Where do new genes come from? It is one case where genes turn on or off, resulting in black or white fur, or where say slightly longer necks are favored over short ones. These changes are based on existing genes. What about the case of completely novel features? How do you go from a bacterium without any concept of arms and legs, teeth, etc. and lacking genes for these, to macroscopic animals having these genes. Macroscopic animals of course descended from single celled organisms. How do you get a gene (or group of genes) for an eye or a pancreas? What sort of mutation can give me a new, useful gene?
It is true that many evolutionary changes are due to changes in how and where genes are turned on and off. Changes in how existing genes are used is not enough to explain all evolutionary change, though, a point emphasized in your question. Changes in the number and type of genes that an organism has are also very important. There are two basic types of mechanism by which an animal might gain new genes. The first is horizontal gene transfer, and the second is gene duplication. Gene duplication occurs in both prokaryotes (single-celled organisms without nuclei) and eukaryotes (cells with nuclei like plants, animals, and fungi). Horizontal transfer is very widespread among prokaryotes but until recently was thought to be infrequent and insignificant in eukaryote evolution.
Horizontal gene transfer is common in prokaryotes such as bacteria. It occurs when a cell acquires DNA by some means other than inheritance from its parent cell. For example, bacteria of the same species may get new genes by conjugation, where two cells exchange pieces of DNA called plasmids. Plasmids contain genes but are separate from a cell’s genome. Individual cells may carry a lot of plasmids or none at all. Genes may also be transferred from one bacterium to another by viruses in a process called transduction. When a virus leaves an infected cell to infect another, it may carry some of the first host’s DNA with it into the second host. In this way, the second host can acquire genes from the first.
One of the most common ways for bacteria to acquire new genes is by transformation. When a bacterial cell encounters a stray piece of DNA in its environment (like from other bacteria that have died), it takes this piece of DNA into the cell. If that piece of DNA carries any useful genetic information, the cell will keep the DNA and benefit from it. This type of gene sharing between different species is very common and is an important part of bacterial evolution. Transformation also has consequences in terms of human health. For example, transformation is how genes for antibiotic resistance are spread from species to species.
The second major source of new genetic material for an organism is gene duplication. Genes may be duplicated due to a DNA replication error when a cell divides or when gametes (reproductive cells like sperm and eggs) are produced. Occasionally, entire genomes may be duplicated, probably due to an error in cell division. Once there are two or more copies of a gene in the cell, then the extra copies are free to diverge or change their function. The function of the original gene is called the “ancestral” function. The duplicated genes may evolve new functions or just subtly change the ancestral function. Over evolutionary time, the differences between the duplicates may become great.
There are many ways in which duplicated genes may diversify. Genes that descend from duplicates tend to be more specialized (either in what they do or in where they do it) than the ancestral gene. One duplicate may retain the ancestral function while the other evolves to perform a new function or performs the ancestral function at a different time or place. Or the ancestral functions could be distributed among the duplicates so that none of the duplicates ends up being functionally equivalent to the ancestral gene. The process of diversification of duplicated genes takes a very, very long time. Gene duplication events occur most frequently on small scales where one or a few genes are duplicated. Whole genome duplications, however, are not uncommon. The vertebrate genome is a classic example of gene duplication. Early in the vertebrate lineage, about 450 million years ago, the entire genome was duplicated twice. That means the ancestor of all vertebrates had four copies of every gene in its genome. Over time, these gene foursomes were free to divvy up their duties while evolving new functions. That’s why today each gene that is present in one copy in a fruit fly exists as approximately four different versions in a human. I say “approximately” because some duplicates may have been lost or duplicated again in the intervening millennia. Whole genome evolution is more common in plants than in animals.
No one type of genetic change is responsible for major evolutionary changes. Gene duplication and horizontal gene transfer are two types of genetic change. In combination with other processes such as recombination, mutation, and epigenetic mechanisms, they contribute to large-scale evolutionary changes. Genetic changes may eventually lead to alteration of an existing structure or development of a new structure. You mentioned legs as an example. Limbs had a huge impact on animal evolution. Let’s consider the limbs of arthropods such as insects, crustaceans, and spiders. The ancestors of arthropods were probably legless, wormlike marine creatures. They were limited as to how fast, how far, and through what sort of substrate they could move. The earliest limbs were probably just little outgrowths of the body wall that might have helped the animal crawl through mud or enabled it to swim better or cling to a rock.
These primitive legs were useful and improved an animal’s survival, so they were favored by evolution (this is called positive selection). Eventually, mutations or gene duplications caused some animal to make a leg with a joint. This made the limb stronger and more flexible, so now that improvement was selected for in the population. Over time, these limbs continued to be refined and altered. Today the arthropods show the most diverse array of limb morphologies of any animal group. The simple jointed limbs of the ancestor have undergone such amazing changes that today we see grasping claws, poison fangs, walking legs, swimming legs, mating appendages, feeding tools, and spear-like hunting appendages, just to mention a few. Such specialization makes it possible for animals to invade new niches and exploit new resources for survival.
Each step in a limb’s evolution was driven by a change in a gene’s function or in where and when that gene is used. Gene duplication is one of many types of genetic change that can provide fuel for such morphological change. Gene duplication has been very important in evolution because it provides new material upon which natural selection may act without the loss of any genetic information. Duplication preserves the normal function of a gene while providing an extra copy of that gene for mutation and natural selection.
I highly recommend Sean Carroll’s book From DNA to Diversity as a good primer on how genes change over time and give rise to new animal forms.
Rivera, M.C., and J.A. Lake. 2004. The ring of life provides evidence for a genome fusion origin of eukaryotes. Nature 431:152–5.
Ge, F., L.S. Wang, and J. Kim. 2005. The cobweb of life revealed by genome-scale estimates of horizontal gene transfer. PloS Biology 3(10):1709–18.
Taylor, J.S., and J. Raes. 2004. Duplication and divergence: the evolution of new genes and old ideas. Annual Reviews in Genetics 38:615–43.
Dehal, P., and J.L. Boore. 2005. Two rounds of whole genome duplication in the ancestral vertebrate. PloS Biology 3(10):1700–8.
Gross, L. Clear evidence for two rounds of vertebrate genome duplication. 2005. PloS Biology 3(10):1676–7. doi:10.1371/journal.pbio.0030344
Wikipedia entries for “horizontal gene transfer” and “gene duplication” are good general overviews.