[Paleopsych] NYT: In Chimpanzee DNA, Signs of Y Chromosome's Evolution

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In Chimpanzee DNA, Signs of Y Chromosome's Evolution
New York Times, 5.9.1
http://www.nytimes.com/2005/09/01/science/01chimp.html

    By [3]NICHOLAS WADE

    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.

    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.