Ever since Emile Zuckerkandl and Morris Goodman independently compared blood proteins of African apes and humans and determined they were indistinguishable, the remarkable molecular similarities between chimpanzees and humans have been obvious. But now with the sequencing and mapping (pinpointing the location of genes on chromosomes) of whole genomes of chimpanzees and humans, it is possible to identify the genes responsible for the expression of the similarities like those blood proteins and also the differences like hair patterns and even brain size.
Aside from humans and chimpanzees, many genomes have been se-quenced and include, for example, the mouse, E. coli, puffer fish, honeybee, silk moth, and rice. Those of gorillas, orangutans, bonobos, and rhesus monkeys are under construction. So far, as one would predict, animals that look similar have similar genomes. Perhaps the most humbling find from the mapping of the human genome is that humans have between 20 and 25,000 genes, which is only about twice that of a worm or fruit fly.
Of course, for investigating human origins we are most interested in how humans and chimpanzees matchup. Sequence comparisons have consistently shown that humans and chimpanzees are the most closely related hominoids sharing about 99 percent of their genetic code. The genomes prove unequivocally that chimpanzees are our closest living relatives, just as Darwin predicted and just as numerous other studies indicated that led up to the whole genome analyses.
Depending upon how one looks at the genomes of humans and chimpanzees, the difference in DNA can be estimated to be larger than 1 percent difference. Some estimates show up to an 8 percent difference. Straight nucleotide base pair differences are very small, on the order of less than 2 percent difference, but if the lens is pulled back and entire genes (segments of base pairs) or gene families (genes that get inherited together or that work together) are considered, then the human-chimpanzee genetic differences can be larger. This makes sense since most of the raw material is the same between chimpanzees and humans, it is just tweaked differently in each one. Both have hair, but it is just differently grown and arranged. Both have arms and legs, but they are just different lengths. Both have larger than normal brains and greater than average intelligence but humans are just more exaggerated. With hardly any sequence differences from chimpanzees, humans are not so derived as was previously assumed and we fit even more comfortably in the Tree of Life.
But humans are clearly different from chimpanzees, so what makes a human not a chimpanzee and conversely, what makes a chimpanzee not a human? Can we find the genes for big brains, language, tooth size, etc? Scientists are comparing, and will be comparing forevermore, the chimpanzee and human genomes to find regions that differ. During a scan of the sequence on a computer, for instance, a scientist may find a particularly interesting region that separates chimpanzees from humans. They will then look to databases of mapped genes in other animals to see if those genes have been identified and if their functions are known. If not, they may knock a gene down (a "candidate gene") in a mouse to see what effects, if any, are visible in the phenotype from the loss of the gene's function. Such an experiment in a model animal helps determine the function of genes since mice have very similar genomes to chimpanzees and humans.
Out of all the chromosomes, the Y chromosome seems to bear many of the differences between chimpanzees and humans. About 30 percent of our proteins are the same and those that differ are only separated by a couple of amino acid changes. Many of the types of genes that have experienced more evolution in humans than in chimpanzees—which is tracked by number sequence changes compared to primitive genomes like mice—are involved in immunity, sperm and egg production, and sensory perception like smelling.
Comparisons between the chimpanzee and human genomes mean nothing without an out-group to help decipher what traits are primitive (shared with the out-group) and what traits are derived (unique to the species). Once the bonobo, gorilla, orangutan, and rhesus monkey genomes are complete it will be possible to tell which genes arose on the chimpanzee lineage and which arose on the human lineage. Having the genomes of closely related out-groups mapped will lead scientists toward the genes that distinguish humans from the other apes.
The practical and promising aspects of whole genome sequencing and mapping involve finding cures for diseases and genetic disorders, but sequencing of whole genomes is vastly improving our understanding of the relationships between genotypes and phenotypes and the complicated biology of inheritance. Looking across genomes, especially at regulatory genes, has shown us that Mendelian inheritance—a biology driven by single genes and discrete traits—is the exception rather than the rule. In reality, many traits are polygenic where different alleles on more than one gene, often on different chromosomes all together, are responsible for a single trait. Also, traits are more likely to be continuous than discrete, ranging across shades of colors, for example, as opposed to being simply black or white. Additive effects are common, in which case the sum of the products of each involved gene results in the phenotype.
It appears that most of the differences between the DNA of humans and chimpanzees have to do with the activity levels of genes rather than the genes themselves. So, regulatory genes that either regulate expression themselves, or express proteins that regulate the activity of other genes, are where the human-chimpanzee variation occurs. A good explanation for this phenomenon could be that turning a gene on or off, or changing the levels of proteins expressed, is evolutionarily easier than changing the genes, amino acids, or proteins themselves.
The function of over 95 percent of our DNA is still a mystery. That is, we have spelled out the code, but have discovered that most of it does not code for proteins. Genes can be separated by a vast desert of noncoding DNA, which is sometimes called "junk" DNA. But is it useless? Probably not, because included among noncoding sequences are the crucial promoter regions which control when genes are turned on or off.
The human genome has more noncoding DNA than any other animal known to date and it is not clear why. At least half of the noncoding sequence is made up ofrecognizable repeated sequences, some ofwhich were inserted by viruses in the past. These repeats may provide some genomic wiggle room. That is, long stretches of noncoding DNA provide a playground for evolution. It may be a huge selective advantage to have all that raw material available to mutate and either modify existing traits and behaviors or express new ones all together. Humans are characterized by the ability to be flexible and to adapt quickly, so our junk DNA is potentially a priceless contribution to our humanness.
An intriguing difference in chimpanzees and humans occurs with the MYH16 gene. A mutation, estimated to have occurred about 2.4 Mya, rendered it inactive in humans but it continues to function well in chimpanzees, rhesus monkeys (Macaca mulatta), and other primates. MYH16 is involved in the development of jaw muscles for chewing so scientists hypothesize that the loss of function of this gene is linked to the drastic change in skull morphology in early members of the genus Homo around 2 Mya. Hominins during that transition time clearly had smaller teeth and chewing muscles and were in the midst of adopting a carnivorous way of life where stone tools began to take much of the functional burden away from the teeth and jaws. Although MYH16 is probably not the only gene involved in the chewing muscle complex (as it did not disappear completely with the mutation), it could definitely reveal a significant event in our evolution.
The mapping of whole genomes has revealed how difficult it is to find the "gene for" most traits, not only because phenotypes are expressed through complicated orchestrations of genes, but also because they can be heavily influenced by the environment during development and during life. When looking for specific genes, geneticists can control for environmental factors by observing identical twins that have essentially identical genotypes but grew up in different environments (i.e., separate bodies). Unfortunately such experiments are impossible to perform with Homo erectus, but understanding the environmental influences on trait development can help paleontologists decipher which traits are important for identifying species and tracking evolution and which traits are useless for those purposes because they are easily changed by nutrition or other nongenetic, environmental factors. An important area of genetic study uses quantitative trait loci or QTLs to determine which skeletal and dental traits of fossils are most informative for understanding evolutionary history, as compared to those that are too easily changed by the environment during life.
The few differences between humans and the great apes are actually the genetic foundation for our rapid cultural evolution and geographic expansion after 200 Kya. Only a few genetic changes were necessary to make human prehistory and history possible.
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