Y-chromosomes exist in the body cells of many kinds of male animals. Found in the nucleus of most living animal cells, the X and Y-chromosomes are condensed structures made of DNA wrapped around proteins called histones. The individual histones bunch into groups that the coiled DNA wraps around called a nucleosome, which are roughly 10 nano-meters (nm) across. The histones bunch together to form a helical fiber (30 nm) that spins into a supercoil (200 nm). During much of a cell's life, DNA exists in the 200 nm supercoil phase. But when DNA replicates itself, supercoils condense further into visible chromosomes with diameters of about 1400 nm. The X- and Y-chromosomes carry the genetic information that determines the sex of many types of animals. The Y-chromosome contains a gene called the sex-determining region Y, or the SRY gene in humans. If a fertilized egg, called a zygote, has the SRY gene, the zygote develops normally into an adult organism with male sex traits. Zygotes without the SRY gene develop to have female traits. Zygotes with Y-chromosomes but mutated SRY genes can develop into adult organisms that have female traits.

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.

The Sex-determining Region Y (Sry in mammals but SRY in humans) is a gene found on Y chromosomes that leads to the development of male phenotypes, such as testes. The Sry gene, located on the short branch of the Y chromosome, initiates male embryonic development in the XY sex determination system. The Sry gene follows the central dogma of molecular biology; the DNA encoding the gene is transcribed into messenger RNA, which then produces a single Sry protein. The Sry protein is also called the testis-determining factor (TDF), a protein that initiates male development in humans, placental mammals, and marsupials. The Sry protein is a transcription factor that can bind to regions of testis-specific DNA, bending specific DNA and activating or enhancing its abilities to promote testis formation, marking the first step towards male, rather than female, development in the embryo.

In humans, sex determination is the process that determines the biological sex of an offspring and, as a result, the sexual characteristics that they will develop. Humans typically develop as either male or female, primarily depending on the combination of sex chromosomes that they inherit from their parents. The human sex chromosomes, called X and Y, are structures in human cells made up of tightly bound deoxyribonucleic acid, or DNA, and proteins. Those are molecules that contain the instructions for the development and functioning of all life forms, including the development of physical traits and body parts that correspond with each biological sex. Humans who inherit two X chromosomes typically develop as females, while humans with one X and one Y chromosome typically develop as males. Sex determination is the beginning of the development of many characteristics that influence how a human looks and functions as well as the societal expectations that other humans have for each other.

Early 1990s research conducted by Peter Koopman, John Gubbay, Nigel Vivian, Peter Goodfellow, and Robin Lovell-Badge, showed that chromosomally female (XX) mice embryos can develop as male with the addition of a genetic fragment from the Y chromosome of male mice. The genetic fragment contained a segment of the mouse Sry gene, which is analogous to the human SRY gene. The researchers sought to identify Sry gene as the gene that produced the testis determining factor protein (Tdf protein in mice or TDF protein in humans), which initiates the formation of testis. Koopman's team published their results in 1991 in Male Development of Chromosomally Female Mice Transgenic for Sry gene. Their results showed that Sry gene partly determines the sex of an embryo and is the only gene on the Y chromosome necessary for initiation of male development in mice.

Studies in Spermatogenesis is a two volume book written by Nettie Maria Stevens, and published by the Carnegie Institution of Washington in 1905 and 1906. In the books Stevens explains the research she conducted on chromosomal sex determination in the sperm and egg cells of insect species while at Bryn Mawr College, near Philadelphia, Pennsylvania. Studies in Spermatogenesis described early examples of chromosomal XY sex-determination.

Carl Richard Moore was a professor and researcher at the University of Chicago in Chicago, Illinois who studied sex hormones in animals from 1916 until his death in 1955. Moore focused on the role of hormones on sex differentiation in offspring, the optimal conditions for sperm production, and the effects of vasectomy or testicular implants on male sex hormone production. Moore's experiments to create hermaphrodites in the laboratory contributed to the theory of a feedback loop between the pituitary and fetal gonadal hormones to control sex differentiation. Moore showed that the scrotal sac controls the temperature for the testes, which is necessary for sperm production. He also helped distinguish the hormones testosterone, and androsterone from testicular extracts.

In the late 1980s, Peter Goodfellow in London, UK led a team of researchers who showed that the SRY gene in humans codes a protein that causes testes to develop in embryos. During this time, scientists in London and Paris, including Peter Koompan and John Gubbay, proposed that SRY was the gene on the Y chromosome responsible for encoding the testis-determining factor (TDF) protein. The TDF is a protein that initiates embryo to develop male characteristics. Looking for evidence that SRY was the TDF, Goodfellow and colleagues examined people who were anatomically female, but whose cells had Y chromosomes. Females normally have cells with two X sex chromosomes (XX), while males normally have cells with one X and one Y chromosome (XY). Goodfellow's team discovered that individuals with Y chromosomes developed as female instead of as male due to inactive SRY sequences on the Y chromosome. Goodfellow and colleagues compiled the results of their experiment in a paper titled Genetic Evidence Equating SRY and the Testis-Determining Factor in 1990. Their results showed that the SRY gene is necessary for male characteristics to develop in embryos, and that SRY encodes the TDF protein.

In 2008 researchers Daniel Warner and Richard Shine tested the Charnov-Bull model by conducting experiments on the Jacky dragon (Amphibolurus muricatus), in Australia. Their results showed that temperature-dependent sex determination(TSD) evolved in this species as an adaptation to fluctuating environmental temperatures. The Charnov-Bull model, proposed by Eric Charnov and James Bull in 1977, described the evolution of TSD, although the model was, for many years, untested. Many reptiles and some fish exhibit non-genetic sex determination, in which an embryos' environment can influence the sex of the adult organism. Environmental conditions such as humidity or population density can alter sex in some organisms, and a widespread form of non-genetic sex determination is temperature-dependent sex determination. TSD reveals how embryonic development can contribute to the evolution of physiological processes. Researchers have documented TSD in a wide range of species, and they continue to investigate how such a sex determining system has evolved.

The Y-chromosome is one of a pair of chromosomes that determine the genetic sex of individuals in mammals, some insects, and some plants. In the nineteenth and twentieth centuries, the development of new microscopic and molecular techniques, including DNA sequencing, enabled scientists to confirm the hypothesis that chromosomes determine the sex of developing organisms. In an adult organism, the genes on the Y-chromosome help produce the male gamete, the sperm cell. Beginning in the 1980s, many studies of human populations used the Y-chromosome gene sequences to trace paternal lineages. In mammals, the Y-chromosomes contain the master-switch gene for sex determination, called the sex-determining region Y, or the SRY gene in humans. In most normal cases, if a fertilized egg cell, called a zygote, has the SRY gene, the zygote develops into an embryos that has male sex traits. If the zygote lacks the SRY gene or if the SRY gene is defective, the zygote develops into an embryo that has female sex traits.