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Thread: A Structured Ancestral Population for the Evolution of Modern Humans

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    Lightbulb A Structured Ancestral Population for the Evolution of Modern Humans

    The view that modern humans evolved through a bottleneck from a single founding group of archaic Homo is being challenged by new analyses of contemporary genetic variation. A wide range of middle to late Pleistocene ages for gene genealogies and evidence for early population structures point to a diverse and scattered ancestry associated with a metapopulation history of local extinctions, re-colonization and admixture. A different balance of the same processes has shaped chimpanzee diversity.

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    Post Re: A structured ancestral population for the evolution of modern humans

    In leyman terms, this means that clusters of different pre-homo sapiens developed into different types of homo sapiens? Perhaps that in junction with lack of gene flow would explain phenotype differences but on a later phase those different groups had gene exchange between them or else there would still be different types of hominids....right?
    That people breed with those they find attractive within their own ethnic population is all the eugenics I think is necessary. - Milesian

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    Post Re: A structured ancestral population for the evolution of modern humans

    Quote Originally Posted by Dr. Solar Wolff
    I can't access PDF files but from your summary, it looks as if this data supports the multi-regionalists. Is that true?

    A structured ancestral population for the evolution of modern humans

    Rosalind M Harding and Gil McVean


    The view that modern humans evolved through a bottleneck from a single founding group of archaic Homo is being challenged by new analyses of contemporary genetic variation. A wide range of middle to late Pleistocene ages for gene
    genealogies and evidence for early population structures point to a diverse and scattered ancestry associated with a metapopulation history of local extinctions, re-colonization and admixture. A different balance of the same processes has shaped chimpanzee diversity.

    For geneticists, studies of modern human origins constitute a search for an ancestral history that can satisfactorily explain patterns of contemporary genetic diversity. The broader evolutionary debate concerns the emergence of a type of human who, by reference to people living now, was anatomically and behaviorally modern [1–9]. Was that emergence a revolutionary event in which a small founding group of anatomically modern Homo sapiens replaced ‘archaic’ species of human [1–5]? Alternatively, was the evolution of a modern complex of traits in sub-Saharan Africa a gradual process, with assimilation of genes from a widely distributed Homo erectus population, including Neanderthals in Europe [8,9]?

    The contribution of genetics to the modern human origins debate has had three phases so far. The first was the realization that genes preserved ancestral history, and that recovering history was a credible scientific endeavor — unlike eugenic efforts to predict or shape the genetic future. Initially, classical polymorphisms were used to study history as population phylogeny [10]. Subsequently, DNA sequence data provided genealogical resolution of relationships among individual gene copies. In this second phase, heralded by the first studies of mitochondrial DNA (mtDNA) diversity, geneticists added time scales to phylogenies and genealogies.

    These studies raised hopes among archaeologists that genetic dating would be a useful tool to augment their methods for dating bones and artifacts [10,11]. In the third and most recent phase, population geneticists have examined diversity in samples from populations to make demographic inferences from tell-tale clues in summaries of data (for example, Tajima’s D, mismatch distributions and the shapes of gene trees [11,12,13]).

    The recent African origin (RAO) model for modern humans describes a speciation bottleneck in sub-Saharan Africa followed by range expansions and subsequent population growth [12]. Diversity in mtDNA provides the clearest genetic evidence for this model. Most analyses of nuclear loci conclude support for this RAO model but the evidence for a speciation bottleneck is equivocal. What do we mean by a bottleneck? The reduction of a widespread subdivided species complex to a single regional population is one form of bottleneck.

    However, we first refer more specifically to a bottleneck in ancestral population size that could have occurred if a large, well-mixed population was reduced to a handful of survivors. If such a bottleneck occurred, it should be detectable in loci
    across the genome, but it is not. The explanation could be that diversity in gene coding regions was protected by balancing selection while the rest was squeezed by the presumed bottleneck [12]. Alternatively, there are demographic
    models that can accommodate a range of patterns in genetic variation including those that appear to suggest balancing selection as well as those indicating bottlenecks.

    We also look to recent studies of chimpanzee diversity for a different perspective on demographic history. Our prediction is that new metapopulation models will provide the key to understanding human demographic history in the context of primate evolution. Genetic evidence for a recent African origin In the decades before mtDNA sequence analysis became routine, geneticists worked from protein polymorphism, which is abundant in human populations [14] and is a valuable proxy for genetic variation in the nuclear genome. The homogeneous distribution of this variation across racial groups [15] showed that modern human diversity did not preserve in situ deep structural differences
    between populations.

    Consequently, multiregional evolution was untenable unless high levels of gene flow between Africa and Eurasia had been sustained throughout the evolution of Homo. With high levels of intercontinental gene flow there would be no reasons to expect either higher diversity in Africa than in Europe or Asia, yet there is, or that the largest genetic distances would be between sub-Saharan African and non-African populations, yet they often are [12]. Recent studies of worldwide
    patterns in human DNA diversity have not neglected or failed to make the same observations.

    One new caveat, however, is that while genetic distances between African and non-African populations are large relative to distances between non-African populations, the largest distances can be found among African populations [16].
    It has also become evident that, although only weakly structured, autosomal variation does carry information about the geographic birthplace of living individuals in both microsatellite mutations and linkage disequilibrium between loci, as well as from gradations in allelefrequency differences [17,18].

    This significant but weak geographic structure owes a lot to recent mutation and recombination events in conjunction with genetic drift, and not much to the preservation of ancient ancestral population structure in situ. Some structure in the ancestral population before the range expansions out of Africa has been detected, however, by clustering methods that do not depend on present day geographic classification of individuals.

    The algorithm STRUCTURE, first used to analyse human autosomal microsatellite variation [18], also has been applied to Helicobacter pylori, a chronic gastric pathogen that has colonized humans worldwide, revealing structure in both recent and ancient ancestral human populations [19]. This study distinguished two ancestral source populations within Africa: one for a range expansion into the rest of Africa, and the other for expansions into Europe and Asia. High levels of resolution of phylo-geographic patterns have been only otherwise achieved by studies of the non-recombining portion of Y chromosomes (NRY)s [20] and mtDNA diversity [21,22].

    The main aim of studies in the third phase has been to refine the mtDNA-based RAO model by detecting and integrating evidence for population size bottlenecks and recoveries with geographic range expansions [12]. Starshaped genealogies, in particular those preserved in mtDNA data [12] and Y chromosomes, [23,24] have been interpreted as clear evidence for population size expansions, and autosomal loci have provided confirmation of population size fluctuations. For example, a bottleneck followed by growth for European demography has been inferred from analyses of autosomal SNPs (single nucleotide polymorphisms) and microsatellites [25,26,27].

    Where a growth signal is lacking in genetic data, despite population size expansion, the explanation can be that subdivision in the ancestral population has not been taken into account [28]. For example, a range expansion by a small founding group could have established several relatively isolated subpopulations which then later increased in size. Any population structure that developed in the initial range expansion could have weakened subsequent growth signals [29,30]. Thus, low levels of phylo-geographic and demographic resolution for autosomal loci compared with mtDNA and NRY chromosomes nonetheless may be compatible with an RAO model that incorporates a speciation bottleneck.

    But we still need to be more quantitative and to progress from statistical analyses of pattern to rigorous model specification [13].


    Was there a speciation bottleneck?

    Despite other more pertinent evidence to hand, it was the estimate of roughly 200 000 years for the time to the most recent common ancestor (TMRCA) of worldwide diversity in mitochondrial DNA lineages [31] that won over majority support in favor of a RAO model. Periodic oscillations in Pleistocene climate caused deterioration and fragmentation of a suitable habitat for modern humans in Africa and a glacial maximum at 120 000 years ago potentially could have squeezed lineage diversity through a small founding group. Diversity in mtDNA is compatible with an expansion out of a bottleneck.

    However, does autosomal diversity also provide evidence of a bottleneck in ancestral population size? Tracing through the 30 000 genes located mainly in our autosomal chromosomes are a large number of different gene genealogies. Most have features that provide a strong contrast to the star-like genealogies for mtDNA and NRYs. With many TMRCA estimates ranging from 500 000 years to a million years, and some that are older than this [12], it is clear that the mtDNA Eve estimate, and its interesting association with dates for the emergence of modern human anatomy in the fossil record, stands firm [32] but stands almost alone.

    A Late Pleistocene bottleneck in ancestral population size would have funneled TMRCA estimates for many loci into a narrow range around the estimate from mtDNA of 200 000 years, and the absence of such clustering argues against population recovery out of a handful of survivors. The range of TMRCA estimates from autosomal loci is compatible with sampling from an effective population size (Ne) of 10 000 [14,25,33] (Table 1) under the assumption that Ne has remained constant over the past million years. The expected demographic signature for a constant sized population of 10 000 has been reported for many studies of African samples [25,33] but not all [34].

    Although the ancestral population may have been restricted to Africa, contemporary populations worldwide preserve an exceptional abundance of high-frequency, completely mismatching common SNP haplotype pairs, referred to as ‘yin yang haplotypes’ [35]. To account for their geographic distribution, their age must predate the phase of modern human range expansions. Yin yang haplotypes capture the same feature of the data that others have reported as positive Tajima’s D statistics [12].

    Possible explanations for yin yang haplotypes of either deep population splits (multiregional evolution model) or maintenance of ancient lineages by balancing selection were discounted by the authors [35]. They concluded that a well-mixed ancestral population, featuring an Ne size of 10 000, has been maintained. However, any population large enough to support an Ne estimate of 10 000 is probably too large not to be structured by non-random mating to some extent.

    It has become easy to accept the recent age for mitochondrial Eve, and also to justify the many older TMRCA estimates for autosomal gene genealogies, by assuming that Ne has not been reduced from 10 000, but an NRY TMRCA estimate of 60 000 years [24], which is so much younger than mitochondrial Eve, has produced a quiet sense of unease. This point estimate for Adam can be stretched to 109 000 years [32] by judicious choice of statistical method, using generation intervals of 30 years instead of 20, and dropping the exponential growth assumption. In fact, the star-shape of the genealogy, which has been interpreted as evidence for growth out of a bottleneck, may actually be an artefact of pooling across ethnicities in fine-scale structured populations [36,37]. However, special pleading for differential reproductive behavior of males and females is required, and no-one has demonstrated that shallow NRY diversity is compatible with a single but well-mixed ancestral population of substantial size in the Late Pleistocene [13].

    Increasingly, population geneticists are directing their attention to structure in the ancestral population from which range expansions across Africa and out of Africa occurred [11,12,13,38]. Several studies have concluded that African populations must have been more strongly subdivided and isolated from each other than non-African populations [11,12,16,39], and that some African populations were not a direct source for the range expansions out of Africa [40]. An additional and more contentious possibility [41–45,46] is that not all modern human diversity presently found outside of Africa evolved from recent African ancestry.

    The greater time-depth of autosomal and X chromosome loci, compared with mtDNA and Y chromosomes, allows subdivision in the ancestral population to date to a time when modern human morphology was evolving from an archaic form. Patterns in these genetic data do suggest admixture between the Late Pleistocene humans, whose range expansions are visible in mtDNA and Y chromosome data, and populations established earlier. Probably, most of this gene flow took place within sub-Saharan Africa, but we cannot rule out admixture elsewhere in the world.


    A metapopulation model for human evolution

    For a more dynamic approximation to human population structure than offered by classical equilibrium island or stepping-stone models, the brightest prospects are given by metapopulation models. Metapopulations are made up of transient populations connected by migration, subject to extinction and rebirth by colonization, as well as to fluctuation in local size [47]. Metapopulation models provide a sufficient approximation to biological reality to be useful in simulation studies of human evolutionary history. Also, recent theoretical work shows how the coalescent process for modeling gene genealogies can be related to evolution in a metapopulation structure [47].

    Although the spread of some genes between populations will be restricted, possibly increasing their ATMRCA times, in contrast, other genes that show no effects of structure due to lucky migrations and colonizations will trace shallow coalescent histories. Consequently, structure in a metapopulation has the potential to elevate both the average level of genomic diversity and expected TMRCA estimates, but makes a particularly substantial impact by increasing the variance in TMRCA estimates.

    Should metapopulation dynamics be applied not only to the recent evolution of modern humans [29] but also to the evolution of Homo throughout the Pleistocene? It is feasible to suppose that there was a higher level of extinction of subpopulations during harsh phases of glacial cycles, reduced diversity and increased coalescenceof geographically scattered lineages. The RAO model assumes an evolutionary history of population splits and a speciation bottleneck associated with extinction of lineages closely related to a core population (Figure 1a). Alternatively, there is no expectation for a bottleneck associated with persistence of a single core population in a metapopulation history (Figure 1b).

    The presence of multiple populations, and their absorption of some admixture before neighboring extinctions, does permit diverse lineages for some but not all genes to continue. Under this model, a wide range of TMRCA estimates for autosomal loci — and a TMRCA for NRY chromosomes that is younger than the TMRCA for mtDNA — does not pose any difficulty. Furthermore, yin yang haplotypes [35], positive Tajima’s D values [12], and some atypically low FST values [48] become easy to account for without generalizing the explanation of balancing selection beyond specific cases of immunity response.


    Perspectives from a non-human genome

    The application of metapopulation models is likely to prove very helpful, not only for understanding how evolutionary processes have shaped human diversity over perhaps the past million years, but also for efforts to understand the evolution of chimpanzee diversity [49,50]. Pan troglodytes is divided among subspecies in western, central and eastern regions of Africa, and finescale structure within some P. troglodytes populations is also notable [50,51]. Diversity is higher than for modern humans. However, surveys of autosomal inter-genic regions, introns and psudogenes [50,52,53,54] report diversity for the P. troglodytes species that is perhaps only 1.5 times or at most twofold higher than for humans (Table 1). This is in marked contrast to reports for threefoldhigher diversity in chimpanzees from studies of X chromosome loci [55–58].


    Current Opinion in Genetics & Development

    Models of population structure. Populations are represented by columns, showing intervals of continuity over time, broken by extinction events. Connectivities through colonization events are represented by lines at the base of each column. Additional lines represent further migration. Time is represented vertically with the present at the top. (a) This radial model for population structure mimics phylogenetic divergence. Contemporary diversity has descended from a persistent core population or lineage, from which other populations have diverged. (b) In the metapopulation model, genetic ancestry can be found across more than one population throughout the evolution of Homo. Re-colonization of populations can be sourced from either single populations or admixtures. Metapopulation models do not require geographical locations to be specified, but in the context of human evolution it is likely that African populations dominate as sources for re-colonization events.

    The magnitude of these discrepancies between autosomal and sex-linked loci reflects different drift histories in structured populations. Phylogeographic structure, within and among chimpanzee populations, makes a contribution to high levels of genetic diversity by increasing the length of gene genealogies, allowing accumulation of more mutational differences.

    Until these comparative studies of autosomal diversity, high mitochondrial diversity for chimpanzees compared with humans was understood as indicating that mid-Pleistocene hominins would have carried substantial diversity within multiple species and sub-species across the Old World. Consequently, the inference was made that modern humans must represent just the subset of this diversity contained by a single regional population [49]. What are the implications of only modest differences between humans and chimpanzees in levels of presumably neutral autosomal diversity?

    First, autosomal diversity for P. troglodytes that is 1.5 times to twofold higher than modern human diversity is compatible with a study that has estimated ancestral population size for humans and chimpanzees at 12 000–21 000, and rejected the notion that modern humans, as a species, have a dramatically reduced Ne [60]. Other studies yield estimates for ancestral population size that are several times larger than contemporary human or chimpanzee Ne estimates [61,62]. This may result from several factors, including model assumptions that fail to account for high variability in gene genealogies associated with metapopulation structure. Feasibly, diversity in Homo sapiens was reduced in phases of greater subpopulation extinction and colonization associated with several dispersals out of Africa, but the loss may have been modest.

    Second, structure within and among chimpanzee subspecies could provide feasible guidelines for population structure within and among populations of humans before the extinction of Neanderthal and other archaic populations. Certainly, the distinctiveness of mtDNA D-loop haplotypes obtained from Neanderthal fossils compared with modern humans, including fossil as well as contemporary sources [63], is comparable to mtDNA differences used to define regional chimpanzee subspecies.

    Diversity among Neanderthals is comparable to levels within either modern humans or a chimpanzee subspecies [64]. It is likely that autosomal diversity in chimpanzees has been modified by ongoing genetic exchange between western and central subspecies [49,50]. Similarly for hominins, Neanderthal gene flow into an early modern human population has not been ruled out by theoretical studies [65–67]. Under the assumption of a metapopulation model, an absence of Neanderthal mtDNA lineages in contemporary human populations could reflect either complete replacement of an extinct Neanderthal population or loss by drift following admixture events.


    Evolution of modern human phenotypes

    The search for an ancestral history that can satisfactorily explain the genetic architecture of modern human phenotypes will require models that include positive selection within a structured population [47]. Compelling genetic evidence has been found for geographically local adaptation from analysis of FST values [48]. However, the relatively small Ne values for humans and other primates, compared with Drosophila or rodents, implies weakened purifying selection and an expectation for some level of polymorphism among slightly deleterious variants [52,68,69].

    It will be easy to misinterpret the latter as evidence for positive selection in the form of local adaptation. Identifying the sites in DNA where positive selection has acted on divergence in morphology or other quantitative traits between humans and chimpanzees, against a likely background of genetic drift during colonization bottlenecks [70], also will be difficult [M Ruvolo, in this issue]. Overall, little evidence may emerge from analyses of non-synonymous coding DNA, because both species have shared similar levels of constraint on evolutionary change [71], and maintain an extraordinary similarity in macromolecular phenotypes [72]. The more promising source of genetic evidence for quantitative trait adaptations lies in regulatory variation, much ofwhich is probably outside of coding regions.

    In the fourth phase of the modern human origins debate, geneticists will analyse the evolution of transcription factor sequences and regulatory motifs to understand the series of changes in gene expression that produced modern human phenotypes. The comparison of human and chimpanzee genomes is already beginning to provide clues about the evolution of Homo [73,74]. Molecular clock dating of a mutation in the human myosin gene to about 2.4 million years ago associates the evolution of a more gracile masticatory apparatus with the emergence of early Homo in the hominin fossil record [75]. Positive selection on genes for speech [76,77], brain size [78–81] and probably olfaction [54,82,83] has produced adaptations during hominin evolution. Phylogenetic analysis of evolutionary rates suggested that the FOXP2 gene may have been the target of selection for more proficient spoken language in the recent evolutionary divergence of modern humans from Neanderthals [76,77]. Other examples are sure to follow.


    Conclusions

    Genetic data provide substantial support for range expansions by modern humans out of Africa but not for an RAO model that constrains all ancestry for modern humans into a speciation bottleneck. At present, there is no evidence to support a major reduction and recovery in ancestral population size, although improved models and methods for analyzing multi-locus data may yet find such evidence.

    Levels of diversity across ancestral Homo could feasibly have been twofold higher than levels in contemporary A structured ancestral population for the evolution of modern humans Harding and McVean 5
    www.sciencedirect.com Current Opinion in Genetics & Development 2004, 14:1–8 modern humans, but probably not much greater, and the inferred Late Pleistocene reduction could reflect loss of structure through extinction of some subpopulations, range expansions of others, and increased migration. Due to admixture, perhaps more so during phases of range contraction than in phases of range expansion, some of our genes could have come through multiple archaic populations and not just down a single lineage in Africa.


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    48. Akey JM, Zhang G, Zhang K, Jin L, Shriver MD: Interrogating a high-density SNP map for signatures of natural selection. Genome Res 2002, 12:1805-1814. This genome-wide analysis of 26 530 single nucleotide polymorphisms, the majority of which are non-coding, identified 174 genes as candidates for selection targets. These included 156with atypically high FST values— reflecting geographically local positive selection—and 18 with atypically low FST values, possibly reflecting balancing selection.
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    8 Genomes and evolution Current Opinion in Genetics & Development 2004, 14:1–8 www.sciencedirect.com

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    Post Re: A structured ancestral population for the evolution of modern humans

    Quote Originally Posted by Dr. Solar Wolff
    I can't access PDF files but from your summary, it looks as if this data supports the multi-regionalists. Is that true?
    The paper is not entirely clear on this but it seems to say that modern humans could be descended from Homo Sapiens mixed with Neanderthals, Homo Erectus and archaic Homo Sapiens. It says that current data does not support a recent African origin (RAO) of humans. Here is the conclusion of the paper:

    Genetic data provide substantial support for range expansions by modern humans out of Africa but not for an RAO model that constrains all ancestry for modern humans into a speciation bottleneck. At present, there is no evidence to support a major reduction and recovery in ancestral population size, although improved models and methods for analyzing multi-locus data may yet find such evidence. Levels of diversity across ancestral Homo could feasibly have been twofold higher than levels in contemporary modern humans, but probably not much greater, and the inferred Late Pleistocene reduction could reflect loss of structure through extinction of some subpopulations, range expansions of others, and increased migration. Due to admixture, perhaps more so during phases of range contraction than in phases of range expansion, some of our genes could have come through multiple archaic populations and not just down a single lineage in Africa.

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    Post Re: A structured ancestral population for the evolution of modern humans

    Quote Originally Posted by Vetinari
    The paper is not entirely clear on this but it seems to say that modern humans could be descended from Homo Sapiens mixed with Neanderthals, Homo Erectus and archaic Homo Sapiens. It says that current data does not support a recent African origin (RAO) of humans. Here is the conclusion of the paper:

    Genetic data provide substantial support for range expansions by modern humans out of Africa but not for an RAO model that constrains all ancestry for modern humans into a speciation bottleneck. At present, there is no evidence to support a major reduction and recovery in ancestral population size, although improved models and methods for analyzing multi-locus data may yet find such evidence. Levels of diversity across ancestral Homo could feasibly have been twofold higher than levels in contemporary modern humans, but probably not much greater, and the inferred Late Pleistocene reduction could reflect loss of structure through extinction of some subpopulations, range expansions of others, and increased migration. Due to admixture, perhaps more so during phases of range contraction than in phases of range expansion, some of our genes could have come through multiple archaic populations and not just down a single lineage in Africa.
    I would say that's pretty clear.

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    Post Re: A structured ancestral population for the evolution of modern humans

    Quote Originally Posted by Manji
    In leyman terms, this means that clusters of different pre-homo sapiens developed into different types of homo sapiens? Perhaps that in junction with lack of gene flow would explain phenotype differences but on a later phase those different groups had gene exchange between them or else there would still be different types of hominids....right?
    Clifford Jolly estimated (though I doubt its reliable) that any hominid sharing a common ancestor less than 4 million years ago, could theoretically hybridise and produce offspring - this is older than Homo.

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    Post Re: A structured ancestral population for the evolution of modern humans

    Quote Originally Posted by atlanto-med
    I would say that's pretty clear.
    The problem is that the paper doesn't really specify which archaic populations were involved so it could include Neanderthals or just archaic Homo Sapiens.

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    Post Re: A structured ancestral population for the evolution of modern humans

    Quote Originally Posted by Vetinari
    The problem is that the paper doesn't really specify which archaic populations were involved so it could include Neanderthals or just archaic Homo Sapiens.
    Qafzeh and other Middle Paleolithic moderns (Stringer refers to them as being a grade of near-moderns) have some archaic features, but I wouldn't expect it to mean the early grade of moderns because archaic usually means phenotypically not modern.

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