our chromosomes are, in fact, an ancient patchwork.

    People often ask me when this chromosome fusion happened in ancient hominins. I think they attribute excessive importance to this event, reasoning that chromosome fusion may have been the cause of some reproductive isolation. For example, they often ask specifically about Neandertals and modern humans, figuring that when we show Neandertals had 48 chromosomes, it will at last explain why they are extinct.

    In reality, the fusion must have happened within a population. The first person who carried it, and his immediate descendants, must have been able to mate and reproduce successfully with people who didn't carry it. This outcome is not uncommon for chromosomal rearrangements. Many create reproductive incompatibility, and those that do are very unlikely to become common within a population. Some become moderately common but create problems for homozygotes who carry two copies of them. Others seem to be neutral and do not cause noticeable problems.

    So why do related species with different chromosome numbers often have trouble producing fertile offspring, even if they can mate successfully? This is likely because many chromosomal rearrangements and other genetic changes have accumulated in each lineage after a long period of reproductive isolation. Each may have been near selectively neutral within the population where it first occurred. A few may start out deleterious in homozygotes, and later may become fixed in the population only after other genetic changes ameliorate (or "rescue") these deleterious effects. Sometimes, positive natural selection can favor changes within one population that decrease carriers' ability to reproduce with members of another population, and in these cases reproductive isolation can appear very rapidly. In other words, the evolutionary constraints on chromosome structure aren't simple.

    Whether fast or slow, as each of the emerging species becomes different from the ancestral genetic background, the potential for reproductive incompatibility increases. This evolution is not a single jump, but a series of steps that may result in gametic incompatibility, hybrid inviability, or hybrid sterility.

    The series of events leading to the fusion of human chromosome 2 are genetically very interesting, as are the repeated instances of rearrangement that Ventura and colleagues illustrate in chimpanzees. But chromosome fusion has no special magical power, and whether it was connected to ancient speciations or other events in our evolution will take a lot of creative hypothesis testing.


    References

  • Dynamics of genetic and morphological variability within Neandertals

    Wed, 2012-07-04 09:23 -- John Hawks
    Research authors: 
    Publication information: 

    A manuscript under submission to the Journal of Anthropological Sciences

    Work status: 

    This manuscript has just been added to the open research queue. Until this status is updated, readers can assume that the manuscript is incomplete and essential parts are being added by one or more authors. It may be an extremely early draft upload awaiting editing and addition of citations, so reader beware.

    Abstract: 

    Genetic comparisons suggest that Neandertals had relatively low genetic variation compared to recent humans, that variation may have been substantially higher among central Asian Neandertals and earlier Neandertals, and that long isolation did not figure into the evolution of later Neandertals. These observations pose a challenge to traditional morphological accounts of Neandertal evolution. These have often featured a long period of isolation in western Europe with the slow accumulation of specialized traits in classic Neandertals. The genetic evidence does appear consistent with archaeological indicators of dispersal and turnover among Neandertals. The morphological evidence as historically considered, with overly broad regional-scale and temporal divisions, may be silent on the interesting aspects of Neandertal population dynamics. New ways of looking at the morphology of Neandertals may yield a better picture of their interactions and movements.

    Genetic evidence from Neandertals may reflect complex population dynamics that a hundred years of morphological comparisons have barely hinted. Neandertal mtDNA and nuclear genomes show that there may have been large population movements and flows across their European and central Asian range. One provocative finding suggests that early European Neandertals such as those from Krapina and Saccopastore may have had little genetic input into later Neandertal populations of Europe because of migration from central Asia [1].

    Following long precedent, I consider Neandertals as an ancient human population extending across Europe and parts of West and Central Asia between approximately 200,000 and 30,000 years ago. The definition oversimplifies. It excludes skeletal samples before 200,000 years ago that display clear anatomical similarities with later Neandertals, even if individual specimens may not possess a full suite of Neandertal-like characteristics. It also excludes people of Upper Paleolithic Europe who followed the Neandertals, and who also share some of their characteristics. As we now understand, most living people share a fraction of Neandertal genes [2]. Most important, the definition oversimplifies by neglecting the morphological diversity across the geographic range it encompasses.

    A look within the core European and Asian range of Neandertals finds great diversity and differentiation. Cranial and postcranial anatomy mark regional differences between Neandertals from Europe and southwest Asia. The southwest Asian Neandertals are outside the anatomical range of European Neandertals for many characteristics, and cannot be easily differentiated from modern humans in that area [3]. Early European Neandertals, chiefly from Krapina and Saccopastore, are morphologically different from most later Neandertals in Europe. Individual specimens far from the Europe or West Asia also share Neandertal similarities, suggestive of gene flow or shared ancestry over a much broader space.

    Putting morphology and genetics together will allow us to build a synthetic view of Neandertal population dynamics. In some instances, the current genetic evidence suggests events that cannot be corroborated by morphological evidence. Far from a unitary group evolving in isolated glacial conditions, the Neandertals appear to have been a highly dynamic population with the potential for rapid migration and long-distance dispersal. This perspective adds context to the archaeological record of Middle Paleolithic and initial Upper Paleolithic cultural changes.

    The context of Neandertal morphological variation

    It has been common for anthropologists to emphasize the unity of Neandertal morphology, instead of its diversity. There have been two reasons for this emphasis in recent years. First, a paramount problem in European prehistory is to identify the biological makers of the earliest Upper Paleolithic industries [4]. Only a small number of skeletal remains have been identified in association with terminal Middle and initial Upper Paleolithic assemblages, nearly all fragmentary. In this context, identifying whether a specimen is "Neandertal" or "modern" can may depend very strongly on a single trait. By decomposing Neandertal identity into the morphology of an individual trait, Neandertals are made to look more morphologically homogeneous than if many traits could be considered together.

    The second reason for emphasizing Neandertal morphological unity has been the assumption that long isolation might explain the evolution of their distinctive traits. This idea can be traced to Howell [5] who introduced the hypothesis that isolation in glacial Europe gave rise to divergent morphological trends in the Late Pleistocene populations of Europe and West Asia. Other workers followed this concept with related models. Hublin [6] suggested that long isolation of Neandertals could explain the evolution of their morphological pattern by genetic drift and local selection, both of which would predict a reduction in the variability of this population. The strength of this explanation was that it provided an explanation for the mosaic appearance of Neandertal traits over time within Middle Pleistocene Europeans [7]. However, even strong genetic drift need not reduce the variability of a population, and in fact morphological variability in Europe did not decrease for most Neandertal traits [8].

    These two concerns are interrelated. Both rest on an assumption that Neandertal populations were relatively static, and could have changed only very slowly. This assumption can be defended in terms of paleoenvironment and cultural dynamics. European Neandertals lived recurrently, if not continuously, in periglacial conditions. Changes in culture, as evidenced by archaeological industries, initially proceeded very slowly, and began to exhibit greater regional diversity and temporal turnover only toward the end of the Neandertals' existence. Their unique anatomical configuration emerged within this context. What could be more natural than to assume that the forces of selection and drift had slowly driven them to greater and greater anatomical specialization within this unique environment?

    Yet, our current understanding of the Neandertals shows that they did not experience a slow, plodding march toward anatomical specialization. With more discoveries from extreme eastern Europe and central Asia, it seems that the center of Neandertal evolution may not have been Europe at all. The anatomical record of western Europe lay at one geographic end of a broad distribution, and the few specimens of Neandertals from central Asia show intriguing differences from Neandertals in the west [9].

    If rapid evolution of earlier Neandertals were possible, then we would not need a long history of isolation to explain Neandertal morphology. If rapid evolution of the latest Neandertals were possible, we would not assume that late Middle and early Upper Paleolithic specimens must either represent earlier Neandertal or later modern populations; they could just as easily be a variable anatomical mixture of these.

    We can adopt a more nuanced view of the diversity within and among Neandertal populations. The main impediment to understanding Neandertal diversity is the limit on the skeletal record. The Neandertals are the best-known of any human population before 40,000 years ago. However, even with hundreds of known specimens, only a few individuals represent any single part of Neandertal anatomy. Today we can talk about the diversity of Neandertals only at the broadest regional scale.

    A history of Neandertal diversity

    An examination of the history of the Neandertal problem adds perspective on how our understanding their morphological diversity can continue to advance. At the beginning, Neandertal "diversity" was defined mostly in terms of their difference from humans and other fossil (or purported fossil) specimens. The initial Neandertal discoveries were specimens from the later part of the Neandertals' existence. First to be recognized was Feldhofer, then Forbes Quarry and Engis (both discovered earlier), Spy and later the classic French specimens from La Ferrassie [10] and La Chapelle-aux-Saints [11]. Only these last were recovered at a time when the morphology of earlier Neandertals, represented at Krapina, had been described [12]. Specimens later recognized as intermediate between modern and Neandertal extremes were discovered relatively late in the process.

    After the first descriptions of Neandertals, some anatomists attempted to accommodate them within human variability by extrapolating from the anatomical patterns of developmental abnormalaties or rare morphological correlates of disease. Rudolf Virchow asserted that the Neandertal skeleton was rachitic [13], while J. Barnard Davis maintained that the Neandertal skull presented an extreme case of synostosis, accounting for its elongated shape and complete suture closure. In the view of these anatomists, the Neandertals presented a logical extreme of morphological tendencies already known in contemporary people, allowing their anatomy to be brought within the compass of morphological "laws." Humans to be compared with Neandertals were pathological variants within populations, not members of very different populations.

    By contrast, others attempted to place Neandertals by considering the gradations among human racial groups. For example, Huxley [14] suggested that human variation was so great that "it is possible to select a series which shall lead by insensible gradations from the Neanderthal skull up to the most ordinary forms". Quatrefages and Hamy [15] put the Neandertal skull as part of a primitive race of humans. The recovery of earlier Neandertals, from the Riss-Würm interglacial and earlier, ultimately showed the anatomical continuity between Neandertals and more ancient human populations.

    Yet, several discoveries from the early twentieth century distracted many anthropologists by appearing to support the argument for an ancient, much more modern "presapiens" form in Europe. Today we appreciate that the supposedly early fossil sample included specimens of questionable or much later provenance, such as Fontéchevade and the infamous Piltdown skull. These did not entirely explain the Presapiens idea, however, which emerged from the alignment of specimens on a morphological axis from modern to Neandertal extremes. For example, Vallois argued that specimens lacking specific Neandertal characters must therefore represent a distinct group with a phyletic connection to modern humans [16]. Weidenreich did not accept a presapiens population as specifically distinct from Neandertals, but did categorize samples as Homo sapiens based on the absence of Neandertal characteristic morphology irrespective of date (e.g., Swanscombe grouped with Skhul as "H. sapiens intermediate" [17]. McCown and Keith [18] described the Neandertal similarities within the sample from Skhul and Tabun as representing a population evolving from a more modern to a more specialized type. These examples illustrate a slow trend toward acceptance two propositions about the evolution of Neandertals and modern humans: "Modern" morphological traits may in many cases be primitive, while the morphological traits of Neandertals may in many cases be derived, or "specialized".

    Neandertal variation and "varieties"

    Howell [19] discussed the variation of Neandertals by describing three varieties. His summary helped to crystallize the description of Neandertal change over time and variation across space. The varieties were:

    "Early Neandertals". This group included Krapina, Saccopastore and Ehringsdorf. Howell additionally mentioned several Asian specimens, including those from Tabun, Zuttiyeh and Teshik-Tash, without explicitly assigning them to this group. Howell distinguished the early Neandertals from classic Neandertals by eight cranial features, largely associated with smaller and more compact vaults and less midfacial prognathism. He also claimed the postcranial skeleton of this early Neandertal sample to be "more anatomically modern" than that of later Neandertals.

    "Classic Neandertals". This group included most of the well-known remains from the Würm glaciation in Europe. Howell characterized this set by cranial features, acknowledging that the sample of Early Neandertal postcrania was not sufficiently numerous to make clear statements about differences with the classic Neandertals. He also pointed out that this set of specimens were known exclusively from southwestern Europe, from western Germany and Italy on the eastern tier.

    "Southwest Asian Neandertals". This group included the entire known fossil record of the region, including Skhul, Tabun, Zuttiyeh, Qafzeh and Shanidar. Howell noted the divergent opinions of anthropologists about the evolutionary scenario that generated this sample. He offered the opinion that the initial population of the Levant represented by Tabun had affinities with Early Neandertal people, and that the region had undergone a trend of "sapiensization" explaining the Skhul sample.

    Howell identified these varieties of Neandertals to clarify his position on the Neandertal ancestry of recent humans. In his view, several previous authors had been too categorical in their insistence that Neandertals could not have been ancestors of modern peoples. He allowed that the classic Neandertals may have been too specialized to have given rise to later populations within Europe. But the early Neandertals were less anatomically specialized and may have been ancestral to modern humans in some other, non-European, region. Moreover, the Southwest Asian Neandertals appeared to provide evidence of an evolutionary trend toward modern humans.

    These groupings have in later years been widely repeated. The differences between classic Neandertals and early Neandertals, such as the Krapina and Saccopastore samples, has repeatedly been observed, as reviewed by Hawks and Wolpoff [8]. The distinction between early and classic Neandertals emerged from the work of Gorjanovic-Kramberger [12], Weidenreich [20], [21], Weinert [22] and Sergi [23].

    Howell's "Southwest Asian Neandertal" sample deserves further comment. At the time he wrote, McCown and Keith's description of the Skhul and Tabun remains [18] had grouped these as representing a single population, anatomically intermediate between classic Neandertals and modern humans. Howell advocated this combined sample as a single population. Some recent authors have followed this position [24], [25], [26]

    Thus, although they served an important role in the history of anthropology, Howell's categories have not been universally accepted. I note them here to consider how the discussion of Neandertal variability emerged during the last 50 years. Today, as we consider paleogenetic evidence, these categories have very little ability to inform us about the relation between morphological and genetic information. Early Neandertals as discussed above have not yet produced any genetic data, except for the Teshik-Tash specimen. None of Howell's Southwest Asian Neandertals are represented by sequence data to date, regardless of their morphological interpretation. New Neandertal specimens from central Asia and extreme eastern Europe have provided an unexpected trove of genetic information, although with the exception of Teshik-Tash they have never figured strongly in the discussion of morphological diversity within Neandertals. All of the remaining genetic data come from Howell's classic Neandertals, the set within which previous morphological studies have least attempted to explain variability. In other words, genetic data require us to redefine historical conceptions of Neandertal groupings and variability.

    Paleogenetics

    The data from paleogenetics of Neandertals have rapidly changed during the past few years. As a result, descriptions of the state of the evidence from as recently as 2005 are now obsolete. In that time, the synthesis of Neandertal DNA evidence has proceeded from a very simple model to one involving more complicated population interactions and movements. No known living people have mtDNA sequences that belong to the clade shared by all known Neandertals. Initially, this fact strongly influenced many researchers to believe that Neandertals had become extinct without issue (e.g., [27], [28]. Later, the sequencing of nuclear genomes of Neandertals demonstrated that a fraction of the ancestry of living non-Africans can be traced to these ancient people [2]. This simple question provides the beginning of our understanding of genetic diversity within Neandertals. We can use samples from different Neandertal individuals, as well as the genetic material they share with some living people, to test hypotheses about the population structure and dynamics of Neandertal populations.

    The complete mitochondrial genomes of more than a dozen Neandertals have been described and small fractions of the mitochondrial sequences are known for many more. These extend from as far east as Okladikov Cave in the low Altai, and as far west as El Sidrón in Spain, encompassing nearly the entire east-west range known for the Neandertals. The north-south extent of data is much more restricted, as none of the sites from present-day Israel or Iraq have yielded genetic evidence. In addition to the mtDNA, three Neandertals from Vindija are represented by substantial sequencing of the nuclear genome, averaging nearly 1x coverage for each of them. Much smaller fractions of the nuclear genome have been recovered from Neandertal specimens from Feldhofer Cave, El Sidrón, and Mezmaiskaya.

    Mitochondrial genomes show that the Neandertal population was far from static across the time of its existence. As a general observation, Neandertal mtDNA diversity is less than is present among humans worldwide, with a common ancestor estimated for Neandertal mtDNA sequences only a little before 110,000 years ago [29]. Late Neandertals in peninsular Europe, including three Vindija specimens and two each from Feldhofer and El Sidrón, form a tight mtDNA clade with an ancestor as recent as 60,000 years ago [1]. For the current discussion, I will term this set as the "late western Neandertals". By contrast, some earlier European and central Asian Neandertals belong to an mtDNA genealogical tree nearly twice as deeply rooted. These include western European specimens such as Valdegoba and Scladina, as well as Neandertals from the very far east, such as Okladnikov and Teshik-Tash. What seems to unite the earlier Neandertals is time, rather than space [1]. Mezmaiskaya and Monte Lessini (from the Caucasus and Italy, respectively) belong to mtDNA branches that cluster with the late western Neandertals. Dalén and colleagues hypothesize a movement of eastern Neandertals into the west sometime around 50,000 years ago, resulting in a partial replacement of western Neandertals.

    Neither geography nor time considered alone are sufficient to explain the grouping of the later, western subset of Neandertals into a tight mtDNA genealogical arrangement. One possible explanation is a movement of Neandertals from the eastern to western part of their range sometime after the origin of this clade, some 60,000 years ago. This movement would have to have replaced a large fraction of the mtDNA gene pool of earlier Neandertals in western Europe; otherwise, clades shared by earlier Neandertals such as Scladina would still be found among the later Neandertals. The replacement of earlier, more diverse mtDNA clades would be easier if the effective number of Neandertals in western Europe was very small. A small effective size does not necessarily imply a very small census population size [30], and might point to a way to uncover population dynamics of this population, as discussed below.

    Nuclear DNA variation among Neandertals is very limited compared to that found in living human populations. By using the genome of the Denisova specimen as an outgroup, Reich and colleagues [31] showed that the variation across the Neandertal geographic range, from Mezmaiskaya to El Sidrón, is very low compared to the variation within humans today, or between Neandertals and the Denisova genome. They interpreted this low variation within Neandertals as evidence for a bottleneck in the population history of Neandertal groups. The nuclear genetic sequences available, from Vindija, Feldhofer, Mezmaiskaya and El Sidrón, are a broader group than the "late western Neandertals" discussed above with low mtDNA variation, because of the addition of Mezmaiskaya. The most striking use of the mtDNA data from Dalen and colleagues [1] is to note just how unrepresentative the nuclear DNA sample from Vindija, El Sidrón, Mezmaiskaya and Feldhofer actually is. These six specimens represent only a single small clade of the Neandertal mtDNA genealogy. Nuclear genetic sampling of a broader range of Neandertals might uncover substantially more variation.

    The reduced variation of nuclear and mtDNA in the late western Neandertals reflects high genetic drift in this component of the Neandertal population. Genetic drift may reflect many different demographic phenomena, including small population size, recurrent movement, extinction and recolonization of small subpopulations, or selection-migration interaction. We do not have nuclear genetic data from earlier Neandertals, and so we cannot directly test the hypothesis of a population bottleneck in the classic or later Neandertals.

    The discussion of genetic diversity among these Neandertals has not yet attempted to reconcile their genealogical arrangement with morphological classification schemes. The set of "late western Neandertals" known to share a close mtDNA genealogical connection (Vindija-Feldhofer-El Sidrón) is not synonymous with "classic Neandertals". The well-known classic Neandertals include specimens such as La Chapelle-aux-Saints, La Ferrassie 1, Monte Circeo 1 (Guattari) as well as Feldhofer (Neandertal) 1. This classic Neandertal sample stretches across a substantial span of time. Most important, the classic Neandertals flank both the earlier and later sides of the 50,000-year-ago event proposed by Dalen and colleagues [1]. The two Vindija mtDNA sequences included by Dalén and colleagues [1] are both from layer G3 of the site, perhaps 40,000 years old, and both are derived from postcranial fragments without diagnostic morphological traits. Even so, the other material from G3 include cranial, mandibular and dental remains that are not synonymous with classic Neandertal morphology [32]. These late Neandertals from Vindija display less pronounced morphology or lacking traits that are common in the earlier classic Neandertals [33]. If these can be lumped together in mtDNA and nuclear DNA diversity with the remains from El Sidrón and Feldhofer, it seems possible that traditional morphological groupings will fail to capture real biological differences among Neandertal populations.

    Two avenues of evidence will provide more insights about Neandertal population dynamics. Obviously, uncovering more nuclear genomes from Neandertals or early Upper Paleolithic humans would advance our knowledge greatly. Tempering this expectation is that the later western Neandertals, with lower genetic diversity, are the ones most likely to provide more genetic data. Earlier Neandertals, and the Neandertals from central Asia, would be most useful to uncover new knowledge about the population dynamics of this ancient group. A second source of evidence may come from the introgression of Neandertal genes into later human populations. As we begin to uncover the genes in living people that came from Neandertals, we face the possibility that these genes may represent different ancient Neandertal groups to greater or lesser degrees. The initial work on Neandertal genetics suggested that most of the population mixture with Neandertals may have happened in west Asia [2]. That would suggest that European Neandertals are themselves somewhat genetically distinct from the population that gave rise to most Neandertal genes in recent populations. Comparing different Neandertals with each other will help us uncover the structure of the population that gave rise to Neandertal ancestry in living people. By doing so, we may gain an additional genetic probe into the period before 60,000 years ago, as Neandertal populations had differentiated before the large-scale encounters with dispersing people from Africa.

    Population dynamics

    From the Altai to Spain, the known geographic range of Neandertals covered more than 7000 kilometers east to west. At least intermittently, this population occupied more than 30 degrees of latitude, as far north as Byzovaya [34] and as far south as the Levant. The excursions of Late Mousterian people north of the Arctic Circle suggest that the Neandertals rapidly colonized new regions when they became suitable for habitation. The paleoecological reconstruction of Mousterian sites encompasses almost the entire range of European ecological contexts, except for Alpine and Arctic biomes [35]. Although the European climatic conditions oscillated considerably during the Late Pleistocene, the Neandertals seem likely to have been capable of adapting to changing conditions, either by tracking ecotones as climate shifted or by changing their subsistence strategies to meet new requirements. In other words, the archaeological record by itself is sufficient to show us that Neandertal populations were highly dynamic in areas where habitation was possible only during intermittent climatic periods.

    Across northwestern Europe, from Britain to Poland, an area of more than a million square kilometers was abandoned by Neandertals during the early stages of the last glaciation and not reinhabited until after approximately 60,000 years ago. The intermittent occupation of these parts of Europe was likely not a function of "habitat tracking" by Neandertals, but instead a record of regional expansions and partial extinctions when climatic conditions deteriorated [36]. White and Pettitt [37] suggest a very small Neandertal population size in northwestern Europe during the late Middle Paleolithic, and consider the possibility that the occupation of Britain was maintained as seasonal hunting camps rather than permanent settlement. This kind of occupation would put movements of several hundred kilometers into the ordinary behavioral pattern of individual Neandertals. At an extreme, the survival of Neandertals on the northwestern tier of Europe may have been precarious [38]. From the perspective of population dynamics, this does not suggest a dense, stable population, but instead one of great mobility and repeated ability to colonize and exploit new opportunities.

    Earlier anthropologists also suggested that the Neandertal population had been dynamic in its potential for dispersal and movement. Most such suggestions centered around the role of the Pleistocene glaciations as an impetus for migration and recurrent isolation. For Howell [5], glacial cycles provided the isolation that enabled classic Neandertals to evolve their specialized anatomy. Weckler [39] argued that isolation was one consequence of glaciations, but that long-distance migrations and recolonizations of formerly periglacial habitat was an important cause of population change in Neandertals and the modern humans who encountered them.

    Genetics now leads us to a picture of a highly dynamic Neandertal population. This should not be a surprise in the context of the archaeological record, which shows abundant evidence for regional-scale population movement and rapid changes to cultures and adaptive strategies. But it is not clear that the genetic and archaeological data actually converge on a single picture of population dynamics.

    A close look at a single archaeological example helps to demonstrate this point. The Quina Mousterian in southwestern France appears to represent a regional Neandertal adaptive pattern. As climate conditions gave rise to a mix of steppe and boreal forest, Neandertals specialized on reindeer, and to a lesser extent horse, replacing an earlier strategy using a broader mix of large fauna. The accompanying toolkit has been recovered from many sites in the region, consistently overlying earlier Denticulate and Typical Mousterian assemblages [40].

    As we consider this kind of technical transition, it is not obvious how the earlier and later Neandertals of southwestern France were related to each other. The transition in this area, around 60,000 years ago, is a temporal boundary between traditions that each lasted for thousands of years. Certainly it is possible that the earlier population underwent cultural adaptive evolution, suiting it better to the changing ecology, and resulting in the later cultural tradition. But it is also possible that ideas and people spread together, as the more effective cultural strategies of northern Neandertals enabled them to make incursions into the territory further to the south. Long-term Pleistocene climate changes may have provided the impetus for both interaction and conflict.

    Cultural change and spatial dispersal were likely interlinked. An effective faunal procurement strategy may open up habitat that earlier Neandertals had less success exploiting. The colder parts of Germany seem to have seen the spread of reindeer hunters during MIS 4, in an occupation that may have been thin on the ground but potentially occupied a broad area [41]. As different Neandertal groups used different adaptive strategies, some would have expanded in range, sometimes into new previously unoccupied territory but often into territories formerly occupied by groups with different cultural strategies. Could northern Neandertal reindeer hunters have followed their herds right down into the heartland of France, as conditions grew colder, replacing their cousins to the south?

    Despite the evidence for cultural change, as far as we know the morphological variation across this cultural transition was continuous. Before 60,000 years ago, southwestern France was inhabited by people we call classic Neandertals. Skeletal associations with Quina Mousterian, for example from Les Pradelles [42] and Combe Grenal, present no obvious appearance of morphological discontinuity with other classic Neandertals. Condemi and colleagues [43] considered the dental sample from the Rhône valley of southeastern France, including the well-known classic and late Neandertal sites of Hortus, Tournal and Le Portel and the older sites of Genay and Payre. Their comparisons were necessarily limited but showed a lack of regional differentiation between this set of Neandertals and the remainder of the Neandertal sample from across Europe. Within Spain, Rosas and colleagues [44] described the mandibular remains from El Sidrón, including them in several comparisons of regional samples of Neandertals. They found evidence for a significant difference in mandibular morphology between "northern" and "southern" samples, which they attribute to a smaller dentition and degree of midfacial prognathism in the southern sample.

    In short, morphological comparisons across the relevant time span in France and Spain are insufficient to support the hypothesis of a large-scale migration bringing in a new mtDNA type. Yet it is difficult to imagine that a widespread movement of Neandertals could reach northern Spain by around 50,000 years ago without passing through southwestern France or affecting the skeletal sample of Spain. Possibly the very small sample of physical remains will simply be insufficient to test hypotheses of population dynamics on this scale.

    We cannot consider Neandertal population dynamics without discussing the probable effects of low population size on their distribution. The estimation of population numbers from archaeological site densities is imprecise with many sources of error. Nevertheless, some estimates of the total number of Neandertals representing traditions such as the Mousterian of Acheulean Tradition (MTA) are as low as a few hundred individuals total [45]. Across peninsular Europe, there may have been fewer than 10,000 Neandertals living at any given time, an indication of the census population size. Certainly, the genetic variation of Neandertals is consistent with a very small effective population size. Many factors reduce genetic variation relative to census population size [30], including two of particular relevance to Neandertal population structure: Extinction and recolonization of groups [46], and broader regional-scale cultural replacement in the presence of selection [47]. Such small groups and regional populations would have very little genetic "inertia" against the long-term effect of gene flow. Genetic continuity in this scenario could never persist for long against even a moderate amount of immigration acting over many generations.

    If the Neandertals of southwestern France, for example, were fewer than 1000 individuals, how could they have maintained identifiable traditions of stone technology for thousands of years? If their gene pool was constantly in flux due to immigration and long-distance movement of individuals, how could their cultures not have rapidly changed beyond recognition? In this scenario it seems necessary to assume very strong reinforcement of technology by learning biases, probably mediated by the observed utility of stone tool choices within the local ecology [48]. Learning and cognition may fundamental supports for a dynamic Neandertal population, enabling their persistence in a tenuous paleoclimatic regime.

    Conclusion

    The genetic data force us to adopt a new stance on the nature of Neandertal populations. A long, slow evolution of Neandertal populations cannot account for the evidence of long-distance interactions and movement on relatively short time scales. The archaeological record may be a more sensitive indicator of regional-scale changes than the morphological record of skeletal biology. Archaeology also gives us insight into the ways the Neandertals maintained their population in the face of regional movements and logistical strategies may have involved temporary summer occupations at some distance from their core territories.

    The redefinition of Neandertal population groupings should begin immediately. We may soon have genetic data from many more Neandertal specimens. Given the unexpected finding of diversity from the Denisova specimen [31], it is possible that some other Asian "Neandertal" populations will turn out to represent equally divergent human populations. We should not too readily assume that Shanidar, or Skhul, or Amud, for example, will lie within the known pattern of Neandertal genetic variability. What we now know is that the traditional category of "classic" Neandertals is insufficient to describe the genetic variability and dynamics of Late Pleistocene Europeans. Obviously we must proceed much further with the comparison of physical remains before we will be able to test any connections between cultural and biological transitions within Neandertals.


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  • Neandertal similarity in the HapMap samples

    Mon, 2012-06-25 11:36 -- John Hawks

    In my last installment on Neandertal introgression in present-day human samples, I covered whole genome data from the 1000 Genomes Project ("Which population in the 1000 Genomes Project samples has the most Neandertal similarity?". For the next few weeks I'll be releasing more of these comparisons, made with the help of my Ph.D. student, Aaron Sams.

    Just to remind about our methods for comparing genomes, what we have done is to examine every base reported as a single nucleotide polymorphism by the 1000 Genomes Project. If the sequencing data had no errors, then this would be an account of every point mutation in the human genome. However, the data are imperfect in various ways, as I'll note below. Likewise, the Neandertal sequence data are imperfect in various ways.

    Here's one of the 1000 Genomes Project comparisons, showing the histogram for pooled European, African, and Chinese samples. In this chart, the number of shared Neandertal derived SNP alleles is the x-axis, divided into bins of around 500. The y-axis is the number of individual genomes in the sample found in each bin. So on this chart, the largest number of European genomes (nearly 120) share very approximately 645,000 derived SNP alleles with the Vindija 33.16 genome.

    Comparison of shared Neandertal derived variants in African, Chinese and European samples

    I find it necessary to be very explicit about these charts, because after showing them to many people I know how easily they can be misinterpreted. It's natural to assume that they are bar charts, where higher y values mean more Neandertal. But with more than 2000 genomes to compare, a bar chart is really just noise. These histograms are much like bell curves, in which the shape of the distribution on the y-axis indicates the dispersion within the population of Neandertal shared alleles.

    Percentages

    Everyone is excited to find out what percentage of Neandertal ancestry people have. I'm hesitant to report percentages, because I think they are misleading on these data. There is some filtering hiding beneath the data. In particular SNP alleles that are found only in one individual ("singletons") are likely to be undersampled by the project's sequence analysis. Because gene variants that have introgressed from Neandertal populations tend to be rare in present-day samples, when we miss some rare alleles, this tends to reduce our estimate of Neandertal similarity. This bias in resequencing data should affect populations roughly in proportion to their Neandertal ancestry. Our comparisons of different populations are therefore likely to give the right order of Neandertal ancestry (e.g., Europeans more than Asians) but may underestimate the total fraction of ancestry by some amount. We are counting human SNP variants and not every base pair in the Neandertal genome data, so the effect of sequencing error in the Neandertals will be minimal, but nevertheless present in a small fraction of comparisons. These errors should be randomly distributed with respect to human population differences, but they also add noise that should decrease the accuracy of percentage estimates.

    For another thing, we don't know where the zero point may be. Europeans have around 3 percent more than Yoruba; Yoruba (as I showed in the last post) have around a half percent more Neandertal similarity than Luhya in the 1000 Genomes Project sample. The Luhya are almost certainly not minimal for living people, in fact I would put some money against it. Since some Neandertal alleles have proceeded right up to high frequencies outside Africa, there has been ample opportunity during the last 30,000 years or more for other alleles to have spread into Africa.

    Our conservative approach is to rely on comparisons of large samples of people, ideally hundreds, and to trust a comparison only when it achieves statistical significance in these samples. That still allows us to detect very slight excesses of Neandertal ancestry in some populations, because the data from hundreds of individuals is very strong evidence. But the overlap among populations is sometimes very extensive even if their means differ significantly.

    Incomplete lineage sorting (ILS) is one pattern by which living people share alleles with Neandertals. ILS should be equally distributed among populations today, under the assumption that Neandertals and ancestral Africans stem from a single unstructured population. Obviously, Europeans and Asians share more derived SNP alleles with Neandertals than do Africans today, so we can strongly reject the hypothesis of isolation between African and Neandertal populations.

    Given that, three patterns of evolution could have caused some populations to share more derived alleles with Neandertals than others.

    1. Population structure in the ancestors of Africans and Neandertals may have caused some populations to share more ILS with Neandertals than others.

    2. Continued gene flow between Neandertals and Africans could have spread Neandertal alleles into Africa and vice-versa.

    3. Recent introgression from Neandertal populations into the ancestors of today's populations may have transferred new Neandertal alleles into recent humans.

    These three processes actually overlap with each other. Very likely all three of them happened -- although to date, the descriptions of Neandertal genome data have accentuated the last and argued that the first two are relatively less important [1] [2]. A "new" allele in a Neandertal may actually have originated from a mutation more than a half million years ago, have been lost within ancient Africans, and transferred into today's Europeans when they encountered and mixed with Neandertals. We cannot tell these processes apart from the standpoint of any single SNP allele. Only by comparing many SNP alleles across many populations can we sort out their relative importance.

    To this end, we have been comparing populations with each other and ancient Neandertals in many different ways. The 1000 Genomes Project has continued to sample and resequence many of the same samples that were initially amassed for the International HapMap Project. The HapMap was a project based on genotyping individuals with microarray technology. Genotypes are just as informative in many cases as whole-genome sequences. If you already know which genetic variations you want to examine, a microarray can save a substantial amount of wasted effort.

    With Neandertal comparisons, we don't start out knowing in advance which genotypes will be useful. For this reason, genotyping data yields a potential bias when comparing to Neandertal or other human genomes. The microarray was designed to include genotypes that were already known to vary in some human population. With the HapMap, this bias tends to overrepresent the genetic variations in the initial HapMap samples -- generally, Utah residents of northern European descent, ethnic Yoruba people from Nigeria, ethnic Han Chinese from Beijing, and Japanese people from Tokyo. If these samples share some common derived SNP alleles with Neandertals, they will very likely be represented in the genotyping array. But very rare alleles won't be represented. And alleles that are uniquely in other populations -- such as East Africans or South Asians -- may not be represented, either. The bias is called "ascertainment bias" because it comes from the "ascertainment" of SNPs, or their initial discovery in some populations but not others.

    It is possible now to find sets of SNP markers that have been statistically chosen to minimize ascertainment biases. The filters used in such comparisons are complex, and in some cases actually rely on the Neandertal genotype, so I haven't used them here. For our first paper we have focused on the whole-genome sequence comparisons, but here I'll give the same comparisons on some HapMap samples to show approximately where they fit. I will focus here on raw comparisons instead of standardizing them in terms of the predictive ability of informative SNPs on whole genome data. Finding the most informative SNPs is part of the process of sorting introgression from earlier population structure, and is rather more complex; I prefer to start with something very simple and visually easy to interpret.

    South Asia

    One interesting place is India. The HapMap includes a sample of Indian-Americans with origins in Gujarat, in western India. Here's a plot comparing the Gujarat ancestry (GIH) sample with the CEU and LWK samples:

    Comparison of shared Neandertal derived variants in CEU, LWK and GIH samples

    The GIH sample has substantially fewer shared Neandertal derived SNP alleles than the CEU sample. What may be more curious is that the GIH sample also has fewer than East Asians on average. The JPT+CHB samples, for example, exceed the GIH mean by around 100 derived SNPs.

    Comparison of shared Neandertal derived variants in JPT+CHB, LWK and GIH samples

    On a mean of more than 43,000, 100 is around a fourth of a percent, so it's not much -- and it may fall within the amount expected from ascertainment bias. It will be much more enlightening to have GIH whole genome data. In the meantime, we can probably confirm the picture from sequence data that indicates Europeans today have the highest degree of Neandertal ancestry.

    East Africa

    The situation within Africa is potentially very complex also. From sequence data, we were able to show that Yoruba (YRI) and Luhya (LWK) population samples have different numbers of shared derived Neandertal SNP alleles. The YRI sample in West Africa has significantly more Neandertal similarity than the LWK sample in East Africa. We speculate that this relation may reflect trans-Saharan gene flow, which has continued throughout history and prehistory.

    Is this a question of east versus west in Africa? That might seem unlikely considering the extent of population movements into northeastern Africa and continued trade along the East African coast throughout historic time.

    The HapMap includes a sample of ethnic Maasai people from Kenya, which allows us to provide another perspective on African variation. Here is the chart, compared to LWK and CEU:

    Comparison of shared Neandertal derived variants in CEU, LWK and MKK samples

    The Maasai have substantially more Neandertal similarity than Luhya, despite their present geographic proximity. In fact, the mean amount of Neandertal similarity in the Maasai is approximately the same as that in the ASW sample, which is composed of African-American ancestry people in the Southwest U.S.:

    Comparison of shared Neandertal derived variants in CEU, LWK and ASW samples

    You see immediately more dispersion in the African-American ancestry sample, because the mixture between African and European ancestors is more variable and much more recent than the events that gave rise to the Neandertal ancestry of Maasai people.

    We speculate that there may have been a substantial amount of interaction in northeast Africa. Obviously this has been true in historic times, but the Maasai suggest that it may go back long before the origins of the present ethnic groups and their movements into this area. The present heterogeneity of Neandertal similarity in these populations suggests a really complex population history. Some of the present Neandertal similarity may derive from ILS within the ancient African population.

    Probing assumptions

    Of course my lab is not the only one presently engaged in comparing the archaic human genomes with recent populations. One of the reasons why we're pursuing a more open science strategy in our reporting is that different groups using different methodologies ought to converge on the same population history. Where we see different results, it's often an indication that the alternative approaches involve substantially different assumptions about the way ancient humans interacted. As we've probed more deeply into the data, we have confronted the reality that long-term population mixture between Neandertal and African ancestral populations is extremely difficult to rule out. Assuming that long-term interactions were impossible because Neandertals and Africans were completely isolated will probably lead to erroneous results. That makes it harder for us to clearly identify gene variants that came from Neandertals within the last hundred thousand years, as opposed to those shared with Neandertals via more ancient gene flow.

    What makes long-term interactions seem more likely is that some of the Neandertal genomes seem to be more closely related to living people than others. More on that in my next installment.


    References

    Synopsis: 
    I examine the pattern of Neandertal ancestry in India and East Africa.
  • Quantum of solace

    Wed, 2012-05-16 22:31 -- John Hawks

    I just want to point out, on the "six generations of daughters" story...

    The family has an astonishing six generations of daughters still living. The matriarch of the family, Mollie Wood, was born in 1901 and just marked her 111th birthday. The youngest addition to the family, Braylin Marie Higgins, was born in March to Wood’s great, great granddaughter.

    ...that the baby and the 111 year old share the same fraction of genes as the average European shares with a Neandertal.

  • Blond as a window to ancient pigmentation variation

    Sat, 2012-05-05 13:57 -- John Hawks

    Blond hair is relatively common in island Melanesia, even though the skin pigmentation of Melanesian peoples is relatively dark. Eimear Kenny and colleagues report in this week's Science that one SNP variant in the gene TYRP1 explains a high proportion of the variance in hair color in this population [1].

    Resequencing of TYRP1 exons detected a single previously unknown polymorphism, a C-to-T transition at chr9:12,694,273 (GrCH37/hg19), that corresponds to a predicted arginine-to-cysteine mutation (R93C) in exon 2 of TYRP1 at amino acid position 93 (TT in blond- and CT or CC in dark-haired individuals)...[more on assessing effect in a GWA panel].

    We genotyped R93C in 918 Solomon Islanders for whom we had measured hair pigmentation with spectrometry. A recessive model provided the best fit for the data, and R93C genotypes accounted for 46.4% of the variance in hair color (linear regression; P = 2.19 × 10−90; Fig. 1D and table S2). The frequency of the 93C allele in the Solomon Islands is 0.26, and genotyping of R93C in an additional 941 individuals from 52 worldwide populations revealed that the 93C allele is rare or absent outside of Oceania (table S3). Furthermore, we found no evidence for recent gene flow from Europe (i.e., admixture) (figs. S5 and S6) nor a strong signature of recent positive selection for the 93C allele (figs. S9 to S11).

    This paper is very short, only a few paragraphs. When I read through it, I got one impression of the results, and that impression changed greatly when I looked into the supplement.

    Some underreported facts:

    1. The blondness allele is present in all the samples from the Solomon Islands, at a frequency as high as 49% in a large sample from Malaita. In this study, the authors found it at its lowest frequency in "Polynesian outlier" islands near the Solomons.

    2. The allele was not found in any of the HGDP samples, even when they were genotyped specifically for this study. That includes the "Melanesian" and "Papuan" samples. These two are relatively small in HGDP (n=14 and n=16 in this study) but even so would probably present this allele were it present at anything like the frequency in the Solomon Islands.

    3. The text of the paper reports that a recessive effect model is the best explanation for the relation of hair pigmentation and TYRP1 genotypes. The supplement shows that the recessive model is only very slightly better than a "codominant" model, as it only explains an additional 3 percent of the variance. In the best case considering this allele along with age and geographic origin of the individuals, only 48% of the variation of hair pigmentation can be explained. That leaves 52% to be explained by other genetic and nongenetic causes. There may be a lot of genetic background, which may include more alleles of large effect.

    4. Skin pigmentation varies greatly among these Solomon Islands samples, with more than a third of the overall variance in skin pigmentation explained by geography. The tables don't make it clear how pigmentation is patterned by geography. The TYRP1 allele that is the subject of this paper does not explain much variation in skin pigmentation.

    5. Sex and age have strong effects on hair pigmentation in this sample, but not on skin pigmentation. Again, these point to background genetic factors. Many populations have sex and age effects on hair pigmentation, so some of the additional causal factors may be widely shared.

    I began looking more deeply into TYRP1 R93C for a couple of reasons. The prehistory of human populations in the Solomon Islands goes back more than 30,000 years. Because this allele is not present in mainland Asian populations, as far as we know, but it is present thoughout the Solomons, suggests that it may have become common at or near the initial founding of this population. The LD pattern around the mutation likewise suggests that it has been segregating in this population for a long time. The data are consistent with the idea that blond phenotypes were present in the Solomon Islands as early as the initial colonists who founded the population.

    It will be interesting to look further into nearby populations to see if it characterized early colonists more broadly. Blond phenotypes occur very commonly in Aboriginal Australians, also age-dependent in expression, as many children have blond hair that darkens with age. Other Melanesian islands, such as Vanuatu and Fiji, also have a high incidence of blondness. For the islands, I expect that the same allele will be responsible for a similar fraction of the variance. For Australia, I would guess that this allele is also present, but with 40,000 years of evolution, there could well be a more diverse genetic explanation.

    Pigmentation variation in Eurasia is clearly a phenotype that has been affected both by recent positive selection and selection on old, standing genetic variants. Europe and East Asia today each have a dozen or more alleles that individually have strong effects on skin, hair, or eye pigmentation. Many of the alleles common in one region are rare in the other. These are well explained by recent selection on pigmentation; if there had been no selection on pigmentation, the populations would not show as extensive a pattern of differences, and new alleles would not have reached high frequencies. But if we had only a single mutation at 30 percent distinguishing one of these populations, which had arisen as early as 30,000 years ago, we would not have a strong case for selection.

    In Melanesia, we have just the opening sketch of pigmentation variation. We know that there is substantial variation in skin and hair pigmentation, and that one mutation unique to this part of the world explains a large fraction (but still a minority) of the variance in hair pigment. The other genes that contribute to variation in hair and skin pigmentation are not known. Possibly, skin pigmentation variation among the geographic regions in this study may reflect late prehistoric migration of people through this region, as agriculture moved into the area and Polynesia was settled. But the genetic part of this story remains to be demonstrated.

    Both Asia and Europe have a similar pattern of selection which has favored new alleles along with some old, standing alleles. Across the temperate regions of Europe, East Asia, and the Americas, it is plausible that the disadvantages of dark pigment for vitamin D production manifested themselves. It is also plausible across these regions that the advantages of dark pigment as protection from UV radiation would have been relaxed, allowing sexual selection on pigmentation to play an important role.

    The evidence here suggests that this allele in Melanesia has not been recently selected from a new mutation. Additionally weighing against recent selection is the observation that the mutation acts recessively on hair pigmentation -- recent selection is much more likely for mutations with dominant or additive effects.

    Together, these observations suggest that variation in human pigmentation emerged in stages. Some genes, such as ASIP, have old alleles that explain some of the variation in pigmentation today and are geographically ubiquitous, in Africa, Eurasia, and the Americas. This genetic variation was older than the Late Pleistocene. Such genes (ASIP is probably an example) today have alleles associated with darker pigment that are common in sub-Saharan Africa. Probably many other genes have variation within Africa that are part of the ancestral pigment variation of humanity. As people dispersed throughout the world, mixing with archaic humans, they carried some of these pigmentation variants along with them.

    What's interesting is that even though some of these ancient alleles lighten skin pigmentation, they remain segregating in today's light-pigmented populations. They were not selected to fixation, even though there was plenty of time for them to increase toward fixation, and even though strong selection on pigmentation appears to have been present in many high-latitude populations. Later mutations that lighten pigmentation were strongly selected in these same populations, some reaching very high frequencies, while the old mutations still were not selected to fixation.

    The story is of course more complex than a simple count of standing and new mutations. Some genetic changes that lighten pigmentation may have countervailing negative effects. Solving the problem of becoming light pigmented in just the right way may really be a different problem in different populations. Founder effects may have shifted the genetic background of early Eurasian populations just enough to create strong path-dependence for later mutations, allowing some to proceed rapidly and blocking the rise of others.

    The story of TYRP1 gives a new perspective on the early evolution of pigmentation outside Africa. Here is a novel allele that originated within the earliest colonists to Oceania, which affects hair pigmentation strongly, in a population that was always low-latitude. It did not come from earlier archaic humans as far as we know so far (not in the Denisova genome). It may have become common by a founder effect. We cannot rule out selection, such as social or sexual selection, as a cause of its initial spread or current geographic distribution, but we have no genetic evidence in favor of such selection. We know from the data that there must be many other loci that affect pigmentation in this population.

    This may have been much like the original pigmentation genetics of early modern human populations. It may also be much like the pattern that accounts for pigmentation variation within Africa today. It is not a simple story in which a few loci of large effect explain the evolutionary pattern. It is a story in which a substantial store of segregating variation persists within populations for tens of thousands of years.

    Why does that matter? Here's one reason: We're looking at possible pigmentation variants in archaic humans, and we have counted many of them. Anyone might begin this project with the presumption that Neandertals and Denisovans had pigmentation variants that were fixed relative to living people. In that context, it would be surprising to find that they had not introgressed.

    But if all these ancient populations had a large store of small-effect variants affecting pigmentation, a mutation that we find in one individual might have been rare in the population. The TYRP1 R93C allele varies from 5 to 50 percent in the Solomon Islands samples. We already know that the MC1R coding variant in some Neandertals is not found in the Vindija genomes. Variation in pigmentation loci may have been ubiquitous in human populations, with few fixed alleles separating populations. The ancient landscape was more like ASIP than SLC24A5.


    References

    Synopsis: 
    Pigmentation genetics in the Solomon Islands gives some perspective on the process of phenotype evolution
  • The Neandertal pigmentation race

    Mon, 2012-03-19 23:41 -- John Hawks

    As regular readers know, I've been detailing some of our work on the pigmentation genes of Neandertal and Denisova genomes. I got interrupted in the middle of my posts on that work undertaken by my undergraduate students, but we've got some interesting results. I've got to get going faster writing them up here, because we now have some competition.

    Traci Watson covers a new, short paper that infers pigmentation phenotypes for Neandertals, the Denisova genome, as well as several modern humans with whole-genome data: "Were Some Neandertals Brown-Eyed Girls?"

    One complication is that traits such as hair color are controlled by multiple genes. To determine the cumulative impact of multiple genes on one trait, the authors assumed they could simply add together the impact of individual genes. The female Neandertal known as Vi33.26, for example, had seven genes for brown eyes, one for "not-brown" eyes, three for blue eyes, and four for "not-blue eyes." By the researchers' reckoning, that means a six-gene balance in favor of brown and a negative balance for blue, so Vi33.26's eyes were probably brown. According to this method, all three Neandertals had a dark complexion and brown eyes, and although one was red-haired, two sported brown locks.

    I'm quoted very extensively in the article, and my basic attitude is that the new paper's results don't match what my students have found. So, time to continue my series!

  • Taking the mtDNA pulse of Neandertal populations

    Tue, 2012-02-28 11:01 -- John Hawks

    Neandertals have strikingly limited genetic variation. They once lived across a range from Spain to Siberia. Yet when we compare sequences across their whole genomes, we find them to be much less different across this geographic range than people living in the same regions today.

    I think this is one of the most fascinating findings of ancient genomics. It may tell us something about Neandertal populations that we did not begin to suspect without their DNA.

    But there is one explanation for this fact that I and others pointed out long before DNA evidence: The Neandertal population was surely much, much smaller than Holocene population of Europe. Small population size over a long time can restrict genetic diversity. So maybe the Neandertals preserved little genetic variation simply because there were so few of them.

    Neandertal mtDNA dynamism

    Love Dalén and colleagues [1] add some perspective to this question. The paper adds one novel mtDNA sequence, of the Neandertal from Valdegoba, Spain, to the record of Neandertals. This builds on earlier work by Ludovic Orlando and colleagues, who performed some analysis of Neandertal variation over time when they reported the sequence of the 100,000-year-old Scladina mtDNA sequence [2]. The main contribution of the current paper is its separation of Neandertals into earlier and later subsamples, showing that the Neandertals after 48,000 years ago in Western Europe have greatly restricted mtDNA diversity compared to the earlier sample of Neandertals.

    That's a tricky comparison. The paper illustrates it with this figure:

    Neandertal mtDNA phylogeny from Dalen et al. 2012

    Figure 1 from Dalén et al. 2012. Original caption: "Figure 1. Phylogenetic relationships and geographic distribution of Neandertals. Recent (<48 kyr) western Neandertals are placed within a well defined monophyletic group (blue box), whereas specimens older than 48 kyr constitute a paraphyletic group together with eastern Neandertals (red box). The sampling locations for the specimens are shown with corresponding colour coding."

    The blue clade includes all Neandertals after 48,000 years ago from Western Europe; the red clade includes earlier Neandertals from the west as well as both earlier and later Neandertals from the east.

    The meat in this phylogram is not only that the later western Neandertals are close relatives, but that they share an ancestor only around 60,000 years ago. That's a mere 20,000 to 25,000 years before the later western Neandertals lived. The variation within these Neandertals is roughly the same as that within a single mtDNA clade within Europe today, such as clade H1.

    Comparing the later Neandertal diversity to the variation of present-day Europeans helps to clarify the meaning of low diversity. Low mtDNA diversity doesn't necessarily imply that the later Neandertals in western Europe were few in number. Certainly there are millions of Europeans today who carry clade H1, for example. Low mtDNA diversity tells us something more limited about the ancestors of these Neandertals. Sometime after 60,000 years ago, a pulse of mitochondria came from the east and were remarkably successful in the west.

    Looking at the red clade in the figure is also illustrative. Eastern Neandertals and earlier western Neandertals had a lot more diversity than the later western Neandertals. We have to remember that the Scladina individual lived 40,000 years before the common ancestor of the blue clade, so that the greater ages of these specimens matters. Still, when we look at the diversity in that red clade, it is greater than the mtDNA diversity today in the most widespread basal clade outside Africa, the M clade. Taking the mtDNA phylogeny alone, we would say that the 13 Neandertals had a greater sequence difference than all the people who with ancestry outside Africa today. Only when we look at the predominantly African clades today (the L clades) do we start to see sequence differences as great as among these Neandertals.

    I began the post by pointing out that small population size alone might explain the low mtDNA diversity of Neandertals. Dalén and colleagues provide a key comparison that helps to reject that hypothesis. Small population size alone cannot explain the discrepancy of mtDNA diversity of these Neandertals across space and time.

    The whole-genome perspective

    Now, the question is whether this pattern holds true only for mtDNA, or whether the rest of the genome also shows some dynamic within Neandertal populations.

    We have quite a lot of information on this point, because the initial sequencing of the Vindija Neandertals was accompanied by a smattering of sequencing of the nuclear genomes of one individual from El Sidrón, the original Feldhofer specimen and the Mezmaiskaya Neandertal specimen. The inclusion of Mezmaiskaya is important, because it alone is not included in the "low mtDNA diversity" red clade pictured above. If the pattern observed for mtDNA is reflected by the rest of the genome, the comparison between Mezmaiskaya and western Neandertal genomes should show substantially more diversity.

    When they published the draft Denisova genome, Reich and colleagues [3] used it as an outgroup to investigate variation among the Neandertals, and they focused initially on Mezmaiskaya:

    Using the 56 Mb of autosomal DNA sequences determined from [the Mezmaiskaya specimen], we estimate that the DNA sequence divergence between the Vindija and Mezmaiskaya Neanderthals corresponds to a date of 140,000 +/- 33,000 years ago (Supplementary Information section 6) (Fig. 1). This remarkably low divergence—which is about one-third of the closest pair of present-day humans that we analysed—is in agreement with the observation that diversity among Neanderthal mtDNAs is low relative to present-day humans and indicates that the Vindija and Mezmaiskaya Neanderthals descend from a common ancestral population that experienced a drastic bottleneck since separating from the ancestors of the Denisova individual.

    That adds substantially to the mtDNA picture. The mtDNA variation of western Neandertals may reflect population turnover after 50,000 years ago. But the nuclear genome comparison cannot be explained by this single event. The variation of nuclear genomes between Mezmaiskaya and El Sidrón spans across more than half the Neandertal geographic range and requires mechanisms that restricted genetic variation across at least the period after 140,000 years ago.

    I think we can do quite a bit better using the nuclear genetic information already available, keeping an explicit phylogeographic model in mind. My view is that Neandertal populations were dynamic throughout their existence, with repeated waves of population turnover across broad geographic scales. The mtDNA of later western Neandertals may reflect a large, recent event. But there must also have been earlier ones to limit variation of the nuclear genome. The implication is that early Neandertals like Krapina may have had relatively little genetic connection to later Neandertals in the same region, like Vindija.

    That picture matches what we are beginning to understand about the population history of Europe during the last 30,000 years. I think that's how human populations have always behaved.

    Revisiting Neandertal races

    I wrote extensively about Neandertal mtDNA in 2009, noting the work of Virginie Fabre and colleagues [4], which showed the geographic structure of Neandertal mtDNA variation ("Neandertal races?"). Fabre and colleagues showed that Neandertal mtDNA variation is apportioned unequally across space, and made sense of the variation using a phylogeographic model with three broad geographic groups. I pointed out then that an alternative explanation might be that the specimens represent different times:

    Many have pointed out, going back to McCown and Keith (1939), that time is another possible cause of morphological differentiation of Neandertals. The mtDNA sequences cover a wide range of times -- the Scladina sequence comes from roughly 100,000 years ago, the others cover the span from 50,000 down to 29,000 years ago. Why not test temporal groups instead of geographic groups? Temporal clusters might reflect interglacial colonizations, differential gene flow, or natural selection. There is a good precedent -- last year a report of complete mtDNA sequences from woolly mammoths found evidence for geographic structure among mtDNA lineages, one of which apparently replaced the other (Gilbert et al. 2008).

    Time is just one example of an alternative model for variation. But I think it helps to clarify the basic problem of the a priori models -- you have to draw boundaries between the specimens somewhere.

    The problem still remains even in the current paper. Why should we divide time arbitrarily at 48,000 years ago? Why divide time in western Europe but not across the eastern part of the Neandertals' range?

    Combining space and time into a single phylogeographic picture is complicated. We end up using a null model to generate millions of pseudosamples to represent the exact time and place we found specimens, hoping to show the null model wrong. Refuting a null model doesn't necessarily tell us much about the behavior of ancient populations that flowed across space and interacted at different times. I think that life was more complicated rather than less, and look to models from more recent populations to understand it.

    How not to publicize your work

    The paper by Dalén and colleagues is such a neat piece of work, I think it's a shame that Uppsala University had to go and spoil it with this silly press release: "European Neanderthals Were On the Verge of Extinction Even Before the Arrival of Modern Humans".

    The paper pointedly does not show that Neandertals were on the "verge of extinction". Neandertals in the eastern part of their range show no sign of any demographic collapse, and the western part of the range arguably only shows signs of recovery and expansion.

    What the paper actually tells us is about the dynamism of Neandertal populations, which is very comparable to that of the Europeans of the last 10,000 years. Keeping this comparison in mind helps remind us that very large groups of people may still have low mtDNA diversity, reflecting the history of population movements and interactions in the past. Comparing the mtDNA with nuclear genetic evidence is also essential to this picture. Neither of these tell us that Neandertals were near extinction.

    Please, if you're putting together a press package about Neandertals, stop framing it around the concept of Neandertal extinction. You aren't going to say anything novel about this, and it just encourages lazy science writing. And it's a false concept. The Neandertals didn't become extinct.

    UPDATE (2012-03-06): A reader points out that several of the dates for specimens in the paper are different than reported in the literature. I noticed that too, and don't know quite what to make of it. I don't think that the differences in dates affect the general result, that later specimens in Western and Central Europe are relatively invariant compared to the Eastern European and Asian sample. But it is a reminder that the results do depend on a certain ordering and geographic sampling of specimens and may change if we fill in the gaps.


    References

    Synopsis: 
    Neandertals in western Europe have a recent mtDNA ancestor, pointing to the dynamics within their population.
  • Mailbag: Neandertal interbreeding

    Mon, 2012-02-13 17:26 -- John Hawks

    Re: Neandertal ancestry

    I stumbled across your (excellent) website this morning and enjoyed a couple of your articles concerning Neandertals. I know you're a busy guy so I'll get straight to it:

    Your articles discuss varying levels of Neandertal DNA in present-day human populations. I thought the issue of whether Neandertals and modern humans successfully interbred was still very much undecided?

    For reasons I've always presumed to be largely sentimental, I hope the Neandertals "survived" via interbreeding, rather than simply disappeared from the face of the Earth. Your articles are very uplifting.

    Great to hear from you and thank you so much for the kind words!

    There is no doubt anymore; many of us have Neandertal ancestors. Now we are working on determining which parts of the genome this involves in different living people, and how the pattern of interbreeding took place.

  • Mailbag: Neandertal genes across the Strait of Gibraltar

    Sun, 2012-02-12 22:03 -- John Hawks

    Re: Neandertal gene variants in Yoruba:

    If you think in terms of ice-age climate, with sea-level about 150 ft lower than at present and the Mediterranean regularly covered by thick arctic-like ice in winter, it is easy to imagine early humans making their way back and forth over an ice-covered strait of Gibraltar or along an ice-free coastal strip connecting western Europe with West Africa. I think the discovery of relatively large number of neanderthal genes in West African tribes like the Yoruba is one of those unexpected and unpredicted facts that on further reflection makes a lot of sense, justifying the statistical analysis used. After all, if a statistical algorithm only shows what's expected, you have to wonder whether all it's done is to give a statistical excuse for what's already believed to be true.

    Indeed, I think this is a possible explanation. On the other hand, there is just as much danger of post hoc generalization the other way!

    Testing that hypothesis will require some more sophisticated estimates of the ages of particular gene regions that have been inherited from Neandertals in West African populations.

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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.