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Ancient humans more diverse?

Researchers have delved back further than ever into the genetic history of humans, and found that the ancient population that gave rise to modern humans may have been nearly twice as genetically diverse than humans today, according a study published this week in Proceedings of the National Academy of Sciences. Scientific reconstruction of a Homo erectusImage: Wikimedia commons, linkurl:Lillyundfreya;http://commons.wikimedia.org/wiki/File:Homo_erectus.JPG While most studies on the genetics of an

By | January 18, 2010

Researchers have delved back further than ever into the genetic history of humans, and found that the ancient population that gave rise to modern humans may have been nearly twice as genetically diverse than humans today, according a study published this week in Proceedings of the National Academy of Sciences.
Scientific reconstruction of a Homo erectus
Image: Wikimedia commons,
linkurl:Lillyundfreya;http://commons.wikimedia.org/wiki/File:Homo_erectus.JPG
While most studies on the genetics of ancient humans have focused on the last half million years, this study looks at particularly old areas of the genome, allowing the researchers to look at the more distant past, said molecular geneticist linkurl:Prescott Deininger;http://129.81.225.52/ of the Tulane Cancer Center in New Orleans, LA, who was not involved in the research. "This [study] is a little window to look back a little bit further," he said. When examining genetic diversity, scientists often use a measure called the effective population size, which describes how big a population has to be to carry its level of genetic diversity. Modern humans have an effective population size of about 10,000 -- a relatively low level of diversity. Chimps and gorillas, for example, both have effective population sizes of greater than 20,000. This estimate of 10,000 has been regarded as stable for about 200,000 to 400,000, maybe "as far back as a million" years, said population geneticist linkurl:Chad Huff;http://jorde-lab.genetics.utah.edu/?page_id=330 of the University of Utah. But looking deeper into human history, Huff and his colleagues determined that before about 1.2 million years ago, the effective population size of our ancestral populations was actually around 18,500. The researchers gained their insight by looking at mobile elements -- bits of DNA that can insert themselves into the genome -- known as Alus. Occurring in an estimated 1 in 21 to 22 births, Alus, which are about 300 base pairs long and the most abundant mobile elements in the human genome, insert into the genome at a rate at least three orders of magnitude rarer than the single nucleotide mutation rate. Because of this rarity, any particular Alu is likely to be much older than an average mutation. Furthermore, because the DNA just outside of these Alu inserts is closely linked to the mobile element, that surrounding DNA is also likely to be relatively old. The researchers can thus "use these elements they call molecular fossils to dig down through the strata of the human genome and arrive at some conclusions about human origin," explained molecular biologist John Goodier of the linkurl:University of Pennsylvania School of Medicine,;http://www.med.upenn.edu/ who did not participate in the research. Comparing these ancient areas of the human reference genome with the genome of a particular individual -- that of genomics guru Craig Venter, as it happens -- the team found that much of the DNA surrounding the Alu inserts was older than would be expected if the effective population size had always been 10,000. Based on their results, they concluded that the effective population size had been nearly double its current level before about 1.2 million years ago. While this is clearly a substantial difference, Huff said he was actually surprised the diversity of the ancient population wasn't even greater. "It is unusual that our [effective population size] is so small for so long," Huff said, especially given the success of our species. If our ancestors "really did live on three continents," he added, "you would expect a much larger [effective] population size." "I also wouldn't have expected our [effective population size] to be 10,000 for so long," Huff added. The small effective population size of modern humans was attributed to a bottleneck event that eliminated a great deal of ancient diversity sometime in the last 400,000 years. But if humans have maintained such low diversity for more than a million years, "I'm wondering if maybe it hasn't been [a] series of bottlenecks or if it's always been relatively small," Huff said. While the exact mechanisms shaping the diversity of ancient humans will undoubtedly require further research, this study makes a good start by identifying a potential tool that can be used to see further back into our history, Deininger said. "I'm always a little bit impressed by how sophisticated some of these population biology studies can be in terms of unraveling ancient details," he said. "It's fun to look at the dynamics of our history."
**__Related stories:__***linkurl:On Human Diversity;http://www.the-scientist.com/article/display/15791/
[24th October 2005]*linkurl:The 0.1% Portrait of Human History;http://www.the-scientist.com/article/display/13907/
[30th June 2003]*linkurl:Genetic Variation Illuminates Murky Human History;http://www.the-scientist.com/article/display/11959/
[24th July 2000]
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Comments

Avatar of: anonymous poster

anonymous poster

Posts: 2

January 19, 2010

Now that I understand the concept of effective population size, can it be an indicator of cooperativeness versus within-group competitiveness?
Avatar of: Blair Bolles

Blair Bolles

Posts: 1

January 19, 2010

I first read about this work in the New York Times, which has a completely different take, arising from a different definition of effective population. They call it the breeding population, which obviously cannot be right if the effective population for modern humans is 10,000. I wonder what definition was used in the PNAS paper itself.
Avatar of: Jef Akst

Jef Akst

Posts: 28

January 19, 2010

Unfortunately, the PNAS article does not offer a definition of effective population size, as it is a very commonly used term in population genetics. You can view the article here: http://www.pnas.org/content/early/2010/01/06/0909000107\n\nI can tell you that Chad Huff defined it for me last week as follows: An effective population size of 10,000 means "we have the genetic diversity of a species that has always had a population size of 10,000. If our population size dropped to 10,000 we would not lose any genetic diversity."\n
Avatar of: Dov Henis

Dov Henis

Posts: 97

August 6, 2010

On Culture And Genetics\n\nSeed of Human-Chimp Genomes Diversity\n\n\nI.\nBook Review:\nAlmost Chimpanzee: Searching for What Makes Us Human, in Rainforests, Labs, Sanctuaries, and Zoos by Jon Cohen\nReview by Bruce Bower\nhttp://www.sciencenews.org/view/generic/id/61609/title/Book_Review_Almost_Chimpanzee_Searching_for_What_Makes_Us_Human%2C_in_Rainforests%2C_Labs%2C_Sanctuaries%2C_and_Zoos_by_Jon_Cohen\n\n\nII.\nSeed of Human-Chimp Genomes Diversity\n\nhttp://pulse.yahoo.com/_2SF3CJJM5OU6T27OC4MFQSDYEU/blog/articles/53079 \n\n2 Nov,2005 Dov, in biologicalEvolution forum. \n\nBiological Evolution's Seeds of Diversity, Human and Chimpanzee/Bonobo Genomes\n\nChapter One, \nIn which some wonder what made us human.\n\nThree recent quotations from Science, representative of many other recent similar statements in various scientific publications:\n\nA) "Understanding the genetic basis of how genotype generates phenotype will require increasing the accuracy and completeness of the currently available chimpanzee genome sequence, as well as sequencing other primate genomes."\n\nB)"Can we now provide a DNA-based answer to the fascinating and fundamental question, "What makes us human?" Not at all! Comparison of the human and chimpanzee genomes has not yet offered any major insights into the genetic elements that underlie bipedal locomotion, big brain, linguistic abilities, elaborated abstract thought, or any other unique aspect of the human phenome."\n\nC)"What makes us human? This question may be answered by comparison of human and chimpanzee genomes and phenomes, and ultimately those of other primates. To this end, we need to understand how genotype generates phenotype, and how this process is influenced by the physical, biological, and cultural environment."\n\nChapter Two,\nIn which is explained plainly and succinctly the obvious route by which we evolved,\n\ni.e. that genotype has not generated phenotype, that we evolved from our genotype via a group of feedback loops. From Science, Vol 308, Issue 5728, 1563-1565 , 10 June 2005, Immunology: Opposites Attract in Differentiating T Cells, Mark Bix, Sunhwa Kim,Anjana Rao:\n\n"During differentiation, precursor cells with progressively narrowed potential give rise to progeny cells that adopt one of two (or more) divergent cell fates. This choice is influenced by intricate regulatory networks acting at multiple levels. Early in differentiation, precursor cells show low-level activation of all progeny genetic programs. Bias toward a given lineage comes from environmental inputs that activate powerful positive- and negative- feedback loops, which work in concert to impose selective gene expression patterns". \n\nChapter Three,\nIn which we explain the revolutionary evolved uniqueness of the human ape's phenotype:\n\nThe 6My-old revolutionary life evolution was initiated by our forefathers who adapted from life in semi- or tropical forest circumstances to life on plains. Changes in living posture and circumstances led to modified perceptive/adaptive experiences and capabilities. Developing employment of tools effected enhanced differentiation of hands from legs and enhanced upstanding posturing. As evolving community culture led to language communication humans have gradually replaced adaptation to changed circumstances with self-evolving cultures/civilizations for control and modification of much of their circumstances. This is essentially similar to early life's celling evolution, but with culture functioning for humans for change/control of circumstances in lieu of genetic and protein toolings that function for the in-cell genomes for adapting their cell's physiology to changing circumstances.\n\nChapter Four,\nIn which appears, may be, genetic evidence/demonstration of the workings of human cultural evolution.\n\n(a) From Science, 2 Sept 2005: "Page's team compared human and chimp Ys to see whether either lineage has lost functional genes since they split.\n\nThe researchers found that the chimp had indeed suffered the slings and arrows of evolutionary fortune. Of the 16 functional genes in this part of the human Y, chimps had lost the function of five due to mutations. In contrast, humans had all 11 functional genes also seen on the chimp Y. "The human Y chromosome hasn't lost a gene in 6 million years," says Page. "It seems like the demise of the hypothesis of the demise of the Y," says geneticist Andrew Clark of Cornell University in Ithaca, New York."\n\n(b) But look at this: From Science, Vol 309, 16 Sept 2005, Evolving Sequence and Expression:"An analysis of the evolution of both gene sequences and expression patterns in humans and chimpanzees...shows that...surprisingly, genes expressed in the brain have changed more on the human lineage than on the chimpanzee lineage, not only in terms of gene expression but also in terms of amino acid sequences".\n\nSurprisingly...???\n\nChapter Five and conclusion,\nIn which I suggest that detailed study of other creatures that, like humans, underwent radical change of living circumstances, for example ocean-dwelling mammals, might bring to light unique evolutionary processes and features of evolutionary implications similar to those of humans.\n\nend. \n\nDov Henis\n(Comments From The 22nd Century)\n03.2010 Updated Life Manifest \nhttp://www.the-scientist.com/community/posts/list/54.page#5065\nCosmic Evolution Simplified\nhttp://www.the-scientist.com/community/posts/list/240/122.page#4427\n"Gravity Is The Monotheism Of The Cosmos"\nhttp://www.the-scientist.com/community/posts/list/260/122.page#4887

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