The brain is made up of soft tissue so it doesn't appear in the fossil record. Skulls or brain cases have been used to postulate brain structure but until the reptiles the brain didn't completely fill the brain case so this use of fossils has only worked on later animals. In 1866, the German biologist Ernst Haeckel proposed his Biogenetic Law that “Ontology Recapitulates Phylogeny.” The idea was that as an embryo develops, it goes through the same stages as it's ancestors. A beginning human embryo looks like a fish embryo, human embryos even have a short tail at some time. This theory was quite popular during the late 19th century but was much too general and for the most part untrue. It lost popularity completely during the 1930's and the synthesis between Darwin's theory and genetics. Unfortunately the synthesis had nothing to say about how organisms developed so embryology became a purely explanatory science, rooted in no theory. (1) In 1961 the Lac Operon was discovered by Monod, Changeux, and Jacob. Complex regulatory control exists at the bacterial level. In 1978 Edward B. Lewis discovered homeotic genes. These genes have been found in all levels of eukaryotes and little changed. This and other discoveries have led to a second synthesis of molecular genetics, phylogeny, and evolutionary biology called evo-devo. (2) The idea is that all eukaryotes have an evolutionary stable set of genes. This set creates all the myriad forms of life through patterning and timing of expression. Patterning is called the transcriptome. The transcriptome and the timing of the transcriptome exposes homology, the connection to a most recent ancestor. These new ideas and technologies have transformed embryology and our knowledge of brain evolution. (6)(4)
This is not to say that Haeckel was all wrong and should be forgotten. There is a relationship between phylogeny and ontogeny and the tools of molecular genetics have transformed descriptive embryology as they inform not only where to look but how to look. Steven Jay Gould wrote about this extensively. How scientific progress depends as much on the failure of ideas as on the success of them. The wonders of the natural world are not there to fit into anyone's theory, they are there to be revealed and maybe even understood. Wherever the journey takes us.. Gould's work as a historian of science is one of his many accomplishments. (1)
The neocortex arose in mammals from a base structure called the posterior pallium that is related to the olfactory bulb. The structure of the pallium has come and gone through different orders. Birds inherited a three layer structure maybe from dinosaurs but it has fused into a single layer. Mammals have a unique 6 layer structure called the neocortex. (5) The hippocampus also evolved from the pallium, the medial pallium. A study of hippocampal volume vs neocortex volume in primate evolution shows that neocortex volume has increased while regions of the hippocampus: CA3, fascia dentata, subiculum, and entorhinal cortex, have decreased. This is perhaps because of color vision in primates at the expense of the sense of smell. In humans, neocortex volume has greatly increased and in the hippocampus, CA3, subculum and entorhinal cortex volume has also increased. (3) As human sense of smell is pretty weak compared to other mammals such as dogs, it looks like there is some re-purposing going on. The subculum and the entorhinal cortex are two of the three regions containing cells used for the cognitive map. (1)
To summarize: The neocortex is a part of the brain only found in mammals that has greatly expanded in primates and hugely expanded in humans. Primate evolution has shown a decrease in some regions of the hippocampus but an increase in humans of the regions that control spatial reasoning.
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(1) Gould, Stephen Jay. “Ontogeny and Phylogeny.” Accessed May 24, 2020. https://www.hup.harvard.edu/catalog.php?isbn=9780674639416.
(2) Jacob, F. “Evolution and Tinkering.” Science 196, no. 4295 (June 10, 1977): 1161–66. https://doi.org/10.1126/science.860134.
(3) Vanier, David R., Chet C. Sherwood, and Jeroen B. Smaers. “Distinct Patterns of Hippocampal and Neocortical Evolution in Primates.” Brain, Behavior and Evolution 93, no. 4 (2019): 171–81. https://doi.org/10.1159/000500625.
(4) Lui, Jan H., David V. Hansen, and Arnold R. Kriegstein. “Development and Evolution of the Human Neocortex.” Cell 146, no. 1 (July 8, 2011): 18–36. https://doi.org/10.1016/j.cell.2011.06.030.
(5) Tosches, Maria Antonietta, and Gilles Laurent. “Evolution of Neuronal Identity in the Cerebral Cortex.” Current Opinion in Neurobiology 56 (June 2019): 199–208. https://doi.org/10.1016/j.conb.2019.04.009.
(6) Rakic, Pasko. “Evolution of the Neocortex: A Perspective from Developmental Biology.” Nature Reviews Neuroscience 10, no. 10 (October 2009): 724–35. https://doi.org/10.1038/nrn2719.
(7) Beaver, Bill. “The Hippocampus as a Cognitive Map.” Emergent Thoughts, May 9, 2020. https://wjbeaver.wixsite.com/mysite/post/the-hippocampus-as-a-cognitive-map.
(8) O’Keefe, John. “Spatial Cells in the Hippocampal Formation - Nobel Lecture,” December 7, 2014.
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