The sex of a reptile embryo partly results from the production of sex hormones during development, and one process to produce those hormones depends on the temperature of the embryo's environment. The production of sex hormones can result solely from genetics or from genetics in combination with the influence of environmental factors. In genotypic sex determination, also called genetic or chromosomal sex determination, an organism's genes determine which hormones are produced. Non-genetic sex determination occurs when the sex of an organism can be altered during a sensitive period of development due to external factors such as temperature, humidity, or social interactions. Temperature-dependent sex determination (TSD), where the temperature of the embryo's environment influences its sex development, is a widespread non-genetic process of sex determination among vertebrates, including reptiles. All crocodilians, most turtles, many fish, and some lizards exhibit TSD.

Wilhelm Johannsen in Denmark first proposed the distinction between genotype and phenotype in the study of heredity in 1909. This distinction is between the hereditary dispositions of organisms (their genotypes) and the ways in which those dispositions manifest themselves in the physical characteristics of those organisms (their phenotypes). This distinction was an outgrowth of Johannsen's experiments concerning heritable variation in plants, and it influenced his pure line theory of heredity. While the meaning and significance of the genotype-phenotype distinction has been a topic of debate-among Johannsen's contemporaries, later biological theorists, and historians of science-many consider the distinction one of the conceptual pillars of twentieth century genetics. Moreover some have used it to characterize the relationships between studies of development, genetics, and evolution.

Tooth enamel contains relics of its formation process, in the form of microstructures, which indicate the incremental way in which it forms. These microstructures, called cross-striations and striae of Retzius, develop as enamel-forming cells called ameloblasts, whcih cyclically deposit enamel on developing teeth in accordance with two different biological clocks. Cross-striations result from a twenty-four hour cycle, called a Circadian rhythm, in the enamel deposition process, while striae of Retzius have a longer periodicity. Unlike other tissues, enamel does not remodel after it forms, leaving those microstructures intact after deposition. Cross-striations and striae of Retzius thus provide evidence of the timing and processes of tooth development, and they indicate how organisms in a lineage differently grow and develop across generations. Researchers have examined those microstructures to investigate human evolution.

In 1868 in England, Charles Darwin proposed his pangenesis theory to describe the units of inheritance between parents and offspring and the processes by which those units control development in offspring. Darwin coined the concept of gemmules, which he said referred to hypothesized minute particles of inheritance thrown off by all cells of the body. The theory suggested that an organism's environment could modify the gemmules in any parts of the body, and that these modified gemmules would congregate in the reproductive organs of parents to be passed on to their offspring. Darwin's theory of pangenesis gradually lost popularity in the 1890s when biologists increasingly abandoned the theory of inheritance of acquired characteristics (IAC), on which the pangenesis theory partially relied. Around the turn of the twentieth century, biologists replaced the theory of pangenesis with germ plasm theory and then with chromosomal theories of inheritance, and they replaced the concept of gemmules with that of genes.

In nineteenth century Great Britain, Thomas Henry Huxley proposed connections between the development of organisms and their evolutionary histories, critiqued previously held concepts of homology, and promoted Charles Darwin's theory of evolution. Many called him Darwin's Bulldog. Huxley helped professionalize and redefine British science. He wrote about philosophy, religion, and social issues, and researched and theorized in many biological fields. Huxley made several methodological contributions to both invertebrate and vertebrate embryology and development, and he helped shape the extra-scientific discourse for these fields.