In a recent post, I wrote about the split between chimpanzees, bonobos, and the Homo genus, and also looked into the possibility that the split took place in Eurasia. In this post we will discuss a little known fat that sets us, humans, apart from all other apes, the fact that we have 23 pairs of chromosomes, while they have 24.
Humans have 23 pairs (46 chromosomes) while the other apes have 24 pairs (48 chromosomes)
We often read that chimpanzees and bonobos share roughly 99% of their genetic material with humans. They are our closest living relatives, but we couldn't mate with them successfully because our number of chromosomes differs.
The African gorillas, chimpanzees, and bonobos, and the Asian orangutans, extant apes, all carry 24 pairs of chromosomes, a total of 48. We, humans (and also our Neanderthal and Denisovan ancestors) carry 23 pairs, with 46 chromosomes in total. This feature sets us apart from all of the great apes.
Changes in the number, shape, or structure of the chromosomes in a species plays a role in evolution, leading to the formation of new species (speciation). This phenomenon, known as "karyotype evolution" (karyotype is the array of chromosomes in a given species) was first detected by Wilson and Painter in 1935, who observed the fusion of chromosomes in fruit flies.
Fusion is what happened to reduce the number of chromosomes carried by humans. Two chromosomes in apes, known as chromosome 2a and chromosome 2b, fused together forming our chromosome 2. So the total count dropped from 24 to 23 pairs.
The following image, from Culajay, 2025, shows how our chromosome 2 (top) aligns with chromosomes 2a and 2b in chimps, gorillas, and orangutans:
The process of fusion of two chromosomes is complex (see Ijdo et al., 1991 and Fan et al., 2002). I prepared the following image to clarify the process. A regular pair of chromosomes, "X" shape to the left is composed of two individual chromosomes linked up at their "centromeres". During cellular division inside a cell, fibers attach to the centromere and and pulls the chromosomes apart, half going to one side, the other half going to the opposite side of the dividing cell. So centromeres play an important role in regulating the division of cells, and reproduction, where the sexual cells carry half the chromosome load compared to regular ones.
The tips of each chromosme have "telomeres", which act as protective caps located and help maintain the chromosome's structure and stability. They are a long DNA helix with a certain sequence combining the bases Cytosine (C), Thymine (T), Adenine (A), and Guanine (G) of the form 5'-(TTAGGG)n-(CCCTAA)m-3' (where 5' and 3' are specific carbon atoms, and "m" and "n" are the number of repeats of each sequence of bases and ranges between 800 and 2,500.
The fusion of chromosomes 2a and 2b led to the telomeres linking up, and to a new, fused, chromosome 2, with two centromeres. For the chromosome to be able to work, and be functional, one of the centromeres became deactivated, and we can see it, surviving as a relict in our chromosome 2. The telomeric regions fused together also survive, in an area known as 2q13 where the vestigial telomeres survive, with their respective 5'-(TTAGGG)n-(CCCTAA)m-3' sequences linked head to head.
This took place as a random mutation in one individual of a group of pre-human apes. And this individual when he or she mated with other members of the group, passed on this new trait to its descent, as we will see below.
Speciation, Homo genus appears
But how could an individual with 47 chromosomes mate with those with 48 chromosomes?
So, by chance or a random event, an individual is born, carrying the fused chromosome 2, a total of 47 chromosomes. It would be a fertile person, and could mate with other members (with 48 chromosomes).
The following image is from Stankiewicz, 2016(One pedigree we all may have come from - did Adam and Eve have the chromosome 2 fusion? Mol Cytogenet. 2016 Sep 26;9:72. doi: 10.1186/s13039-016-0283-3. PMID: 27708712; PMCID: PMC5037601). It is a diagram showing how one, the first, unique individual with 47 chromosomes can mate with others, despite carrying 47 chromosomes, and how, in a few generations, some individuals end up with 46 chromosomes (which include two copies of the fused chromosome 2), and speciation becomes fixed.
Stankiewicz proposes that the original group where the mutation arose was a "gorilla-like polygamous pedigree of a putative early modern human clan" It was in this group that the fused chromosome 2 became fixed as a homozygous element. The diagram shows a two parents, a male ◻ and a female ◯, in Generation I, who have one son, a male, of Generation II, who was the first to carry the fused chromosome 2 in a heterozygous form. This male is represented by ◩. He mates with different females ◯ who carry 48 chromosomes. They produce offspring in Generation III, some are of the regular "normal" kind, with 48 chromosomes both boys (◻) and a girls (◯), others carry 47 chromosomes boys (◩) and girls (◐). There are a number of miscarriages or stillborn babies caused by "chromosome imbalances" (▲)
Those who are heterozygous in the 3rd Generation, and mate with each other (◩ and ◐) will produce offspring in Generation IV, some of them will not be viable (▲), others will have 48 chromosomes like the original population (◻ and ◯), others will carry a heterozygous form with 47 chromosomes (◩, ◐), but some, few, will have 46 chromosomes, homozygous for the fused chromosome 2: boys (■) and girls (⚫)
Benefits of the fused chromosome
According to Stankiewicz, the 46 chromosome variant spread in this population because it provided an evolutionary advantage possibly linked to higher fertility or to improved brain and cognitive development. Furthermore, it could have promoted bipedalism, or physiological aspects such as "endurance running, or improved thermo-regulation by an enhanced sweating capacity".
Culajay, 2025 highlights the impact of the fused chromosome 2 on human evolution. The change altered the shape and therefore the functioning of our genome. It led to modifications in the shape of our pelvis that resulted in our bipedalism.
When did this event take place?
The short answer is that we don't know. Nevertheless, there are some educated guesses, as we will see below.
According to Jiang et al., 2024, the chromosome 2 fusion event "is not a recent evolutionary event but potentially occurred during African great ape speciation" adding that "Given fossil evidence that Australopithecus existed around 2-4 mya, Paranthropus around 1-3 mya, and the earliest Homo fossils around 2-3 mya, we speculate that this fusion event did arise in the genus Homo but rather occurred in ancestral great ape populations that would give rise to humans" (highlight is mine)
We know that this trait, the fused chromosome 2, is shared by our relatives, the Denisovans and Neanderthals: "We conclude that Denisovans and modern humans (and presumably Neandertals) shared a karyotype consisting of 46 chromosomes." (Reich et al., 2012). So the event that led to the fusion took place before the split between Neanderthals & Denisovans, and Humans. This makes it older than 800,000 years.
Research published by Dreszer et al., 2007. (Biased clustered substitutions in the human genome: The footprints of male-driven biased gene conversion. Genome Research, 17(10), 1420–1430. https://doi.org/10.1101/gr.6395807) analyzing "unexpected biased clustered substitutions (UBCS)" found close to telomeres, estimated that "the fusion occurred as recently as 740,000 years ago and no more than ∼3 million years ago." This is a wide range, spanning from the Denisovan-Neanderthal-Human split, backwards into the Homo erectus, Homo antecessor, or even the Homo naledi all of which may have shared with us the fused chromosome 2.
These UBCS statistics used by Dreszer were revised and improved by Poszewiecka et al., 2022 (Revised time estimation of the ancestral human chromosome 2 fusion. BMC Genomics. 2022 Aug 25; 23 (Suppl 6):616. doi: 10.1186/s12864-022-08828-7. PMID: 36008753; PMCID: PMC9413910). Their study of chromosome 2 (highlight is mine) "estimated its formation time at 0.9 Mya with a 95% confidence interval of 0.4-1.5 Mya"
Culajay, 2025, focusing on the effects of the fusion on bipedalis and pelvic shape argues that the date of this event is older than 5 million years ago because it ties in with the modification of hip shape observed in Australopithecus afarensis and the even earlier Ardipithecus ramidus (4.4 Mya): "The timing of the Chromosome 2 fusion is best placed more than 5 million years ago, possibly 6.9–7.4 Mya, near the divergence of humans and chimpanzees." (Highlight is mine)
Comments
Perhaps we may be able to obtain the genome of Homo erectus, or Homo floresiensis or other ancient hominins, and check if they have 46 or 48 chromosomes. This would help us learn if they are members of our "human" tree or not.
Another interesting point is that the fusion of chromosome 2 is clear scientific proof of evolution in action. A random event produces a mutant, and the mutation leads to a new species. This is a thorn in the side of "creationists" who can't explain it away. They do, of course, come up with ridiculous alternatives: they argue that the telomere fusion and centromere deactivation is a misinterpretation of the data; that God created humans with 46 chromosomes, and created apes with 46. God can create as he wishes. I rest my case.
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