Human evolutionary genetics

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Human evolutionary genetics studies how one human genome differs from another human genome, the evolutionary past that gave rise to the human genome, and its current effects. Differences between genomes have anthropological, medical, historical and forensic implications and applications. Genetic data can provide important insights into human evolution.

Contents

Origin of apes

The taxonomic relationships of hominoids Hominoid taxonomy 7.svg
The taxonomic relationships of hominoids

Biologists classify humans, along with only a few other species, as great apes (species in the family Hominidae). The living Hominidae include two distinct species of chimpanzee (the bonobo, Pan paniscus , and the chimpanzee, Pan troglodytes ), two species of gorilla (the western gorilla, Gorilla gorilla , and the eastern gorilla, Gorilla graueri), and two species of orangutan (the Bornean orangutan, Pongo pygmaeus , and the Sumatran orangutan, Pongo abelii). The great apes with the family Hylobatidae of gibbons form the superfamily Hominoidea of apes.

Apes, in turn, belong to the primate order (>400 species), along with the Old World monkeys, the New World monkeys, and others. Data from both mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) indicate that primates belong to the group of Euarchontoglires, together with Rodentia, Lagomorpha, Dermoptera, and Scandentia. [1] This is further supported by Alu-like short interspersed nuclear elements (SINEs) which have been found only in members of the Euarchontoglires. [2]

Phylogenetics

A phylogenetic tree is usually derived from DNA or protein sequences from populations. Often, mitochondrial DNA or Y chromosome sequences are used to study ancient human demographics. These single-locus sources of DNA do not recombine and are almost always inherited from a single parent, with only one known exception in mtDNA. [3] Individuals from closer geographic regions generally tend to be more similar than individuals from regions farther away. Distance on a phylogenetic tree can be used approximately to indicate:

  1. 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]
  2. 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:

General observations

As discussed before, different parts of the genome show different sequence divergence between different hominoids. It has also been shown that the sequence divergence between DNA from humans and chimpanzees varies greatly. For example, the sequence divergence varies between 0% to 2.66% between non-coding, non-repetitive genomic regions of humans and chimpanzees. [8] The percentage of nucleotides in the human genome (hg38) that had one-to-one exact matches in the chimpanzee genome (pantro6) was 84.38%. Additionally gene trees, generated by comparative analysis of DNA segments, do not always fit the species tree. Summing up:

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

The sequences of the DNA segments diverge earlier than the species. A large effective population size in the ancestral population (left) preserves different variants of the DNA segments (=alleles) for a longer period of time. Therefore, on average, the gene divergence times (tA for DNA segment A; tB for DNA segment B) will deviate more from the time the species diverge (tS) compared to a small ancestral effective population size (right). SpeciesVsGeneDivergenceTime.svg
The sequences of the DNA segments diverge earlier than the species. A large effective population size in the ancestral population (left) preserves different variants of the DNA segments (=alleles) for a longer period of time. Therefore, on average, the gene divergence times (tA for DNA segment A; tB for DNA segment B) will deviate more from the time the species diverge (tS) compared to a small ancestral effective population size (right).

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)

A and B are two different loci. In the upper figure they fit to the species tree. The DNA that is present in today's gorillas diverged earlier from the DNA that is present in today's humans and chimps. Thus both loci should be more similar between human and chimp than between gorilla and chimp or gorilla and human. In the lower graph, locus A has a more recent common ancestor in human and gorilla compared to the chimp sequence. Whereas chimp and gorilla have a more recent common ancestor for locus B. Here the gene trees are incongruent to the species tree. Ancestralsizehuman.svg
A and B are two different loci. In the upper figure they fit to the species tree. The DNA that is present in today's gorillas diverged earlier from the DNA that is present in today's humans and chimps. Thus both loci should be more similar between human and chimp than between gorilla and chimp or gorilla and human. In the lower graph, locus A has a more recent common ancestor in human and gorilla compared to the chimp sequence. Whereas chimp and gorilla have a more recent common ancestor for locus B. Here the gene trees are incongruent to the species tree.

Another study (Chen & Li, 2001) sequenced 53 non-repetitive, intergenic DNA segments from human, chimpanzee, gorilla and orangutan. [8] When the DNA sequences were concatenated to a single long sequence, the generated neighbor-joining tree supported the Homo-Pan clade with 100% bootstrap (that is that humans and chimpanzees are the closest related species of the four). When three species are fairly closely related to each other (like human, chimpanzee and gorilla), the trees obtained from DNA sequence data may not be congruent with the tree that represents the speciation (species tree).

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 parsimonious analysis revealed that 24 loci supported the Homo-Pan clade, 7 supported the Homo-Gorilla clade, 2 supported the Pan-Gorilla clade and 20 gave no resolution. Additionally they took 35 protein coding loci from databases. Of these 12 supported the Homo-Pan clade, 3 the Homo-Gorilla clade, 4 the Pan-Gorilla clade and 16 gave no resolution. Therefore, only ~70% of the 52 loci that gave a resolution (33 intergenic, 19 protein coding) support the 'correct' species tree. From the fraction of loci which did not support the species tree and the internodal time span they estimated previously, the effective population of the common ancestor of humans and chimpanzees was estimated to be ~52 000 to 96 000. This value is not as high as that from the first study (Takahata), but still much higher than present day effective population size of humans.

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 olfactory receptors. Genes involved in chemoreception and immune response are overrepresented. [17] Another study estimated that 86 genes had been lost. [18]

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 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. [20]

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

Segmental duplications (SDs or LCRs) have had roles in creating new primate genes and shaping human genetic variation.

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

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. [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 segmental duplications in the two genomes, [24] 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 [8]
LocusHuman-ChimpHuman-GorillaHuman-Orangutan
Alu elements2--
Non-coding (Chr. Y)1.68 ± 0.192.33 ± 0.25.63 ± 0.35
Pseudogenes (autosomal)1.64 ± 0.101.87 ± 0.11-
Pseudogenes (Chr. X)1.47 ± 0.17--
Noncoding (autosomal)1.24 ± 0.071.62 ± 0.083.08 ± 0.11
Genes (Ks)1.111.482.98
Introns0.93 ± 0.081.23 ± 0.09-
Xq13.30.92 ± 0.101.42 ± 0.123.00 ± 0.18
Subtotal for X chromosome1.16 ± 0.071.47 ± 0.08-
Genes (Ka)0.80.931.96

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 elements diverge 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. [25]

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 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. [26] [27] [28]

Genetic differences among modern humans

Homo sapiens is thought to have emerged about 300,000 years ago. It dispersed throughout Africa, and after 70,000 years ago throughout Eurasia and Oceania. A 2009 study identified 14 "ancestral population clusters", the most remote being the San people of Southern Africa. [29] [30]

With their rapid expansion throughout different climate zones, and especially with the availability of new food sources with the domestication of cattle and the development of agriculture, human populations have been exposed to significant selective pressures since their dispersal. For example, the ancestors of East Asians are thought to have undergone processess of selection for a number of alleles, including variants of the EDAR, ADH1B, ABCC1, and ALDH2 genes.

The East Asian types of ADH1B in particular are associated with rice domestication and would thus have arisen after the development of rice cultivation roughly 10,000 years ago. [31] Several phenotypical traits of characteristic of East Asians are due to a single mutation of the EDAR gene, dated to c. 35,000 years ago. [32]

As of 2017, 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 genetics studies using artificial intelligence (AI), that suggest the existence of an unknown human ancestor species, not Neanderthal, Denisovan or human hybrid (like Denny (hybrid hominin)), in the genome of modern humans. [37] [38]

Research studies

In March 2019, Chinese scientists reported inserting the human brain-related MCPH1 gene into laboratory rhesus monkeys, resulting in the transgenic monkeys performing better and answering faster on "short-term memory tests involving matching colors and shapes", compared to control non-transgenic monkeys, according to the researchers. [39] [40]

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 human ancestor population bottleneck occurred "around 930,000 and 813,000 years ago ... lasted for about 117,000 years and brought human ancestors close to extinction." [43] [44]

See also

Related Research Articles

<span class="mw-page-title-main">Human evolution</span> Evolutionary process leading to anatomically modern humans

Human evolution is the evolutionary process within the history of primates that led to the emergence of Homo sapiens as a distinct species of the hominid family that includes all the great apes. This process involved the gradual development of traits such as human bipedalism, dexterity, and complex language, as well as interbreeding with other hominins, indicating that human evolution was not linear but weblike. The study of the origins of humans, variously known by the terms anthropogeny, anthropogenesis, or anthropogony, involves several scientific disciplines, including physical and evolutionary anthropology, paleontology, and genetics.

<span class="mw-page-title-main">Homininae</span> Subfamily of mammals

Homininae, also called "African hominids" or "African apes", is a subfamily of Hominidae. It includes two tribes, with their extant as well as extinct species: 1) the tribe Hominini ―and 2) the tribe Gorillini (gorillas). Alternatively, the genus Pan is sometimes considered to belong to its own third tribe, Panini. Homininae comprises all hominids that arose after orangutans split from the line of great apes. The Homininae cladogram has three main branches, which lead to gorillas and to humans and chimpanzees. There are two living species of Panina and two living species of gorillas, but only one extant human species. Traces of extinct Homo species, including Homo floresiensis have been found with dates as recent as 40,000 years ago. Organisms in this subfamily are described as hominine or hominines.

<span class="mw-page-title-main">Human genome</span> Complete set of nucleic acid sequences for humans

The human genome is a complete set of nucleic acid sequences for humans, encoded as DNA within the 23 chromosome pairs in cell nuclei and in a small DNA molecule found within individual mitochondria. These are usually treated separately as the nuclear genome and the mitochondrial genome. Human genomes include both protein-coding DNA sequences and various types of DNA that does not encode proteins. The latter is a diverse category that includes DNA coding for non-translated RNA, such as that for ribosomal RNA, transfer RNA, ribozymes, small nuclear RNAs, and several types of regulatory RNAs. It also includes promoters and their associated gene-regulatory elements, DNA playing structural and replicatory roles, such as scaffolding regions, telomeres, centromeres, and origins of replication, plus large numbers of transposable elements, inserted viral DNA, non-functional pseudogenes and simple, highly repetitive sequences. Introns make up a large percentage of non-coding DNA. Some of this non-coding DNA is non-functional junk DNA, such as pseudogenes, but there is no firm consensus on the total amount of junk DNA.

<span class="mw-page-title-main">Mitochondrial Eve</span> Matrilineal most recent common ancestor of all living humans

In human genetics, the Mitochondrial Eve is the matrilineal most recent common ancestor (MRCA) of all living humans. In other words, she is defined as the most recent woman from whom all living humans descend in an unbroken line purely through their mothers and through the mothers of those mothers, back until all lines converge on one woman.

<span class="mw-page-title-main">Ape</span> Branch of primates

Apes are a clade of Old World simians native to sub-Saharan Africa and Southeast Asia, which together with its sister group Cercopithecidae form the catarrhine clade, cladistically making them monkeys. Apes do not have tails due to a mutation of the TBXT gene. In traditional and non-scientific use, the term ape can include tailless primates taxonomically considered Cercopithecidae, and is thus not equivalent to the scientific taxon Hominoidea. There are two extant branches of the superfamily Hominoidea: the gibbons, or lesser apes; and the hominids, or great apes.

In human genetics, the Y-chromosomal most recent common ancestor is the patrilineal most recent common ancestor (MRCA) from whom all currently living humans are descended. He is the most recent male from whom all living humans are descended through an unbroken line of their male ancestors. The term Y-MRCA reflects the fact that the Y chromosomes of all currently living human males are directly derived from the Y chromosome of this remote ancestor. The analogous concept of the matrilineal most recent common ancestor is known as "Mitochondrial Eve", the most recent woman from whom all living humans are descended matrilineally. As with "Mitochondrial Eve", the title of "Y-chromosomal Adam" is not permanently fixed to a single individual, but can advance over the course of human history as paternal lineages become extinct.

The molecular clock is a figurative term for a technique that uses the mutation rate of biomolecules to deduce the time in prehistory when two or more life forms diverged. The biomolecular data used for such calculations are usually nucleotide sequences for DNA, RNA, or amino acid sequences for proteins.

In biology and genetic genealogy, the most recent common ancestor (MRCA), also known as the last common ancestor (LCA), of a set of organisms is the most recent individual from which all the organisms of the set are descended. The term is also used in reference to the ancestry of groups of genes (haplotypes) rather than organisms.

The humanzee is a hypothetical hybrid of chimpanzee and human, thus a form of human–animal hybrid. Serious attempts to create such a hybrid were made by Soviet biologist Ilya Ivanovich Ivanov in the 1920s, and possibly by researchers in China in the 1960s, though neither succeeded.

<span class="mw-page-title-main">Timeline of human evolution</span>

The timeline of human evolution outlines the major events in the evolutionary lineage of the modern human species, Homo sapiens, throughout the history of life, beginning some 4 billion years ago down to recent evolution within H. sapiens during and since the Last Glacial Period.

<span class="mw-page-title-main">Hominini</span> Tribe of mammals

The Hominini form a taxonomic tribe of the subfamily Homininae ("hominines"). Hominini includes the extant genera Homo (humans) and Pan and in standard usage excludes the genus Gorilla (gorillas).

<span class="mw-page-title-main">Chimpanzee genome project</span> Effort to determine the DNA sequence of the chimpanzee genome

The Chimpanzee Genome Project was an effort to determine the DNA sequence of the chimpanzee genome. Sequencing began in 2005 and by 2013 twenty-four individual chimpanzees had been sequenced. This project was folded into the Great Ape Genome Project.

Molecular anthropology, also known as genetic anthropology, is the study of how molecular biology has contributed to the understanding of human evolution. This field of anthropology examines evolutionary links between ancient and modern human populations, as well as between contemporary species. Generally, comparisons are made between sequences, either DNA or protein sequences; however, early studies used comparative serology.

<span class="mw-page-title-main">Human genetic variation</span> Genetic diversity in human populations

Human genetic variation is the genetic differences in and among populations. There may be multiple variants of any given gene in the human population (alleles), a situation called polymorphism.

<span class="mw-page-title-main">Hominidae</span> Family of primates

The Hominidae, whose members are known as the great apes or hominids, are a taxonomic family of primates that includes eight extant species in four genera: Pongo ; Gorilla ; Pan ; and Homo, of which only modern humans remain.

The chimpanzee–human last common ancestor (CHLCA) is the last common ancestor shared by the extant Homo (human) and Pan genera of Hominini. Estimates of the divergence date vary widely from thirteen to five million years ago.

The human mitochondrial molecular clock is the rate at which mutations have been accumulating in the mitochondrial genome of hominids during the course of human evolution. The archeological record of human activity from early periods in human prehistory is relatively limited and its interpretation has been controversial. Because of the uncertainties from the archeological record, scientists have turned to molecular dating techniques in order to refine the timeline of human evolution. A major goal of scientists in the field is to develop an accurate hominid mitochondrial molecular clock which could then be used to confidently date events that occurred during the course of human evolution.

Incomplete lineage sorting, also termed hemiplasy, deep coalescence, retention of ancestral polymorphism, or trans-species polymorphism, describes a phenomenon in population genetics when ancestral gene copies fail to coalesce into a common ancestral copy until deeper than previous speciation events. It is caused by lineage sorting of genetic polymorphisms that were retained across successive nodes in the species tree. In other words, the tree produced by a single gene differs from the population or species level tree, producing a discordant tree. Whatever the mechanism, the result is that a generated species level tree may differ depending on the selected genes used for assessment. This is in contrast to complete lineage sorting, where the tree produced by the gene is the same as the population or species level tree. Both are common results in phylogenetic analysis, although it depends on the gene, organism, and sampling technique.

The myth of the one percent refers to the 1975 study done by Wilson and King that asserted that human-chimpanzee divergence is about 1%. Humans share a common ancestor with chimpanzees, and the rapid evolution of chimpanzees and humans, along with gorillas and bonobos, has led to difficulties in creating an accurate lineage or tree topology. Chimpanzees and humans were found to be a monophyletic clade, leading to the question of how closely related the two are.

References

  1. ↑ Murphy, W.J.; Eizirik, E.; O'Brien, S.J.; Madsen, O.; Scally, M.; Douady, C.J.; Teeling, E.; Ryder, O.A.; Stanhope, M.J.; de Jong, W.W.; Springer, M.S. (2001). "Resolution of the early placental mammal radiation using Bayesian phylogenetics". Science. 294 (5550): 2348–2351. Bibcode:2001Sci...294.2348M. doi:10.1126/science.1067179. PMID   11743200. S2CID   34367609.
  2. ↑ Kriegs, J.O.; Churakov, G.; Kiefmann, M.; Jordan, U.; Brosius, J.; Schmitz, J. (2006). "Retroposed elements as archives for the evolutionary history of placental mammals". PLOS Biol. 4 (4): e91. doi: 10.1371/journal.pbio.0040091 . PMC   1395351 . PMID   16515367.
  3. ↑ Schwartz M, Vissing J (2002). "Paternal Inheritance of Mitochondrial DNA". N Engl J Med. 347 (8): 576–580. doi: 10.1056/NEJMoa020350 . PMID   12192017.
  4. ↑ ""Human Chromosome 2." PBS". PBS . Archived from the original on 2018-07-31. Retrieved 2017-08-31.
  5. ↑ 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. Bibcode:2015Natur.526...68T. doi:10.1038/nature15393. PMC   4750478 . PMID   26432245.
  6. ↑ "134 to 188 ka": Fu Q, Mittnik A, Johnson PL, Bos K, Lari M, Bollongino R, Sun C, Giemsch L, Schmitz R, Burger J, Ronchitelli AM, Martini F, Cremonesi RG, Svoboda J, Bauer P, Caramelli D, Castellano S, Reich D, Pääbo S, Krause J (March 21, 2013). "A revised timescale for human evolution based on ancient mitochondrial genomes". Current Biology. 23 (7): 553–59. Bibcode:2013CBio...23..553F. doi:10.1016/j.cub.2013.02.044. PMC   5036973 . PMID   23523248..
  7. ↑ Patterson N, Richter DJ, Gnerre S, Lander ES, Reich D (2006). "Genetic evidence for complex speciation of humans and chimpanzees". Nature. 441 (7097): 1103–8. Bibcode:2006Natur.441.1103P. doi:10.1038/nature04789. PMID   16710306. S2CID   2325560.
  8. 1 2 3 Chen, F.C.; Li, W.H. (2001). "Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees". Am J Hum Genet. 68 (2): 444–456. doi:10.1086/318206. PMC   1235277 . PMID   11170892.
  9. ↑ Ken Miller in the Kitzmiller v. Dover trial transcripts.
  10. ↑ Sarich, V.M.; Wilson, A.C. (1967). "Immunological time scale for hominid evolution". Science. 158 (3805): 1200–1203. Bibcode:1967Sci...158.1200S. doi:10.1126/science.158.3805.1200. PMID   4964406. S2CID   7349579.
  11. ↑ Venn, Oliver; Turner, Isaac; Mathieson, Iain; de Groot, Natasja; Bontrop, Ronald; McVean, Gil (June 2014). "Strong male bias drives germline mutation in chimpanzees". Science. 344 (6189): 1272–1275. Bibcode:2014Sci...344.1272V. doi:10.1126/science.344.6189.1272. PMC   4746749 . PMID   24926018.
  12. ↑ Yoder, A.D.; Yang, Z. (1 July 2000). "Estimation of primate speciation dates using local molecular clocks". Mol Biol Evol. 17 (7): 1081–1090. doi: 10.1093/oxfordjournals.molbev.a026389 . PMID   10889221.
  13. ↑ Takahata, N.; Satta, Y.; Klein, J. (1995). "Divergence time and population size in the lineage leading to modern humans". Theor Popul Biol. 48 (2): 198–221. doi: 10.1006/tpbi.1995.1026 . PMID   7482371.
  14. ↑ Yang, Z. (1 December 2002). "Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci" (abstract page). Genetics. 162 (4): 1811–1823. doi:10.1093/genetics/162.4.1811. PMC   1462394 . PMID   12524351. Archived from the original on 16 February 2011. Retrieved 25 August 2006.
  15. 1 2 3 4 Chimpanzee Sequencing; Analysis Consortium (2005). "Initial sequence of the chimpanzee genome and comparison with the human genome". Nature. 437 (7055): 69–87. Bibcode:2005Natur.437...69.. doi: 10.1038/nature04072 . PMID   16136131.
  16. ↑ Olson, M.V. (1999). "When less is more: gene loss as an engine of evolutionary change". Am J Hum Genet. 64 (1): 18–23. doi:10.1086/302219. PMC   1377697 . PMID   9915938.
  17. 1 2 Wang, X.; Grus, W.E.; Zhang, J. (2006). "Gene losses during human origins". PLOS Biol. 4 (3): e52. doi: 10.1371/journal.pbio.0040052 . PMC   1361800 . PMID   16464126.
  18. ↑ Demuth, Jeffery P.; Bie, Tijl De; Stajich, Jason E.; Cristianini, Nello; Hahn, Matthew W. (December 2006). Borevitz, Justin (ed.). "The Evolution of Mammalian Gene Families". PLOS ONE. 1 (1): e85. Bibcode:2006PLoSO...1...85D. doi: 10.1371/journal.pone.0000085 . PMC   1762380 . PMID   17183716.
  19. ↑ Winter, H.; Langbein, L.; Krawczak, M.; Cooper, D.N.; Suarez, L.F.J.; Rogers, M.A.; Praetzel, S.; Heidt, P.J.; Schweizer, J. (2001). "Human type I hair keratin pseudogene phihHaA has functional orthologs in the chimpanzee and gorilla: evidence for recent inactivation of the human gene after the Pan-Homo divergence". Hum Genet. 108 (1): 37–42. doi:10.1007/s004390000439. PMID   11214905. S2CID   21545865.
  20. ↑ Stedman, H.H.; Kozyak, B.W.; Nelson, A.; Thesier, D.M.; Su, L.T.; Low, D.W.; Bridges, C.R.; Shrager, J.B.; Purvis, N.M.; Mitchell, M.A. (2004). "Myosin gene mutation correlates with anatomical changes in the human lineage". Nature. 428 (6981): 415–418. Bibcode:2004Natur.428..415S. doi:10.1038/nature02358. PMID   15042088. S2CID   4304466.
  21. ↑ Perry, G.H.; Verrelli, B.C.; Stone, A.C. (2005). "Comparative analyses reveal a complex history of molecular evolution for human MYH16". Mol Biol Evol. 22 (3): 379–382. doi: 10.1093/molbev/msi004 . PMID   15470226.
  22. ↑ Hellen, Elizabeth H. B.; Kern, Andrew D. (2015-04-01). "The Role of DNA Insertions in Phenotypic Differentiation between Humans and Other Primates". Genome Biology and Evolution. 7 (4): 1168–1178. doi:10.1093/gbe/evv012. ISSN   1759-6653. PMC   4419785 . PMID   25635043.
  23. ↑ Bird, Christine P.; Liu, Maureen; et al. (2007). "Fast-evolving noncoding sequences in the human genome". Genome Biology. 8 (6): R118. doi: 10.1186/gb-2007-8-6-r118 . PMC   2394770 . PMID   17578567.
  24. ↑ Cheng, Z.; Ventura, M.; She, X.; Khaitovich, P.; Graves, T.; Osoegawa, K.; Church, D; Pieter DeJong, P.; Wilson, R. K.; Paabo, S.; Rocchi, M; Eichler, E. E. (2005). "A genome-wide comparison of recent chimpanzee and human segmental duplications". Nature. 437 (1 September 2005): 88–93. Bibcode:2005Natur.437...88C. doi:10.1038/nature04000. PMID   16136132. S2CID   4420359.
  25. ↑ Kaessmann, H.; Heissig, F.; von Haeseler, A.; Pääbo, S. (1999). "DNA sequence variation in a non-coding region of low recombination on the human X chromosome". Nat Genet. 22 (1): 78–81. doi:10.1038/8785. PMID   10319866. S2CID   9153915.
  26. ↑ Saey, Tina Hesman (2009). "Story one: Team decodes neandertal DNA: Genome draft may reveal secrets of human evolution". Science News. 175 (6): 5–7. doi:10.1002/scin.2009.5591750604.
  27. ↑ Green, Richard E.; Krause; Briggs; Maricic; Stenzel; Kircher; Patterson; Li; Zhai; Fritz; Hansen; Durand; Malaspinas; Jensen; Marques-Bonet; Alkan; Prüfer; Meyer; Burbano; Good; Schultz; Aximu-Petri; Butthof; Höber; Höffner; Siegemund; Weihmann; Nusbaum; Lander; et al. (2010-05-07). "A Draft Sequence of the Neandertal Genome". Science. 328 (5979): 710–722. Bibcode:2010Sci...328..710G. doi:10.1126/science.1188021. PMC   5100745 . PMID   20448178.
  28. ↑ "NEANDERTALS LIVE!". john hawks weblog. 6 May 2010. Archived from the original on 2010-12-16. Retrieved 2010-12-31.
  29. ↑ Tishkoff, SA.; Reed, FA.; Friedlaender, FR.; Ehret, C.; Ranciaro, A.; Froment, A.; Hirbo, JB.; Awomoyi, AA.; et al. (May 2009). "The genetic structure and history of Africans and African Americans". Science. 324 (5930): 1035–44. Bibcode:2009Sci...324.1035T. doi:10.1126/science.1172257. PMC   2947357 . PMID   19407144.
  30. ↑ BBC World News "Africa's genetic secrets unlocked" Archived 2009-07-01 at the Wayback Machine , 1 May 2009.
  31. ↑ Peng, Y.; et al. (2010). "The ADH1B Arg47His polymorphism in East Asian populations and expansion of rice domestication in history". BMC Evolutionary Biology. 10 (1): 15. Bibcode:2010BMCEE..10...15P. doi: 10.1186/1471-2148-10-15 . PMC   2823730 . PMID   20089146.
  32. ↑ Traits affected by the mutation are sweat glands, teeth, hair thickness and breast tissue. Kamberov; et al. (2013). "Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant". Cell. 152 (4): 691–702. doi:10.1016/j.cell.2013.01.016. PMC   3575602 . PMID   23415220. East Asian Physical Traits Linked to 35,000-Year-Old Mutation Archived 2021-08-13 at the Wayback Machine , NYT, 14 February 2013.
  33. ↑ NCBI (2017-05-08). "dbSNP's human build 150 has doubled the amount of RefSNP records!". NCBI Insights. Archived from the original on 2020-04-08. Retrieved 2017-05-16.
  34. ↑ Jorde, LB; Wooding, SP (2004). "Genetic variation, classification and 'race'". Nature Genetics . 36 (11s): S28–33. doi: 10.1038/ng1435 . PMID   15508000.
  35. ↑ Tishkoff, SA; Kidd, KK (2004). "Implications of biogeography of human populations for 'race' and medicine". Nature Genetics . 36 (11s): S21–7. doi: 10.1038/ng1438 . PMID   15507999.
  36. ↑ The 1000 Genomes Project Consortium (2015-10-01). "A global reference for human genetic variation". Nature. 526 (7571): 68–74. Bibcode:2015Natur.526...68T. doi:10.1038/nature15393. ISSN   0028-0836. PMC   4750478 . PMID   26432245.{{cite journal}}: CS1 maint: numeric names: authors list (link)
  37. ↑ Mondal, Mayukh; Bertranpedt, Jaume; Leo, Oscar (16 January 2019). "Approximate Bayesian computation with deep learning supports a third archaic introgression in Asia and Oceania". Nature Communications . 10 (246): 246. Bibcode:2019NatCo..10..246M. doi:10.1038/s41467-018-08089-7. PMC   6335398 . PMID   30651539.
  38. ↑ 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.
  39. ↑ 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.
  40. ↑ Shi, Lei; et al. (27 March 2019). "Transgenic rhesus monkeys carrying the human MCPH1 gene copies show human-like neoteny of brain development". Chinese National Science Review . 6 (3): 480–493. doi: 10.1093/nsr/nwz043 . PMC   8291473 . PMID   34691896. Archived from the original on 4 October 2022. Retrieved 30 December 2019.
  41. ↑ 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.
  42. ↑ Ragsdale,vAaron P.; et al. (17 May 2023). "A weakly structured stem for human origins in Africa". Nature . 167 (7962): 755–763. Bibcode:2023Natur.617..755R. doi:10.1038/s41586-023-06055-y. PMC   10208968 . PMID   37198480.
  43. ↑ 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.
  44. ↑ Hu, Wangjie; et al. (31 August 2023). "Genomic inference of a severe human bottleneck during the Early to Middle Pleistocene transition". Science . 381 (6661): 979–984. Bibcode:2023Sci...381..979H. doi:10.1126/science.abq7487. PMID   37651513. S2CID   261396309. Archived from the original on 1 September 2023. Retrieved 2 September 2023.

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