[Paleopsych] SW: On Early Emigrations from Africa
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Anthropology: On Early Emigrations from Africa
http://scienceweek.com/2005/sw050610-1.htm
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
(2003)
Science http://www.sciencemag.org
--------------------------------
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ANTHROPOLOGY: NEW EVIDENCE FOR OUT OF AFRICA MODEL
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
years.
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
--------------------------------
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ANTHROPOLOGY: ANCIENT DNA AND THE ORIGIN OF MODERN HUMANS
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:
ANTHROPOLOGY: RECOMBINATION IN HOMINID MITOCHONDRIAL DNA
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
#1]
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
286:2524):
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
reconsidered."
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
troglodytes).
--------------------------------
Related Material:
IN FOCUS: ON MITOCHONDRIA, DNA, AND SPERM CELLS
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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