Genetic differences between humans and other great apes[edit]
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.[12]
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[edit]
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).[13]
80 genes were lost in the human lineage after separation from the last common ancestor with the chimpanzee. 36 of those were for olfactory receptors. Genes involved in chemoreception and immune response are overrepresented.[14] Another study estimated that 86 genes had been lost.[15]
Hair keratin gene KRTHAP1[edit]
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. The gene loss occurred relatively recently in human evolution—less than 240,000 years ago.[16]
Myosin gene MYH16[edit]
Stedman et al. (2004) stated that the loss of the sarcomeric myosin gene MYH16 in the human lineage led to smaller masticatory muscles. They estimated that the mutation that led to the inactivation (a two base pair deletion) occurred 2.4 million years ago, predating the appearance of Homo ergaster/erectus in Africa. The period that followed was marked by a strong increase in cranial capacity, promoting speculation that the loss of the gene may have removed an evolutionary constraint on brain size in the genus Homo.[17]
Another estimate for the loss of the MYH16 gene is 5.3 million years ago, long before Homo appeared.[18]
- CASPASE12, a cysteinyl aspartate proteinase. The loss of this gene is speculated to have reduced the lethality of bacterial infection in humans.[14]
Gene addition[edit]
Segmental duplications (SDs or LCRs) have had roles in creating new primate genes and shaping human genetic variation.
Human-specific DNA insertions[edit]
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.[19]
Selection pressures[edit]
Human accelerated regions are areas of the genome that differ between humans and chimpanzees to a greater extent than can be explained by genetic drift over the time since the two species shared a common ancestor. These regions show signs of being subject to natural selection, leading to the evolution of distinctly human traits. Two examples are HAR1F, which is believed to be related to brain development and HAR2 (a.k.a. HACNS1) that may have played a role in the development of the opposable thumb.
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.[20]
Sequence divergence between humans and apes[edit]
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.[12] 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.[12]
A companion paper examined segmental duplications in the two genomes,[21] whose insertion and deletion into the genome account for much of the indel sequence. They found that a total of 2.7% of euchromatic sequence had been differentially duplicated in one or the other lineage.
Percentage sequence divergence between humans and other hominids[5]| 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. Alu elementsdiverge quickly due to their high frequency of CpG dinucleotides which mutate roughly 10 times more often than the average nucleotide in the genome. The mutation rate is higher in the male germ line, therefore the divergence in the Y chromosome—which is inherited solely from the father—is higher than in autosomes. The X chromosome is inherited twice as often through the female germ line as through the male germ line and therefore shows slightly lower sequence divergence. The sequence divergence of the Xq13.3 region is surprisingly low between humans and chimpanzees.[22]
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.[12] 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[edit]
An international group of scientists completed a draft sequence of the Neanderthal genome in May 2010. The results indicate some breeding between modern humans (Homo sapiens) and Neanderthals (Homo neanderthalensis), as the genomes of non-African humans have 1-4% more in common with Neanderthals than do the genomes of subsaharan Africans. Neanderthals and most modern humans share a lactose-intolerant variant of the lactase gene that encodes an enzyme that is unable to break down lactose in milk after weaning. Modern humans and Neanderthals also share the FOXP2 gene variant associated with brain development and with speech in modern humans, indicating that Neanderthals may have been able to speak. Chimps have two amino acid differences in FOXP2 compared with human and Neanderthal FOXP2.[23][24][25]
Modern humans[edit]
Molecular biologists starting with Wesley Brown[26] on mtDNA and Allan Wilson[26] on mtDNA have produced observations relevant to human evolution.
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