The Domain Eukarya arose from the first prokaryotic organisms more than 1.7 billion years ago. It includes all of the organisms with eukaryotic cells--that is, those with membranous organelles (including mitochondria and chloroplasts). The organisms in this domain will be the focus of our classifications; indeed, they represent the vast majority of organisms we see each day. In terms of our classification questions, members of the domain have the following characteristics:
One of the key branches of evolutionary biology in recent decades has been the examination of the evolution of eukaryotes from these early prokaryotes (see Bacteria and Archaea). The evolution of the domain Eukarya is believed to have occurred by two primary processes. These evolutionary events are explained briefly below, but for more information please see our Conclusions.
All of the membranous organelles except for the mitochondria and chloroplasts are ultimately continuous with the plasma membrane and with each other. They comprise the endomembrane system, and are highly dependent on each other for the partitioning of the cell for metabolic activity. The organelles of the endomembrane system include the nucleus (surrounded by a double membrane), rough and smooth endoplasmic reticulum, Golgi apparatus, lysosomes, peroxisomes, vacuoles, and transport vesicles that move between the components. The eukaryotic endomembrane system arose by a process known as membrane infolding. The plasma membranes of the original prokaryotic cells that gave rise to the first eukaryote ones folded inward. Originally, this membrane may have formed small vesicles around the nucleus, which then grew outward to form a perforated double membrane. The inner projections of the plasma membrane (projecting out from the nuclear membrane) pinched off from the plasma membrane, forming the endoplasmic reticulum. From these organelles, the Golgi apparatus was derived, probably to improve the efficiency of protein synthesis.
The mitochondria and chloroplasts of eukaryotic cells arose in a different fashion. Most scientists now follow the endosymbiosis model, developed by Dr. Lynn Margulis of the University of Massachusetts. Because of the similarity of these organelles to prokaryotic cells, the endosymbiotic model proposes that they arose from small prokaryotes that established residence inside larger ones, deriving their outer membranes from the plasma membrane of the host cell. Mitochondria arose from small heterotrophic prokaryotes that had great efficiency in aerobic respiration, and chloroplasts arose from small photosynthetic autotrophs. Because the organelles could not be digested, they eventually evolved to assume a closely interdependent relationship with the cell, and today could not even survive on their own.
Here are a number of other resources:
A flowchart dealing with characteristics of the eukaryotic cell
A virtual cell
The University of Arizona's Phylogenetic project
There is truly immense diversity within the Domain Eukarya. It includes the kingdoms Protista, Fungi, Plantae, and Animalia. Protista includes the protists--unicellular, colonial, or multicellular, with a wide variety of reproductive cycles and energy and carbon derivation. Fungi are chemoheterotrophic, mostly multicellular decomposers with a unique reproductive cycle. Plantae are multicellular photoautotrophs with an alternation-of-generations life cycle and rigid cell walls. Finally, Animalia are multicellular chemoheterotrophs with a simple life cycle and no cell walls.