New Developments in the Genetic Evidence for Modern Human Origins

Transcription

1 Evolutionary Anthropology 17:69 80 (2008) Articles New Developments in the Genetic Evidence for Modern Human Origins TIMOTHY D. WEAVER AND CHARLES C. ROSEMAN The genetic evidence for modern human origins was reviewed recently in Evolutionary Anthropology by Pearson, 1 so our goal is to highlight new developments rather than attempt a comprehensive review. For years, polarized Multiregional and Out-of-Africa models for modern human origins were debated vigorously, but today there is substantial agreement among specialists. One area of broad consensus is that Africa or, more accurately, sub-saharan Africa, played a predominant role in the origins of modern humans. This view is found even among researchers who argue against complete replacement of nonmodern Eurasians. 2 7 The importance of Africa is clear not only from genetics, but also from the fossil record. 1,8 On the other hand, most researchers also agree that, at least in principle, modern humans and nonmodern Eurasians, such as Neandertals, could have interbred with each other. The fossil record suggests that Neandertals and modern humans constituted independent evolutionary lineages, 9 but their recent common ancestry leaves open the possibility of admixture. 10 The open question is whether there is any evidence of admixture. 1 Timothy D. Weaver is a paleoanthropologist in the Department of Anthropology at the University of California, Davis. His research focuses on the origins, evolution, and disappearance of Neandertals, and the related question of the origins of humans who were anatomically and behaviorally modern. He strives to integrate approaches and datasets from genetics with traditional studies of the fossil record. Charles C. Roseman is an evolutionary anthropologist at the University of Illinois, Urbana-Champaign. He is interested in the genetic basis and evolution of morphological variation. His research deals with identifying those parts of the genome that contribute to individual differences in the skeletal morphology of model organisms, and using population and quantitative genetic models to test evolutionary hypotheses. Department of Anthropology, University of California, One Shields Avenue, Davis, CA 95616, USA. tdweaver@ucdavis.edu Department of Anthropology, University of Illinois at Urbana-Champaign, 109 Davenport Hall, 607 South Matthews Avenue, Urbana, IL 61801, USA Key words: genetics; modern human origins; population size; Neandertals; natural selection VC 2008 Wiley-Liss, Inc. DOI /evan Published online in Wiley InterScience ( While there is much agreement about modern human origins, there are still areas of disagreement, which we place into three categories: 1. Population size versus time. Although most current Multiregional models recognize Africa s predominant role in modern human origins, this is argued to be due to a larger long-term population in Africa than occurred in other geographic regions. 4,11 13 A larger African population size would have led to greater African genetic diversity and larger genetic distances to Africa, even with equal numbers of migrants per generation and no range expansions out of Africa. A related point is that most Multiregional models tend to be equilibrium or near-equilibrium models, meaning that migration patterns between different regions are thought to have persisted long enough that a balance was reached among migration, mutation, and genetic drift. Consequently, the genetic signatures of any population branching that may have occurred in the past have been erased by more recent migration. Many Multiregional models argue that isolation by distance has produced patterns of human genetic variation. 5,13,14 Isolation by distance occurs when individuals tend to migrate short distances to find mates and, at equilibrium, it predicts a positive relationship between genetic and geographic distance The implication is that the patterns of genetic diversity within and among human populations today were produced by a long history of predominantly short-range migrations, with infrequent longer ones, rather than a recent range expansion out of Africa. In contrast, Out-of-Africa models emphasize recent range expansions of modern humans out of Africa These expansions would have led to the replacement or genetic swamping of nonmodern Eurasian populations such as Neandertals. The frequent founding of new populations is emphasized rather than small numbers of migrants moving between relatively stable existing populations. According to Out-of-Africa models, present patterns of human genetic diversity were produced very recently, so that they still reflect a history of range expansions and founder effects, the reason being that not enough time has elapsed to reach a new equilibrium state. 17,22 African populations are thought to be the most diverse because they have existed the longest and because populations outside of Africa were founded from a subset of the diversity that existed within Africa Admixture. Multiregional models emphasize the magnitude and

2 70 Weaver and Roseman Articles Box 1. Glossary Admixture transfer of genes between two populations that had previously been isolated from each other. Ancient DNA a DNA sequence retrieved from a biological sample of a dead organism, often coming from an extinct taxon. Ascertainment bias genetic loci are usually discovered by finding differences among individuals in a small sample, then typed for a larger sample. This nonrandom discovery process often biases estimates of population genetic parameters such as measures of within-population genetic diversity, among-population differentiation, linkage disequilibrium, and tests for departures from mutation-drift-equilibrium. The only way to eliminate ascertainment bias is to completely resequence all the individuals in the study; that is, the discovery sample is the same as the study sample. Autosomal locus a position on one of the paired (non-sex) chromosomes. Bottleneck a sharp contraction followed by a recovery in population size. Census population size the actual number of individuals in a population. Coalescence time the time in the past when all DNA sequences in a sample shared a last common ancestor (time to the most recent common ancestor). Directional natural selection when natural selection favors a phenotype that differs from the population mean, resulting in a shift of the mean. Effective population size a population genetics parameter that equals the number of breeding individuals in an idealized population that would have as much genetic drift as is in the actual population. Founder effect when a small subset of a population moves to a new geographic region, its genetic diversity is lower than and is often unrepresentative of the original population. A founder effect produces a genetic signature similar to a bottleneck. Gene flow transfer of genes between populations by migration of individuals between the populations and subsequent mating. Gene tree a tree that shows the evolutionary relationships among a sample of DNA sequences. Genetic distance a statistic that reflects some aspect of genetic variation between two populations, sometimes standardized by the variation found within them. Genetic drift chance genetic changes in a population due to finite size. Genetic locus a particular position in the genome. Haplotype the presence of particular nucleotides over a stretch of DNA that tend to be inherited together. Isolation by distance an equilibrium model that predicts a positive relationship between genetic and geographic distance. This relationship occurs because individuals tend to migrate short distances to find mates and because long-range migrations are rare. Linkage disequilibrium deviation from a random association of the nucleotides present at a set of genetic loci. Microsatellite a rapidly evolving block of DNA in which a simple DNA sequence is repeated multiple times and individuals vary in their number of repeats. Mitochondrial DNA a short DNA molecule that is found outside of the cell nucleus. It traces maternal lines of descent because it is inherited only from the mother. Mutation-drift-equilibrium a population is said to be at mutation-drift-equilibrium when a balance (equilibrium) has been reached between the genetic variation introduced by mutation and that lost by genetic drift. Negative natural selection when natural selection acts to remove low-frequency novel genotypes from a population. Nuclear DNA the bulk of an individual s DNA, which is found within the cell nucleus. Population subdivision or structure a population is said to be subdivided or structured when it is divided into a set of local groups and there is nonrandom mating across groups. Population tree a tree that shows the evolutionary relationships among a set of populations. Positive natural selection when natural selection acts to shift low-frequency novel genotypes to high frequency or fixation within a population. Purifying natural selection another term for negative natural selection. Range expansion an increase in the geographic range occupied by a population or species. Range expansions are often linked with increases in population size. Short tandem repeat (STR) another term for a microsatellite. Single nucleotide polymorphism (SNP) a position in the genome where individuals differ with regard to which nucleotide is present. Stabilizing natural selection when natural selection favors the mean phenotype, preventing a shift of the mean. Y-chromosome a sex chromosome that is paired with the X chromosome in males, whereas females have two X chromosomes. The nonrecombining portion traces paternal lines of descent.

3 Articles Genetic Evidence for Modern Human Origins 71 adaptive significance of admixture in modern human origins. 3,24 In contrast, Out-of-Africa models often argue for minimal to no admixture Natural selection. Multiregional models emphasize the importance of natural selection in shaping present human diversity, both genetic and anatomical. Natural selection is argued to explain how modern human anatomical features became common globally after about 50,000 years ago. 2,25,26 Similar arguments are made about genetics. For example, present patterns of mitochondrial DNA (mtdna) variation are said to be due to natural selection rather than population history. 27,28 In contrast, Out-of-Africa models tend to explain the prevalence of these genetic and anatomical features with range expansions out of Africa and population replacements, although the importance of natural selection is recognized in shaping some features. 18,19,21 As with most scientific debates, diverse opinions exist that cannot be categorized easily, but these three categories capture the spirit of the differences between most Multiregional and Out-of-Africa models. Since Pearson s article 1 was published in Evolutionary Anthropology, there have been new developments in genetics that bear on these points of disagreement. Importantly, advances in DNA sequencing technology mean that data on human genetic diversity is accumulating rapidly. 29 It is now possible to examine genetic diversity across numerous autosomal loci instead of basing interpretations solely on mtdna and the nonrecombining portion of the Y-chromosome. What are the implications with regard to our understanding of modern human origins? DOES HIGHER AFRICAN GENETIC DIVERSITY REFLECT LARGER POPULATION SIZE OR GREATER TIME DEPTH? The existence of higher African genetic diversity was noted by Cann, Stoneking, and Wilson 30 in their pioneering study of human mtdna. They proposed that African populations were more diverse because they had existed longer. However, if genetic variation has reached equilibrium, then differences in within-population diversity would be due to unequal population sizes or, more correctly, effective population sizes, rather than founding time. 4,11,12 For populations far away from equilibrium, differences in within-population diversity could be due to differences in time since the founding of the populations from small numbers of individuals. 17,22 mtdna variation illustrates the basic interpretive problem. Multiple studies have shown that African populations are more diverse than are other human populations. 30,31 This pattern also holds for many other genetic loci. 23,32,33 The usual interpretation is that African populations are older, or have existed longer, because non-african populations were founded quite recently as modern humans expanded from Africa. When a new population is founded from a small number of individuals it tends to be genetically more homogeneous than is the source population. Even if the population subsequently grows in size, it will take some time for genetic diversity to accumulate again from new mutations. Eventually, a balance will be reached between the genetic variation introduced by mutations and that lost by genetic drift (mutationdrift-equilibrium); the population will no longer preserve the low diversity that was a genetic signature of its recent founding. It follows that if non-african populations were founded quite recently from subsets of African populations, we would expect them to be less diverse than are African populations. However, an alternative interpretation is that human population size has been larger in Africa than elsewhere for a long time. 4,11,12 Differences in effective population size between Africa and the rest of the world could reflect either actual census size differences or differences in the frequency of local population extinctions, 34 with extinctions being less frequent in Africa. At mutationdrift equilibrium, within-population genetic diversity is proportional to population size. If European and Asian populations have been small relative to those in Africa since the initial migration of humans out of Africa, sometime after 1.8 million years ago, then differences in genetic diversity could be explained without invoking recent range expansions out of Africa. The first interpretation could be considered to support Outof-Africa but the second to support Multiregionalism, 4 depending on precisely how these two models are defined. 35 Definitions aside, until recently it is has been difficult to distinguish between these two possible interpretations, time and size. But new genetic data now make the second interpretation unlikely. A series of recent studies have analyzed a dataset 36 of numerous individuals from globally distributed populations (Fig. 1) typed for microsatellite or short tandem repeat (STR) genetic loci. 14,17,22,33,37 39 (The exact numbers of individuals, populations, and loci vary among the different studies.) There are two important features of this STR dataset. First, because STRs evolve rapidly, it is possible, more accurately than with most other nuclear loci, to assess of the amount of variation found within populations, regardless of how the genetic loci were ascertained. 32,40,41 Genetic loci are usually discovered by finding differences among individuals in a sample set. For slowly evolving nuclear loci such as single nucleotide polymorphisms (SNPs), the populations represented in the sample set will tend to appear more diverse than other populations, making it difficult to assess within-population genetic diversity accurately. STRs are not free of ascertainment bias, 42 but the bias is usually less than that for many other nuclear loci. Second, each individual was typed for numerous loci. Natural selection can affect patterns of genetic variation in ways that mimic population history and, even in the absence of natural selection, by chance, the history of any particular genetic locus will often be very different from the history of the populations under study. Consequently, to infer human population history accu-

4 72 Weaver and Roseman Articles Figure 1. Geographic locations of the human populations in the global STR dataset. Each population is indicated by a triangle. rately, it is crucial to analyze multiple independently evolving loci 5,43,44 (Box 2). One of the first analyses done on the STR dataset was of genetic distances among human populations. 33 Genetic distances can be calculated at either local or global scales. At the local scale, there is a tendency for genetic and geographic distances to be positively correlated. 15 This typical pattern is also found for the STR dataset but, in this case, it is found at the global scale. 14,17 Interestingly, morphological distances based on cranial measurements are also correlated with geographic distances among globally distributed human populations. 14,45 At the local scale, the relationship between genetic and geographic distances is usually thought to be due to isolation by distance, which is an equilibrium model. 17 Taken at face value, consistency at the global scale with an equilibrium model would appear to support Multiregionalism, or at least make it unnecessary to invoke recent range expansions out of Africa to explain patterns of human genetic diversity. However, genetic distances are not the only relevant feature of the data. Because STRs are not as affected by ascertainment bias as are many other nuclear loci, it is possible to assess within-population genetic variation more accurately. The resulting pattern is that the amount of genetic... it is not just that African populations are more diverse than other populations, but that there is a sequential decrease in diversity with distance from Africa. With some exceptions, this sequential decrease was invisible to earlier studies,... variation found within a population declines predictably with that population s distance from Africa (Fig. 2). 17,22,33,46 An important early observation made about human genetic diversity was that African populations were the most diverse. This observation could be explained either by differences in population size or differences in time since the founding of the populations. Based on STRs, it turns out that it is not just that African populations are more diverse than other populations, but that there is a sequential decrease in diversity with distance from Africa. With some exceptions, 23 this sequential decrease was invisible to earlier studies, in part because of ascertainment bias, and also because diversity tended to be assessed across three large regions, Africa, Asia, and Europe, rather than population by population. It is difficult to imagine an ecological reason to explain why, moving away from Africa, each successive region would have a smaller population than the previous one. Relative to Europe and Asia, Africa does have a large equatorial land mass, which could have resulted in a larger human population size, given that humans, like other primates, are tropically derived animals. But this rationale cannot readily explain why European populations are more diverse than eastern Asian populations or why both are more diverse

5 Articles Genetic Evidence for Modern Human Origins 73 Box 2. Genetic Inferences of Human Population History Because gene trees are not equivalent to population trees, single genetic loci rarely provide much power to distinguish between competing models. The basic problem of relying on a single locus is illustrated nicely by simulations conducted by Harpending and colleagues. 79 These authors consider two populations that differ from each other genetically about as much as two human populations from different continents. The populations have always been constant in size and are connected by gene flow at a rate of one individual exchanged every two generations. The simulated situation can be thought of as a simple Multiregional model consisting of two continental populations, say Africa and Europe, that have been connected by gene flow for a long time. Unlike real genetic data, the evolutionary history of the simulated populations is known and gene trees for a single genetic locus can be generated multiple times. Even though the evolutionary history of the populations is always the same, the gene trees that are generated often differ substantially from each other in features such as branch lengths and the clustering of individuals from the two populations. Harpending and colleagues 79 present four gene trees that are representative of the results of their simulations. In one of these, individuals from only one population cluster on one side of the primary split and individuals from both populations are found on the other side. The presence of African populations on both sides of the primary split of the human mtdna tree, 31 an African root, is often interpreted as strong evidence of the Out-of-Africa model. However, even though the simulated populations were constant in size and geographically fixed, a tree was produced that is rooted within one population. The other three trees all show a mix of individuals from both populations on both sides of the primary split. If we assume that these four trees are representative of the probability of generating a tree rooted in one population and the two populations represent Africa and Europe, then the probability of an African root would be 1/4 3 1/2 ¼ 1/ 8 ¼ (the probability of rooting within one population multiplied by the probability that the root population is Africa). This probability is not particularly high, but it is still higher than the 0.05 significance level typically required to reject a hypothesis. Analyses of the Y-chromosome produce trees with topography similar to that of the mtdna tree 108 and the Y-chromosome is inherited independently of mtdna. Considering both loci together, the probability of the data for the simple two-region Multiregional model now becomes (1/8) 2 ¼ 1/64 ¼ While we cannot reject the simple multiregional model with one genetic locus, it is possible to rule it out with two independent loci. The basic point is that information from multiple genetic loci is often needed to robustly infer the history of human populations, with more loci needed the more similar the competing models. Only consistent areas of the trees are likely to reflect population history rather than the idiosyncratic history of a particular genetic locus. than Oceanian populations. Alternatively, stabilizing natural selection could be responsible for limiting variation in the number of STR repeats, 27 as seems to have occurred at higher taxonomic levels, such as in comparisons of humans, chimpanzees, gorillas, and orangutans. 32 To be viable, this explanation would need to account for the fact that stabilizing natural selection was more severe in a stepwise manner with distance from Africa. As humans expanded out of Africa, stabilizing natural selection would, if anything, be expected to be stronger in the populations who remained in African environments rather than in those who encountered new environments. In addition, the circumstances leading to natural selection would have to be relatively uniform across numerous genetic loci. Eswaran and colleagues 2,47 have proposed an intricate natural selective model that may be consistent with this pattern, which we will discuss later in the context of admixture and the question of whether natural selection explains the spread of modern human anatomical features. Importantly, decreasing genetic diversity with distance from Africa is not only found with STRs. When analyzed properly, other nuclear datasets show exactly the same pattern of decreasing diversity. The same individuals as in the STR dataset have also been typed for almost 3,000 SNPs. Once ascertainment bias is minimized in the SNP dataset by assessing variation at stretches of DNA considered together (long haplotypes) instead of at single SNPs sites, it turns out that within-population SNP diversity is almost perfectly correlated with within-population STR diversity (Fig. 3). As in the STR dataset, African populations are the most diverse, followed in order by European, eastern Asian, and Oceanian populations. 48 There is also some evidence that within-population cranial diversity decreases with geographic distance from Africa, although the strength of this relationship is much weaker than that for genetics. 49 The consistency across the STR and SNP datasets is more readily explained by population history and demography, which would be expected to affect all loci uniformly, rather than by natural selection, which could be quite variable in its effects. The most plausible interpretation of decreasing genetic diversity with distance from Africa is that differences in within-population diversity are due to differences in founding time, because human populations were founded recently enough that they

6 74 Weaver and Roseman Articles The spectacular recovery of Neandertal ancient DNA offers the most direct line of evidence for evaluating genetic admixture. mtdna has been extracted from thirteen Neandertal fossils; nuclear DNA from both autosomal loci and the Y-chromosome has been retrieved from multiple individuals. So far, no positive evidence of admixture has been detected However, because past DNA lineages could have been lost by genetic drift over the approximately 40,000 years since modern humans entered Europe, the lack of evidence of admixture does not rule Figure 2. Relationship of within-population genetic variation with geographic distance from eastern Africa. Heterozygosity is the measure of within-population variation; the distances are in kilometers. Each star represents one population from Fig. 1. Modified from Prugnolle, Manica, and Baloo. 22 have not yet reached equilibrium. As modern humans expanded out of Africa, the most distant regions would be the least diverse because of serial loss of diversity with each founding event and because the youngest populations are the furthest from equilibrium. 17,22,37,38,41 Liu and colleagues 38 have conducted simulations to determine how well this particular Out-of-Africa model fits the STR data and to estimate the parameter values that produce the best fit. The overall fit of the model is extremely good. A crucial test for alternative models would be to show that they have similar probabilities of producing the observed STR data. The best-fitting parameter values suggest that modern humans expanded out of Africa starting about 50,000 years ago from a founding population with an effective size of about 1,000 individuals. Archeological evidence appears to indicate reductions in human population size in southern Africa around 50,000 years ago, probably caused by increasing aridity, 50 which may be related to the timing of the modern human expansion out of Africa. Returning again to the global relationship between genetic and geographic distances, the interpretation is quite different under an equilibrium isolation-by-distance model than under a model of serial founder events during a range expansion out of Africa. Under isolation by distance, geographically neighboring populations will be genetically similar because they often exchange migrants, so that genetic similarity is primarily due to gene flow. Under a serial-founder-event model, similarity among populations is primarily due to common history, either by ancestor-descendent relationships or by descent from a common source population. Geographically neighboring populations are genetically similar because they diverged quite recently. Related to this, it has long been observed that human populations are genetically quite similar to one another, with only about 5% 15% of the total genetic variation found between populations. 39,51 A serialfounder-event model suggests that the limited genetic differences among human populations are primarily the consequence of a short history of divergence rather than a long history of divergence masked by gene flow. IS THERE GENETIC EVIDENCE OF ADMIXTURE BETWEEN MODERN HUMANS AND NONMODERN EURASIANS? mtdna has been extracted from thirteen Neandertal fossils; nuclear DNA from both autosomal loci and the Y-chromosome has been retrieved from multiple individuals. So far, no positive evidence of admixture has been detected. However, because past DNA lineages could have been lost by genetic drift over the approximately 40,000 years since modern humans entered Europe, the lack of evidence of admixture does not rule out a Neandertal genetic contribution to early modern human populations. out a Neandertal genetic contribution to early modern human populations. 56,57 How much admixture is consistent with the data depends on demographic assumptions about the modern human population of 40,000 years ago, including whether it was growing rapidly in size, how subdivided it was, and how long Neandertals and modern humans overlapped

7 Articles Genetic Evidence for Modern Human Origins 75 Figure 3. Relationship between SNP haplotype and STR within-population genetic variation. Heterozygosity is the measure of within-population variation. Each star represents one population from Fig. 1. Modified from Conrad and coworkers. 48 in time and space. 55,56,58,59 The statistical power to detect ancient admixture increases rapidly with the number of independent genetic loci, 60,61 so further analyses of Neandertal nuclear DNA could prove fruitful. Perhaps the largest obstacles will be establishing that extracted nuclear DNA actually comes from the Neandertal fossils and is not simply contaminating modern human DNA, and that the original sequence has not been obscured by chemical changes after death. 55,62 65 Wall and Kim 66 estimated when Neandertal and modern European lineages split and the amount of admixture between the two groups based on the sequences presented in the two studies of Neandertal nuclear DNA. 52,53 They argue quite convincingly that large discrepancies between the two studies indicate substantial contamination problems for at least one of the studies. Neandertal mtdna is distinctive enough 55,63,67 that its authenticity can be established from the sequence itself. However, this is not the case for most nuclear regions, which are expected to coalesce before the split between the Neandertal and modern human lineages. 68 Ancient DNA from early modern humans in Europe could provide another test for admixture, but so far the potential for contamination has made it impossible to verify that DNA extracted from modern human fossils 69,70 is actually endogenous. 62 A more indirect approach to detecting admixture is to examine extant human genetic variation. Taking this approach, Templeton 5,71,72 used nested clade analysis (NCA) to identify what appear to be numerous episodes of gene flow between African and Eurasian populations starting as early as 1.5 million years ago. In support of these inferences, the same analyses also identified three range expansions out of Africa with dates that are broadly concordant with the initial dispersal of human ancestors out of Africa, the colonization of Europe, and the spread of modern humans out of Africa. While intriguing, these analyses have two potential shortcomings. First, the inferred episodes of gene flow could have been among African populations, 1,2 because the ancestors of today s Eurasians may have been part of one subdivision of a structured African population at the time when the gene flow occurred. While not directly contradicting Out-of- Africa, this interpretation does suggest that modern humans originated from a relatively large and subdivided African population rather than from a small population whose descendants replaced other African populations as well as Eurasian populations. The second problem has to do with statistical testing. According to Templeton, 5,72 based on his inferences of gene flow, a complete replacement Out-of-Africa model can be rejected with high statistical confidence. However, his statistical test assumes that NCA never produces false positives of gene flow. The test considers confidence intervals for the timing of the inferred episodes of gene flow, but not the possibility that a gene flow inference could be completely incorrect. For an appropriate statistical test, this additional uncertainty must be incorporated. False positives are a real possibility, given that NCA often inferred population structure and range expansions in simulations of populations for which mating was entirely random across all the populations. 77 The best way evaluate Templeton s model of three range expansions coupled with gene flow would be to simulate it, along with a complete replacement Out-of-Africa model, and determine the probabilities that both models will produce the observed NCA inferences. It may be that a complete replacement Out-of- Africa model and Templeton s model have a similar probability of producing the observed data. Templeton 5,72 dismisses the simulation approach because it can only evaluate the goodness of fit of a limited set of models, leaving open the possibility that the best-fitting model is not considered at all. NCA supposedly overcomes this problem by making inferences directly from the data using a specific set of rules. These rules, the inference key, are generalizations based on a combination of population-genetic theory and empirical examples from circumstances where it is deemed that secure, independent information about population history is available. However, by including a limited number of known examples and results from theory that are entirely equivalent to results drawn from simulations, the inference key implicitly limits the space of models that are considered, which is equivalent to the explicit limiting of the simulation approach. Once NCA has been used to infer a particular model, it seems reasonable to use simulations to evaluate this model against other competing models. The mtdna of many human populations indicates that they either passed through a bottleneck or grew rapidly from a small size, but some nuclear datasets appear to show a population crash instead, with only limited expansion afterward. 81 Admixture could be the explanation, 2,47 but this discrepancy could be more apparent than real, because ascertainment bias affects many nuclear datasets. 48,59,82,83 Studies that make corrections for ascertainment bias 48,84 and datasets for which individuals have been sequenced completely (no ascertainment bias) do show genetic signatures of bottlenecks, at least for non-african populations, and are generally more consistent with mtdna. The decrease in within-population STR diversity with distance from Africa also indicates a series of

8 76 Weaver and Roseman Articles Box 3. Does the mtdna Coalescence Time Indicate the Origin of Modern Humans? The human mtdna coalescence time of about 150,000 years ago could indicate a bottleneck or speciation event that signals the origin of modern humans, but all mtdna variants present today will eventually coalesce sometime in the past regardless of whether there was a bottleneck or not. If there was a severe bottleneck around 150,000 years ago, then the reduction in population size could cause mtdna lineages to coalesce rapidly around this time, and the coalescence time would reflect an actual demographic event (A). However, the same coalescence time could be produced in a constantsized population with an average (harmonic mean) population size the same as that of the severely bottlenecked population (B). In this case, the mtdna coalescence time would not reflect a demographic event at all. One way to look at the problem is to compare mtdna and autosomal coalescence times. In contrast to mtdna, autosomal loci coalesce, on average, about 450,000 years ago. 52 Does this indicate that modern humans originated from a bottleneck 450,000 years ago? A roughly fourfold difference in coalescence times between mtdna and the autosomes is actually consistent with a human population that was approximately constant in size around 150,000 years ago. mtdna will coalesce in approximately one-fourth the time as will autosomal loci because it is passed only through females and is haploid (unpaired), whereas autosomal DNA is inherited from both parents on diploid (paired) chromosomes. This is not to say that a bottleneck or speciation event at 150,000 years ago is inconsistent with mtdna evidence, just that the mtdna coalescence time should not be assumed to indicate a bottleneck when constant population size is also a plausible explanation. Bottlenecks do appear to have happened, but most data suggest that they occurred when modern humans expanded out of Africa about 50,000 years ago, 17,22,84 86 not at 150,000 years ago within Africa. The shallow mtdna coalescence time does indicate that the effective population size of humans has been quite small on average. This is more consistent with an Outof-Africa than a Multiregional model because it is difficult to imagine a small population spread across the entire Old World. 79 However, this interpretation is complicated by the fact that effective size can sometimes be much smaller than census size. 34 The basic point is that there is no reason to suspect that the mtdna coalescence time represents an actual demographic event such as the origin of modern humans. founder events as modern humans expanded out of Africa. 17,22,33,38 Highly divergent haplotype pairs indicated either by extended linkage disequilibrium 61,88 or deep coalescence times 73,74 could be due to admixture. Linkage disequilibrium breaks down over time by mutation and recombination, so extensively linked regions of the human genome may have been introduced by admixture with individuals from a population with a highly divergent history, such as Neandertals or other nonmodern Eurasians. Alternatively, extensive linkage could be a signature of a recent sweep of an adaptive allele and its surrounding DNA through human populations by directional natural selection. 89 The human mtdna coalescence time of about 150,000 years ago 31 is sometimes taken to date a bottleneck or speciation event that signals the origin of modern humans. 90 If this were the case, depending on the severity and duration of the bottleneck, finding loci with coalescence times substantially older than 150,000 years could indicate admixture. 74 However, the mtdna coalescence time may not correspond to a demographic event at all (Box 3). Moreover, even with-

9 Articles Genetic Evidence for Modern Human Origins 77 out admixture, we expect many autosomal loci to have deep coalescence times both within and outside of Africa. 87 Consequently, to demonstrate admixture one must show that there are too many highly divergent loci to be compatible with a complete replacement Out-of-Africa model, 73 which inevitably involves numerous assumptions that are difficult to validate. Other confounding factors are the possibility of balancing natural selection, 91 population structure in Africa, and inadequate African sampling. 92 While multiple studies have noted patterns of human genetic variation that may be consistent with admixture, to make a convincing case it will probably be necessary to examine individual loci in detail to rule out other explanations. One locus, microcephalin, has been examined in detail, 93 and the argument for admixture is reasonably convincing. Not only do two haplotypes coalesce about 1.7 million years ago, but, in addition the D haplotype appears to have risen in frequency about 37,000 years ago. Arguably, positive natural selection caused this frequency increase after the D haplotype was introduced by a rare admixture event between two deeply diverged populations, but it may be explained by neutral demographic processes. 96 In support of the neutral explanation, microcephalin was not one of the genes detected in recent genome scans for natural selection. 97,98 It should be noted, however, that the different statistical tests to detect natural selection do vary in the circumstances under which they are most sensitive. 98,99 The adaptive advantage of the D haplotype is still unknown, but it appears to not be related to brain size or cognition. 100,101 While the case for admixture is reasonably convincing, the identity of the admixing populations is unclear. Because the D haplotype is common outside of Africa today, admixture may have occurred between modern humans and nonmodern Eurasians such as Neandertals. 93,94 However, given that only 9 of the 89 individuals genotyped were from sub-saharan Africa, 93 another possibility is that the African frequency of the D haplotype is underestimated because of limited sampling. If this is the case, then admixture between different African populations would be equally likely. DOES NATURAL SELECTION EXPLAIN THE SPREAD OF MODERN HUMAN mtdna VARIANTS AND ANATOMICAL FEATURES? One locus, microcephalin, has been examined in detail, and the argument for admixture is reasonably convincing. Not only do two haplotypes coalesce about 1.7 million years ago, but, in addition the D haplotype appears to have risen in frequency about 37,000 years ago. The rapid accumulation of nuclear sequence data has lead to multiple genome scans for signatures of natural selection in human populations. 89,97,98 One interesting observation from these scans is that many signatures of natural selection appear to be population-specific, 97 indicating adaptation to local environments. Genome scans have the potential to provide much insight into recent human evolution and diversification, as well as into broader questions such as how much of the human genome has been shaped by natural selection rather than by neutral evolutionary forces such as mutation, genetic drift, and gene flow. So far, however, these studies have yet to provide direct insights into modern human origins. Consequently, this section focuses on the issues of whether natural selection can explain the spread of modern human mtdna variants and anatomical features rather than being a more general review of the influence of natural selection on the human genome. Neandertal and extant human mtdna variants can be readily distinguished from each other. 55,63,67 This suggests limited admixture under some demographic scenarios, because if Neandertals and modern humans interbred we would expect at least some extant humans to have mtdna variants similar to those of Neandertals. 55,58,59 An alternative explanation is that mutation produced a highly adaptive mtdna variant that spread through the human population by natural selection, replacing other variants such as those extracted from Neandertal fossils. 27,28 Given that most Neandertal fossils are on the order of 50,000 years old and their mtdna sequences fall outside the variation found in living humans, 55,63,67 the sweep must have occurred after this time for it to have eliminated Neandertal variants. The coalescence time of human mtdna is substantially older than 50,000 years ago, 31 so the signature of this selective event, if it happened, should still be preserved in patterns of living human mtdna variation. Detailed analyses do suggest that human mtdna variation has been influenced by natural selection, but it seems to have been mainly purifying natural selection 102 and not selective sweeps (directional natural selection). Purifying natural selection removes deleterious variants from the population and will slightly bias coalescence time estimates for recent nodes in the mtdna tree, but it will not strongly affect the branching order of the tree. 102 This suggests that the human mtdna tree mainly reflects the history of human populations rather than directional natural selection. A related issue is whether natural selection explains the worldwide spread of modern human anatomical features after about 50,000 years ago. This spread is typically taken to reflect a replacement of Eurasian

10 78 Weaver and Roseman Articles populations, such as Neandertals, by expanding Africans, but if the anatomy is adaptive the action of natural selection could mimic a range expansion. The argument is essentially the same as for mtdna except that natural selection would have acted on a gene complex instead of a single genetic locus. Eswaran and colleagues 2,47 have proposed a model under which a highly adaptive phenotype is spread from Africa by local migration and natural selection, but because, at any given time, admixture occurs only within a narrow geographic region, some genetic loci will appear to show a series of founder events but others will not. Founder events would occur because in the narrow admixture region the small number of individuals carrying the adaptive modern phenotype would expand at the expense of resident nonmodern and hybrid individuals. This process could explain why some genetic loci indicate bottlenecks whereas others appear not to do so. African-derived alleles would have spread across the world either by being linked to the adaptive gene complex or by chance, and would show signatures of a series of founder events. On the other hand, the Eurasian-derived alleles that spread would preserve the signature of a relatively large, nonmodern population. This model was originally proposed to explain the lack of signatures of bottlenecks in some nuclear loci. However, as discussed earlier, another possible explanation is ascertainment bias. In addition, as Eswaran and colleagues 2,47 recognized, one potential problem with this model is that it cannot explain the spread of modern human anatomical features unless they themselves are the phenotypic advantage. It would also be necessary to identify which features of modern human anatomy were so adaptive that they rapidly spread through the global human population. Therefore, a relevant question is whether or not the anatomical differences between Neandertals and modern humans are adaptive. Evolutionary quantitative genetic analyses, in fact, show that Neandertal and modern human cranial differences There is strong genetic evidence of range expansions out of Africa, as well as evidence that the reduced genetic diversity of non-africa populations is because they originated more recently rather than because they were smaller. can be explained by genetic drift, 103 making it unlikely, at least for the cranium, that modern human anatomical features were spread by natural selection rather than a range expansion out of Africa. An important point is that these analyses do not simply compare the magnitude of the morphological differences between Neandertals and modern humans; they are multivariate tests of how the patterns of covariation across different cranial measurements compare to those expected for divergence by genetic drift. Natural selective hypotheses designed to account for Neandertal and modern human cranial differences would also need to show multivariate consistency with the observed patterns of variation. While it may be possible to imagine natural selective scenarios that mimic genetic drift for a single measurement, such as fluctuating directional natural selection, the scenarios become much less plausible for multivariate patterns of variation. While cranial form appears not to be a candidate phenotype to bolster phenotypic sweep models, we cannot rule out that a yet unknown set of features was subject to directional selection leading to the spread of alleles out of Africa. The evolutionary pictures obtained from comparisons of Neandertal and modern human mtdna and cranial form are very similar overall. 103 A recurring pattern is congruence between craniometrics and genetics for humans and Neandertals, 14,49, which seems inconsistent with the hypothesis that natural selection has obscured or removed the signatures of population history or phylogeny in both. CONCLUSIONS Genetic and fossil evidence indicate that Africa played a predominant role in the origins of modern humans. New genetic data further imply that this was not simply because Africa had a larger longterm population size than elsewhere. There is strong genetic evidence of range expansions out of Africa, as well as evidence that the reduced genetic diversity of non-africa populations is because they originated more recently rather than because they were smaller. It is unclear whether these range expansions resulted in the complete replacement of nonmodern Eurasians or if admixture occurred. For at least one gene, microcephalin, a reasonably convincing case can be made for admixture. At minimum, the African population that gave rise to these range expansions seems to have been quite structured, with exchanges of migrants between deep subdivisions. This implies that modern humans did not originate from a bottleneck about 150,000 years ago within Africa, although there were founder events as modern humans expanded their range outside of Africa. Taken together, these lines of evidence support an Out-of-Africa model of modern human origins, although not necessarily complete replacement of nonmodern Eurasians. ACKNOWLEDGMENTS We thank John Fleagle, Henry Harpending, Richard Klein, Teresa Steele, and two anonymous reviewers for providing valuable comments on earlier drafts of this paper. REFERENCES 1 Pearson OM Has the combination of genetic and fossil evidence solved the riddle of modern human origins? Evol Anthropol 13:

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