In the 1850s, Austrian monk Gregor Mendel experimented with pea plants to unravel the basic principles of inheritance. His findings were ignored at the time, but later, when scientists learned about chromosomes and the process of meiosis, Mendel's theory gained prominence as the physical basis of inheritability became clearer. One of the principles Mendel described, now called Mendel's second law, was that alleles of different genes assort independently during gamete formation. Since Mendel's time, we have discovered that the law of independent assortment applies to many genes, but is not universal. When geneticist T. H. Morgan began studying the genetics of fruit flies, he discovered that some genes sort together when they are located on the same chromosome.
Geneticist T. H. Morgan, in his work with fruit flies, showed that traits encoded by genes that are located on the same chromosome may not obey Mendel's second law—the law of independent assortment. Because they are physically linked, alleles of these genes are less likely to separate from one another during gamete formation than are alleles of genes located on different chromosomes.
However, alleles of linked genes can be shuffled by crossing over, in which two homologous chromatids exchange corresponding chromosomal segments. A portion of the chromatid physically breaks off and is reattached to the homologous chromatid. In this way, the maternal allele of one gene can be passed down together with the paternal allele of another gene on that same chromosome. Crossing over is an essential process for maintaining a wealth of genetic diversity, even though a species may have a small number of chromosomes.
Textbook Reference: Concept 8.3 Genes Are Carried on Chromosomes