It will take years and many morediscoveries before we determine all the human specific populations thatoccupied the earth before the general post ice age radiation. We have already posted that it is possibleand even probable that there existed a range of sub populations quite variant throughoutthe globe and additionally that the Neanderthals at least perhaps helped forman initial human population that then modernized on the coastal plains.
Most likely all subgroupsmodernized and transitioned to space based forms that then migrated off planet. Modern humanity is a recent manufacturedesigned specifically to terraform Earth after the Pleistocene Nonconformity (orDeluge) that ended the Ice Age.
That the Denisova variant isstrongly reflected in Melanesian human stock is a further reminder of theextent of pre deluge genetic mixing that we will recover over time.
Huge human populations are now completingthe job of subsuming local populations of unusual genetic material which is notlost so much as protectively dispersed.
The Denisova discovery: Ancient genomics shed new light on humanorigins
By Thomas H. Douglass
17 January 2011
An international team of scientists made headlines at the end of lastyear when they used genetic evidence to show that an ancient people, onceliving in the Altai Mountains of southern Siberia, were distant cousins of theNeanderthals and contributed to the modern human genome before theirextinction.
The discovery is a triumph of modern genomics and decades of publiclyfunded science research in the United States and elsewhere, which has led tothe sequencing of the human genome and promises to revolutionize our understandingof 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 substantialcontributions 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 humanoccupation for over 250,000 years. Early humans often sought out caves assources of shelter and protection as they dispersed, repeatedly, from Africainto Eurasia and beyond. Like a number ofother sites, Denisova cave is important because stone tool technology suggeststhat different peoples occupied the site at different times toward the end ofthe Pleistocene age (2.6 million to 10,000 years ago), as modernHomosapiens began to disperse from Africa andgenerally 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 extractedancient DNA from a phalanx bone, or digit, to map its DNA onto known human andNeanderthal genomes. Surprisingly, the Denisovans proved to be distinct fromboth humans and Neanderthals known to have been living elsewhere in Eurasia at the time. Instead, researchers found that theDenisovans were distant cousins of the Neanderthals from Europe ,apparently having branched off from other Neanderthal populations shortly afterNeanderthals branched from modern humans, 300,000-450,000 years ago.
Unlike their Neanderthal cousins in Europe, who contributed anestimated 1-4 percent of genomic material among modern humans living throughoutEurasia , the Denisovans did not contributeto the DNA of these populations. Perhaps most surprisingly however, beforetheir disappearance from southern Siberia theDenisovans did contribute approximately 4-6 percent of modern Melanesian DNA.
This finding adds to a series of others in the last decade, somegenetic and some paleontological, which paint an increasingly complex pictureof human origins within Africa and beyond.Future work will investigate the distribution of Denisovans across Asia, thecontext of their mixing with modern humans leaving Africa ,and the possible existence of other archaic populations that may havecontributed to the modern human genome.
Human genetics in the 21st century
While the Denisova discovery enriches our understanding of humanevolution, it does not overthrow but rather contributes to a consensus amonghuman geneticists regarding the remarkable genetic similarity of humanindividuals and populations around the globe.
Humans are unusually genetically homogeneous as a species, a result ofour recent, common origin from small populations in Africa in the past 150,000-200,000 years. Populations of chimpanzees or other primatesseparated by rivers or other barriers are often genetically distinct from oneanother, interbreeding very little and maintaining separate populations despitetheir close proximity. Human populations, by contrast, are remarkably identicaldespite their distribution across distant regions of the earth.
Early studies in the 1970s, since corroborated by modern sequencingmethods, showed that 85-90 percent of genetic diversity within the entire humanspecies is contained within any given group. By contrast, only 10-15 percent ofhuman genetic variation distinguishes one group from another, or is exclusiveof certain groups. If all people on earth had their DNA at a specific locationsequenced, 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 anygiven population. Only very few variants would be found in one population andnot in another.
Decades of research into DNA sequencing methods have generated ongoing,international projects to document human genetic diversity. Among theseprojects are the Human Genome Diversity Panel (HGDP), the International HapMapProject, and the Centre d’Etudes du Polymorphisme Humain (CEPH). These projectssequence entire genomes or portions of genomes in thousands of individualsacross the globe in an effort to understand diversity, relatedness, migrationand settlement histories, and vulnerability to disease in differentpopulations.
Such an understanding is provided by analysis of segments of varyinggenetic code called single-nucleotide polymorphisms (SNPs, pronounced “snips”),repetitive microsatellite sequences, DNA copy number variations (CNVs) andduplications or deletions of genes and other segments. SNPs are small variants ofbase 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 describinghow 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 relatednesspatterns and migration routes from Africa . Thestudy, examining 650,000 DNA sites in almost 1,000 individuals from 50 humanpopulations, illustrates how early humans peopled the world in a sequentialseries of dispersals beginning in sub-Saharan Africa and continuing on to NorthAfrica, the Middle East, Europe, South and Central Asia, East Asia, Oceania andAmerica.
While the geneticists were able to distinguish between sub-SaharanAfricans and individuals outside Africa , theiranalyses did not reconstruct “racial groups” previously recognized forpolitical or social purposes. For instance, almost all Middle Easternindividuals have enormous contributions of DNA variants that are found inhigher frequencies in Africa, Europe, Central and South Asia , reflecting mixed ancestry and continued gene flow acrosscontinents.
Importantly, Li and Absher also found that 85-95 percent of geneticvariation found among all people is common to all groups, while only a smallamount of variation can be used to distinguish one group from another.
Despite efforts by corporations to copyright genetic material, andprivatize or profit from methods developed through publicly funded research,dozens of complete and annotated genomes from living organisms around the worldare 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 hasbeen applied not only to living populations, but also to fossil specimens. Thesimilarities in physiology and form between closely related species have preventedscientists from determining, previously, whether populations outside Africalike 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-scalemixing and continuous gene flow between populations outside and within Africa , both before and after modern human migrationsthat supposedly replaced Neanderthals. In this sense, multiregionalists likeProfessor Milford Wolpoff at the University of Michigan claimed thatNeanderthals never wholly disappeared, but rather became incorporated into thepopulations leaving Africa and settling the Middle East and Europe.
The “Out of Africa” or “Recent African Origin” model of humanevolution, ultimately supported by most scientists in the field, claimed thathuman populations leaving Africa in recent history did replace Neanderthals andother archaic populations throughout Eurasia, citing African technologicalinnovations in the middle to late Stone Age, and similar osteologicalcharacteristics like “gracile” or finer features seeming to unite all modernhumans to the exclusion of Neanderthals.
Mitochondrial analysis of all living humans and extraordinary work toextract mitochondrial DNA from Neanderthal remains gave support in recentdecades to the African Origin model of evolution. This work showed all livinghumans to have a recent common mitochondrial ancestor, nicknamed “Eve,” wholived 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 Neanderthalshad mixed with modern humans and left nuclear, but not mitochondrial DNA amongtheir living descendents.
Extracting and sequencing DNA from fossils is notoriously difficult.The human genome is 3 billion base pairs long, and is contained within eachcell of the body in 23 volumes called chromosomes. The chromosomes themselvesrange from 50 million to 250 million base pairs long each, and altogether holdabout 23,000 genes that code for proteins, the machinery of our cells. But whenorganisms die, their many base pairs quickly break down: Neanderthal remainstypically offer DNA in small fragments an average of 50 base pairs in size,difficult to retrieve and analyze. Further complicating any study of ancientDNA 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 ancientbones are 95-99 percent bacterial, with a small remainder belonging to theorganism we mean to study.
A new form of DNA sequencing, however, has given scientists the abilityto analyze ancient DNA as never before. Called “pyrosequencing,” the techniqueuses millions of microscopic beads, each functioning as a DNA copying factory,to faithfully preserve and amplify even severely damaged DNA. Innovations bySvaante Pääbo’s team in Leipzig
The result has been a revolution in ancient DNA studies, and thecomplete sequencing of the Neanderthal genome using multiple Neanderthalremains across Europe .
A draft sequence of the Neanderthal genome published last year providedstrong evidence that Neanderthals interbred with modern humans in the MiddleEast as they dispersed from Africa , perhaps50,000-80,000 years ago. After screening dozens of Neanderthal remains for thepresence of DNA, scientists chose three from Vindija Cave in Croatia from whichto extract bone powder and, ultimately, ancient DNA.
The scientists consistently found Neanderthals to be slightly moreclosely related to Eurasians than to sub-Saharan Africans, suggesting thatapproximately 1-4 percent of modern Eurasian DNA is inherited fromNeanderthals. This Neanderthal contribution to the modern human genome, whichis substantial, may imply only a small amount of interbreeding; a variety ofhistorical scenarios describing modern human and Neanderthal interactions arecompatible with the available data.
The sequencing of Denisovan remains at the end of last year providesfurther evidence for interbreeding between dispersing populations of modernhumans, and archaic populations inhabiting Eurasia .
Previous sequencing of the mitochondrial genome, using DNA from afinger bone, found Denisovans to be the descendants of an ancient populationthat split apart from a lineage common to both Neanderthals and modern humans.This meant that humans and Neanderthals were more closely related to oneanother than to Denisovans, our ancient cousins. This discovery fueledwidespread interest because it implied that descendents of our ancientancestors Homo erectus or Homo heidelbergensis, having dispersedfrom Africa a million years ago or even before, persisted in Eurasia until 30,000 years ago.
Homo erectus and heidelbergensis were descendants ofancientAustralopithecines like “Lucy,” who, after evolving in Africa, thendispersed into the Middle East, Europe and Asia between 800,000 and 2 million years ago. Homo heidelbergensis isthought to have given rise to both modern humans in Africa and to Neanderthalsin Europe; it was not anticipated that a third lineage, the Denisovans, mighthave 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 thatancestors like Homo erectus may have dispersed from Africa as early as 2 million years ago. Like the discovery of the “hobbit” remainsfound on the Indonesian island of Flores , however, the sequencing of Denisovanmitochondrial DNA raised the possibility that ancient ancestors left Africa and persisted, possibly without interaction withlater Neanderthals or modern humans, all the way into the late Stone Age.
Now, complete sequencing of the Denisovan nuclear genome has shown thatthese individuals were in fact distant cousins of Neanderthals, and moreclosely related to them than to us. A tooth in Denisova cave, which theresearchers interpret as being larger than those found in modern humans orNeanderthals, appears to corroborate what has been revealed by DNA: theDenisovans belonged to a population anciently diverged from Neanderthals.
But the sequencing of the Denisovan genome reveals an extraordinarytwist: while Neanderthals and Denisovans shared a common lineage hundreds ofthousands of years ago, in the last 50,000 years the Denisovans appear to havecontributed to a significant portion―about 5 percent―of the modern human genomeamong Melanesians in southeast Asia and the southwest Pacific.
It is unclear whether the Denisovans contributed to the modern humangenome because they inhabited a swath of territory extending down into southeastAsia, or whether modern peoples dispersing from Africa may have passed throughsouthern Siberia .
Constructing plausible historical scenarios for such an interaction iscomplicated by the difficulty of determining the precise timing of Denisovanoccupation in the Altai Mountains . Caves arenotoriously complex geologically because they house unusual patterns of waterflow, sediment deposition and animal presence over many millennia. Radiocarbondating of animal bones altered by human tools suggest at least two periods ofoccupation at Denisova: one 50,000 years ago or older, and another only15,000-30,000 years ago.
The sequencing of the Denisovan genome illustrates the remarkableadvances in genetic technology and international scientific collaboration thatare advancing the field of biology. More than 150 years after Darwin
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