Human Evolutionary Genetics - Wikipedia

8/10/2019 Human Evolutionary Genetics - Wikipedia

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Human evolutionary geneticsFrom Wikipedia, the free encyclopedia

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Human evolutionary genetics studies how one human genome differs from the other, theevolutionary past that gave rise to it, and its current effects. Differences between genomes haveanthropological , medical and forensic implications and applications. Genetic data can provideimportant insight into human evolution .

Contents

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1 Origin of apes 2 Cladistics 3 Speciation of humans and the African apes

o 3.1 General observations o 3.2 Divergence times o 3.3 Divergence times and ancestral effective population size

4 Genetic differences between humans and other great apes o 4.1 Gene loss

4.1.1 Hair keratin gene KRTHAP1 4.1.2 Myosin gene MYH16 4.1.3 Other

o 4.2 Gene addition o 4.3 Selection pressures

5 Genetic differences between humans and Neanderthals 6 Sequence divergence between humans and apes 7 Modern humans

o 7.1 Age of the common ancestor o 7.2 African origin for modern humans o 7.3 Y chromosome findings

8 See also 9 References 10 External links

[edit ] Origin of apes

Taxonomic relationships of hominoids
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Biologists classify humans , along with only a few other species , as great apes (species in thefamily Hominidae ). The Hominidae include two distinct species of chimpanzee (the bonobo , Pan

paniscus , and the common chimpanzee , Pan troglodytes ), two species of gorilla (the westerngorilla , Gorilla gorilla , and the eastern gorilla , Gorilla graueri ), and two species of orangutan (theBornean orangutan , Pongo pygmaeus , and the Sumatran orangutan , Pongo abelii ).

Apes, in turn, belong to the primates order (>400 species). Data from both mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) indicates that primates belong to the group ofEuarchontoglires , together with Rodentia , Lagomorpha , Dermoptera , and Scandentia .[1] This isfurther supported by Alu-like short interspersed nuclear elements (SINEs) which have been foundonly in members of the Euarchontoglires .[2]

[edit ] Cladistics

A phylogenetic tree like the one shown above is usually derived from DNA or protein sequences from populations. Often mitochondrial DNA or Y chromosome sequences are used to studyancient human demographics. These single -locus sources of DNA do not recombine and arealmost always inherited from a single parent, with only one known exception in mtDNA (Schwartzand Vissing 2002). Individuals from the various continental groups tend to be more similar to oneanother than to people from other continents. The tree is rooted in the common ancestor ofchimpanzees and humans, which is believed to have originated in Africa . Horizontal distancecorresponds to two things:

1. Genetic distance . Given below the diagram, the genetic difference between humans andchimps is roughly 2%, or 20 times larger than the variation among modern humans.

2. Temporal remoteness of the most recent common ancestor. Rough estimates are givenabove the diagram, in millions of years. The mitochondrial most recent common ancestorof modern humans lived roughly 200,000 years ago, latest common ancestors of humansand chimps between four and seven million years ago.

Chimpanzees and humans belong to different genera , indicated in red. Formation of species andsubspecies is also indicated, and the formation of "races" is indicated in the green rectangle to theright (note that only a very rough representation of human phylogeny is given). Note that verticaldistances are not meaningful in this representation.

[edit ] Speciation of humans and the African apes

The separation of humans from their closest relatives, the African apes (chimpanzees and gorillas)has been studied for more than a century and the amount of scientific publications on that subject ishuge. 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?
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genyhttp://en.wikipedia.org/w/index.php?title=Human_evolutionary_genetics&action=edit&section=3http://en.wikipedia.org/w/index.php?title=Human_evolutionary_genetics&action=edit&section=3http://en.wikipedia.org/wiki/Effective_population_sizehttp://en.wikipedia.org/wiki/Effective_population_sizehttp://en.wikipedia.org/wiki/Effective_population_sizehttp://en.wikipedia.org/wiki/Effective_population_sizehttp://en.wikipedia.org/w/index.php?title=Human_evolutionary_genetics&action=edit&section=3http://en.wikipedia.org/wiki/Phylogenyhttp://en.wikipedia.org/wiki/Subspecieshttp://en.wikipedia.org/wiki/Specieshttp://en.wikipedia.org/wiki/Genushttp://en.wikipedia.org/wiki/Mitochondrialhttp://en.wikipedia.org/wiki/Africahttp://en.wikipedia.org/wiki/Chimpanzeehttp://en.wikipedia.org/wiki/Genetic_recombinationhttp://en.wikipedia.org/wiki/Locus_(genetics)http://en.wikipedia.org/wiki/Y-chromosomal_Adamhttp://en.wikipedia.org/wiki/Mitochondrial_DNAhttp://en.wikipedia.org/wiki/DNA_sequencehttp://en.wikipedia.org/wiki/Proteinhttp://en.wikipedia.org/wiki/DNAhttp://en.wikipedia.org/wiki/Phylogenetic_treehttp://en.wikipedia.org/w/index.php?title=Human_evolutionary_genetics&action=edit&section=2http://en.wikipedia.org/wiki/Human_evolutionary_genetics#cite_note-Kriegs-1http://en.wikipedia.org/wiki/Short_interspersed_nuclear_elementhttp://en.wikipedia.org/wiki/Human_evolutionary_genetics#cite_note-Murphy-0http://en.wikipedia.org/wiki/Scandentiahttp://en.wikipedia.org/wiki/Dermopterahttp://en.wikipedia.org/wiki/Lagomorphahttp://en.wikipedia.org/wiki/Rodenthttp://en.wikipedia.org/wiki/Euarchontoglireshttp://en.wikipedia.org/wiki/Nuclear_DNAhttp://en.wikipedia.org/wiki/Mitochondrial_DNAhttp://en.wikipedia.org/wiki/Primatehttp://en.wikipedia.org/wiki/Sumatran_orangutanhttp://en.wikipedia.org/wiki/Bornean_orangutanhttp://en.wikipedia.org/wiki/Orangutanhttp://en.wikipedia.org/wiki/Eastern_gorillahttp://en.wikipedia.org/wiki/Western_gorillahttp://en.wikipedia.org/wiki/Western_gorillahttp://en.wikipedia.org/wiki/Gorillahttp://en.wikipedia.org/wiki/Common_chimpanzeehttp://en.wikipedia.org/wiki/Bonobohttp://en.wikipedia.org/wiki/Chimpanzeehttp://en.wikipedia.org/wiki/Hominidaehttp://en.wikipedia.org/wiki/Family_(biology)http://en.wikipedia.org/wiki/Great_apehttp://en.wikipedia.org/wiki/Specieshttp://en.wikipedia.org/wiki/Human


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Are there traces of population structure (subpopulations) preceding the speciation or partialadmixture succeeding it?

What were the specific events (including fusion of chromosomes 2a and 2b) prior to andsubsequent to the separation?

[edit ] General observationsAs discussed before, different parts of the genome show different sequence divergence betweendifferent hominoids . It has also been shown that the sequence divergence between DNA fromhumans 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 .[3] Additionally gene trees, generated by comparative analysis of DNA segments, do not always fitthe species tree. Summing up:

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 have23 pairs of chromosomes, while chimpanzees, gorillas, and orangutans have 24. Humanchromosome 2 is a fusion between two chromosomes that remained separate in the other

primates .[4]

[edit ] Divergence times

The divergence time of humans from other apes is of great interest. One of the first molecularstudies, published in 1967 measured immunological distances (IDs) between different primates .[5] 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 andtherefore weaker immunological response to each other's antigens. The immunological responseof a species to its own antigens (e.g. human to human) was set to be 1. The ID between humans andgorillas was determined to be 1.09, that between humans and chimpanzees was determined as1.14. However the distance to six different Old World monkeys was on average 2.46 indicatingthat the African apes are far closer related to humans than to monkeys. The authors consider thedivergence 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. Thatwas 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. Laterstudies based on molecular genetics were able to resolve the trichotomy: chimpanzees are

phylogenetically closer to humans than to gorillas. However, the divergence times estimated later(using much more sophisticated methods in molecular genetics) do not substantially differ fromthe very first estimate in 1967.

[edit ] Divergence times and ancestral effective population size
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The sequences of the DNA segments diverge earlier than the species. A large effective populationsize 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 (t A for DNA segmentA; t B for DNA segment B) will deviate more from the time the species diverge (t S) compared to asmall ancestral effective population size (right).

Current methods to determine divergence times use DNA sequence alignments and molecularclocks . Usually the molecular clock is calibrated assuming that the orangutan split from theAfrican apes (including humans) 12-16 MYA. Some studies also include some old world monkeysand 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 .[6] If these dates are revised, the divergencetimes estimated from molecular data will change as well. However, the relative divergence timesare unlikely to change. Even if we can't tell absolute divergence times exactly, we can be prettysure 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 sequence from different regions of the genomefrom human and chimpanzee and 7 DNA sequences from human, chimpanzee and gorilla .[7] Theydetermined that chimpanzees are more closely related to humans than gorillas. Using variousstatistical methods, they estimated the divergence time human-chimp to be 4.7 MYA and thedivergence time between gorillas and humans (and chimps) to be 7.2 MYA. Additionally theyestimated 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 humansis estimate to be only ~10,000. If true that means that the human lineage would have experiencedan 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 andchimps. Thus both loci should be more similar between human and chimp than between gorilla andchimp or gorilla and human. In the lower graph, locus A has a more recent common ancestor inhuman and gorilla compared to the chimp sequence. Whereas chimp and gorilla have a morerecent 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 ahuman, a chimpanzee, a gorilla, and orangutan .[3] When the DNA sequences were concatenated toa single long sequence, the generated neighbor-joining tree supported the Homo - Pan clade with100% 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 thespeciation (species tree). The shorter internodal time span (T IN) the more common are incongruentgene trees. The effective population size (N e) of the internodal population determines how longgenetic lineages are preserved in the population. A higher effective population size causes moreincongruent 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.
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When each segment was analyzed individually, 31 supported the Homo - Pan clade, 10 supportedthe Homo -Gorilla clade, and 12 supported the Pan -Gorilla clade. Using the molecular clock theauthors estimated that gorillas split up first 6.2-8.4 MYA and chimpanzees and humans split up1.6-2.2 million years later (internodal time span) 4.6-6.2 MYA. The internodal time span is usefulto 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. Additionallythey 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% ofthe 52 loci that gave a resolution (33 intergenic, 19 protein coding) support the 'correct' speciestree. From the fraction of loci which did not support the species tree and the internodal time spanthey estimated previously, the effective population of the common ancestor of humans andchimpanzees was estimated to be ~52 000 to 96 000. This value is not as high as that from the firststudy (Takahata), but still much higher than present day effective population size of humans. [dubious discuss ]

A third study (Yang, 2002) used the same dataset that Chen and Li used but estimated the ancestraleffective population of 'only' ~12,000 to 21,000, using a different statistical method .[8]

[edit ] Genetic differences between humans and other greatapes

The alignable sequences within genomes of humans and chimpanzees differ by about 35 millionsingle nucleotide substitutions. Additionally about 3% of the complete genomes differ by

deletions, insertions and duplications .[9]

Since mutation rate is relatively constant, roughly one half of these changes occurred in the humanlineage. Only a very tiny fraction of those fixed differences gave rise to the different phenotypes ofhumans and chimpanzees and finding those is a great challenge. The vast majority of thedifferences are neutral and do not affect the phenotype. [citation needed ]

Molecular evolution may act in different ways, through protein evolution, gene loss, differentialgene regulation and RNA evolution. All are thought to have played some part in human evolution.

[edit ] 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 couldthus be a common mechanism of evolutionary adaptation (the "less-is-more" hypothesis) .[10]

80 genes were lost in the human lineage after separation from the last common ancestor with thechimpanzee. 36 of those were olfactory receptors . Genes involved in chemoreception and immuneresponse are overrepresented .[11] Another study estimated that 86 genes had been lost .[12]
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[edit ] Hair keratin gene KRTHAP1

A gene for type I hair keratin was lost in the human lineage. Keratins are a major component ofhairs. Humans still have nine functional type I hair keratin genes but the loss of that particular genemay have caused the thinning of human body hair. The gene loss occurred relatively recently in

human evolution less than 240,000 years ago .[13]

[edit ] Myosin gene MYH16

Stedman et al. (2004) stated that the loss of the sarcomeric myosin gene MYH16 in the humanlineage led to smaller masticatory muscles . They estimated that the mutation that led to theinactivation (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 incranial capacity , promoting speculation that the loss of the gene may have removed anevolutionary constraint on brain size in the genus Homo .[14]

Another estimate for the loss of the MYH16 gene is 5.3 million years ago, long before Homo appeared .[15]

[edit ] Other

CASPASE12 , a cysteinyl aspartate proteinase [16]

[edit ] Gene addition

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

[edit ] Selection pressures

Human accelerated regions are areas of the genome that differ between humans and chimpanzeesto a greater extent than can be explained by genetic drift over the time since the two species shareda common ancestor. These regions show signs of being subject to natural selection, leading to theevolution 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 ofthe opposable thumb .

[edit ] Genetic differences between humans and Neanderthals

An international group of scientists has completed a draft of 63 percent of the Neanderthal genome, consisting of 3.7 billion base pairs .[17] Some parts of the Neanderthal genome have morein common with chimps than humans [clarification needed ], while other parts are shared by both

Neanderthals and humans. Neanderthals and most humans share a lactose-intolerant variant of thelactase gene that encodes an enzyme that is unable to break down lactose in milk after weaning.Humans and Neanderthals also share the FOXP2 gene variant associated with brain developmentand with speech in humans, indicating that Neanderthals may have been able to speak. Chimps
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ipedia.org/wiki/HAR1Fhttp://en.wikipedia.org/wiki/Human_accelerated_regionshttp://en.wikipedia.org/w/index.php?title=Human_evolutionary_genetics&action=edit&section=13http://en.wikipedia.org/wiki/Low_copy_repeatshttp://en.wikipedia.org/wiki/Segmental_duplicationhttp://en.wikipedia.org/w/index.php?title=Human_evolutionary_genetics&action=edit&section=12http://en.wikipedia.org/wiki/Human_evolutionary_genetics#cite_note-15http://en.wikipedia.org/wiki/Caspase_12http://en.wikipedia.org/w/index.php?title=Human_evolutionary_genetics&action=edit&section=11http://en.wikipedia.org/wiki/Human_evolutionary_genetics#cite_note-Perry-14http://en.wikipedia.org/wiki/Human_evolutionary_genetics#cite_note-Stedman-13http://en.wikipedia.org/wiki/Cranial_capacityhttp://en.wikipedia.org/wiki/Homo_ergasterhttp://en.wikipedia.org/wiki/Masticatory_muscleshttp://en.wikipedia.org/wiki/MYH16http://en.wikipedia.org/wiki/Myosinhttp://en.wikipedia.org/w/index.php?title=Human_evolutionary_genetics&action=edit&section=10http://en.wikipedia.org/wiki/Human_evolutionary_genetics#cite_note-Winter-12http://en.wikipedia.org/wiki/Keratinhttp://en.wikipedia.org/w/index.php?title=Human_evolutionary_genetics&action=edit&section=9


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have two amino acid differences in FOXP2 compared with human FOXP2. In may 2010 the entire Neanderthal genome was completed and the results were published in the journal Nature. Theresults indicate some breeding between humans and Neanderthals as the genomes of non-Africanhumans are 1-4% Neanderthal.

[edit ] Sequence divergence between humans and apesThe draft sequence of the common chimpanzee genome published in the summer 2005 showed theregions that are similar enough to be aligned with one another account for 2400 million of thehuman genomes 3164.7 million base s[18] that is, 75.8% of the genome. This 75.8% of the humangenome is 1.23% different from the chimpanzee genome in single nucleotide polymorphisms [18] (chang es of single DNA letters in the genome). Another type of difference, called indels (insertions/deletions) account for another ~3 % difference between the alignable sequences .[18] Inaddition, variation in copy number of large segments (> 20 kb) of similar DNA sequence providesa further 2.7% difference between the two species .[19] Hence the total similarity of the genomescould be as low as about 70%.

The figures above do not take into account differences in the organization of the alignablesequences within the genomes of humans and chimps. Short stretches of alignable sequence may

be in very different orders and locations within the two genomes. At present we cannot fully assessthe difference in structure of the two genomes, because the human genome was used as a scaffoldwhen the chimpanzee draft genome was assembled. When genomes are sequenced, relatively shortsequences of DNA are produced, and these sequences have to be fitted together like a jigsaw

puzzle. This requires multiple overlapping reads to accurately assemble the overall sequence. Thehuman genome sequence is relatively accurate, with 8 to 9 -fold coverage , but the chimpanzee draftgenome only has 3.6-fold coverage .[18] The human genome was sequenced using a hierarchicalshotgun method which can deal with duplications and difficult-to-assemble sequences better thanthe whole genome shotgun method that was used for the chimpanzee draft genome. The humangenome was used as a template for the assembly of the draft chimpanzee genome, on theassumption that the two genomes would be similar.

Almost half of that 1.23% SNP change belongs to the human at 0.53%, whose genetic variance islower than a chimp, and just over half to the chimp at 0.7%. If we also take into account thatrandom "genetic drift " takes up the bulk of the 0.54% difference, then that percentage differencewhere SNPs have a potential positive impact on human abilities, is between 0.01% and 0.02%. The

bonobo is a sibling species of common chimpanzee and is genetically about as different fromhumans as are common chimps.

Percentage sequence divergence between humans and other hominids Locus Human-Chimp Human-Gorilla Human-Orangutan

Alu elements 2 - -Non-coding (Chr. Y) 1.68 0.19 2.33 0.2 5.63 0.35Pseudogenes (autosomal) 1.64 0.10 1.87 0.11 -Pseudogenes (Chr. X) 1.47 0.17 - -
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Noncoding (autosomal) 1.24 0.07 1.62 0.08 3.08 0.11Genes (K s) 1.11 1.48 2.98Introns 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 (K a) 0.8 0.93 1.96

The sequence divergence has generally the following pattern: Human-Chimp < Human-Gorilla


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Mitochondrial Eve . The observation that the mtMRCA is the direct matrilineal ancestor of allliving humans does not mean either that she was the first anatomically modern human, nor that noother female humans lived concurrently with her. Other women would have lived at the same timeand passed nuclear genes down to living humans, but their mitochondrial lineages were lost overtime. This could be due to random events such as producing only male children.

[edit ] African origin for modern humans

There is evidence that modern human mtDNA has an African origin: "We infer from the tree ofminimum length... that Africa is a likely source of the human mitochondrial gene pool. Thisinference comes from the observation that one of the two primary branches leads exclusively toAfrican mtDNAs... while the second primary branch also leads to African mtDNAs... By

postulating that the common ancestral mtDNA... was African, we minimize the number ofintercontinental migrations needed to account for the geographic distribution of mtDNA types. "[21]

The broad study of African genetic diversity headed by Sarah Tishkoff found the San people to

express the greatest genetic diversity among the 113 distinct populations sampled, making themone of 14 "ancestral population clusters". The research also located the origin of modern humanmigration in south-western Africa, near the coastal border of Namibia and Angola .[22]

[edit ] Y chromosome findings

The Y chromosome is much larger than mtDNA, and is relatively homogeneous; therefore it hastaken much longer to find distinct lineages and to analyse them. Conversely, because the Ychromosome is so large by comparison, it holds more genetic information. Y chromosome studiesshow similar findings to those made with mtDNA. The estimate for the age of the ancestral Ychromosome for all extant Y chromosomes is given at about 70,000 years ago and is also placed in

Africa; the individual who contributed this Y chromosomal heritage is sometimes referred to as Ychromosome Adam . The difference in dates between Y chromosome Adam and mitochondrial Eveis usually attributed to a higher extinction rate for Y chromosomes due to greater differentialreproductive success between individual men, which means that a small number of very successfulmen may produce many children, while a larger number of less successful men will produce farfewer children.

[edit ] See also

The Journey of Man: A Genetic Odyssey Chromosome 2 (human) Chimpanzee genome project Genetic history of Europe Genetic history of South Asia

[edit ] References
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a

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