Human evolutionary genetics
Human evolutionary genetics studies how one
Origin of apes
million years ago ) |
Biologists classify
Apes, in turn, belong to the
Phylogenetics
A
- Genetic distance. The genetic difference between humans and chimpanzees is less than 2%,[4] or three times larger than the variation among modern humans (estimated at 0.6%).[5]
- Temporal remoteness of the most recent common ancestor. The mitochondrial most recent common ancestor of modern humans is estimated to have lived roughly 160,000 years ago,[6] the latest common ancestors of humans and chimpanzees roughly 5 to 6 million years ago.[7]
Speciation of humans and the African apes
The separation of humans from their closest relatives, the non-human African apes (chimpanzees and gorillas), has been studied extensively for more than a century. Five major questions have been addressed:
- Which apes are our closest ancestors?
- When did the separations occur?
- What was the effective population size of the common ancestor before the split?
- Are there traces of population structure (subpopulations) preceding the speciation or partial admixture succeeding it?
- What were the specific events (including fusion of chromosomes 2a and 2b) prior to and subsequent to the separation?
General observations
As discussed before, different parts of the genome show different sequence divergence between different
- The sequence divergence varies significantly between humans, chimpanzees and gorillas.
- For most DNA sequences, humans and chimpanzees appear to be most closely related, but some point to a human-gorilla or chimpanzee-gorilla clade.
- The human genome has been sequenced, as well as the chimpanzee genome. Humans have 23 pairs of chromosomes, while Human chromosome 2 is a fusion of two chromosomes 2a and 2b that remained separate in the other primates.[9]
Divergence times
The divergence time of humans from other apes is of great interest. One of the first molecular studies, published in 1967 measured immunological distances (IDs) between different primates.[10] Basically the study measured the strength of immunological response that an antigen from one species (human albumin) induces in the immune system of another species (human, chimpanzee, gorilla and Old World monkeys). Closely related species should have similar antigens and therefore weaker immunological response to each other's antigens. The immunological response of a species to its own antigens (e.g. human to human) was set to be 1.
The ID between humans and gorillas was determined to be 1.09, that between humans and chimpanzees was determined as 1.14. However the distance to six different Old World monkeys was on average 2.46, indicating that the African apes are more closely related to humans than to monkeys. The authors consider the divergence time between Old World monkeys and hominoids to be 30 million years ago (MYA), based on fossil data, and the immunological distance was considered to grow at a constant rate. They concluded that divergence time of humans and the African apes to be roughly ~5 MYA. That was a surprising result. Most scientists at that time thought that humans and great apes diverged much earlier (>15 MYA).
The gorilla was, in ID terms, closer to human than to chimpanzees; however, the difference was so slight that the trichotomy could not be resolved with certainty. Later studies based on molecular genetics were able to resolve the trichotomy: chimpanzees are phylogenetically closer to humans than to gorillas. However, some divergence times estimated later (using much more sophisticated methods in molecular genetics) do not substantially differ from the very first estimate in 1967, but a recent paper[11] puts it at 11–14 MYA.
Divergence times and ancestral effective population size
Current methods to determine divergence times use DNA sequence alignments and molecular clocks. Usually the molecular clock is calibrated assuming that the orangutan split from the African apes (including humans) 12-16 MYA. Some studies also include some old world monkeys and set the divergence time of them from hominoids to 25-30 MYA. Both calibration points are based on very little fossil data and have been criticized.[12]
If these dates are revised, the divergence times estimated from molecular data will change as well. However, the relative divergence times are unlikely to change. Even if we can't tell absolute divergence times exactly, we can be pretty sure that the divergence time between chimpanzees and humans is about sixfold shorter than between chimpanzees (or humans) and monkeys.
One study (Takahata et al., 1995) used 15 DNA sequences from different regions of the genome from human and chimpanzee and 7 DNA sequences from human, chimpanzee and gorilla.[13] They determined that chimpanzees are more closely related to humans than gorillas. Using various statistical methods, they estimated the divergence time human-chimp to be 4.7 MYA and the divergence time between gorillas and humans (and chimps) to be 7.2 MYA.
Additionally they estimated the effective population size of the common ancestor of humans and chimpanzees to be ~100,000. This was somewhat surprising since the present day effective population size of humans is estimated to be only ~10,000. If true that means that the human lineage would have experienced an immense decrease of its effective population size (and thus genetic diversity) in its evolution. (see Toba catastrophe theory)
Another study (Chen & Li, 2001) sequenced 53 non-repetitive, intergenic DNA segments from human,
The shorter internodal time span (TIN) the more common are incongruent gene trees. The effective population size (Ne) of the internodal population determines how long genetic lineages are preserved in the population. A higher effective population size causes more incongruent gene trees. Therefore, if the internodal time span is known, the ancestral effective population size of the common ancestor of humans and chimpanzees can be calculated.
When each segment was analyzed individually, 31 supported the Homo-Pan clade, 10 supported the Homo-Gorilla clade, and 12 supported the Pan-Gorilla clade. Using the molecular clock the authors estimated that gorillas split up first 6.2-8.4 MYA and chimpanzees and humans split up 1.6-2.2 million years later (internodal time span) 4.6-6.2 MYA. The internodal time span is useful to estimate the ancestral effective population size of the common ancestor of humans and chimpanzees.
A
A third study (Yang, 2002) used the same dataset that Chen and Li used but estimated the ancestral effective population of 'only' ~12,000 to 21,000, using a different statistical method.[14]
Genetic differences between humans and other great apes
The alignable sequences within genomes of humans and chimpanzees differ by about 35 million single-nucleotide substitutions. Additionally about 3% of the complete genomes differ by deletions, insertions and duplications.[15]
Since mutation rate is relatively constant, roughly one half of these changes occurred in the human lineage. Only a very tiny fraction of those fixed differences gave rise to the different phenotypes of humans and chimpanzees and finding those is a great challenge. The vast majority of the differences are neutral and do not affect the phenotype.[citation needed]
Molecular evolution may act in different ways, through protein evolution, gene loss, differential gene regulation and RNA evolution. All are thought to have played some part in human evolution.
Gene loss
Many different mutations can inactivate a gene, but few will change its function in a specific way. Inactivation mutations will therefore be readily available for selection to act on. Gene loss could thus be a common mechanism of evolutionary adaptation (the "less-is-more" hypothesis).[16]
80 genes were lost in the human lineage after separation from the last common ancestor with the chimpanzee. 36 of those were for
Hair keratin gene KRTHAP1
A gene for type I hair keratin was lost in the human lineage. Keratins are a major component of hairs. Humans still have nine functional type I hair keratin genes, but the loss of that particular gene may have caused the thinning of human body hair. Based on the assumption of a constant molecular clock, the study predicts the gene loss occurred relatively recently in human evolution—less than 240 000 years ago, but both the Vindija Neandertal and the high-coverage Denisovan sequence contain the same premature stop codons as modern humans and hence dating should be greater than 750 000 years ago. [19]
Myosin gene MYH16
Stedman et al. (2004) stated that the loss of the sarcomeric
Another estimate for the loss of the MYH16 gene is 5.3 million years ago, long before Homo appeared.[21]
Other
- CASPASE12, a cysteinyl aspartate proteinase. The loss of this gene is speculated to have reduced the lethality of bacterial infection in humans.[17]
Gene addition
Human-specific DNA insertions
When the human genome was compared to the genomes of five comparison primate species, including the chimpanzee, gorilla, orangutan, gibbon, and macaque, it was found that there are approximately 20,000 human-specific insertions believed to be regulatory. While most insertions appear to be fitness neutral, a small amount have been identified in positively selected genes showing associations to neural phenotypes and some relating to dental and sensory perception-related phenotypes. These findings hint at the seemingly important role of human-specific insertions in the recent evolution of humans.[22]
Selection pressures
It has also been hypothesized that much of the difference between humans and chimpanzees is attributable to the regulation of gene expression rather than differences in the genes themselves. Analyses of conserved non-coding sequences, which often contain functional and thus positively selected regulatory regions, address this possibility.[23]
Sequence divergence between humans and apes
When the draft sequence of the common chimpanzee (Pan troglodytes) genome was published in the summer 2005, 2400 million bases (of ~3160 million bases) were sequenced and assembled well enough to be compared to the human genome.[15] 1.23% of this sequenced differed by single-base substitutions. Of this, 1.06% or less was thought to represent fixed differences between the species, with the rest being variant sites in humans or chimpanzees. Another type of difference, called indels (insertions/deletions) accounted for many fewer differences (15% as many), but contributed ~1.5% of unique sequence to each genome, since each insertion or deletion can involve anywhere from one base to millions of bases.[15]
A companion paper examined
Locus | Human-Chimp | Human-Gorilla | Human-Orangutan |
---|---|---|---|
Alu elements | 2 | - | - |
Non-coding (Chr. Y) | 1.68 ± 0.19 | 2.33 ± 0.2 | 5.63 ± 0.35 |
Pseudogenes (autosomal) | 1.64 ± 0.10 | 1.87 ± 0.11 | - |
Pseudogenes (Chr. X) | 1.47 ± 0.17 | - | - |
Noncoding (autosomal) | 1.24 ± 0.07 | 1.62 ± 0.08 | 3.08 ± 0.11 |
Genes (Ks) | 1.11 | 1.48 | 2.98 |
Introns | 0.93 ± 0.08 | 1.23 ± 0.09 | - |
Xq13.3 | 0.92 ± 0.10 | 1.42 ± 0.12 | 3.00 ± 0.18 |
Subtotal for X chromosome | 1.16 ± 0.07 | 1.47 ± 0.08 | - |
Genes (Ka) | 0.8 | 0.93 | 1.96 |
The sequence divergence has generally the following pattern: Human-Chimp < Human-Gorilla << Human-Orangutan, highlighting the close kinship between humans and the African apes.
Mutations altering the amino acid sequence of proteins (Ka) are the least common. In fact ~29% of all orthologous proteins are identical between human and chimpanzee. The typical protein differs by only two amino acids.[15] The measures of sequence divergence shown in the table only take the substitutional differences, for example from an A (adenine) to a G (guanine), into account. DNA sequences may however also differ by insertions and deletions (indels) of bases. These are usually stripped from the alignments before the calculation of sequence divergence is performed.
Genetic differences between modern humans and Neanderthals
An international group of scientists completed a draft sequence of the
Genetic differences among modern humans
With their rapid expansion throughout different climate zones, and especially with the availability of new food sources with the
genes.The East Asian types of ADH1B in particular are associated with
As of 2017[update], the Single Nucleotide Polymorphism Database (dbSNP), which lists SNP and other variants, listed a total of 324 million variants found in sequenced human genomes.[33] Nucleotide diversity, the average proportion of nucleotides that differ between two individuals, is estimated at between 0.1% and 0.4% for contemporary humans (compared to 2% between humans and chimpanzees).[34][35] This corresponds to genome differences at a few million sites; the 1000 Genomes Project similarly found that "a typical [individual] genome differs from the reference human genome at 4.1 million to 5.0 million sites … affecting 20 million bases of sequence."[36]
In February 2019, scientists discovered evidence, based on
Research studies
In March 2019, Chinese scientists reported inserting the human brain-related
In May 2023, scientists reported, based on genetic studies, a more complicated pathway of human evolution than previously understood. According to the studies, humans evolved from different places and times in Africa, instead of from a single location and period of time.[41][42]
On 31 August 2023, researchers reported, based on genetic studies, that a
See also
- Chimpanzee genome project
- FOXP2 and human evolution
- Genetics and archaeogenetics of South Asia
- Genetic history of Europe
- Genetic history of indigenous peoples of the Americas
- Genetic history of Italy
- Genetic history of the British Isles
- Genetic history of the Middle East
- Homininae
- List of haplogroups of historical and famous figures
- The Journey of Man: A Genetic Odyssey
- Y-DNA haplogroups by ethnic groups
- Race and genetics
- Recent human evolution
References
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- ^ As of 2015, the typical difference between the genomes of two individuals was estimated at 20 million base pairs (or 0.6% of the total of 3.2 billion base pairs):
"a typical [individual] genome differs from the reference human genome at 4.1 million to 5.0 million sites [...] affecting 20 million bases of sequence"
Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, et al. (October 2015). "A global reference for human genetic variation". Nature. 526 (7571): 68–74. PMID 26432245.
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- ^ Dockrill, Peter (11 February 2019). "Artificial Intelligence Has Found an Unknown 'Ghost' Ancestor in The Human Genome". ScienceAlert.com. Archived from the original on 23 April 2022. Retrieved 11 February 2019.
- ^ Burrell, Teal (29 December 2019). "Scientists Put a Human Intelligence Gene Into a Monkey. Other Scientists are Concerned". Discover. Archived from the original on 30 December 2019. Retrieved 30 December 2019.
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- ^ Zimmer, Carl (17 May 2023). "Study Offers New Twist in How the First Humans Evolved - A new genetic analysis of 290 people suggests that humans emerged at various times and places in Africa". The New York Times. Archived from the original on 17 May 2023. Retrieved 18 May 2023.
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- ^ Zimmer, Carl (31 August 2023). "Humanity's Ancestors Nearly Died Out, Genetic Study Suggests - The population crashed following climate change about 930,000 years ago, scientists concluded. Other experts aren't convinced by the analysis". the New York Times. Archived from the original on 31 August 2023. Retrieved 2 September 2023.
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Further reading
- Jobling, Mark A.; Hollox, Edward; Hurles, Matthew; Kivisild, Toomas; Tyler-Smith, Chris (2013). Human Evolutionary Genetics. New York: Garland Science. OCLC 829099073.
- Rannala B, Yang Z (August 2003). "Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci". Genetics. 164 (4): 1645–56. PMID 12930768.