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Human Evolution and Human Genome at a Glance

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Evolution of the Human Genome I

Part of the book series: Evolutionary Studies ((EVOLUS))

Abstract

The long-term human evolution is first explained. Starting from the origin of life, emergence of mammals and evolution of primates and hominoids are outlined, followed by classification of family Hominidae. We then move to the human genome. Its structure in terms of chromosomes and dichotomy of coding and noncoding regions are discussed, followed with general description on various types of mutations such as nucleotide substitutions, insertions and deletions, repeat number changes, and gene duplications.

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References

  • Babarinde IA, Saitou N (2013) Heterogeneous tempo and mode of conserved noncoding sequence evolution among four mammalian orders. Genome Biol Evol 5:2330–2343

    Article  PubMed  PubMed Central  Google Scholar 

  • Babarinde IA, Saitou N (2016) Genomic locations of conserved noncoding sequences and their proximal protein-coding genes in mammalian expression dynamics. Mol Biol Evol 33:1807–1817

    Article  CAS  PubMed  Google Scholar 

  • Bejerano G et al (2004) Ultraconserved elements in the human genome. Science 304:1321–1325

    Article  CAS  PubMed  Google Scholar 

  • Birney E et al (2007) Identifi cation and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799–816

    Article  CAS  PubMed  Google Scholar 

  • Brown TA (2007) Genomes 3. Garland Science Publishing, New York

    Google Scholar 

  • Carbone L et al (2014) Gibbon genome and the fast karyotype evolution of small apes. Nature 513:195–201

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen FC, Li WH (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 68:444–456

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Clamp M et al (2007) Distinguishing protein-coding and noncoding genes in the human genome. Proc Natl Acad Sci U S A 104:19428–19433

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Darwin C (1871) The descent of man and selection in relation to sex. Appleton, New York

    Book  Google Scholar 

  • Dehal P et al (2002) The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science 298:2157–2167

    Article  CAS  PubMed  Google Scholar 

  • Djebali S et al (2012) Landscape of transcription in human cells. Nature 489:101–108

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Eddy S (2012) The C-value paradox, junk DNA and ENCODE. Curr Biol 22:R898

    Article  CAS  PubMed  Google Scholar 

  • Ezawa K, Ikeo K, Gojobori T, Saitou N (2011) Evolutionary patterns of recently emerged animal duplogs. Genome Biol Evol 3:1119–1135

    Article  PubMed  PubMed Central  Google Scholar 

  • Fujiyama A, Watanabe H, Toyoda A, Taylor TD, Itoh T, Tsai SF, Park HS, Yaspo ML, Lehrach H, Chen Z, Fu G, Saitou N, Osoegawa K, de Jong PJ, Suto Y, Hattori M, Sakaki Y (2002) Construction and analysis of a human-chimpanzee comparative clone map. Science 295:131–134

    Article  PubMed  Google Scholar 

  • Gagneux P, Wills C, Gerloff U, Tautz D, Morin PA, Boesch C, Fruth B, Hohmann G, Ryder OA, Woodruff DS (1999) Mitochondrial sequences show diverse evolutionary histories of African hominoids. Proc Natl Acad Sci U S A 96:5077–5082

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Garner KJ, Ryder O (1996) Mitochondrial DNA diversity in gorillas. Mol Phylogenet Evol 6:39–48

    Article  CAS  PubMed  Google Scholar 

  • Gerstein MB et al (2012) Architecture of the human regulatory network derived from ENCODE data. Nature 489:91–100

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gonder MK, Oates JF, Disotell TR, Forstner MR (1997) A new west African chimpanzee subspecies? Nature 388:337

    Article  CAS  PubMed  Google Scholar 

  • Gonder MK, Distill TR, Oates JF (2006) New genetic evidence on the evolution of chimpanzee populations and implications for taxonomy. Int J Primatol 27:1103–1127

    Article  Google Scholar 

  • Goodman M (1962) Evolution of the immunologic species specificity of human serum proteins. Hum Biol 34:104–150

    CAS  PubMed  Google Scholar 

  • Graur D (2018) Chapter 2. Rubbish DNA: the functionless fraction of the human genome. In: Saitou N (ed) Evolution of the human genome I. Springer, Tokyo, pp 19–60

    Google Scholar 

  • Graur D, Zheng Y, Price N, Azevedo RBR, Zufall RA, Elhaik E (2013) On the immortality of television sets: function in the human genome according to the evolution-free gospel of ENCODE. Genome Biol Evol 5:578–590

    Article  PubMed  PubMed Central  Google Scholar 

  • Gregory TR (ed) (2005) The evolution of the genome. Elsevier Academic, Burlington

    Google Scholar 

  • Gribbin J, Charfas J (1982) The monkey puzzle. Pantheon Books, New York

    Google Scholar 

  • Groves CP (1997) Taxonomy and phylogeny of primates. In: Blancher A, Klein J, Socha W (eds) Molecular biology and evolution of blood group and MHC antigens in primates. Springer, Berlin, pp 3–23

    Google Scholar 

  • Hara Y, Satta Y, Imanishi T (2012) Reconstructing the demographic history of the human lineage using whole-genome sequences from human and three great apes. Genome Biol Evol 4:1133–1145

    Article  PubMed  PubMed Central  Google Scholar 

  • Hinshaw G et al (2009) Maps, & basic results. Astrophys J Suppl Ser 180:225

    Article  Google Scholar 

  • Horai S, Hayasaka K, Kondo R, Tsugane K, Takahata N (1995) Recent African origin of modern humans revealed by complete sequences of hominoid mitochondrial DNAs. Proc Natl Acad Sci U S A 92:532–536

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Imanishi T (2018) Chapter 4. Protein-coding and non-coding RNA genes. In: Saitou N (ed) Evolution of the human genome I. Springer, Tokyo, pp 93–115

    Google Scholar 

  • Imanishi T et al (2004) Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol 2:856–875

    Article  CAS  Google Scholar 

  • International Chimpanzee Chromosome 22 Consortium (2004) DNA sequence and comparative analysis of chimpanzee chromosome 22. Nature 429:382–388

    Article  Google Scholar 

  • International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921

    Article  Google Scholar 

  • International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature 431:931–945

    Article  Google Scholar 

  • Kitano T (2018) Chapter 5. Duplicated genes. In: Saitou N (ed) Evolution of the human genome I. Springer, Tokyo, pp 117–130

    Google Scholar 

  • Kitano T, Liu Y-H, Ueda S, Saitou N (2004) Human specific amino acid changes found in 103 protein coding genes. Mol Biol Evol 21:936–944

    Article  CAS  PubMed  Google Scholar 

  • Locke DP et al (2011) Comparative and demographic analysis of orang-utan genomes. Nature 469:529–533

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Matsunami M, Saitou N (2013) Vertebrate paralogous conserved noncoding sequences may be related to gene expressions in brain. Genome Biol Evol 5:140–150

    Article  PubMed  Google Scholar 

  • Montanucci L, Bertranpetit J (2018) Chapter 6. Recombination. In: Saitou N (ed) Evolution of the human genome I. Springer, Tokyo, pp 131–142

    Google Scholar 

  • Morin PA, Moor JJ, Woodruff DS (1992) Identification of chimpanzee subspecies with DNA from hair and allele-specific probes. Proc R Soc Lond B 249:293–297

    Article  CAS  Google Scholar 

  • Myers RH, Shafer DA (1979) Hybrid ape offspring of a mating of gibbon and siamang. Science 205:308–310

    Article  CAS  PubMed  Google Scholar 

  • Napier JR, Napier PH (1985) The natural history of the primates. MIT Press, Cambridge, MA

    Google Scholar 

  • Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York

    Google Scholar 

  • Neph S et al (2012) An expansive human regulatory lexicon encoded in transcription factor footprints. Nature 489:83–90

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ngai MY, Saitou N (2016) The effect of perfection statuses on mutation rates of microsatellites in primates. Anthropoid Sci. (in press) 124:85–92

    Article  Google Scholar 

  • Nowark RM (1991) Walker’s mammals of the world, vol I, 5th edn. The Johns Hopkins University Press, Baltimore

    Google Scholar 

  • Nozawa M, Kawahara Y, Nei M (2007) Genomic drift and copy number variation of sensory receptor genes in humans. Proc Natl Acad Sci U S A 104:20421–20426

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • O’huigin C, Satta Y, Takahata N, Klein J (2002) Contribution of homoplasy and of ancestral polymorphism to the evolution of genes in anthropoid primates. Mol Biol Evol 19:1501–1513

    Article  PubMed  Google Scholar 

  • Oates JF, Groves CP, Jenkins PD (2009) The type locality of Pan troglodytes vellerosus (Gray, 1862), and implications for the nomenclature of West African chimpanzees. Primates 50:78–80

    Article  PubMed  Google Scholar 

  • Ohno S (1972) So much “junk” DNA in our genome. Brookhaven Symp Biol 23:366–370

    CAS  PubMed  Google Scholar 

  • Oota S (2018) Chapter 3. GC content heterogeneity. In: Saitou N (ed) Evolution of the human genome I. Springer, Tokyo, pp 61–92

    Google Scholar 

  • Oota S, Kawamura K, Kawai Y, Saitou N (2010) A new framework for studying the isochore evolution: estimation of the equilibrium GC content based on the temporal mutation rate model

    Google Scholar 

  • Prado-Martinez et al (2013) Great ape genetic diversity and population history. Nature 499:471–475

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Prüfer K et al (2012) The bonobo genome compared with the chimpanzee and human genomes. Nature 486:527–531

    Article  PubMed  PubMed Central  Google Scholar 

  • Putnam NH et al (2008) The amphioxus genome and the evolution of the chordate karyotype. Nature 453:1064–1071

    Article  CAS  PubMed  Google Scholar 

  • Rhesus Macaque Genome Sequencing and Analysis Consortium (2006) Evolutionary and biomedical insights from the rhesus macaque genome. Science 316:222–234

    Article  Google Scholar 

  • Ruiz-Trills I, Roger AI, Burger G, Gray MW, Lang BF (2008) A phylogenomic investigation into the origin of Metazoa. Mol Biol Evol 25:664–672

    Article  Google Scholar 

  • Saber MM, Babarinde IA, Hettiarachchi N, Saitou N (2016) Emergence and evolution of Hominidae-specific coding and noncoding genomic sequences. Genome Biol Evol. (advance access) 8:2076–2092

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Saitou N (1991) Reconstruction of molecular phylogeny of extant hominoids from DNA sequence data. Am J Phys Anthropol 84:75–85

    Article  CAS  PubMed  Google Scholar 

  • Saitou N (2005) Evolution of hominoids and the search for a genetic basis for creating humanness. Cytogenet Genome Res 108:16–21

    Article  CAS  PubMed  Google Scholar 

  • Saitou N (2013) Introduction to evolutionary genomics. Springer, Berlin

    Google Scholar 

  • Satta Y, Klein J, Takahata N (2000) DNA archives and our nearest relative: the trichotomy problem revisited. Mol Phylogenet Evol 14:259–275

    Article  CAS  PubMed  Google Scholar 

  • Scally A et al (2012) Insights into hominid evolution from the gorilla genome sequence. Nature 483:169–175

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shulte P et al (2010) The Chicxulub asteroid impact and mass extinction at the cretaceous-paleogene boundary. Science 327:1214–1218

    Article  Google Scholar 

  • Sibley CG, Ahlquist JE (1984) The phylogeny of the hominoid primates, as indicated by DNA-DNA hybridization. J Mol Evol 20:2–15

    Article  CAS  PubMed  Google Scholar 

  • Sibley CG, Ahlquist JE (1987) DNA hybridization evidence of hominoid phylogeny: results from an expanded data set. J Mol Evol 26:99–121

    Article  CAS  PubMed  Google Scholar 

  • Sleep NH, Zahnle KJ, Kasting JF, Morowitz HJ (1989) Annihilation of ecosystems by large asteroid impacts on the early earth. Nature 342:139–142

    Article  CAS  PubMed  Google Scholar 

  • Steiper ME, Young NM (2009) Chapter 74: Primates (primates). In: Hedges SB, Kumar S (eds) The timetree of life. Oxford University Press, Oxford, pp 482–486

    Google Scholar 

  • Takahashi M, Saitou N (2012) Identification and characterization of lineage-specific highly conserved noncoding sequences in mammalian genomes. Genome Biol Evol 4:641–657

    Article  PubMed  PubMed Central  Google Scholar 

  • Takahata N, Satta Y (1997) Evolution of the primate lineage leading to modern humans: phylogenetic and demographic inferences from DNA sequences. Proc Natl Acad Sci U S A 94:4811–4815

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Takezaki N (2018) Chapter 7. CNVs and microsatellite DNA polymorphism. In: Saitou N (ed) Evolution of the human genome I. Springer, Tokyo, pp 143–155

    Google Scholar 

  • The Chimpanzee Sequencing and Analysis Consortium (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437:69–87

    Article  Google Scholar 

  • The ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489:57–74

    Article  PubMed Central  Google Scholar 

  • Thurman RE et al (2012) The accessible chromatin landscape of the human genome. Nature 489:75–82

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tilton GG (1988) Age of the solar system. In: Meteorites and the early solar system. University of Arizona Press, Tucson, pp 259–275

    Google Scholar 

  • van Bakel H, Nislow C, Blencowe BJ, Hughes TR (2010) Most “dark matter” transcripts are associated with known genes. PLoS Biol 8:e1000371

    Article  PubMed  PubMed Central  Google Scholar 

  • Venter JC et al (2001) The sequence of the human genome. Science 291:1304–1351

    Article  CAS  PubMed  Google Scholar 

  • Vervaecke H, van Elsacker L (1992) Hybrids between common chimpanzees (Pan troglodytes) and pygmy chimpanzees (Pan paniscus) in captivity. Mammalia 56:667–669

    Google Scholar 

  • Wildman DE, Uddin M, Liu G, Li G, Goodman M (2003) Implications of natural selection in shaping 99.4% nonsynonymous DNA identity between humans and chimpanzees: enlarging genus Homo. Proc Natl Acad Sci U S A 100:7181–7188

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xu X, Arnason U (1996) The mitochondrial DNA molecule of Sumatran orangutan and a molecular proposal for two (Bornean and Sumatran) species of orangutan. J Mol Evol 43:431–437

    Article  CAS  PubMed  Google Scholar 

  • Yunis JJ, Prakash O (1982) The origin of man: a chromosomal pictorial legacy. Science 215:1525–1530

    Article  CAS  PubMed  Google Scholar 

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Authors and Affiliations

  1. Division of Population Genetics, National Institute of Genetics, Mishima, Japan

    Naruya Saitou

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  1. Naruya Saitou
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Correspondence to Naruya Saitou .

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  1. Division of Population Genetics, National Institute of Genetics, Mishima, Japan

    Naruya Saitou

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Saitou, N. (2017). Human Evolution and Human Genome at a Glance. In: Saitou, N. (eds) Evolution of the Human Genome I. Evolutionary Studies. Springer, Tokyo. https://doi.org/10.1007/978-4-431-56603-8_1

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