John H. Renwick first coined the term “synteny” in 1971, which refers to the genes present on the same chromosomes, even if they are not genetically linked. The species with common ancestry tend to show conserved syntenic regions. Therefore, the concept of synteny is nowadays used to describe the evolutionary relationship between species.

Around 80 million years ago, the human and mice lineages diverged from the common ancestor. During the course of evolution, the ancestral chromosome underwent several rearrangements, breakage, and fusion events to evolve into the chromosomes of mice and humans. For example, it took around 180 chromosomal breakage-and-rejoining events for the evolution of ancestral chromosomes into human and mice chromosomes. Yet, several regions of chromosomes in both mice and humans have maintained common gene order or synteny. For example, over 510,000 base pairs of mouse chromosome 12 share syntenic blocks with human chromosome 14. In the future, when the evolutionary distance between two species will increase, the number of chromosomal breakage-and-rejoining events will increase, and the synteny will decrease.

Primate ancestral karyotype

Based on synteny relation and DNA sequence analysis, scientists have predicted the karyotype of all primate ancestors. Synteny between humans and other primates such as chimpanzees, gorillas, and other living primate species reveals that human chromosomes are derived from ancestral chromosomes by several chromosomal breakage-and-rejoining events. Such large-scale chromosome rearrangements are rare, like once in 5 million years. But whenever they occur, they are most likely to lead to the evolution of a new species. A comparison between human chromosomes with the proposed primate ancestral karyotype shows several chromosome rearrangements. For example, the fusion of ancestral chromosomes 9 and 11 formed the human chromosome 2; or the reciprocal translocation of ancestral chromosomes 14 and 21 led to the evolution of human chromosomes 12 and 22.