Analogous structures are anatomical structures that have similar functions, but arose independently. Due to environmental stresses and natural selection, organisms of different species evolved and adapted independently, resulting in the existence of body parts with similar functions. This refers to convergent evolution. An example of analogous structures are the wings of several different animals. A moth, hummingbird, and a bat are only extremely distantly evolutionarily related, yet they all have wings of some sort, which serve the common purpose of transportation through air. Homologous structures are body parts that are anatomically similar and may share similar anatomical forms, but are not the result of convergent evolution, rather they are the result of divergent evolution. These commonalities within organisms show descent from a common ancestor. An example of homologous structures are the "arms" of three different mammals, a human, a bat, and a whale. Each "arm" has very similar anatomical organization of bones, but is used for very different functions.

A vestigial trait is an attribute that has lost its function but has been retained through evolution. Examples include the formation of goose bumps in humans and pelvic remnants in boas and pythons. A change in the DNA sequence (genome) of a cell is a mutation. A trait that makes an organism better suited for a habitat is an adaption. Structures that arise in organisms that share a common ancestor, but perform different structures are called homologous structures. An example of a homologous structure is the "arm" of a mammal. Mammals have very similar bone and muscle organization in their arms (whales, humans, bats), but the function of each is much different (swimming, grabbing, flying).

It is believed that all organisms are descended from a common ancestor. Evidence of this includes morphological similarities, vestigial characteristics, and observations made within the fossil record. Recently, phylogenetic trees and cladograms are made using DNA sequence analysis to determine the similarity in the genomes of organisms. 

When parts of an animal serve different functions but have similar placement and bone structure (such as a wolf forearm and a whale flipper) and are derived from a common ancestor, these two structures are homologous. Convergent evolution is a process during which two non-related organisms develop analogous structures that serve the same function but have different structures. The bottleneck effect refers to the decrease in genetic diversity that occurs when a population goes through sudden decline and then expands again. Mendel's laws of inheritance refer to the rules by which different traits, or alleles, are passed on from one generation to the next as discrete units of inheritance called genes.

By definition, vestigial structures are structures that are thought to have had a biological function a long time ago but have since lost that function due to evolutionary changes. The human appendix is considered to be an example of a vestigial structure.

Homologous structures show the existence of a shared ancestry through the observation of structural similarities between different species; however, while a human's hand and a cat's paw are structurally similar, they have very different functions.

When a mutation in a gene prevents it from being read, it may be advantageous if the compound produced by the encoded enzyme can be readily obtained from outside sources, saving energy needed to produce the compound on one's own.

A well-known example of this is the GLO gene for vitamin C production. In fruit-eating animals like bats, guinea pigs, and humans, the gene is still present but has a broken promoter, rendering it nonfunctional.

An atavistic trait is a rare appearance of an ancestral structure in an evolved organism. Since dolphins evolved from four-legged mammals, a dolphin born with a pair of hind flippers shows is an atavism, an evolutionary throwback.

Ear wiggling is a an example of a vestigial trait. A rhino's horn in relation to a ram's horn represents an analogous vs. homologous structure. Facial recognition in crows is believed to be a product of coevolution.

Before any truly accurate scientific work on evolution and inheritance could be done, the academic community had to accept the notion that the Earth and its species change over time. If species were fixed, then genetic variation, natural selection, and evolution could not be plausible. Once the scientific community acknowledged the changes in organisms, they were able to proceed into studies to determine why and how such changes occur.

The answer is homoplasy, which is another term for convergent evolution. Humans and squid evolved the eye independently, which explains the differences in structure despite similar function.