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Early history of brain development
Scientists can infer that the first brain structure appeared at least 521 million years ago, with fossil brain tissue present in sites of exceptional preservation.

Before the evolutionary development of the brain, nerve nets, the simplest form of a nervous system developed. These nerve nets, which were first observed in Cnidaria, consist of a number of neurons spread apart that allow the organism to respond to physical contact. They are able to rudimentarily detect food and other chemicals but these nerve nets do not allow them to detect the source of the stimulus.

Ctenophores also demonstrate this crude precursor to a brain or centralized nervous system, however, they phylogenetically diverged before the phylum Porifera and Cnidaria. There are two current theories on the emergence of nerve nets. One theory is that nerve nets may have developed independently in Ctenophores and Cnidarians and the other theory states that a common ancestor may have developed nerve nets, but this was lost in Porifera.

A trend in brain evolution according to a study done with mice, chickens, monkeys and apes concluded that more evolved species tend to preserve the structures responsible for basic behaviors. A long term human study comparing the human brain to the primitive brain found that the modern human brain contains the primitive hindbrain region – what most neuroscientists call the protoreptilian brain. The purpose of this part of the brain is to sustain fundamental homeostatic functions. The pons and medulla are major structures found there. A new region of the brain developed in mammals about 250 million years after the appearance of the hindbrain. This region is known as the paleomammalian brain, the major parts of which are the hippocampi and amygdalas, often referred to as the limbic system. The limbic system deals with more complex functions including emotional, sexual and fighting behaviors. Of course, animals that are not vertebrates also have brains, and their brains have undergone separate evolutionary histories.

The brainstem and limbic system are largely based on nuclei, which are clusters of tightly-packed neurons and the axon fibers that connect them to each other and to neurons in other locations. The other two major brain areas (the cerebrum and cerebellum) are based on a cortical architecture. At the outer periphery of the cortex, the neurons are arranged into layers (the number of which vary according to species and function) a few millimeters thick. There are axons that travel between the layers, but the majority of axon mass is below the neurons themselves. Since cortical neurons and most of their axon fiber tracts don't have to compete for space, cortical structures can scale more easily than nuclear ones. A key feature of cortex is that because it scales with surface area, "more" of it can be fit inside a skull by introducing convolutions, in much the same way that a dinner napkin can be stuffed into a glass by wadding it up. The degree of convolution is generally greater in more evolved species, which benefit from the increased surface area.

The cerebellum, or "little brain," is behind the brainstem and below the occipital lobe of the cerebrum in humans. Its purposes include the coordination of fine sensorimotor tasks, and it may be involved in some cognitive functions, such as language. Human cerebellar cortex is finely convoluted, much more so than cerebral cortex. Its interior axon fiber tracts are called the arbor vitae, or Tree of Life.

The area of the brain with the greatest amount of recent evolutionary change is called the cerebrum, or neocortex. In reptiles and fish, this area is called the pallium, and is smaller and simpler relative to body mass than what is found in mammals. According to research, the cerebrum first developed about 200 million years ago. It's responsible for higher cognitive functions - for example, language, thinking, and related forms of information processing. It's also responsible for processing sensory input (together with the thalamus, a part of the limbic system that acts as an information router). Most of its function is subconscious, that is, not available for inspection or intervention by the conscious mind. Neocortex is an elaboration, or outgrowth, of structures in the limbic system, with which it is tightly integrated.

Human brain size in the fossil record
The evolutionary history of the human brain shows primarily a gradually bigger brain relative to body size during the evolutionary path from early primates to hominids and finally to Homo sapiens. Brain size and some of its structure can be studied using endocasts, which are the internal casts created by using a skull as a mold. Endocasts can help scientists study superficial brain areas and their relative sizes, although they cannot reveal brain structure, particularly of deeper brain structures.

Human brain size has been trending upwards since 2 million years ago, with a 3 factor increase. Early australopithecine brains were a little larger than chimpanzee brains. The increase has been seen as larger human brain volume as we progressed along the human timeline of evolution (see Homininae), starting from about 600 cm3 in Homo habilis up to 1600 cm3 in Homo neanderthalensis (male averages). The increase in brain size topped with Neanderthals, possibly due to their larger visual systems. Brain size of Homo sapiens varies significantly between population (races), with male averages ranging between about 1,200 to 1,450 cm3.

In addition to just the size of the brain, scientists have observed changes in the folding of the brain, as well as in the thickness of the cortex. The more convoluted the surface of the brain is, the greater the surface area of the cortex which allows for an expansion of cortex, the most evolutionarily advanced part of the brain. Greater surface area of the brain is linked to higher intelligence as is the thicker cortex but there is an inverse relationship-- the thicker the cortex, the more difficult it is for it to fold.

Embryology
Further information: Embryology and Neural Induction In addition to studying the fossil record, evolutionary history can be investigated via embryology. An embryo is an unborn/unhatched animal and evolutionary history can be studied by observing how processes in embryonic development are conserved (or not conserved) across species. Similarities between different species may indicate evolutionary connection. One way anthropologists study evolutionary connection between species is by observing orthologs. An ortholog is defined as two or more homologous genes between species that are evolutionarily related by linearly descent.

The separation of neural and glial cells from other tissue is the first step of neural induction, the process by which the nervous system is generated. In invertebrates, the ventrolateral region of the embryo gives rise to the neurogenic region. As the neural groov e starts to close, the neurogenic region becomes more ventral. The seam of the neural tube closure is the site of neurogenesis, from where the neuroblasts delaminate, or enlarge and squeeze away from the epithelial layer. These neuroblasts divide to form ganglion mother cells (GMC), which then form neurons and glia.

In vertebrates, the zygote is polarized after the fertilization to form two hemispheres: the animal and vegetal hemispheres. After multiple rounds of cell division, a blastula is formed. The fluid-filled cavity of the blastula is called the blastocoel. Via gastrulation, the gastrula is formed which ultimately leads to the formation of the neurula. This neurogenic regions becomes the neural plate, which folds on itself to form the neural tube the top of which becomes the neural crest. The neural tube gives rise to central nervous system, while the cells from the neural crest give rise to the peripheral nervous system.

Bone Morphogenetic Protein (BMP), a growth facto r that plays a significant role in embryonic neural development, is highly conserved amongst vertebrates, as is Sonic Hedgehog (shh), a morphogen that inhibits BMP to allow neural crest development.