Coevolution happens at many levels, not just the level of species. Organelles such as mitochondria and chloroplasts serve as good intracellular examples. Other living things make up a crucial component of an organism's environment. Coevolution can occur in helpful ways (symbiosis) and in harmful ways (parasitism). Many factors can influence coevolution, such the frequency and degree of interaction.

The fossil record holds a lot of evolutionary information that can't be seen on shorter time scales, although the more recent fossil record is more complete. Among other things, the fossil record demonstrates that extinctions can open up ecological space for new speciation and radiation, and that life forms tend to begin small and evolve to be bigger over time.

Geology and climate have shaped the development of life tremendously. This has occurred in the form of processes such as the oxygenation of the atmosphere, mass extinctions, tectonic drift, and disasters such as floods and volcanic eruptions. Life, particularly bacteria, has also been able to impact the geological makeup of the planet through metabolic processes.

The history of life and evolution has been characterized by several key events. These events can be grouped as new hierarchal levels of selection coming into play, as biological units coming together in symbiosis and specialization, or in a number of other ways. Other important events are situations of conflict resolution or information transmission, from the genetic to the cultural level.

We can use methods of genetic analysis to connect phylogenic information to geographical histories. Human migration has left genetic traces on every continent, and allows us to trace our roots back to Africa. Molecular genetic methods allow us to determine whether or not trait states were ancestral, which can have profound implications for fundamental biological ideas.

The Tree of Life must be discovered through rigorous analysis. Genetic information is crucial because appearances can be deceiving, and species that look similar can prove to be genetically very dissimilar and not share recent common ancestors. Two criteria, used to determine what the "correct" Tree is, are simplicity and whether the tree maximizes the probability of observing what we actually see.

Speciation is the process through which species diverge from each other and/or from a common ancestor. There are several definitions of species, most of which focus on reproductive isolation and/or phylogenetic similarities. This can cause some controversy. Speciation can result from geographical separation or ecological specialization. There are stages of speciation in which organisms cluster first into distinct populations before finally becoming different species.

Sexual selection is a component of natural selection in which mating success is traded for survival. Natural selection is not necessarily survival of the fittest, but reproduction of the fittest. Sexual dimorphism is a product of sexual selection. In intersexual selection, a sex chooses a mate. In intrasexual selection, individuals of one sex compete among themselves for access to mates. Often honest, costly signals are used to help the sex that chooses make decisions.

Sex allocation is an organism's decision on how much of its reproductive investment should be distributed to male and female functions and/or offspring. Under most conditions, the optimal ratio is 50:50, but that can change under certain circumstances. Sex allocation determines what sexes sequential hermaphrodites should be at each part of their life as well as how simultaneous hermaphrodites should behave. Some species have more control over the sexes of their offspring than others, and adjust the sex ratios of their offspring depending on the environment and conditions.

Life history covers three main classes of traits in organisms: age and size at maturity, number and size of offspring, and lifespan and reproductive investment. Organisms must make tradeoffs among these traits that typically cause them to come to evolutionary equilibrium at intermediate values.