It will take years and many more
discoveries before we determine all the human specific populations that
occupied the earth before the general post ice age radiation. We have already posted that it is possible
and even probable that there existed a range of sub populations quite variant throughout
the globe and additionally that the Neanderthals at least perhaps helped form
an initial human population that then modernized on the coastal plains.
Most likely all subgroups
modernized and transitioned to space based forms that then migrated off planet. Modern humanity is a recent manufacture
designed specifically to terraform Earth after the Pleistocene Nonconformity (or
Deluge) that ended the Ice Age.
That the Denisova variant is
strongly reflected in Melanesian human stock is a further reminder of the
extent of pre deluge genetic mixing that we will recover over time.
Huge human populations are now completing
the job of subsuming local populations of unusual genetic material which is not
lost so much as protectively dispersed.
The Denisova discovery: Ancient genomics shed new light on human
origins
By Thomas H. Douglass
17 January 2011
An international team of scientists made headlines at the end of last
year when they used genetic evidence to show that an ancient people, once
living in the Altai Mountains of southern Siberia, were distant cousins of the
Neanderthals and contributed to the modern human genome before their
extinction.
The discovery is a triumph of modern genomics and decades of publicly
funded science research in the United States and elsewhere, which has led to
the sequencing of the human genome and promises to revolutionize our understanding
of evolution, disease, and global genetic diversity.
While geneticists and paleontologists at the Max Planck Institute in Leipzig , Germany ,
at Harvard and at MIT spearheaded the work, there were also substantial
contributions by scientists throughout the United
States , Spain ,
Canada , Russia , and China
Denisova cave is located in the Altai Mountains of southern Siberia , and has been an important site of human
occupation for over 250,000 years. Early humans often sought out caves as
sources of shelter and protection as they dispersed, repeatedly, from Africa
into Eurasia and beyond. Like a number of
other sites, Denisova cave is important because stone tool technology suggests
that different peoples occupied the site at different times toward the end of
the Pleistocene age (2.6 million to 10,000 years ago), as modernHomo
sapiens began to disperse from Africa and
generally replace other, older populations.
The scientists wanted to know if human remains in the cave,
30,000-50,000 years old, were Neanderthals or modern humans, and so extracted
ancient DNA from a phalanx bone, or digit, to map its DNA onto known human and
Neanderthal genomes. Surprisingly, the Denisovans proved to be distinct from
both humans and Neanderthals known to have been living elsewhere in Eurasia at the time. Instead, researchers found that the
Denisovans were distant cousins of the Neanderthals from Europe ,
apparently having branched off from other Neanderthal populations shortly after
Neanderthals branched from modern humans, 300,000-450,000 years ago.
Unlike their Neanderthal cousins in Europe, who contributed an
estimated 1-4 percent of genomic material among modern humans living throughout
Eurasia , the Denisovans did not contribute
to the DNA of these populations. Perhaps most surprisingly however, before
their disappearance from southern Siberia the
Denisovans did contribute approximately 4-6 percent of modern Melanesian DNA.
This finding adds to a series of others in the last decade, some
genetic and some paleontological, which paint an increasingly complex picture
of human origins within Africa and beyond.
Future work will investigate the distribution of Denisovans across Asia, the
context of their mixing with modern humans leaving Africa ,
and the possible existence of other archaic populations that may have
contributed to the modern human genome.
Human genetics in the 21st century
While the Denisova discovery enriches our understanding of human
evolution, it does not overthrow but rather contributes to a consensus among
human geneticists regarding the remarkable genetic similarity of human
individuals and populations around the globe.
Humans are unusually genetically homogeneous as a species, a result of
our recent, common origin from small populations in Africa
in the past 150,000-200,000 years. Populations of chimpanzees or other primates
separated by rivers or other barriers are often genetically distinct from one
another, interbreeding very little and maintaining separate populations despite
their close proximity. Human populations, by contrast, are remarkably identical
despite their distribution across distant regions of the earth.
Early studies in the 1970s, since corroborated by modern sequencing
methods, showed that 85-90 percent of genetic diversity within the entire human
species is contained within any given group. By contrast, only 10-15 percent of
human genetic variation distinguishes one group from another, or is exclusive
of certain groups. If all people on earth had their DNA at a specific location
sequenced, and 100 genetic variants were found in the human species at that location,
what these studies show is that 85-90 of those variants would be found in any
given population. Only very few variants would be found in one population and
not in another.
Decades of research into DNA sequencing methods have generated ongoing,
international projects to document human genetic diversity. Among these
projects are the Human Genome Diversity Panel (HGDP), the International HapMap
Project, and the Centre d’Etudes du Polymorphisme Humain (CEPH). These projects
sequence entire genomes or portions of genomes in thousands of individuals
across the globe in an effort to understand diversity, relatedness, migration
and settlement histories, and vulnerability to disease in different
populations.
Such an understanding is provided by analysis of segments of varying
genetic code called single-nucleotide polymorphisms (SNPs, pronounced “snips”),
repetitive microsatellite sequences, DNA copy number variations (CNVs) and
duplications or deletions of genes and other segments. SNPs are small variants of
base pairs within the DNA sequence, which act like letters in the genetic code.
Microsatellites, by contrast, are approximately of word length, and genes,
which are long strings of coding base pairs, are like short manuals describing
how to build proteins, the machinery of the cell.
In 2008, geneticists Li and Absher from Stanford and the University of Michigan
used data collated from HGDP and CEPH to reconstruct global human relatedness
patterns and migration routes from Africa . The
study, examining 650,000 DNA sites in almost 1,000 individuals from 50 human
populations, illustrates how early humans peopled the world in a sequential
series of dispersals beginning in sub-Saharan Africa and continuing on to North
Africa, the Middle East, Europe, South and Central Asia, East Asia, Oceania and
America.
While the geneticists were able to distinguish between sub-Saharan
Africans and individuals outside Africa , their
analyses did not reconstruct “racial groups” previously recognized for
political or social purposes. For instance, almost all Middle Eastern
individuals have enormous contributions of DNA variants that are found in
higher frequencies in Africa, Europe, Central and South
Asia , reflecting mixed ancestry and continued gene flow across
continents.
Importantly, Li and Absher also found that 85-95 percent of genetic
variation found among all people is common to all groups, while only a small
amount of variation can be used to distinguish one group from another.
Despite efforts by corporations to copyright genetic material, and
privatize or profit from methods developed through publicly funded research,
dozens of complete and annotated genomes from living organisms around the world
are now freely availably online, and contribute to the burgeoning field of genomics.
Ancient DNA and Denisova
The discovery at Denisova is an example of how genetic analysis has
been applied not only to living populations, but also to fossil specimens. The
similarities in physiology and form between closely related species have prevented
scientists from determining, previously, whether populations outside Africa
like the Neanderthals mixed with modern populations migrating from Africa 150,000 to 200,000 years ago.
The “multiregional” model of human evolution argued for large-scale
mixing and continuous gene flow between populations outside and within Africa , both before and after modern human migrations
that supposedly replaced Neanderthals. In this sense, multiregionalists like
Professor Milford Wolpoff at the University of Michigan claimed that
Neanderthals never wholly disappeared, but rather became incorporated into the
populations leaving Africa and settling the Middle East and Europe.
The “Out of Africa” or “Recent African Origin” model of human
evolution, ultimately supported by most scientists in the field, claimed that
human populations leaving Africa in recent history did replace Neanderthals and
other archaic populations throughout Eurasia, citing African technological
innovations in the middle to late Stone Age, and similar osteological
characteristics like “gracile” or finer features seeming to unite all modern
humans to the exclusion of Neanderthals.
Mitochondrial analysis of all living humans and extraordinary work to
extract mitochondrial DNA from Neanderthal remains gave support in recent
decades to the African Origin model of evolution. This work showed all living
humans to have a recent common mitochondrial ancestor, nicknamed “Eve,” who
lived in Africa about 200,000 years ago;
Neanderthal mitochondrial lineages are by contrast distinct from modern humans.
But this evidence could not rule out the possibility that Neanderthals
had mixed with modern humans and left nuclear, but not mitochondrial DNA among
their living descendents.
Extracting and sequencing DNA from fossils is notoriously difficult.
The human genome is 3 billion base pairs long, and is contained within each
cell of the body in 23 volumes called chromosomes. The chromosomes themselves
range from 50 million to 250 million base pairs long each, and altogether hold
about 23,000 genes that code for proteins, the machinery of our cells. But when
organisms die, their many base pairs quickly break down: Neanderthal remains
typically offer DNA in small fragments an average of 50 base pairs in size,
difficult to retrieve and analyze. Further complicating any study of ancient
DNA are the myriad species of bacteria that colonize our bodies when we die,
and leave their genomes alongside our own. The DNA retrieved from most ancient
bones are 95-99 percent bacterial, with a small remainder belonging to the
organism we mean to study.
A new form of DNA sequencing, however, has given scientists the ability
to analyze ancient DNA as never before. Called “pyrosequencing,” the technique
uses millions of microscopic beads, each functioning as a DNA copying factory,
to faithfully preserve and amplify even severely damaged DNA. Innovations by
Svaante Pääbo’s team in Leipzig
The result has been a revolution in ancient DNA studies, and the
complete sequencing of the Neanderthal genome using multiple Neanderthal
remains across Europe .
A draft sequence of the Neanderthal genome published last year provided
strong evidence that Neanderthals interbred with modern humans in the Middle
East as they dispersed from Africa , perhaps
50,000-80,000 years ago. After screening dozens of Neanderthal remains for the
presence of DNA, scientists chose three from Vindija Cave in Croatia from which
to extract bone powder and, ultimately, ancient DNA.
The scientists consistently found Neanderthals to be slightly more
closely related to Eurasians than to sub-Saharan Africans, suggesting that
approximately 1-4 percent of modern Eurasian DNA is inherited from
Neanderthals. This Neanderthal contribution to the modern human genome, which
is substantial, may imply only a small amount of interbreeding; a variety of
historical scenarios describing modern human and Neanderthal interactions are
compatible with the available data.
The sequencing of Denisovan remains at the end of last year provides
further evidence for interbreeding between dispersing populations of modern
humans, and archaic populations inhabiting Eurasia .
Previous sequencing of the mitochondrial genome, using DNA from a
finger bone, found Denisovans to be the descendants of an ancient population
that split apart from a lineage common to both Neanderthals and modern humans.
This meant that humans and Neanderthals were more closely related to one
another than to Denisovans, our ancient cousins. This discovery fueled
widespread interest because it implied that descendents of our ancient
ancestors Homo erectus or Homo heidelbergensis, having dispersed
from Africa a million years ago or even before, persisted in Eurasia
until 30,000 years ago.
Homo erectus and heidelbergensis were descendants of
ancientAustralopithecines like “Lucy,” who, after evolving in Africa, then
dispersed into the Middle East, Europe and Asia
between 800,000 and 2 million years ago. Homo heidelbergensis is
thought to have given rise to both modern humans in Africa and to Neanderthals
in Europe; it was not anticipated that a third lineage, the Denisovans, might
have also evolved and then remained in southern Siberia until quite recently.
Using fossils from the Atapuerca
Caves in Spain ,
Dminisi Cave
in Georgia and Mojokerto in Indonesia , scientists have long known that
ancestors like Homo erectus may have dispersed from Africa
as early as 2 million years ago. Like the discovery of the “hobbit” remains
found on the Indonesian island of Flores , however, the sequencing of Denisovan
mitochondrial DNA raised the possibility that ancient ancestors left Africa and persisted, possibly without interaction with
later Neanderthals or modern humans, all the way into the late Stone Age.
Now, complete sequencing of the Denisovan nuclear genome has shown that
these individuals were in fact distant cousins of Neanderthals, and more
closely related to them than to us. A tooth in Denisova cave, which the
researchers interpret as being larger than those found in modern humans or
Neanderthals, appears to corroborate what has been revealed by DNA: the
Denisovans belonged to a population anciently diverged from Neanderthals.
But the sequencing of the Denisovan genome reveals an extraordinary
twist: while Neanderthals and Denisovans shared a common lineage hundreds of
thousands of years ago, in the last 50,000 years the Denisovans appear to have
contributed to a significant portion―about 5 percent―of the modern human genome
among Melanesians in southeast Asia and the southwest Pacific.
It is unclear whether the Denisovans contributed to the modern human
genome because they inhabited a swath of territory extending down into southeast
Asia, or whether modern peoples dispersing from Africa may have passed through
southern Siberia .
Constructing plausible historical scenarios for such an interaction is
complicated by the difficulty of determining the precise timing of Denisovan
occupation in the Altai Mountains . Caves are
notoriously complex geologically because they house unusual patterns of water
flow, sediment deposition and animal presence over many millennia. Radiocarbon
dating of animal bones altered by human tools suggest at least two periods of
occupation at Denisova: one 50,000 years ago or older, and another only
15,000-30,000 years ago.
The sequencing of the Denisovan genome illustrates the remarkable
advances in genetic technology and international scientific collaboration that
are advancing the field of biology. More than 150 years after Darwin
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