Natural Genetic Engineering and Evolutionary Genomic Innovation

(Hedges and Batzer 2005; Giraud, Refregier et al. 2008; Scheifele and Boeke 2008; Dobrindt, Chowdary et al. 2010; Kaessmann 2010; Rothschild 2010; Portnoy, Bezdan et al. 2011)

Horizontal DNA transfer and formation of chimeric sequences originating in more than one cell lineage

(Daniels, Peterson et al. 1990; Kordis and Gubensek 1998; Bird and Koltai 2000; Bergthorsson, Adams et al. 2003; Bergthorsson, Richardson et al. 2004; Davis and Wurdack 2004; Odom, Shenkenberg et al. 2004; Rogers and Keeling 2004; Dagan and Martin 2006; Diao, Freeling et al. 2006; Fiebig, Hartmann et al. 2006; Richards, Dacks et al. 2006; Simoes-Barbosa, Arganaraz et al. 2006; Choi and Kim 2007; Marri, Hao et al. 2007; Nisa-Martinez, Jimenez-Zurdo et al. 2007; Bratke and McLysaght 2008; Davids and Zhang 2008; Fortune, Roulin et al. 2008; Pace, Gilbert et al. 2008; Price, Dehal et al. 2008; Sanchez-Puerta, Cho et al. 2008; Tamames and Moya 2008; Xie, Fu et al. 2008; Bock 2009; Boyer, Yutin et al. 2009; Emiliani, Fondi et al. 2009; Koonin 2009; Mitreva, Smant et al. 2009; Pontiroli, Rizzi et al. 2009; Hecht, Nitz et al. 2010; Liu and Zhu 2010; Schaack, Gilbert et al. 2010; Snir and Trifonov 2010; Thomas, Schaack et al. 2010; Corander, Connor et al. 2011; Creevey, Doerks et al. 2011; Haegeman, Jones et al. 2011; Kikuchi, Cotton et al. 2011; Maruyama, Suzaki et al. 2011; Mayer, Schuster et al. 2011; Richards, Soanes et al. 2011; Sanchez 2011; Scholl and Bird 2011; Yoshida, Claverie et al. 2011)

Viruses and proviruses

(Schon, Seifarth et al. 2001; Dunn, Medstrand et al. 2003; Mallet and Prudhomme 2004; Dunn, van de Lagemaat et al. 2005; Buzdin, Kovalskaya-Alexandrova et al. 2006; Dunn, Romanish et al. 2006; Kovalskaya, Buzdin et al. 2006; Nellaker, Yao et al. 2006; Sin, Huh et al. 2006; Moyes, Griffiths et al. 2007; Conley, Piriyapongsa et al. 2008; Huh, Kim et al. 2008; Lee, Malim et al. 2008; Tumapa, Holden et al. 2008; Balada, Ordi-Ros et al. 2009; Boyer, Yutin et al. 2009; Gogvadze, Stukacheva et al. 2009; Schon, Diem et al. 2009; Wang, Kim et al. 2009; Fujii 2010; Perron and Lang 2010; 2011; Coolen 2011; Nascimento, Gongora et al. 2011; Rasko, Webster et al. 2011)

Endogenous retroviruses

(Hefti and Panem 1981; Urnovitz and Murphy 1996; Schon, Seifarth et al. 2001; Pelisson, Mejlumian et al. 2002; Dunn, Medstrand et al. 2003; Dunn, van de Lagemaat et al. 2005; Yano, Panbehi et al. 2005; Dunn, Romanish et al. 2006; Kovalskaya, Buzdin et al. 2006; Nellaker, Yao et al. 2006; Moyes, Griffiths et al. 2007; Balada, Ordi-Ros et al. 2009; Gogvadze, Stukacheva et al. 2009; Schon, Diem et al. 2009; Perron and Lang 2010; Wang, Liska et al. 2010; Nascimento, Gongora et al. 2011)

“Point” mutations and the role of “cryptic” sequence variation

(Kugelberg, Kofoid et al. 2010; Hayden, Ferrada et al. 2011)

Chromosome restructuring, fragile sites, maintenance of syntenic regions and karyotype evolution

(Carson 1973; Carson 1983; Tonzetich, Lyttle et al. 1988; Martin and Lister 1989; Lyttle and Haymer 1992; Bennetzen and Freeling 1993; Lim and Simmons 1994; Qumsiyeh 1994; Moore 1995; Moore, Devos et al. 1995; Bennetzen 1998; Slijepcevic 1998; Favia and Louis 1999; Mathiopoulos, della Torre et al. 1999; Stanyon, Yang et al. 1999; Evgen'ev, Zelentsova et al. 2000; Heslop-Harrison 2000; Singh 2001; Bennetzen and Ramakrishna 2002; Ilic, SanMiguel et al. 2003; Moriarty and Webster 2003; Sankoff 2003; Bourque, Pevzner et al. 2004; Doebley 2004; Ishii and Furukawa 2004; Wienberg 2004; Ayala and Coluzzi 2005; Bourque, Zdobnov et al. 2005; Coghlan, Eichler et al. 2005; Olmo 2005; Yancopoulos, Attie et al. 2005; O'Keefe and Richards 2006; Povirk 2006; Bennetzen 2007; Ferguson-Smith and Trifonov 2007; Casola, Hucks et al. 2008; Friedberg, Darling et al. 2008; Giraud, Refregier et al. 2008; Mezey, Nuzhdin et al. 2008; Misceo, Capozzi et al. 2008; Pichiorri, Ishii et al. 2008; Presgraves 2008; Raskina, Barber et al. 2008; Stanyon, Rocchi et al. 2008; Villasante, de Pablos et al. 2008; Burrow, Williams et al. 2009; Kitano, Ross et al. 2009; Parisod, Salmon et al. 2009; Sun and Xu 2009; Alekseyev and Pevzner 2010; Branzei and Foiani 2010; Brown and O'Neill 2010; Carneiro, Blanco-Aguiar et al. 2010; Devos 2010; Lobo, Sangare et al. 2010; Xia, Sharakhova et al. 2010; Zhang, Gostissa et al. 2010; Alfoldi, Di Palma et al. 2011; Amores, Catchen et al. 2011; Argout, Salse et al. 2011; Borneman, Desany et al. 2011; Carvalho, Ramocki et al. 2011; Furuta, Kawai et al. 2011; Goodwin, M'Barek S et al. 2011; Gostissa, Alt et al. 2011; Graphodatsky, Trifonov et al. 2011; Janssen, van der Burg et al. 2011; Klein, Resch et al. 2011; Nambiar and Raghavan 2011; Neumann, Navratilova et al. 2011; Schmidt and Robin 2011; Sharakhova, Xia et al. 2011; Steiner, Davidow et al. 2011; Stephens, Greenman et al. 2011)

Sex chromosomes

(Bachtrog 2006; Jamilena, Mariotti et al. 2008; Kazama and Matsunaga 2008; Nam and Ellegren 2008; Zhou, Wang et al. 2008; Kejnovsky, Hobza et al. 2009; Lemaitre, Braga et al. 2009; Charlesworth and Mank 2010; Connallon and Clark 2010; Kvikstad and Makova 2010; Meisel, Hilldorfer et al. 2010; O'Meally, Patel et al. 2010; Tracy, Rio et al. 2010; Dyer, White et al. 2011; Gallach, Domingues et al. 2011; Pokorna, Kratochvil et al. 2011)

Genome architecture

(Hurst, Pal et al. 2004; Shaw and Lupski 2004; Galagan, Henn et al. 2005; Sakharkar, Chaturvedi et al. 2005; Batada and Hurst 2007; Lynch 2007; Michalak 2008; Koonin 2009; Al-Shahrour, Minguez et al. 2010; Edlund, Chaumont et al. 2011; Ellison, Stajich et al. 2011; Warnecke and Hurst 2011; Woo and Li 2011)

Mobile Genetic Elements

(van de Lagemaat, Landry et al. 2003; Bartholomeeusen, Christ et al. 2009; Vaknin, Goren et al. 2009; Venner, Feschotte et al. 2009; Britten 2010; Warnefors, Pereira et al. 2010; Hollister, Smith et al. 2011; Janicki, Rooke et al. 2011; Jurka, Bao et al. 2011; Kazazian 2011; Lerat, Burlet et al. 2011; Lynch, Leclerc et al. 2011; Oliver and Greene 2011; Stewart, Kural et al. 2011)

DNA transposons: (Daniels, Peterson et al. 1990; Schnetz and Rak 1992; Wong and Choo 2004; de Boer, Yazawa et al. 2007; Pritham and Feschotte 2007; Gonzalez, Lenkov et al. 2008; Li, Mulligan et al. 2010; Lisson, Hellert et al. 2010; Marin 2010; Martin and Bendahmane 2010; Schaack, Choi et al. 2010; Sela, Kim et al. 2010; Thomas, Schaack et al. 2010; Magwire, Bayer et al. 2011; Takahashi, Ohashi et al. 2011; Thomas, Sorourian et al. 2011)

Retrotransposons and retroviruses: (Panem and Kirsten 1973; Panem, Prochownik et al. 1975; Panem, Ordonez et al. 1976; Panem, Ordonez et al. 1978; Panem and Reynolds 1979; Bergholz, Reynolds et al. 1980; Errede, Cardillo et al. 1980; Reynolds and Panem 1981; Panem 1983; Errede, Company et al. 1985; Hickey and Benkel 1986; Company and Errede 1987; Company and Errede 1988; Mellentin-Michelotti, John et al. 1994; Benit, Lallemand et al. 1999; Nigumann, Redik et al. 2002; Wong and Choo 2004; Grahn, Rinehart et al. 2005; Lenoir, Pelissier et al. 2005; Marques, Dupanloup et al. 2005; Uren, Kool et al. 2005; Watanabe, Kobayashi et al. 2005; Yohn, Jiang et al. 2005; Jern, Sperber et al. 2006; Ustyugova, Lebedev et al. 2006; Villasante, Abad et al. 2007; Gonzalez, Lenkov et al. 2008; Villasante, de Pablos et al. 2008; Zhang, Zhou et al. 2008; Cordaux and Batzer 2009; Kanazawa, Liu et al. 2009; Uchiyama, Fujino et al. 2009; Xiong, Wang et al. 2009; Zhou and Eickbush 2009; Ewing and Kazazian 2010; Konkel and Batzer 2010; Kvikstad and Makova 2010; Martin and Bendahmane 2010; Pi, Zhu et al. 2010; Sela, Kim et al. 2010; Eickbush and Eickbush 2011; Granzotto, Lopes et al. 2011; Grechko, Kosushkin et al. 2011; Hedges and Belancio 2011; Kumari, Sharma et al. 2011; Neumann, Navratilova et al. 2011; Polavarapu, Arora et al. 2011; Siol, Spaller et al. 2011; Taniguchi-Ikeda, Kobayashi et al. 2011; Tubio, Tojo et al. 2011; Walters-Conte, Johnson et al. 2011)

Exons and genetic loci encoding novel proteins (“neogene” formation)

(Nahon 2003; Ohshima, Hattori et al. 2003; Krull, Brosius et al. 2005; Marques, Dupanloup et al. 2005; Levine, Jones et al. 2006; Amit, Sela et al. 2007; Begun, Lindfors et al. 2007; Hasler, Samuelsson et al. 2007; Lev-Maor, Sorek et al. 2007; Piriyapongsa, Polavarapu et al. 2007; Corvelo and Eyras 2008; Lev-Maor, Ram et al. 2008; Lin, Shen et al. 2008; Moller-Krull, Zemann et al. 2008; Shepard and Hertel 2008; Zhou and Wang 2008; Heinen, Staubach et al. 2009; Knowles and McLysaght 2009; Lin, Jiang et al. 2009; Naamati, Fromer et al. 2009; Schwartz, Gal-Mark et al. 2009; Toll-Riera, Castelo et al. 2009; Volff 2009; Xiao, Liu et al. 2009; Fitzpatrick, Johnson et al. 2010; Kaessmann 2010; Li, Dong et al. 2010; Borneman, Desany et al. 2011; Guerzoni and McLysaght 2011; Tautz and Domazet-Loso 2011; Wilson and Masel 2011; Wu, Irwin et al. 2011; Yang and Huang 2011; Zhang, Landback et al. 2011)

Introns and splicing patterns

(Hickey and Benkel 1986; Cavalier-Smith 1991; Doolittle 1991; Purugganan and Wessler 1992; Dai and Zimmerly 2002; Dai and Zimmerly 2003; Munoz-Adelantado, San Filippo et al. 2003; Rogozin, Wolf et al. 2003; Koonin 2006; Lin, Zhu et al. 2006; Rodriguez-Trelles, Tarrio et al. 2006; Rodriguez-Trelles, Tarrio et al. 2006; Carmel, Rogozin et al. 2007; Carmel, Rogozin et al. 2007; Irimia, Penny et al. 2007; Nisa-Martinez, Jimenez-Zurdo et al. 2007; Irimia and Roy 2008; Irimia, Rukov et al. 2008; Lev-Maor, Ram et al. 2008; McGuire, Pearson et al. 2008; Raghavan, Hicks et al. 2008; Sanchez-Puerta, Cho et al. 2008’Steinbauerova, 2008 #4837; Tarrio, Ayala et al. 2008; Catania, Gao et al. 2009; Fablet, Bueno et al. 2009; Gao and Lynch 2009; Garcia-Espana, Mares et al. 2009; Li, Tucker et al. 2009; McNeal, Kuehl et al. 2009; Nielsen and Johansen 2009; Pastor, Talotti et al. 2009; Roy 2009; Roy and Irimia 2009; Tsirigos and Rigoutsos 2009; Lisson, Hellert et al. 2010; Mohr, Ghanem et al. 2010; Chillon, Martinez-Abarca et al. 2011; Farlow, Meduri et al. 2011; Koralewski and Krutovsky 2011; Leclercq, Giraud et al. 2011; Mudge, Frankish et al. 2011; Szczesniak, Ciomborowska et al. 2011)

Insertion of cDNA from processed RNA into the genome

(Esnault, Maestre et al. 2000; Ohshima, Hattori et al. 2003; Dewannieux and Heidmann 2005; Ding, Lin et al. 2006; Pavlicek, Gentles et al. 2006; Neumann, Yan et al. 2007; Sakai, Koyanagi et al. 2007; Blower, Pei et al. 2011; Steele, Williamson et al. 2011)