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Synteny refers to genes present on the same chromosome, like beads on a string. In evolutionary perspective, it describes the co-localization of genes on chromosomes across two or more different species. For example, genes A, B, and C on one species' chromosome correspond to alleles A1, B1, and C1 on another species' chromosome, representing synteny between those species.

Conserved syntenic blocks are genes present in common chromosomal regions across multiple species, indicating shared ancestry. Humans and tree shrews, which diverged 85 million years ago, show conserved synteny in some regions of human chromosome 10 and tree shrew chromosome 16. This pattern demonstrates that an ancestral mammalian chromosome evolved into both modern chromosomes, revealing evolutionary relationships through genome comparisons.

Ancestral chromosomes underwent several rounds of chromosome rearrangement, fusion, and breakage to facilitate diversity and speciation in primates. For example, the fusion of ancestral chromosomes 9 and 11 formed human chromosome 2, while reciprocal translocation of ancestral chromosomes 14 and 21 led to human chromosomes 12 and 22. These large-scale rearrangements occur rarely, approximately once every 5 million years.

Approximately 180 chromosomal breakage-and-rejoining events occurred as ancestral chromosomes evolved into human and mouse chromosomes after their lineages diverged around 80 million years ago. Despite these extensive rearrangements, several chromosome regions in both species maintained common gene order or synteny. For instance, over 510,000 base pairs of mouse chromosome 12 share syntenic blocks with human chromosome 14.

Scientists use synteny analysis combined with high-resolution DNA data from all known modern primates to propose ancestral karyotypes. By comparing conserved sequences and evolutionary relationships across primate species, researchers identified which ancestral chromosomes gave rise to modern chromosomes. Matching colors in human and ancestral chromosome diagrams indicate conserved syntenic blocks derived from specific ancestral chromosomes.

As evolutionary time increases between species, more chromosomal breakage-and-rejoining events accumulate, disrupting the original gene order. Over millions of years, these rearrangements gradually eliminate conserved syntenic blocks. Therefore, species that diverged more recently show greater synteny, while distantly related species show less synteny due to accumulated chromosomal changes.

John Renwick coined the term synteny in 1971, defining it as genes present on the same chromosomes, even if they are not genetically linked. His terminology enabled scientists to describe evolutionary relationships between species based on gene organization. Today, synteny analysis remains a fundamental tool for understanding how chromosomes evolved and how species are related through their genomic architecture.