(2/3) The light of evolution: What would be lost


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Section 3 Conservation genetics
So far we've largely focused on issues directly concerning humans. What about non-human genetic
markers and non-human evolution?
The field of conservation genetics is an interdisciplinary field of study that looks at how to conserve
the diversity of life by understanding evolution and genetics. One of the principle areas of
study is genetic diversity. Diversity is even more important than simple numbers when organisms
begin to dwindle. A population that loses its diversity is very prone to disease, infant
mortality, and rapid decline in population, even if its numbers are relatively high.
For example, the Giant Panda is very near to extinction. We know that there are about
270 in captivity, but the wild populations have been harder to estimate. Based on computations
of genetic diversity that were developed from evolutionary population genetics, it would
appear that the panda population is not as endangered as once thought. The wild populations
may be as high as 3000 individuals, and the diversity is relatively high.
The other important area is identifying which populations are actually distinct species
or genetically divergent subgroups. While a fisherman may not be able to tell the difference
between different types of salmon, a biologist using DNA technology and an understanding
of evolutionary change can determine that a certain river is home to a rare and unique
species of salmon that should be conserved.
Section 4 Agriculture
The other major application for non-human genetics and evolution might be agriculture.
We are highly dependent on only a few crops for most of our food, and evolution can help
us understand how to manage that delicate situation.
The obvious use for evolution in agriculture is in understanding how to improve yields
by artificial selection. Humans have been doing this type of manipulation since we were
hunter-gatherers, harvesting and spreading the seeds of easy to pick and palatable wild
crops. In the last 60 years, however, we have added new technologies to that selection.
We can now map genomes, determine which genes control which traits, and carefully select
the true-breeding strains with the best yields, disease resistance, and marketability. We
can do all of this without introducing foreign DNA, simply from our understanding of inheritance
with modification. The type of study is referred to as quantitative trait loci mapping, and
it started the green revolution in crop development decades before modern transgenic techniques
existed.
As in conservation genetics, understanding evolution can aid us in maintaining adequate
diversity in our crops, in detecting the spread of transgenes or horizontally transferred
genes from other plants, and to determine the true genetic identity of newly emerged
strains.
Evolutionary theory is used to understand selection pressures placed on plant pathogens,
like insects and blights, or weed plants that compete with crops. It can also help us to
reconstruct the evolutionary history of a crop or livestock, so we can identify what
genetic changes have occurred over time. Such studies on corn's closest relatives in central
Mexico have identified ancestral strains with remarkable disease resistance. Similar studies
on ancestral cow population in South American have uncovered existing resistance genes to
common cattle diseases. Cross-breeding efforts could secure a more hardy and resistant food
source.
PART 2 I'm now going to transition over to talking
about applications of what could be called macroevolution, a term not often found in
the scientific literature simply because the distinction is completely artificial.
Section 5 Cladistics and reconstructing phylogenies
One of the most striking evidences for evolution is the nested heirarchy. Organisms can be
grouped on the basis of their genetic homology, and the resulting tree or cladogram matches
up remarkably well with many other lines of evidence. We also see common patterns of divergence.
Organisms that are closely related will share the most sequence, but as we choose comparisons
between organisms that diverged a much longer time ago, the homologies become weaker. There
are some notable exceptions. Some sequences show large differences, some show very little
difference. How should we explain this deviation from the expected substitution rates?
The answer, primarily, is selection. Those gene products that are essential for basic
functions in the organism do not change very much at all over time. Silent mutations, those
that do not affect the function of the gene product, continue to accumulate, but few changes
occur in the protein sequence because if they did, it would result in a decrease in fitness.
We'll talk a bit more about this in the next section.
The fields of bioinformatics and genomics focus on these types of analyses between the
genomes of different organisms. What kinds of applications can we find for bioinformatics,
comparative genomics, and phylogenetics?
Perhaps the most relevant is in the field of emerging diseases. Suppose tomorrow that
a new illness began taking lives in Southern Texas, primarily children and newborns. Hospital
labs, state health agencies, and eventually national agencies like the CDC and USAMRID
would be on the scene, looking for a cause. Suppose we culture out an unidentified bactera
from the lungs of very sick children in the region. What tools would we have to understand
this new lethal pathogen? We'd sequence the DNA, and we'd look at what conditions the
bacteria likes the most, but without a knowledge of macroevolutionary change, we would be missing
the most important tool of all. The ability to interrogate the new genome in relation
to other, well-characterized pathogens. Suppose, in this case, we find that this germ is very
closely related to a pathogen of cattle, but with an inserted region that matches most
closely the presence of a virus of bacteria. We would have valuable information about how
to treat the disease and save children's lives, and how to manage the disease's spread.
Going back to the idea of conservation genetics from Section 3, one application of phylogeny
is in preserving near-extinct species. As an example, take the story of Lonesome George,
the last known individual of the Pinta Island Tortoise, a subspecies of Galapagos tortoise.
Poor George, believed to be around 80 years old, was believed to be the last of his kind,
and with no female, we were facing the end of his subspecies. Then evolutionary biologists,
using DNA technology, discovered a very closely related subspecies that appeared to have interbred
with the Pinta island group in the recent past. Another individual of the same group
was also discovered at the Prague Zoo among other Galapagos tortoises. Unfortunately for
George, it was another male. Current efforts are underway to see if George and females
from a related subspecies can create a hybrid offspring to preserve some of his genes, so
far they have been unsuccessful.
So our understanding of how different groups of organisms are related to each other can
benefit our stewardship of our planet, but can also help to save human lives.
Section 6 Discovering genes and regulatory regions
Once the Human Genome Project had a fairly complete database of sequence, scientists
had a very powerful tool available for the mapping of human genes, but how can they detect
the important sequences, the ones that have some important function in the cell or organism?
One very powerful approach is called selective sweeps. Selective sweeps compare the frequency
of certain markers to their theoretically expected distribution in the absence of selection
pressures.
We also use comparisons of the same sequences between species. Certain regions will show
a high amount of conservation, they don't change very much. Those are regions that are
likely to have some function. The more highly conserved, the more likely those regions have
some crucial role in the cell. For biologists, this was like a high-resolution pirate map
of the Carribean filled with X's. There were so many exciting new genes to be discovered,
and we knew exactly where many of them were. All that remained was to identify what they
did.
Even within a gene, looking at the DNA bases that are most highly conserved often tells
us something about the active site of that gene product. This approach has led to a wealth
of information about genes are regulated, by identifying regulatory and promoter regions.
We've also learned a great deal about how genes are expressed by looking at the similarities
and differences in how different animals develop as embryos. It's hard to pick out a specific
example, because all of modern molecular genetics is based on comparisons of genomes between
widely ranging species.
The other important concept in genetic analysis by macroevolution is the ability to use model
organisms to stand in for humans. For ethical and safety reasons, we prefer not to experiment
on humans. But when we use a non-human substitute for testing and analysis, we need to understand
the differences produced by macroevolutionary change. This is real information we can't
get from intelligent design or other creationist belief system.
Take the case of the Rous sarcoma virus in chickens. In 1911, Francis Rous identified
a retrovirus that could cause cancer in chickens, the rouse sarcoma virus, work which earned
him the 1966 Nobel Prize in Medicine. In 1979, Bishop and Varmus noticed that the retrovirus
actually contained a defective version of a chicken gene. That chicken gene, now called
src or "sarc" is what is known as a proto-oncogene. The million dollar question was whether humans
would have the same gene, with the same potential to cause cancer. Humans and chickens are seperated
by a great deal of evolution, but this gene plays such a crucial role, we would expect
it to be highly conserved. And, in 1981, Varmus and Bishop, using their work on the chicken
src gene, discovered the first human oncogene, earning them a 1989 Nobel and leading to the
development of a class of chemotherapeutics, the classic example of which is Glivec.