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Chromosome 2

Human chromosome

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Chromosome 2 contains the HOXD homeobox gene cluster.

Fusion

Humans have only twenty-three pairs of chromosomes, while all other extant members of Hominidae have twenty-four pairs. Sequencing supports the idea that Neanderthals and Denisovans also had twenty-three pairs.

Human chromosome 2 is a result of an end-to-end fusion of two ancestral chromosomes. The evidence for this includes:

  • The correspondence of chromosome 2 to two ape chromosomes. The closest human relative, the chimpanzee, has nearly identical DNA sequences to human chromosome 2, but they are found in two separate chromosomes. The same is true of the more distant gorilla and orangutan.
  • The presence of a vestigial centromere. Normally a chromosome has just one centromere, but in chromosome 2 there are remnants of a second centromere in the q21.3–q22.1 region.
  • The presence of vestigial telomeres. These are normally found only at the ends of a chromosome, but in chromosome 2 there are additional telomere sequences in the q13 band, far from either end of the chromosome.

We conclude that the locus cloned in cosmids c8.1 and c29B is the relic of an ancient telomere-telomere fusion and marks the point at which two ancestral ape chromosomes fused to give rise to human chromosome 2.

— Jacob W. Ijdo

The timing of the fusion has been differently estimated by different researchers.

The telomere-to-telomere genome assembly and improved genome assembly techniques have enabled a closer look at the repeat-rich fusion site and the two ancestral centromere sites. The chimp and bonobo chromosome 2A and 2B respectively had an end region similar to chromosome 9 (p end) and chromosome 22 (q end). This likely happened in their common ancestor and was fueled by a pericentromeric inversion in each of their ends (the 2A inversion was only seen in these two species; the 2B inversion also in gorillas). The tips of these two end regions were themselves copies of a common ancestor and they were accidentally misaligned together in a human ancestor and lost. The residual segments similar to 9p24.3 and 22q13.33 around the fusion site support this idea. What appears as the modern vestigial telomere was already vestigial at the time of the fusion, as it was actually from the two ancient inversion events.

In 2026, it was reported that incomplete lineage sorting of segmental duplications defines the human chromosome 2 fusion site early during African great ape speciation.

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