[Paleopsych] SW: On Early Emigrations from Africa

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Anthropology: On Early Emigrations from Africa

    The following points are made by P. Forster and S. Matsumura (Science
    2005 308:965):
    1) By analyzing the DNA of living humans from different locations,
    geneticists are able to assemble a detailed reconstruction of
    prehistoric human colonization of the world. This research endeavor
    was championed by the late Allan Wilson and his colleagues [1,2], who
    led the way with their studies of maternally inherited mitochondrial
    DNA (mtDNA). Their work led to the proposal of a recent African origin
    for modern humans some 5000 generations ago. Anthropologists and
    geneticists have since joined forces to create a broad framework of
    possible prehistoric human migration routes and time scales [3-5].
    2) Our current understanding is that modern humans arose ~150,000
    years ago, possibly in East Africa, where human genetic diversity is
    particularly high. Subsequent early colonization within Africa is
    supported by old genetic mtDNA and Y chromosome branches (often called
    "haplogroups" in the Bushmen or Khoisan of the Kalahari Desert, and in
    certain pygmy tribes in the central African rainforest. Early humans
    even ventured out of Africa briefly, as indicated by the
    90,000-year-old Skhul and Qafzeh fossils found in Israel. The next
    event clearly visible in the mitochondrial evolutionary tree is an
    expansion signature of so-called L2 and L3 mtDNA types in Africa about
    85,000 years ago, which now represent more than two-thirds of female
    lineages throughout most of Africa. The reason for this remarkable
    expansion is unclear, but it led directly to the only successful
    migration out of Africa, and is genetically dated by mtDNA to have
    occurred some time between 55,000 and 85,000 years ago. Studies of the
    paternally inherited Y chromosome yield time estimates for the African
    exodus that are in broad agreement with those derived from mtDNA.
    3) It is at this point in the narrative that studies by Thangaraj et
    al (2005) and Macaulay et al (2005) come into the picture. Which route
    did the first Eurasians take out of Africa? Most obvious, perhaps, is
    the route along the Nile and across the Sinai Peninsula leading into
    the rest of the world. But if that were so, why was adjacent Europe
    settled thousands of years later than distant Australia? In Europe,
    Neanderthals were replaced by modern humans only about 30,000 to
    40,000 years ago, whereas southern Australia was definitely inhabited
    46,000 years ago and northern Australia and Southeast Asia necessarily
    even earlier. Or did our ancestors instead depart from East Africa,
    crossing the Red Sea and then following the coast of the Indian Ocean?
    A purely coastal "express train" would conveniently explain the early
    dates for human presence in Australia, but would require that humans
    were capable of crossing the mouth of the Red Sea some 60,000 years
    ago. Why, then, was this feat not repeated by any later African
    emigrants, particularly when the Red Sea level dropped to a minimum
    about 20,000 years ago?
    4) Ideally, these questions would be answered by investigating ancient
    fossils and DNA from the Arabian Peninsula. But because this option is
    currently not available, Thangaraj et al (2005) and Macaulay et al
    (2005) have centered their investigation on the other side of the
    Indian Ocean, in the Andaman Islands and Malaysian Peninsula. Both
    groups used genetic studies of relict populations known to differ
    substantially from their Asian neighbors to estimate the arrival time
    of the first humans in these locations. Thangaraj and colleagues
    sampled the Andamanese, who were decimated in the 19th century by
    diseases imported by the British and then suffered displacement by
    modern Indian immigration. Macaulay and co-workers sampled the native
    tribal people of Malaysia, called the Orang Asli ("original people").
    5) The two teams arrived at compatible conclusions. In the Andaman
    Islands, Thangaraj et al identified the M31 and M32 mtDNA types among
    indigenous Andamanese. These two mtDNA types branched directly from M
    mtDNA, which arose as a founder 65,000 years ago. This time estimate
    for the arrival of M founder mtDNA is matched by that of Macaulay and
    co-workers. These investigators found mtDNA types M21 and M22 in their
    Malaysian data set. These M types are geographically specific branches
    of M that branched off from other Asian mtDNA lineages around 60,000
    years ago. Thus, the first Eurasians appear to have reached the coast
    of the Indian Ocean soon after leaving Africa, regardless of whether
    they took the northern or the southern route.
    References (abridged):
    1. R. L. Cann, M. Stoneking, A. C. Wilson, Nature 325, 31 (1987)
    2. L. Vigilant, M. Stoneking, H. Harpending, K. Hawkes, A. C. Wilson,
    Science 253, 1503 (1991)
    3. P. Endicott et al., Am. J. Hum. Genet. 72, 178 (2003)
    4. R. Cordaux, M. Stoneking, Am. J. Hum. Genet. 72, 1586 (2003)
    5. P. A. Underhill, Cold Spring Harbor Symp. Quant. Biol. 68, 487
    Science http://www.sciencemag.org
    Related Material:
    The following points are made by Chris Stringer (Nature 2003 423:692):
    1) The idea that modern humans originated in Africa, with populations
    subsequently spreading outwards from there, has continued to gain
    support lately. But much of that support has come from analyses of
    genetic variation in people today, and from fossil and archaeological
    discoveries dated to within the past 120,000 years -- after our
    species evolved. Hard evidence for the inferred African origin of
    modern humans has remained somewhat elusive, with relevant material
    being fragmentary, morphologically ambiguous, or uncertainly dated.
    Thus the fossilized partial skulls from Ethiopia recently described by
    White et al (Nature 2003 423:742) are probably some of the most
    significant discoveries of early Homo sapiens so far, owing to their
    completeness and well-established antiquity of approximately 160,000
    2) There are two broad theories about the origins of H. sapiens. A few
    researchers still support a version of the "multiregional" hypothesis,
    arguing that the anatomical features of modern humans arose in
    geographically widespread hominid populations throughout the
    Pleistocene epoch (which lasted from around 1.8 million to some 12,000
    years ago). But most researchers now espouse a version of the "out of
    Africa" model, although there are differences of opinion over the
    complexity of the processes of origin and dispersal, and over the
    amount of mixing that might subsequently have occurred with archaic
    (non-modern) humans outside of Africa. Within Africa, uncertainties
    still surround the mode of modern human evolution -- whether it
    proceeded in a gradual and steady manner or in fits and starts
    (punctuational evolution). Other questions concern the relationship
    between genetic, morphological and behavioral changes, and the precise
    region, or regions, of origin.
    3) For instance, possible early H. sapiens fossils, dating from about
    260,000 to 130,000 years ago, are scattered across Africa at sites
    such as Florisbad (South Africa), Ngaloba (Tanzania), Eliye Springs
    and Guomde (Kenya), Omo Kibish (Ethiopia), Singa (Sudan) and Jebel
    Irhoud (Morocco). But the best dated of these finds, from Florisbad
    and Singa, are problematic because of incompleteness and, in the
    latter case, evidence of disease. Meanwhile, the more complete or
    diagnostically modern specimens suffer from chronological
    uncertainties. So the most securely dated and complete early fossils
    that unequivocally share an anatomical pattern with today's H. sapiens
    are actually from Israel, rather than Africa. These are the partial
    skeletons from Skhul and Qafzeh, dating from around 115,000 years ago.
    Their presence in the Levant is usually explained by a range expansion
    from ancestral African populations, such as those sampled at Omo
    Kibish or Jebel Irhoud around 125,000 years ago.
    4) The new cranial material from Herto, Ethiopia -- described by White
    et al -- adds significantly to our understanding of early H. sapiens
    evolution in Africa. The fossils are complete enough to show a suite
    of modern human characters, and are well constrained by argon-isotope
    dating to about 160,000 years ago. Three individuals are represented
    by separate fossils: a nearly complete adult cranium (skull parts
    excluding the lower jaw), a less complete juvenile cranium, and some
    robust cranial fragments from another adult. All display evidence of
    human modification, such as cut marks, considered to represent
    mortuary practices rather than cannibalism. Associated layers of
    sediment produced evidence of the butchery of large mammals such as
    hippopotamuses and bovines, as well as assemblages of artefacts
    showing an interesting combination of Middle Stone Age and late
    Acheulean technology.
    Nature http://www.nature.com/nature
    Related Material:
    Notes by ScienceWeek:
    Mitochondria are double-membrane enclosed organelles of cells, the
    mitochondria involved with several important biochemical pathways,
    including electron transport and oxidative metabolism. Various types
    of cells containing internal membrane-bound organelles (eukaryotic
    cells) may contain from a few to several thousand mitochondria in each
    cell type. The mitochondria are relatively large cylindrical
    structures up to 10 microns long and up to 2 microns in diameter, and
    most biologists believe mitochondria are cell organelles that may have
    originated as separate organisms that became resident in eukaryotic
    cells. Mitochondrial DNA is independent of nuclear DNA, consisting of
    a circular molecule, 16,569 base pairs long in humans, with a known
    nucleotide sequence.
    Investigations of human mitochondrial DNA have revealed two facts
    relevant to questions of human origins: a) the variation among modern
    human populations is small compared, for example, to that between apes
    and monkeys, which has been interpreted to indicate the recency of
    human origins; b) there is a distinction between African and other
    human mitochondrial types, which has been interpreted to indicate the
    relative antiquity of the African peoples and the relative recency of
    other human populations.
    Interpretations of mitochondrial DNA evidence have been much debated
    in anthropology. Such evidence is a crucial part of the "single
    origin" model of human origins, which proposes that one early
    population of modern humans spread out of Africa approximately 60,000
    to 100,000 years ago and eventually replaced all less modern
    populations of the genus Homo worldwide. Thus, the difference between
    "African" and "non-African" mitochondrial DNA is explained by the idea
    that small "founder" populations left Africa, carrying with them only
    a small sample of the genetic variation found in Africa as a whole,
    and that such founder populations then expanded as they occupied
    Eurasia, growing into a large population with a distinctly non-African
    mitochondrial DNA structure. This idea became popular in the late
    1980s, when it was called the "Mitochondrial Eve" or "Out of Africa"
    hypothesis. Although since then this hypothesis has lost some support,
    it is still one of the major ideas concerning human origins.
    Support for the opposing "regional-continuity" model is based
    primarily on evidence of gradual morphological change, mainly of the
    skull, from ancient to modern inhabitants in different parts of the
    world. In this scenario, modern humans developed almost simultaneously
    in various geographical regions around the world, replacing less
    evolved Homo species beginning approximately 1.5 million years ago.
    These are only the general outlines of a hotly debated complex area of
    research in human evolution.
    The following points are made by G.J. Adcock et al (Proc. Natl. Acad.
    Sci. 2001 98:537):
    1) The authors point out that since its beginning more than 25 years
    ago, the debate over recent human origins has focused on two models.
    The regional-continuity hypothesis postulates that ever since humans
    began to migrate out of Africa more than 1.5 million years ago, there
    has been a single evolving species, Homo sapiens, distributed
    throughout the Old World, with all regional populations connected, as
    they are today, by gene flow. Some skeletal features developed and
    persisted for varying periods in the different regions, so that
    recognizable regional morphologies have developed in Africa, Europe,
    and Asia.
    2) The other view, the "recent out of Africa" model, argues that over
    the period since humans began to leave Africa, there have been several
    species of Homo. In this model, H. sapiens emerged in Africa
    approximately 100,000 years ago and then spread globally, replacing
    other species of Homo that it encountered during the expansion. This
    model proposes that all current regional morphologies, especially
    those outside Africa, developed within the last 100,000 years.
    3) These alternative models arose from interpretations of
    morphological evidence. During the last 15 years, molecular data,
    particularly nucleotide sequences drawn from populations of living
    humans, have made an increasing contribution to the debate. Analysis
    has demonstrated that humans have remarkably little mitochondrial DNA
    sequence variation, and that the earliest branching lineages are found
    in East Africa. These findings were interpreted as strongly supporting
    the "recent out of Africa" model. The authors suggest, however, that
    this interpretation fails to recognize that the demographic history of
    a species cannot be inferred from the pattern of variation of a single
    nucleotide segment. Patterns of variation in different regions of the
    genome must be considered and interpreted in the context of
    paleontological and archeological evidence.
    4) The authors report mitochondrial DNA sequence evidence from 10
    fossils, all agreed to be anatomically modern, rather than archaic,
    Homo sapiens (4 "*gracile" and 6 "*robust" specimens). The 10 fossils
    range in age from less than 10,000 years ago to approximately 60,000
    years ago. The authors report that in one fossil (Lake Mungo 3, dated
    at 60,000 years ago), the mitochondrial DNA sequence is the most
    divergent of all of the Australian fossils analyzed, and this is
    evidently an example of a mitochondrial DNA lineage that existed in an
    ancient modern human but is absent in living human mitochondria. The
    authors state: "Our data present a serious challenge to interpretation
    of contemporary human mitochondrial DNA variation as supporting the
    'recent out of Africa' model. A separate mitochondrial DNA lineage in
    an individual whose morphology is within the contemporary range and
    who lived in Australia would imply [from the out of Africa model and
    its usage of mitochondrial DNA data] both that anatomically modern
    humans were among those that were replaced and that part of the
    replacement occurred in Australia."
    In a commentary on this work, John H. Relethford (Proc. Natl. Acad.
    Sci. US 16 Jan 01 98:390) states: "If the mitochondrial DNA present in
    a modern human (Lake Mungo 3) can become extinct, then perhaps
    something similar happened to the mitochondrial DNA of Neanderthals.
    If so, then the absence of Neanderthal mitochondrial DNA in living
    humans does not reject the possibility of _some_ genetic continuity
    with modern humans... The modern human origins debate can be informed
    by genetic data, both living and ancient, but can only be resolved by
    also considering the fossil and archeological evidence. The picture
    presented by Adcock et al suggests that modern human origins were more
    complicated than once envisioned."
    Proc. Nat. Acad. Sci. http://www.pnas.org
    Notes by ScienceWeek:
    gracile: In general, a Homo fossil with a lightly built skull. The
    Lake Mungo 3 fossil is a gracile specimen.
    robust: In general, a Homo fossil with a heavily built skull.
    Related Material:
    Notes by ScienceWeek:
    The origin of modern humans is an ongoing major focus of research in
    anthropology and paleontology, and also a research area that has seen
    its share of contentious disputes. There are two conflicting views
    concerning the geographic aspects of human origins: 1) in one view,
    the geographic origins of modern man are multiple, with modern man
    (Homo sapiens) appearing more or less at the same time on various
    continents; while in the second view b) modern man originated in
    Africa approximately 200,000 years ago, with modern humans migrating
    from Africa to the rest of the globe.
    The major evidence for the "Out of Africa" hypothesis was published in
    the late 1980s by R.L. Cann et al (1987), the evidence based primarily
    on analysis of mitochondrial DNA in diverse existing human groups...
    In the late 1980s, most anthropologists and paleontologists believed
    that the mitochondria of sperm cells do not enter the egg cell (or if
    they do, are quickly destroyed upon entry), so that male sperm
    mitochondrial DNA does not mix (*recombine) with female egg
    mitochondrial DNA. The idea, therefore, was that mitochondrial DNA is
    of pure maternal lineage, and since analysis of human mitochondrial
    DNA suggested a single origin of Homo sapiens in Africa, the notion of
    an "African Eve" was quickly publicized by the popular media [*Note
    In recent years, however, the notion that mitochondria are of pure
    maternal lineage has been challenged, and the dispute among
    anthropologists and paleontologists concerning multiple-origins vs. a
    single-origin for Homo sapiens has flared up again.
    The following points are made by P. Awadalla et al (Science 1999
    1) For many years it has been accepted that mitochondria are inherited
    exclusively from the mother in mammals, and that the inheritance of
    mitochondrial DNA is therefore "clonal". This assumption has been used
    extensively to date events in human prehistory, including the age of
    our last common female ancestor, called "Eve", and to date the spread
    of Homo sapiens in Asia and Europe. However, mitochondria do contain
    the enzymes necessary for *homologous recombination, and there are at
    least two routes by which the rule of strict maternal inheritance of
    mitochondrial DNA could be broken: a) the entrance of paternal
    mitochondria into the egg cell at fertilization [*Note #2]; and b) the
    transfer of nuclear genome copies of mitochondrial DNA sequences back
    to mitochondrial DNA.
    2) The assumption that human mitochondrial DNA is inherited from one
    parent only and therefore does not recombine is questionable. The work
    of the authors indicates that *linkage disequilibrium in human and
    chimpanzee mitochondrial DNA declines as a function of the distance
    between genome sites, and this pattern can be attributed to one
    mechanism only: recombination.
    3) The authors conclude: "Many inferences about the pattern and tempo
    of human evolution and mtDNA evolution have been based on the
    assumption of clonal inheritance. These inferences will now have to be
    Science http://www.sciencemag.org
    Notes by ScienceWeek:
    recombine: In this context, the term "recombination" refers to a
    genome with a combination of genes other than those that occurred in
    the precursor genome(s), the recombination, in this context, produced
    naturally. Thus, if mitochondrial DNA has naturally spliced into it
    one or more sequences of nuclear DNA or DNA from another line of
    mitochondria, the mix is called "recombination". (See note below on
    "homologous recombination".)
    Note #1: Apart from its proposed exclusive maternal lineage (which has
    now been challenged), mitochondrial DNA has a number of research
    advantages: a) The complete nucleotide sequence of human mitochondrial
    DNA is known, the genome identified as a circular DNA molecule of
    16,569 base pairs. b) Since there are as much as thousands of copies
    of mitochondrial DNA per cell, mitochondrial DNA can be more easily
    isolated from human tissues than nuclear DNA, which has only two
    copies per cell. c) It is believed that mutations occur in
    mitochondria 10 times more frequently than in nuclear DNA, and the
    consequent rapid evolution of the mitochondrial genome enables
    comparisons between groups that would be more difficult to
    differentiate using slower and more complex nuclear DNA sequences.
    homologous recombination: In general, the term "homologous
    recombination" refers to genetic recombination that occurs between
    DNAs with long stretches of homology, and which is mediated by certain
    enzymes involved in DNA repair and replication. In this context, the
    terms "homologous" and "homology" refer to sequences having
    fundamental similarities due to the same evolutionary origin, even if
    the functions of the two sequences are quite different.
    Note #2: See relevant background material below.
    linkage disequilibrium: In this context, the term "linkage" refers to
    gene sequences (genetic loci) that tend to be inherited together more
    often than would be expected by chance. Genetic linkage is a
    reflection of the physical location of the loci on the same chromosome
    segment or DNA molecule. Loci which are close together are less likely
    to be separated by recombination and are therefore more likely to be
    inherited together. The distance between linked loci is measured in
    terms of the frequency of recombination events occurring between them.
    The term "linkage disequilibrium" refers to a situation in which a
    particular combination of gene variants (alleles) at two closely
    linked loci appears more frequently than would be expected by chance.
    The essential idea of the authors in this report is that recombination
    can be detected by considering the relation between linkage
    disequilibrium and gene loci distance (genetic distance). As the
    distance between loci increases, the effect of recombination should
    increase, and recombination should therefore manifest itself as a
    significant decline in linkage disequilibrium with distance. The study
    of the authors consisted of analysis of previously published data
    concerning mtDNA sequences in humans and chimpanzees (Pan
    Related Material:
    Notes by ScienceWeek:
    During the maturation of sperm cells in the human testes
    (spermiogenesis), the mitochondria of sperm cells are relocated: the
    mature sperm cell consists of 3 parts, the head, midpiece, and tail
    (flagellum), and all the mitochondria are densely packed into the
    midpiece of the mature sperm cell.
    One of the major techniques used to investigate ancient human lineages
    involves the genetic analysis of mitochondrial DNA, with such DNA
    considered to be primarily of maternal origin. However, there is
    apparently some confusion about the reasons for the primarily maternal
    origin of mitochondrial DNA. For example, the 1998 textbook
    _Principles of Human Evolution_ by Roger Lewin (Harvard University,
    US) [*Note #1] contains on page 414 an illustrative drawing depicting
    the fate of sperm mitochondria, the drawing showing the midpiece and
    tail of the sperm cell "discarded" upon fertilization of the egg cell.
    The drawing has the following caption: "Unlike nuclear DNA, for which
    we inherit half from our mother and half from our father,
    mitochondrial DNA is passed on only by females. When the sperm
    fertilizes the egg, it leaves behind all of its mitochondria: the
    developing fetus therefore inherits mitochondria only from the
    mother's egg."
    The above presentation by Lewin contradicts current information in
    cell biology. The idea that sperm lose their mitochondria at
    fertilization as a result of extracellular "discard" of the midpiece
    and tail is not correct. The current view in cell biology is that the
    entire human sperm cell (head, midpiece, and tail) penetrates the egg
    cell during the fertilization process. Sperm mitochondria are
    apparently lost (destroyed) shortly after penetration of the egg by
    specific enzymatic reactions, but the destruction of sperm
    mitochondria inside the egg cell is believed to be not always
    complete. The current view in cell biology is that since the sperm
    mitochondria and the sperm flagellum disintegrate inside the egg, very
    few, if any, sperm-derived mitochondria are found in developing or
    adult organisms. In mice it is estimated that only 1 out of every
    10,000 mitochondria are sperm-derived. Nevertheless, the significance
    of contaminating paternal mitochondria in the use of mitochondrial DNA
    to establish genetic lineages is in controversy in the literature, and
    the issue is not yet resolved [*Note #2]. [The Editors wish to thank
    James M. Cummins, Murdoch University (AU) for calling our attention to
    the question of the fate of sperm cell mitochondria.]
    Notes by ScienceWeek:
    Note #1: Roger Lewin: Principles of Human Evolution, Blackwell
    Science, 1998, p.414.
    Note #2: For additional material, cf. F. Ankel-Simons and J.M. Cummins
    (Proc. Natl. Acad. Sci. US 1996 93:13859) and Jim Cummins (Rev. of
    Reproduction 1998 3:172).

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