Gastrulation
Gastrulation is a phase early in the development of animal embryos, during which the morphology of the embryo is dramatically restructured by cell migration. Gastrulation varies in different phyla. Gastrulation is followed by organogenesis, when individual organs develop within the newly formed germ layers.

# Mammals

## Preparation
In mammals, gastrulation occurs after implantation, around day 16 after fertilization in human embryogenesis. As the outer cell mass invades the endometrium, the inner cell mass divides into two layers: the epiblast and hypoblast. The hypoblast spreads out and covers the blastocoel to form the yolk sac. The yolk sac is an extraembryonic tissue that produces blood cells similar to the structure that surrounds the yolk in birds. The epiblast further divides into two more layers. The amnion layer forms the fluid filled cavity to surround and protect the embryo during pregnancy. The embryonic epiblast undergoes gastrulation.

## Gastrulation itself
Gastrulation in mammals is similar to that in birds with the formation of the primitive streak and Hensen's node and the ingression of cells through the primitive groove to form the endoderm and the mesoderm. Thus, gastrulation creates all three germ layers of the embryo: ectoderm, mesoderm, and endoderm
During gastrulation, extraembryonic mesoderm forms within the hypoblast or embryonic mesoderm and migrates out to form the blood vessels of the chorion and connect the chorion to the embryo through the umbilical cord.

# Sea urchins
The following description concerns gastrulation in echinoderms, representative of the triploblasts, or animals with three embryonic germ layers. The illustration, however, depicts the gastrulation of a diploblast, animals with two germ layers.
Sea urchins deviate from simple cleavage at the fourth cleavage. The four vegetal blastomeres divide unequally to produce four micromeres at the vegetal pole and four macromeres in the middle of the embryo. The animal cells divide meridionally and produce mesomeres.
At the beginning of vertebrate gastrulation, the embryo is a hollow ball of cells known as the blastula, with an animal pole and a vegetal pole. The vegetal pole begins to flatten to form the vegetal plate.  Some of the cells of the vegetal pole detach and through ingression become primary mesenchyme cells. The mesenchyme cells divide rapidly and migrate along the extracellular matrix (basal lamina) to different parts of the blastocoel. The migration is believed to be dependent upon sulfated proteoglycans on the surface of the cells and molecules on the basal lamina such as fibronectin. The cells move by forming filopodia that identify the specific target location. These filopodia then organize into syncytial cables that deposit the calcium carbonate that makes up the spicules (the skeleton of the pluteus larva).
During the second phase of gastrulation, the vegetal plate invaginates into the interior, replacing the blastocoelic cavity and thereby forming a new cavity, the archenteron (literally: primitive gut), the opening into which is the blastopore. The arechenteron is elongated by three mechanisms.
First, the initial invagination is caused by a differential expansion of the inner layer made of fibropellins and outer layer made of hyalin to cause the layers to bend inward.
Second, the archenteron is formed through convergent extension. Convergent extension results when cells intercalate to narrow the tissue and move it forward.
Third, secondary mesenchyme pull the tip of the archenteron towards the animal pole. Secondary mesenchyme are formed from cells that ingress from, but remain attached to, the roof of the archenteron. These cells extend filopodia that use guidance cues to find the future mouth region. Upon reaching the target site, the cells contract to pull the archenteron to fuse with the ectoderm. Once the archenteron reaches the animal pole, a perforation forms, and the archenteron becomes a digestive tract passing all the way through the embryo.
The three embryonic germ layers have now formed. The endoderm, consisting of the archenteron, will develop into the digestive tract. The ectoderm, consisting of the cells on the outside of the gastrula that played little part in gastrulation, will develop into the skin and the central nervous system. The mesoderm, consisting of the mesenchyme cells that have proliferated in the blastocoel, will become all the other internal organs.

# Amphibians
During cleavage in amphibians, a higher density of yolk in the vegetal half of the embryo results in the blastocoel cavity being placed asymmetrically in the animal half of the embryo. Unlike in sea urchins, the cells surrounding the blastocoel are thicker than a monolayer. The blastocoel cavity prevents signaling between the animal cap and provides a space for involuting cells during gastrulation.
There are four kinds of cell movements that drive gastrulation in Xenopus: invagination, involution, convergent extension and epiboly. At the dorsal marginal zone, cells change from a columnar shape to become a bottle cell and form an invagination. At this invagination, cells begin to involute into the embryo. This site of involution is called the dorsal lip. The involuting cells migrate along the inside of the blastocoel toward the animal cap. This migration is mediated by fibronectin of the extracellular matrix (ECM) secreted by the blastocoel roof. Eventually, cells from the lateral and ventral sides begin to involute to form a ring of involuting cells surrounding the yolk plug. These involuting cells will eventually form the archenteron which displaces and eventually replaces the blastocoel. Cells from the lateral marginal zone migrate toward the dorsal midline and intercalate with the cells there. This causes the dorsal involuting cells to undergo convergent extension. The dorsal cells become the first to migrate along the roof of the blastocoel cavity and form the anterior/posterior axis of the embryo. During the involution of cells, the cells of the animal cap undergo epiboly and spread toward the vegetal pole.

# Fish
At the time of mid-blastula transition, the zebrafish embryo is composed of three distinct cell layers: the enveloping layer (EVL), deep cells, and the yolk syncytial layer (YSL) formed from the fusion of cells adjacent to the yolk cells.
The first stage of gastrulation begins with the epiboly of the EVL and the deep cells over the YSL. This epiboly is driven by the migration of nuclei and cytoplasm in the YSL and attachments between the YSL and the EVL. Intercalation of the deep cells with the EVL help drive this movement. At about 50% of epiboly, a fate map similar to that of the Xenopus can be derived. The EVL develops into an extraembryonic membrane and does not contribute to the embryo.
The second stage of gastrulation occurs when the leading edge of the epibolizing blastoderm thickens. The dorsal side forms a larger thickening and is known as the embryonic shield. The deep cells in the embryonic shield form two layers. The epiblast forms near the surface and will give rise to the ectoderm. The hypoblast forms next to the YSL and will form a mixture of endoderm and mesoderm. The hypoblast is formed through involution and/or ingression. The movement of cells in the hypoblast are similar to the involuting mesoderm of amphibians. The end result of gastrulation is an asymmetric involution of cells that form the dorsal structures of the embryo.

# Birds
After cleavage, the blastoderm of chick embryos that sits above the yolk secretes fluid into the basally into the space between the yolk and the blastoderm called the subgerminal space. The region of the blastoderm above the subgerminal space is called the area pellucida. The region of the blastoderm above the yolk is the area opaca. The region where these two zones meet is called the marginal zone. At the posterior marginal zone (PMZ), there is a condensation of cells that is important in gastrulation. Within the PMZ, there is another thickening of cells called the Koller's sickle. Before gastrulation begins, the blastoderm forms two layers: the epiblast and the hypoblast. The epiblast gives rise to the embryo and some of the extraembryonic structures while the hypoblast contributes entirely to the extraembryonic membranes. The hypoblast comes from the primary hypoblast which delaminate out of the epiblast. This structure is equivalent to the organizer in amphibians and the embryonic shield in fish. Cells ingress through the primitive groove into the blastocoel cavity, migrate anteriorly through Hensen's node and then laterally through the rest of the groove. Cells that are fated to become the endoderm migrate to the bottom of the cavity and replace the hypoblast cells. Cells that are fated to become mesoderm remain in between the future endoderm cells and the epiblast and the epiblast cells remain to become ectodermal cells. The ectoderm, however, is undergoing epiboly to surround the yolk mass. The cells at the edge of the area opaca send out long filopida that attach to fibronectin in the vitelline membrane surrounding the embryo and yolk mass and pull the ectodermal cells toward the vegetal pole.
As gastrulation proceeds, the primitive streak regresses posteriorly with pharyngeal endoderm, the head process, and the notochord being laid down as it recedes. This results in a temporal gradient of development with the anterior forming organs while the posterior is still going through gastrulation.