Bensasson D, Zhang D-X, Hartl DL, Hewitt GM. Mitochondrial pseudogenes: evolution’s misplaced witnesses. Trends Ecol Evol. 2001; 16(6):314–21. https://doi.org/10.1016/S0169-5347(01)02151-6. Accessed 2018-11-05.
CAS
PubMed
Google Scholar
Richly E, Leister D. NUMTs in sequenced eukaryotic genomes. Mole Biol Evol. 2004; 21(6):1081–4.
CAS
Google Scholar
Mourier T, Hansen AJ, Willerslev E, Arctander P. The Human Genome Project Reveals a Continuous Transfer of Large Mitochondrial Fragments to the Nucleus. Mole Biol Evol. 2001; 18(9):1833–7. https://doi.org/10.1093/oxfordjournals.molbev.a003971. Accessed 2018-11-05.
CAS
Google Scholar
Ricchetti M, Tekaia F, Dujon B. Continued Colonization of the Human Genome by Mitochondrial DNA. PLOS Biol. 2004; 2(9):273. https://doi.org/10.1371/journal.pbio.0020273. Accessed 2018-02-01.
Google Scholar
Hazkani-Covo E, Covo S. Numt-Mediated Double-Strand Break Repair Mitigates Deletions during Primate Genome Evolution. PLOS Genet. 2008; 4(10):1000237. https://doi.org/10.1371/journal.pgen.1000237. Accessed 2018-02-12.
Google Scholar
Hazkani-Covo E, Zeller RM, Martin W. Molecular Poltergeists: Mitochondrial DNA Copies (numts) in Sequenced Nuclear Genomes. PLOS Genet. 2010; 6(2):1000834. https://doi.org/10.1371/journal.pgen.1000834. Accessed 2018-02-12.
Google Scholar
Calabrese FM, Simone D, Attimonelli M. Primates and mouse NumtS in the UCSC Genome Browser. BMC Bioinformatics. 2012; 13(4):15. https://doi.org/10.1186/1471-2105-13-S4-S15. Accessed 2018-11-01.
Google Scholar
Dayama G, Emery SB, Kidd JM, Mills RE. The genomic landscape of polymorphic human nuclear mitochondrial insertions. Nucleic Acids Res. 2014; 42(20):12640–9. https://doi.org/10.1093/nar/gku1038. Accessed 2017-11-20.
CAS
PubMed
PubMed Central
Google Scholar
Tsuji J, Frith MC, Tomii K, Horton P. Mammalian NUMT insertion is non-random. Nucleic Acids Res. 2012; 40(18):9073–88. https://doi.org/10.1093/nar/gks424. Accessed 2018-10-27.
CAS
PubMed
PubMed Central
Google Scholar
Perna NT, Kocher TD. Mitochondrial DNA: molecular fossils in the nucleus. Curr Biol. 1996; 6(2):128–9.
CAS
PubMed
Google Scholar
Pakendorf B, Stoneking M. Mitochondrial DNA and human evolution. Ann Rev Genomics Human Genet. 2005; 6:165–83. https://doi.org/10.1146/annurev.genom.6.080604.162249.
CAS
Google Scholar
Keller I, Bensasson D, Nichols RA. Transition-Transversion Bias Is Not Universal: A Counter Example from Grasshopper Pseudogenes. PLOS Genet. 2007; 3(2):22. https://doi.org/10.1371/journal.pgen.0030022. Accessed 2018-11-05.
Google Scholar
Schmitz J, Piskurek O, Zischler H. Forty Million Years of Independent Evolution: A Mitochondrial Gene and Its Corresponding Nuclear Pseudogene in Primates. J Mole Evol. 2005; 61(1):1–11. https://doi.org/10.1007/s00239-004-0293-3. Accessed 2018-11-05.
CAS
Google Scholar
Zischler H, Geisert H, von Haeseler A, Pääbo S. A nuclear ’fossil’ of the mitochondrial D-loop and the origin of modern humans. Nature. 1995; 378(6556):489–92. https://doi.org/10.1038/378489a0. Accessed 2018-03-04.
CAS
PubMed
Google Scholar
THOMAS R, ZISCHLER H, PÄÄBO S, STONEKING M. Novel Mitochondrial DNA Insertion Polymorphism and Its Usefulness for Human Population Studies. Human Biol. 1996; 68(6):847–54. Accessed 2018-03-04.
CAS
PubMed
Google Scholar
Lang M, Sazzini M, Calabrese FM, Simone D, Boattini A, Romeo G, Luiselli D, Attimonelli M, Gasparre G. Polymorphic NumtS trace human population relationships. Human Genet. 2012; 131(5):757–71. https://doi.org/10.1007/s00439-011-1125-3. Accessed 2018-03-04.
Google Scholar
Baldo L, de Queiroz A, Hedin M, Hayashi CY, Gatesy J. Nuclear–Mitochondrial Sequences as Witnesses of Past Interbreeding and Population Diversity in the Jumping Bristletail Mesomachilis. Mole Biol Evol. 2011; 28(1):195–210. https://doi.org/10.1093/molbev/msq193. Accessed 2018-11-05.
CAS
Google Scholar
Wang B, Zhou X, Shi F, Liu Z, Roos C, Garber PA, Li M, Pan H. Full-length Numt analysis provides evidence for hybridization between the Asian colobine genera Trachypithecus and Semnopithecus. Am J Primatol. 2015; 77(8):901–10. https://doi.org/10.1002/ajp.22419. Accessed 2018-11-05.
CAS
PubMed
Google Scholar
Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH-Y, Hansen NF, Durand EY, Malaspinas A-S, Jensen JD, Marques-Bonet T, Alkan C, Prüfer K, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Höber B, Höffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, et al. A Draft Sequence of the Neandertal Genome. Science. 2010; 328(5979):710–22. https://doi.org/10.1126/science.1188021. Accessed 2018-11-06.
CAS
PubMed
PubMed Central
Google Scholar
Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PLF, Maricic T, Good JM, Marques-Bonet T, Alkan C, Fu Q, Mallick S, Li H, Meyer M, Eichler EE, Stoneking M, Richards M, Talamo S, Shunkov MV, Derevianko AP, Hublin J. -J., Kelso J, Slatkin M, Pääbo S. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature. 2010; 468(7327):1053–60. https://doi.org/10.1038/nature09710. Accessed 2018-02-12.
CAS
PubMed
PubMed Central
Google Scholar
Meyer M, Kircher M, Gansauge M-T, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prüfer K, Filippo Cd, Sudmant PH, Alkan C, Fu Q, Do R, Rohland N, Tandon A, Siebauer M, Green RE, Bryc K, Briggs AW, Stenzel U, Dabney J, Shendure J, Kitzman J, Hammer MF, Shunkov MV, Derevianko AP, Patterson N, Andrés AM, Eichler EE, et al. A High-Coverage Genome Sequence from an Archaic Denisovan Individual. Science. 2012; 338(6104):222–6. https://doi.org/10.1126/science.1224344. Accessed 2018-08-30.
CAS
PubMed
PubMed Central
Google Scholar
Prüfer K, Racimo F, Patterson N, Jay F, Sankararaman S, Sawyer S, Heinze A, Renaud G, Sudmant PH, de Filippo C, Li H, Mallick S, Dannemann M, Fu Q, Kircher M, Kuhlwilm M, Lachmann M, Meyer M, Ongyerth M, Siebauer M, Theunert C, Tandon A, Moorjani P, Pickrell J, Mullikin JC, Vohr SH, Green RE, Hellmann I, Johnson PLF, Blanche H, et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature. 2014; 505(7481):43–9. https://doi.org/10.1038/nature12886. Accessed 2018-11-03.
PubMed
Google Scholar
Qin P, Stoneking M. Denisovan Ancestry in East Eurasian and Native American Populations. Mole Biol Evol. 2015; 32(10):2665–74. https://doi.org/10.1093/molbev/msv141. Accessed 2018-10-25.
CAS
Google Scholar
Fu Q, Posth C, Hajdinjak M, Petr M, Mallick S, Fernandes D, Furtwängler A, Haak W, Meyer M, Mittnik A, Nickel B, Peltzer A, Rohland N, Slon V, Talamo S, Lazaridis I, Lipson M, Mathieson I, Schiffels S, Skoglund P, Derevianko AP, Drozdov N, Slavinsky V, Tsybankov A, Cremonesi RG, Mallegni F, Gély B, Vacca E, Morales MRG, Straus LG, et al. The genetic history of Ice Age Europe. Nature. 2016; 534(7606):200–5. https://doi.org/10.1038/nature17993. Accessed 2018-12-24.
CAS
PubMed
PubMed Central
Google Scholar
Kuhlwilm M, Gronau I, Hubisz MJ, de Filippo C, Prado-Martinez J, Kircher M, Fu Q, Burbano HA, Lalueza-Fox C, de la Rasilla M, Rosas A, Rudan P, Brajkovic D, Kucan Z, Gušic I, Marques-Bonet T, Andrés AM, Viola B, Pääbo S, Meyer M, Siepel A, Castellano S. Ancient gene flow from early modern humans into Eastern Neanderthals. Nature. 2016; 530(7591):429–33. https://doi.org/10.1038/nature16544. Accessed 2018-12-24.
CAS
PubMed
PubMed Central
Google Scholar
Vernot B, Tucci S, Kelso J, Schraiber JG, Wolf AB, Gittelman RM, Dannemann M, Grote S, McCoy RC, Norton H, Scheinfeldt LB, Merriwether DA, Koki G, Friedlaender JS, Wakefield J, Pääbo S, Akey JM. Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals. Science. 2016; 352(6282):235–9. https://doi.org/10.1126/science.aad9416. Accessed 2017-12-06.
CAS
PubMed
PubMed Central
Google Scholar
Browning SR, Browning BL, Zhou Y, Tucci S, Akey JM. Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture. Cell. 2018; 173(1):53–619. https://doi.org/10.1016/j.cell.2018.02.031. Accessed 2018-12-24.
CAS
PubMed
PubMed Central
Google Scholar
Jacobs GS, Hudjashov G, Saag L, Kusuma P, Darusallam CC, Lawson DJ, Mondal M, Pagani L, Ricaut F-X, Stoneking M, Metspalu M, Sudoyo H, Lansing JS, Cox MP. Multiple deeply divergent Denisovan ancestries in Papuans. Cell. 2019; 177:1010–21. https://doi.org/10.1016/j.cell.2019.02.035.
CAS
PubMed
Google Scholar
Mallick S, Li H, Lipson M, Mathieson I, Gymrek M, Racimo F, Zhao M, Chennagiri N, Nordenfelt S, Tandon A, Skoglund P, Lazaridis I, Sankararaman S, Fu Q, Rohland N, Renaud G, Erlich Y, Willems T, Gallo C, Spence JP, Song YS, Poletti G, Balloux F, Driem G. v., Knijff P. d., Romero IG, Jha AR, Behar DM, Bravi CM, Capelli C, et al. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature. 2016; 538(7624):201–6. https://doi.org/10.1038/nature18964. Accessed 2018-07-10.
CAS
PubMed
PubMed Central
Google Scholar
The 1000 Genomes Project Consortium T. A global reference for human genetic variation. Nature. 2015; 526(7571):68–74. https://doi.org/10.1038/nature15393. Accessed 2018-07-11.
Meyer M, Arsuaga J-L, de Filippo C, Nagel S, Aximu-Petri A, Nickel B, Martínez I, Gracia A, de Castro JMB, Carbonell E, Viola B, Kelso J, Prüfer K, Pääbo S. Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins. Nature. 2016; 531(7595):504–7. https://doi.org/10.1038/nature17405. Accessed 2018-02-12.
CAS
PubMed
Google Scholar
Li H. Toward better understanding of artifacts in variant calling from high-coverage samples. Bioinformatics. 2014; 30(20):2843–51. https://doi.org/10.1093/bioinformatics/btu356. Accessed 2018-11-08.
CAS
PubMed
PubMed Central
Google Scholar
Lander ES, Waterman MS. Genomic mapping by fingerprinting random clones: A mathematical analysis. Genomics. 1988; 2(3):231–9. https://doi.org/10.1016/0888-7543(88)90007-9. Accessed 2018-11-05.
CAS
PubMed
Google Scholar
Ajay SS, Parker SCJ, Abaan HO, Fajardo KVF, Margulies EH. Accurate and comprehensive sequencing of personal genomes. Genome Res. 2011; 21(9):1498–505. https://doi.org/10.1101/gr.123638.111. Accessed 2018-11-05.
PubMed
PubMed Central
Google Scholar
Green RE, Malaspinas A-S, Krause J, Briggs AW, Johnson PLF, Uhler C, Meyer M, Good JM, Maricic T, Stenzel U, Prüfer K, Siebauer M, Burbano HA, Ronan M, Rothberg JM, Egholm M, Rudan P, Brajković D, Kućan Z, Gušić I, Wikström M, Laakkonen L, Kelso J, Slatkin M, Pääbo S. A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing. Cell. 2008; 134(3):416–26. https://doi.org/10.1016/j.cell.2008.06.021. Accessed 2018-11-04.
CAS
PubMed
PubMed Central
Google Scholar
Krause J, Fu Q, Good JM, Viola B, Shunkov MV, Derevianko AP, Pääbo S. The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature. 2010; 464(7290):894–7. https://doi.org/10.1038/nature08976. Accessed 2018-10-17.
CAS
PubMed
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics (Oxford, England). 2009; 25(16):2078–9. https://doi.org/10.1093/bioinformatics/btp352.
Google Scholar
Behar D, van Oven M, Rosset S, Metspalu M, Loogväli E-L, Silva N, Kivisild T, Torroni A, Villems R. A “Copernican” Reassessment of the Human Mitochondrial DNA Tree from its Root. Am J Human Genet. 2012; 90(4):675–84. https://doi.org/10.1016/j.ajhg.2012.03.002. Accessed 2018-08-01.
CAS
Google Scholar
Li H, Durbin R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics. 2009; 25(14):1754–60. https://doi.org/10.1093/bioinformatics/btp324. Accessed 2018-07-28.
CAS
PubMed
PubMed Central
Google Scholar
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010; 20(9):1297–303. https://doi.org/10.1101/gr.107524.110. Accessed 2018-07-28.
CAS
PubMed
PubMed Central
Google Scholar
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004; 32(5):1792–7. https://doi.org/10.1093/nar/gkh340. Accessed 2018-07-28.
CAS
PubMed
PubMed Central
Google Scholar
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014; 30(9):1312–3. https://doi.org/10.1093/bioinformatics/btu033. Accessed 2018-07-28.
CAS
PubMed
PubMed Central
Google Scholar
Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP. Integrative genomics viewer. 2011. https://doi.org/10.1038/nbt.1754. https://www.nature.com/articles/nbt.1754. Accessed 2018-08-28.
CAS
PubMed
PubMed Central
Google Scholar
Thorvaldsdóttir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinforma. 2013; 14(2):178–92. https://doi.org/10.1093/bib/bbs017. Accessed 2018-08-28.
Google Scholar