Genomes

No, Not Those Things on Your Lawn

A genome is the full complement of genes in an organism. Genomes range in size from 5000 bases (5 kb) in viruses to upward of 150 billion bases. It is amazing how much information is in DNA. The human genome, for example, has about 3 billion letters, or the same number of letters that occur in 5 copies of War and Peace. If you have read War and Peace, you will remember how long it is. Imagine reading it five times.

The word "genome" may be slightly misleading. While some people argue that the genome is the full catalog of genes required to make an organism, most scientists refer to the full complement of nucleotides in a haploid cell of an organism as the genome. The complete set of nucleotides in an infectious virus particle is also called a genome. The rest is what most people call "junk DNA", but it includes sequences responsible for regulating gene expression in unknown mechanisms. Therefore, one man's junk is another man's treasure. Or, if you're Chinese, one man's junk is another man's ship. We at Shmoop apologize for that awful pun, but nobody makes Chinese nautical jokes anymore. It's a shame.



Much of the human genome is composed of "junk DNA," which is mostly introns and retrotransposons. It is unclear why there is so much "junk DNA" in humans, though the amount of junk DNA changes from organism to organism. Bacteria have little junk DNA, while viruses have genes packed over each other, with the same stretch of nucleotides encoding gene products in both the sense and antisense orientation. Next time you get scolded for being messy, just say, "You should see the amount of junk I've got in my DNA!"



Why do we have so much junk DNA, but bacteria and viruses do not? When we compare eukaryotes to bacteria and viruses, we see that our genomes are loaded with junk. The reason is that our average replication cycles are much slower on the cellular and organism levels. However, when we compare eukaryotes to each other, there is no relationship between genome size and complexity. All mammals have around 2-8 billion bases, while flowering plants range from 70 million to 150 billion. You may be thinking, "But, I'm way better than a plant!" Sorry, according to your genome size, you are not. Nothing like genome comparisons to give you a new perspective on eating vegetables.

Marrying Your Cousin and Other DNA-Based Relationships

Since Carolus Linneaus decided to start identifying species of plants and animals in Sweden, biologists have been trying to identify relationships between species. Charles Darwin developed a theory of natural selection, and in his The Descent of Man, implied that we humans came from a common ancestor. Before you start yelling "I ain't no ape!" at your monitor, remember that evolution implies that you and apes originated from a common ancestor—not that you came from apes. Therefore, chimpanzees are not our ancestors; they are our siblings.

There are many ways of determining relationships between organisms. The most common way is looking at the organisms' genes. We share many of the same genes as yeast, fruit flies, worms, and plants, though their genes have slightly different bases in the coding of the genes. These differences can be used to determine relationships. Our genes are most similar to other primates (sorry, anti-evolutionists), and become progressively different as we work our way up the tree to rodents, cows, and other mammals. At some point, we will arrive at our last common ancestor (LCA) with all other species of life on Earth, but we have not gotten that far science-wise. What the hay, Science? In the meantime, we can use phylogenetics to determine how similar species are to each other. We most often determine species relationships by making phylogenetic trees.

The Living Tree

Phylogenetic trees are basically graphs that show the evolutionary relationships among existing organisms, called taxa. Taxa is a shortened version of the obnoxiously-scientific term "taxonomical unit" that basically means "some living organism." Evolution suggests that all organisms are linked to some common ancestor if you go back far enough (just like all humans are related to each other if you go back far enough).

Therefore, how do we know that organisms are evolutionarily related? Most of the time scientists have no idea, and most phylogenetic trees are good estimates rather than definitive maps of true relationships.

There are two types of evolutionary trees:

• Those where groups are organized based upon morphological features, such as beak structure, number of legs, and type of eye.
   
• Those based on DNA sequence.
   

There has been much dispute at phylogenetic tree conferences over the best way to make a tree. Yes, hundreds of people meet every year and argue over the best way to make a tree. The most popular approach, however, is based on statistical evaluation of the probability that two species would be most similar to any other species with a given inheritable trait. Congratulations, you are now a phylogenetics nerd. It is a gift, and it is a curse.