Eukaryotic cells (large, complex cells which share a nucleus and other membrane-bound structures) have not always existed in the fossil record, nor have modern eukaryotes existed since the first appearance of fossil eukaryotes. The earliest fossil eukaryotes were preceded by prokaryotic cells for 1 ½ billion years. If eukaryotes have descended from a common ancestor more recently than the last common ancestors of all life, then modern eukaryotes should share a number of traits which are not found in prokaryotes. In support of the evolutionary model, eukaryotes as diverse as multicellular humans and unicellular yeast share many common features which are not found in prokaryotic cells.

Modern eukaryotes form a clade whose diverse modern lineages share a number of features such as a nuclear membrane, golgi, endoplasmic reticulum, a new ribosomal subunit, and a greater use of introns to separate coding regions of genes. Modern eukaryotes share signaling pathways (such as specific kinases), pathways which regulate and limit cell division (cyclins, checkpoints, apoptotic mechanisms), a cytoskeleton (composed of actins, myosin, tubulin), collagen (which is the most abundant protein in the human body), proteins used for cell to cell interactions (cadherins, lectins, integrins, and immunoglobulins), and additional transcription factors (HTH, HMG, homeodomains).

Many features of mitochondria and chloroplasts support their evolutionary origin as endosymbiotic prokaryotes that adapted to survive inside ancestral eukaryotic cells. The great similarity between these organelles and certain bacteria is inconsistent with a unique, special creation with “irreducibly complex” molecular pathways.

Instead of being as unrelated to humans as bacteria, all eukaryotes form a clade—a group related by common descent as evidenced by a long list of shared anatomical and molecular traits. The comparisons of genetic sequences support this clade as a real group which excludes prokaryotes. Within eukaryote lineages, a number of subdivisions occurred before giving rise to animals (with fungi and choanoflagellates being more closely related to animals than are plants, algae, paramecia, and amoebae). Unicellular eukaryotes possess some, but not all, of the components of the more complex systems of multicellular eukaryotes which undermines the “irreducible complexity” argument of intelligent design.