PHYLOGENY IS ALL ABOUT BEING CONNECTED TO LIFE
Darwin was the first to sketch a simple branched diagram showing how life is connected through evolution. By the time I was a teenager I was enjoying phylogenetic trees that classified all living things into two kingdoms –plants and animal. Some fifty years later that classification has given way to 96 phyla distributed among three domains. The domains are given the technical names eukaryotes, eubacteria, and archaebacteria. You and almost everything you know that is living are eukaryotes. Your cells have nuclei. But bacteria and archaebacteria have a different structure—they do not have nuclei and their cells are much smaller. That cell structure is called prokaryotic (next time you get a strep throat, think of prokaryotes gathering in multitudes reddening those tissues).
In 2006 scientists compared the complete genome sequences of 191 species that shared in common some 31 genes. There were 11 multicelled animals among these 191 and they represented the major animal phyla (worms, jellyfish, mollusks, arthropods, vertebrates, echinoderms, etc.). Most of the completed sequences were from prokaryotes. The most familiar domain of the prokaryotes belong to the eubacteria (the ones dealing with the germ theory, with spoiled food, rotting carcasses, and some commercially useful bacteria that make vinegar and a variety of cheeses, and other dairy products). The ones we almost never encounter live in extreme environments such as ocean vents, geysers, and sometimes miles down in the earth. The reason they are put into two domains has to do with their organization of their genes. The archaebacteria have split genes as do the eukaryotes but they have a prokaryotic organization. Most prokaryotes are killed when scalded but archaebacteria flourish in hot water that can be very hostile. A few of the eubacteria are also capable of thriving in hot water or extreme environments and they are among the oldest of the forms of life on our evolutionary tree. The archaebacteria arose from the eubacteria and the eukaryotes arose from the archaebacteria.
The phylogenetic tree which relates the genomes to their mutational differences, as one form of life arose from an earlier one, gives a picture strikingly similar to the phylogenetic trees constructed from the fossil record. The age of these ancestors is also determined independently by isotopic analysis of the rocks they are in and the mutational differences among their common genes. Those who think evolution is “just a theory” have a lot of explaining to do because that relation between complexity and time fits evolution and not special creation in any of its forms. The evolutionary theory based on the older fossil record predicted the molecular phylogenetic tree would resemble it in its major features and it did. Science makes predictions and the data lets the scientist see if the theory still holds. It does for the phylogenetic theory.
What is remarkable about this computer generated phylogenetic tree is that new genome sequences can be added as all of the 96 phyla are eventually sequenced and the tree will become more elaborate. Just as a genealogist finds family members in the thousands when dedicated to searching for one’s ancestors, the scientist finds the major family members of all life on earth. Some day a fourth domain, the viruses, may be connected to the first and most ancient cells. We are kin to everything alive
Showing posts with label cell evolution. Show all posts
Showing posts with label cell evolution. Show all posts
Saturday, December 11, 2010
Friday, November 26, 2010
Life Lines 59
SWAPPING GENES HELPS A PARASITE AND ITS HOST
Aphids are sometimes called plant lice. They are sometimes seen in large numbers sucking sap out of stems of leafy plants. The aphids don’t reveal to anyone but a scientist that they are also being parasitized by a bacterium. The bacterium, called Buchnera, has one of the smallest genomes of any cellular organism, a mere 460 genes. It lives in the cells of the aphid. The aphid, curiously, has one of the largest genomes of any cellular organism, over 35, 000 genes, almost twice that of a human. Only a few of its genes have been given to it by Buchnera. Most of its genes are due to numerous duplication of genes. Among the genes given by Buchnera to the aphid are genes for making amino acids. Eleven of these genes came from Buchnera to help make six amino acids. But for two of these amino acids the last step in making the amino acid is done by a gene of the aphid. This makes those two amino acids examples of a mutually beneficial system. Each helps the other for amino acids they both need and neither can survive without the presence of the other.
We often think of animals at war with each other and for predator and prey relations that is true. But many organisms form mutually beneficial relations. Most ecologists would argue that the world of life is interdependent, with all animals dependent ultimately on the foods made by plants through photosynthesis. There are more intimate relations than the groceries we select for our meals. Most trees have roots penetrated with bacteria or fungi that make nitrogen or other essential nutrients for the plant. In return the fungi or bacteria living in the roots have protection and nourishment.
I have often wondered why the public image [“nature red in tooth and claw”] of evolution is based on the predator-prey relation and not the mutualistic or beneficial interplay of organisms with one another. We need a Tennyson to interpret that more positive image of evolution for us. My own feeble effort of “nature rich in share and change” wouldn’t resonate to our emotions nor would it convey the powerful imagery of that bloody evolution as we imagine dinosaurs tearing hunks of flesh from their victims. There is far more mutual benefit going on in nature than an unceasing warfare between species. When we cut up land with roads and fences we quickly eliminate the migration of many species that will perish because they do not have territory to breed or forage. Our image is the hunter with the rifle but the reality for most deer, pheasants, and small mammals is the difficulty of finding food when human barriers isolate them. Organisms die from diseases and malnutrition more often than they do from carnivorous predators devouring them. Evolution is an outcome of both beneficial and horrifying ways to live. A grandmother making clothing is as beneficial as a young hunter bringing home game for all to eat. What is remarkable in the Buchnera-aphid story is the cooperation in amino acid synthesis that developed at a molecular level. It is a relatively recent event, not as ancient as our own cellular ancestry. All of our cells have mitochondria that were derived from bacteria in the early emergence of eukaryotic cells (cells with nuclei). Most of those bacterial genes entered the nuclei of our cells or were permanently lost as our mitochondria became transformed into oxygen breathing and energy producing organelles of our cells.
Aphids are sometimes called plant lice. They are sometimes seen in large numbers sucking sap out of stems of leafy plants. The aphids don’t reveal to anyone but a scientist that they are also being parasitized by a bacterium. The bacterium, called Buchnera, has one of the smallest genomes of any cellular organism, a mere 460 genes. It lives in the cells of the aphid. The aphid, curiously, has one of the largest genomes of any cellular organism, over 35, 000 genes, almost twice that of a human. Only a few of its genes have been given to it by Buchnera. Most of its genes are due to numerous duplication of genes. Among the genes given by Buchnera to the aphid are genes for making amino acids. Eleven of these genes came from Buchnera to help make six amino acids. But for two of these amino acids the last step in making the amino acid is done by a gene of the aphid. This makes those two amino acids examples of a mutually beneficial system. Each helps the other for amino acids they both need and neither can survive without the presence of the other.
We often think of animals at war with each other and for predator and prey relations that is true. But many organisms form mutually beneficial relations. Most ecologists would argue that the world of life is interdependent, with all animals dependent ultimately on the foods made by plants through photosynthesis. There are more intimate relations than the groceries we select for our meals. Most trees have roots penetrated with bacteria or fungi that make nitrogen or other essential nutrients for the plant. In return the fungi or bacteria living in the roots have protection and nourishment.
I have often wondered why the public image [“nature red in tooth and claw”] of evolution is based on the predator-prey relation and not the mutualistic or beneficial interplay of organisms with one another. We need a Tennyson to interpret that more positive image of evolution for us. My own feeble effort of “nature rich in share and change” wouldn’t resonate to our emotions nor would it convey the powerful imagery of that bloody evolution as we imagine dinosaurs tearing hunks of flesh from their victims. There is far more mutual benefit going on in nature than an unceasing warfare between species. When we cut up land with roads and fences we quickly eliminate the migration of many species that will perish because they do not have territory to breed or forage. Our image is the hunter with the rifle but the reality for most deer, pheasants, and small mammals is the difficulty of finding food when human barriers isolate them. Organisms die from diseases and malnutrition more often than they do from carnivorous predators devouring them. Evolution is an outcome of both beneficial and horrifying ways to live. A grandmother making clothing is as beneficial as a young hunter bringing home game for all to eat. What is remarkable in the Buchnera-aphid story is the cooperation in amino acid synthesis that developed at a molecular level. It is a relatively recent event, not as ancient as our own cellular ancestry. All of our cells have mitochondria that were derived from bacteria in the early emergence of eukaryotic cells (cells with nuclei). Most of those bacterial genes entered the nuclei of our cells or were permanently lost as our mitochondria became transformed into oxygen breathing and energy producing organelles of our cells.
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