Post by Bozur on Sept 27, 2005 4:43:20 GMT -5
In Chimpanzee DNA, Signs of Y Chromosome's Evolution
By NICHOLAS WADE
Published: September 1, 2005
Scientists have decoded the chimp genome and compared it with that of humans, a major step toward defining what makes people human and developing a deep insight into the evolution of human sexual behavior.
Yerkes National Primate Research Center, via Associated Press
Scientists sequenced the DNA of a chimpanzee named Clint and compared it with that of humans.
The comparison pinpoints the genetic differences that have arisen in the two species since they split from a common ancestor some six million years ago.
The realization that chimpanzees hold a trove of information about human evolution and nature comes at a time when they and other great apes are under harsh pressures in their native habitat. Their populations are dwindling fast as forests are cut down and people shoot them for meat. They may soon disappear from the wild altogether, primatologists fear, except in the few sanctuaries that have been established.
Chimpanzees and people possess almost identical sets of genes, so the genes that have changed down the human lineage should hold the key to what makes people human.
Biologists suspect that only a handful of genes are responsible for the major changes that reshaped the apelike ancestor of both species into a human and that these genes should be identifiable by having evolved at a particularly rapid rate.
The comparison of the human and chimp genomes, reported in today's issue of Nature, takes a first step in this direction but has not yet tracked down the critical handful of genes responsible for human evolution.
One problem is the vast number of differences - some 40 million - in the sequence of DNA units in the chimp and human genomes. Most are caused by a random process known as genetic drift and have little effect. For now, their large numbers make it difficult for scientists to find the changes caused by natural selection.
But another aspect of the comparison has yielded insights into a different question, the evolution of the human Y chromosome. The new finding implies that humans have led sexually virtuous lives for the last six million years, at least in comparison with the flamboyant promiscuity of chimpanzees.
Some 300 million years ago, the Y chromosome used to carry the same 1,000 or so genes as its partner, the X chromosome. But because the Y cannot exchange DNA with the X and update its genes, in humans it has lost all but 16 of its X-related genes through mutation or failure to stay relevant to their owner's survival. However, the Y has gained some genes from other chromosomes because it is a safe haven for genes that benefit only men, since it never enters a woman's body. These added genes, not surprisingly, all have functions involved in making sperm.
The scientific world's leading student of the Y chromosome, David Page of the Whitehead Institute in Cambridge, Mass., has been seeking to understand whether the Y will lose yet more genes and lapse into terminal decay, taking men with it.
The idea of the Y's extinction "was so delicious from the perspective of gender politics," Dr. Page said. "But many of my colleagues became confused with this blending of gender politics with scientific predictions."
Two years ago, he discovered a surprising mechanism that protects the sperm-making genes. Those genes exist in pairs, arranged so that when the DNA of the chromosome is folded back on itself, the two copies of the gene are aligned. If one copy of the gene has been hit by a mutation, the cell can repair it by correcting the mismatch in DNA units.
The 16 X-related genes are present in only single copies. Dr. Page and his colleagues thought the chimpanzee genome might show how they were protected. To their surprise, they report in Nature, the protection was not there.
The chimp Y chromosome has lost the use of 5 of its 16 X-related genes. The genes are there, but have been inactivated by mutation. The explanation, in his view, lies in the chimpanzee's high-spirited sexual behavior. Female chimps mate with all males around, so as to make each refrain from killing a child that might be his.
The alpha male nonetheless scores most of the paternities, according to DNA tests. This must be because of sperm competition, primatologists believe - the alpha male produces more and better sperm, which outcompete those of rival males.
This mating system puts such intense pressure on the sperm-making genes that any improved version will be favored by natural selection. All the other genes will be dragged along with it, Dr. Page believes, even if an X-related gene has been inactivated.
If chimps have lost five of their X-related genes in the last six million years because of sperm competition, and humans have lost none, humans presumably had a much less promiscuous mating system. But experts who study fossil human remains believe that the human mating system of long-term bonds between a man and woman evolved only some 1.7 million years ago.
Males in the human lineage became much smaller at this time, a sign of reduced competition.
The new result implies that even before that time, during the first four million years after the chimp-human split, the human mating system did not rely on sperm competition.
Dr. Page said his finding did not reach to the nature of the joint chimp-human ancestor, but that "it's a reasonable inference" that the ancestor might have been gorillalike rather than chimplike, as supposed by some primatologists.
The gorilla mating system has no sperm competition because the silverback maintains exclusive access to his harem.
Frans B. M. de Waal of the Yerkes National Primate Research Center in Atlanta said he agreed with fossil experts that the human pair bonding system probably evolved 1.7 million years ago but that the joint ancestor could have resembled a chimp, a bonobo, a gorilla, or something else entirely.
The scientists who have compared the whole genomes of the two species say they have found 35 million sites on the aligned genomes where there are different DNA units, and another five million where units have been added or deleted. Each genome is about three billion units in length.
The chimp genome was completed in draft form in December 2003 by the Broad Institute in Cambridge and Washington University in St. Louis.
Statistical tests for accelerated evolution are not yet powerful enough to identify the major genes that have shaped humans. "We knew that this was only a beginning, but from a general standpoint we have captured the vast majority of the differences between human and chimps," said Robert H. Waterston of the University of Washington, Seattle, the senior author of the report. The genome of a third primate, the orangutan, is now in progress and will help identify the genes special to human evolution, he said.
At the level of the whole animal, primatologists have uncovered copious similarities between the social behavior of chimpanzees, bonobos and humans, some of which may eventually be linked to genes. But this rich vein of discovery may be choked off if the great apes can no longer be studied in the wild.
"The situation is very bad, and our feeling is that by 2040 most of the habitat will be gone, except for those little regions we have set aside," Dr. de Waal said.
By NICHOLAS WADE
Published: September 1, 2005
Scientists have decoded the chimp genome and compared it with that of humans, a major step toward defining what makes people human and developing a deep insight into the evolution of human sexual behavior.
Yerkes National Primate Research Center, via Associated Press
Scientists sequenced the DNA of a chimpanzee named Clint and compared it with that of humans.
The comparison pinpoints the genetic differences that have arisen in the two species since they split from a common ancestor some six million years ago.
The realization that chimpanzees hold a trove of information about human evolution and nature comes at a time when they and other great apes are under harsh pressures in their native habitat. Their populations are dwindling fast as forests are cut down and people shoot them for meat. They may soon disappear from the wild altogether, primatologists fear, except in the few sanctuaries that have been established.
Chimpanzees and people possess almost identical sets of genes, so the genes that have changed down the human lineage should hold the key to what makes people human.
Biologists suspect that only a handful of genes are responsible for the major changes that reshaped the apelike ancestor of both species into a human and that these genes should be identifiable by having evolved at a particularly rapid rate.
The comparison of the human and chimp genomes, reported in today's issue of Nature, takes a first step in this direction but has not yet tracked down the critical handful of genes responsible for human evolution.
One problem is the vast number of differences - some 40 million - in the sequence of DNA units in the chimp and human genomes. Most are caused by a random process known as genetic drift and have little effect. For now, their large numbers make it difficult for scientists to find the changes caused by natural selection.
But another aspect of the comparison has yielded insights into a different question, the evolution of the human Y chromosome. The new finding implies that humans have led sexually virtuous lives for the last six million years, at least in comparison with the flamboyant promiscuity of chimpanzees.
Some 300 million years ago, the Y chromosome used to carry the same 1,000 or so genes as its partner, the X chromosome. But because the Y cannot exchange DNA with the X and update its genes, in humans it has lost all but 16 of its X-related genes through mutation or failure to stay relevant to their owner's survival. However, the Y has gained some genes from other chromosomes because it is a safe haven for genes that benefit only men, since it never enters a woman's body. These added genes, not surprisingly, all have functions involved in making sperm.
The scientific world's leading student of the Y chromosome, David Page of the Whitehead Institute in Cambridge, Mass., has been seeking to understand whether the Y will lose yet more genes and lapse into terminal decay, taking men with it.
The idea of the Y's extinction "was so delicious from the perspective of gender politics," Dr. Page said. "But many of my colleagues became confused with this blending of gender politics with scientific predictions."
Two years ago, he discovered a surprising mechanism that protects the sperm-making genes. Those genes exist in pairs, arranged so that when the DNA of the chromosome is folded back on itself, the two copies of the gene are aligned. If one copy of the gene has been hit by a mutation, the cell can repair it by correcting the mismatch in DNA units.
The 16 X-related genes are present in only single copies. Dr. Page and his colleagues thought the chimpanzee genome might show how they were protected. To their surprise, they report in Nature, the protection was not there.
The chimp Y chromosome has lost the use of 5 of its 16 X-related genes. The genes are there, but have been inactivated by mutation. The explanation, in his view, lies in the chimpanzee's high-spirited sexual behavior. Female chimps mate with all males around, so as to make each refrain from killing a child that might be his.
The alpha male nonetheless scores most of the paternities, according to DNA tests. This must be because of sperm competition, primatologists believe - the alpha male produces more and better sperm, which outcompete those of rival males.
This mating system puts such intense pressure on the sperm-making genes that any improved version will be favored by natural selection. All the other genes will be dragged along with it, Dr. Page believes, even if an X-related gene has been inactivated.
If chimps have lost five of their X-related genes in the last six million years because of sperm competition, and humans have lost none, humans presumably had a much less promiscuous mating system. But experts who study fossil human remains believe that the human mating system of long-term bonds between a man and woman evolved only some 1.7 million years ago.
Males in the human lineage became much smaller at this time, a sign of reduced competition.
The new result implies that even before that time, during the first four million years after the chimp-human split, the human mating system did not rely on sperm competition.
Dr. Page said his finding did not reach to the nature of the joint chimp-human ancestor, but that "it's a reasonable inference" that the ancestor might have been gorillalike rather than chimplike, as supposed by some primatologists.
The gorilla mating system has no sperm competition because the silverback maintains exclusive access to his harem.
Frans B. M. de Waal of the Yerkes National Primate Research Center in Atlanta said he agreed with fossil experts that the human pair bonding system probably evolved 1.7 million years ago but that the joint ancestor could have resembled a chimp, a bonobo, a gorilla, or something else entirely.
The scientists who have compared the whole genomes of the two species say they have found 35 million sites on the aligned genomes where there are different DNA units, and another five million where units have been added or deleted. Each genome is about three billion units in length.
The chimp genome was completed in draft form in December 2003 by the Broad Institute in Cambridge and Washington University in St. Louis.
Statistical tests for accelerated evolution are not yet powerful enough to identify the major genes that have shaped humans. "We knew that this was only a beginning, but from a general standpoint we have captured the vast majority of the differences between human and chimps," said Robert H. Waterston of the University of Washington, Seattle, the senior author of the report. The genome of a third primate, the orangutan, is now in progress and will help identify the genes special to human evolution, he said.
At the level of the whole animal, primatologists have uncovered copious similarities between the social behavior of chimpanzees, bonobos and humans, some of which may eventually be linked to genes. But this rich vein of discovery may be choked off if the great apes can no longer be studied in the wild.
"The situation is very bad, and our feeling is that by 2040 most of the habitat will be gone, except for those little regions we have set aside," Dr. de Waal said.