The field of developmental biology has expanded greatly in the past few decades. Through the combination of genetics and modern techniques in molecular biology, we now understand many more of the processes that direct the development of animals. Epigenesis describes the set of ideas that were first described in the 1700s, which describe that the fertilized egg contains a set of genetic information that directs the embryonic development, and new structures are formed as a result of these genetic instructions. As the embryo develops, the processes of cytoplasmic localization and induction determine the fate of certain cells.

Fertilization typically precedes development of the zygote, but not in the case of parthenogenesis. However, in most species, the developmental process proceeds as follows. Oocyte maturation involves growth of the egg, and morphogenetic determinants exist which will act later in the postfertilization development. The egg accumulates lipid reserves and much mRNA. The nucleus becomes so large that it is now called the germinal vesicle. For an egg to become fertilized, there must be both contact and recognition between egg and sperm, particularly important in animals that undergo external fertilization. Much of our understanding of this process comes from early studies on sea urchins. There is typically a chemical, species-specific reactant seen in invertebrates such as this. Further, binding between the egg and sperm allows for specificity. When the sperm contacts the egg, a number of changes occur to prevent polyspermy. The first sperm to enter causes an immediate electrical potential change in the egg membrane (the fast block), followed by the cortical reaction. Then, in sea urchins and similar invertebrates, a fertilization membrane forms, further preventing polyspermy.

The sperm nucleus enters the egg, and contacts the female pronucleus, and fuse to form the now diploid zygote nucleus. This activates the egg to begin a series of changes. Cleavage occurs rapidly without growth of the zygote, yielding a mass of cells called blastomeres. Variations in cleavage are seen, and occur along the polar axis, forming a polarity in the resultant zygote. Patterns of cleavage depend on the amount of yolk, as well as whether the organism is a protostome or deuterostome. In eggs with little yolk (isolethical eggs), cleavage is relatively equal, known as holoblastic cleavage. This pattern is seen in a variety of animals, including echinoderms, lower chordates, most molluscs, as well as mammals. In mesolethical eggs, cleavage is also holoblastic, but cleavage is slower in the yolk-rich vegetal pole, and more rapid in the animal pole. Animals that exhibit this show either superficial cleavage, or discoidal cleavage. Eggs of most higher vertebrates (excluding mammals, except for the oviparous forms), are telolethical, and cleavage is meroblastic, or partial, resulting in a large amount of yolk, with the embryo undergoing cleavage lying on top.

Zygotes with little yolk, such as aquatic invertebrates rely on a metamorphic life style, called indirect development. The larval form typically has a different feeding mode than the adult. In animals such as mammals, which also have little yolk, the placenta is the attachment for nutrition, and they show direct development.

Cleavage may be radial-cleavage is oriented either parallel or perpendicular to the animal-vegetal axis of the egg as it is in the deuterostomes, or spiral-cleavage is oblique to the animal-vegetal axis as it is in the protostomes. This difference represents the early evolutionary split between these two groups. Mammals have isolethical eggs, but have rotational cleavage, and development is slower than in any other animal groups. Further, early divisions are asynchronous. The outer cells form a trophoblast, which forms the embryonic portion of the placenta. The cells that become the embryo itself are called the inner cell mass.

Ultimately, a cluster of cells called a blastula is formed, typically surrounding a cavity called the blastocoel. The polarity (symmetry or other axes) of the organism may be set by this point.

Gastrulation is characterized by an invagination. The newly formed internal cavity is called the archenteron. The blastopore is the point of the invagination, and may be the future anus or the future mouth of the organism. In the cnidarians, only two cell layers are formed, but in all other animals, the embryo is triploblastic. The gastrula has three cell layers; the endoderm, mesoderm, and ectoderm. Ectoderm gives rise in vertebrates to the epithelia and the nervous system. The digestive tube is derived from the endoderm, as well as organs such as the lungs, liver, and pancreas. The mesoderm gives rise to the skeletal, muscular, and circulatory structures, and the kidney.

Gastrulation in amphibians is oriented in a different way than in other vertebrates. Gastrulation in reptiles, birds, and mammals starts with the formation of the primitive streak, and this then directs the axes of the embryo. Gastrulation in mammals is similar. Coelom formation may be schizocoelous (in protostomes), or enterocoelous (in deuterostomes). This is another example of the basic dichotomy between these two evolutionary lineages. Since the variety of structures of a multicellular organism came from a single cell, and these millions or trillions of cells carry the same DNA, it was a dilemma for early scientists to discover how cells differentiate. Nuclear equivalence describes the answer to this question. Spemann's experiments showed that all cells contained the same nuclear information (of the organism of which they are a part), and the cytoplasm of the area of the gray crescent contains information for normal development. But there is more to the story. Further experiments have shown that the separation of determinative molecules and induction also play a part in the fate of cells during development. Induction is the capacity of one cell or tissue to cause responses in another, and is still only one part of the answer. It is a widespread phenomenon in development. Scientists have identified both primary inductive and secondary inductive processes. Also, mosaic development shows that cell fate can be determined without the effect of the adjacent cells, as well as regulative development, which describes the fact that cells of an early blastomere do have the capacity to follow different paths of differentiation. Maternal mRNA may also influence protein synthesis early in development as well. And if you can follow all of that, you're doing well!

Developmental biology is very complex. But there is more. Homeotic genes are regulatory genes that ensure the orderly development of the embryo, and were first studied in fruit flies. One short DNA sequence is called the homeobox and codes for regulatory proteins. The amazing similarity of homeobox sequences in animals from fruit flies to humans reminds us of our enormous genetic similarities.

Development of the embryo may be within an egg in oviparous animals, within an egg retained in the body of the female (ovoviviparous animals), or nourished within the oviduct or uterus of the female (viviparous animals). Vertebrate animals show a similar pattern of development because they are all amniotes. Even though most mammals do not lay eggs, many of the extraembryonic membranes are retained in the mammalian placenta and embryo. The amnion is the fluid filled sac that protects the embryo, the allantois stores wastes, the yolk sac provides nutrition, and the chorion encloses the rest of the membranes.

The mammalian placenta retains modified membranes of the original reptilian amniotic egg. The amnion remains as a fluid-filled sac. The yolk sac contains no yolk, but is the source of stem cells that give rise to blood and lymphoid cells. The allantois contributes to the umbilical cord. The placenta, however, is unique, and contains both embryonic (derived from the trophoblast, and then the chorionic villi) and maternal tissues with the circulatory vessels in close proximity to allow exchanges. Most major organs in the human embryo develop by the end of the first month. In humans, the embryonic period lasts until the 2 month mark, after which it is referred to as a fetus.

Developmental patterns are seen when the embryo forms three cell layers. The ectoderm is the origin of the neural plate, which rises up, and the two "lips" fuse to form the hollow neural tube. Many cells associated with this tube are the important neural crest cells, which form a variety of unique structures seen only in vertebrates. Endoderm comes from the embryonic archenteron, and forms the gut, and many associated structures such as the lungs, liver and pancreas, as well as the characteristic gill pouches seen in some stage of the life of all vertebrates. In animals such as fish, these persist as gills. But in terrestrial vertebrates, these contributed to structures that you might not surmise- such as the tonsils, the lower jaw, and bones of the inner ear! Mesodermal tissues ultimately form the skeletal and muscular tissues, the circulatory system, and urinary, and reproductive structures. Amazingly, the heart begins to beat before there is any blood to pump!