
The earth is full of an incredible diversity of wondrous creatures. How did this diversity come to pass? At first scientists thought that all evolution was based on Darwin’s theory of natural selection and survival of the fittest. Then we understood how the genome fit into the story, thinking that genes alone control inheritance. And when we first produced the Shape of Life, developmental biology (how a fertilized egg turns into a whole organism) was becoming an important part of evolutionary theory.
Now how we understand evolution is evolving: researchers have discovered that evolution is way more complex than previously thought. They now know that there are multiple processes entirely outside the genome that are important drivers of diversity. “These extra-genetic kinds of inheritance give organisms the flexibility to make rapid adjustments to environmental challenges, dragging genetic change in their wake.“ These include epigenetics, microorganisms and cultural evolution.
Epigenetics
If you train mice to be afraid of a particular smell, that fear is inherited by the offspring of those mice and passed on future generations. The training affected which genes were activated, and this gene regulation was inherited. This is epigenetic inheritance. The genome was changed during the life of the mice and this change was inherited. This was not considered possible until recently. The environment can affect evolution; everything from diet to air pollution to parental behavior can influence gene expression.
“Another way of looking at epigenetics is that while traditional genetics describes the ways the DNA sequences in our genes are passed from one generation to the next, epigenetics describes passing on the way genes are used.”

Bacteria and other symbionts
Organisms can evolve through the bacteria and other symbionts living within them.
Many animals rely on bacteria in their guts to help them obtain and digest their food (for example, Mojave woodrats, termites, cows). The bacteria are not part of the genome, but are passed down through the generations. Without these microorganisms the animals wouldn’t survive.
For example, the Mojave woodrats pass down bacteria in their guts that enable them to eat the creosote bush, which contains toxins that the rats couldn’t otherwise digest. Young woodrats acquire the beneficial microbes by woodrat feces and eating soil. And cows have microbes in their rumen (the first compartment of a cow’s stomach) that help the cows digest and provides them with protein. These microbes can be inherited and passed on to their offspring.
Corals contain microscopic photosynthetic organisms called zooxanthellae. These supply the coral with the building blocks for making proteins, fats, and carbohydrates, and produce calcium carbonate. This leads to coral growth and reproduction. The evolution of the coral is directly influenced by the adaptation and changes occurring within these symbionts over time. As the symbionts evolve to better suit their environment, the coral host also evolves to maintain this beneficial relationship.

Cultural
At first cultural inheritance was thought to happen only in humans, but now it is well established throughout the animal kingdom. Primates, birds and whales all have been shown to have cultural traditions. These cultural adaptations spread through animal populations, can drive evolution, and can even change the physical traits of an organism that are then inherited.
For example, culturally learned foraging traditions of orcas – where different groups specialize in particular types of fish, seals or dolphins – is thought to be driving them to split into several species. The head shape and digestive physiology of the orcas have evolved through the natural selection of genes that are suited to the learned feeding behavior. Watch the Whales and Their Tales video.
Humpback whales also have feeding traditions that spread through populations and distinguish them from other populations of the whales. Off the east coast of the U.S. there’s a population that feeds by a whale slamming its tail fin to force fish into a tight school and then trapping them in bubble nets. Off the west coast small groups of whales create bubble nets to trap fish. Both of these methods spread through populations by cultural transmission. Watch the Whales and Their Tales video.