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; Grbic, Van Leeuwen 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; Mueller, Coleman 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 (including cancer cells)

(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; Gilbert, Takebayashi et al. 2010; Lobo, Sangare et al. 2010; Mani and Chinnaiyan 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; De and Michor 2011; Fudenberg, Getz 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; Hastings and Rosenberg 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; Teixeira and Heim 2011; Crasta, Ganem et al. 2012; Greaves and Maley 2012; Le Scouarnec and Gribble 2012)

            Homoeologous recombination: (Nicolas, Le Mignon et al. 2007; Nicolas, Leflon et al. 2008; Panjabi, Jagannath et al. 2008; Nicolas, Leflon et al. 2009; Gaeta and Chris Pires 2010; Mason, Nelson et al. 2011; Nicolas, Monod et al. 2012)

Sex chromosomes

(Jablonka 2004; 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; Osbourn and Field 2009; Al-Shahrour, Minguez et al. 2010; Mizutani and Ohta 2010; Chavali, Morais et al. 2011; Chu, Wegel et al. 2011; Edlund, Chaumont et al. 2011; Ellison, Stajich et al. 2011; Field, Fiston-Lavier et al. 2011; Warnecke and Hurst 2011; Woo and Li 2011; Baker 2012)

            Speciation by chromosome and karyotype changes: (White 1945 (4th ed 1973); White 1949; Stebbins 1966; Stebbins 1971; White 1978; King 1995; Levin 2002)

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; Gompel, Prud'homme et al. 2005; 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; Gombart, Saito et al. 2009; Heinen, Staubach et al. 2009; Knowles and McLysaght 2009; Lin, Jiang et al. 2009; Mueller, Coleman 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 (“retrogenes”)

(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)

Exon shuffling and protein families

(Hall, Liu et al. 1989; Hiller, Hetzer et al. 2000; Liu and Grigoriev 2004; Morgante, Brunner et al. 2005; Babushok, Ohshima et al. 2007; Jones-Rhoades, Borevitz et al. 2007; Cancherini, Franca et al. 2010; Elrouby and Bureau 2010; Snider, Geng et al. 2010; Crona, Moffatt et al. 2011; Diekmann, Seixas et al. 2011; Grbic, Van Leeuwen et al. 2011; Hoffmann, Opazo et al. 2011; Storz, Opazo et al. 2011; Zmasek and Godzik 2011)

Novel and mobile cis-regulatory sites and CRMs

(Errede, Cardillo et al. 1980; Errede, Company et al. 1985; Company and Errede 1987; Company and Errede 1988; Mastrangelo, Weinstock et al. 1992; Schnetz and Rak 1992; Schon, Seifarth et al. 2001; Nigumann, Redik et al. 2002; Dunn, Medstrand et al. 2003; Dunn, van de Lagemaat et al. 2005; Gompel, Prud'homme et al. 2005; Uren, Kool et al. 2005; Buzdin, Kovalskaya-Alexandrova et al. 2006; Dunn, Romanish et al. 2006; Pomerantseva, Biryukova et al. 2006; Sin, Huh et al. 2006; Ustyugova, Lebedev et al. 2006; Chen and Rajewsky 2007; Chung, Bogwitz et al. 2007; McGregor, Orgogozo et al. 2007; Conley, Piriyapongsa et al. 2008; Huh, Kim et al. 2008; Tomilin 2008; Urrutia, Ocana et al. 2008; Gogvadze, Stukacheva et al. 2009; Ho, Johnsen et al. 2009; Kamachi, Iwafuchi et al. 2009; Kim, He et al. 2009; Pastor, Talotti et al. 2009; Schon, Diem et al. 2009; Uchiyama, Fujino et al. 2009; Kalay and Wittkopp 2010; Borneman, Desany et al. 2011; Cui, Sirotin et al. 2011; Eichenlaub and Ettwiller 2011; Fraser, Babak et al. 2011; Huda, Bowen et al. 2011; Huda, Tyagi et al. 2011; Lynch, Leclerc et al. 2011; Nourmohammad and Lassig 2011; Pandey, Mandal et al. 2011; Teng, Firpi et al. 2011)

(Lindblad-Toh, Garber et al. 2011) (“We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements.”)

“Focusing on regulatory motifs overrepresented at specific locations within or near the promoter, we find that a surprisingly large number of cis-regulatory elements have been subject to coordinated genome-wide modifications during vertebrate evolution, such that the motif frequency changes on a single branch of vertebrate phylogeny. This was found to be the case even between closely related mammal species, with nearly a third of all location-specific consensus motifs exhibiting significant modifications within the human or mouse lineage since their divergence.” (Yokoyama, Thorne et al. 2011)

“Non-coding” regulatory RNA (including mi-, si- and piRNA)

(Ambros 2001; Xie, Johansen et al. 2004; Axtell and Bartel 2005; Chen and Rajewsky 2007; Voss, Gierga et al. 2007; Dinger, Amaral et al. 2008; Ghildiyal, Seitz et al. 2008; Heimberg, Sempere et al. 2008; Mercer, Dinger et al. 2008; Morin, Aksay et al. 2008; Royo and Cavaille 2008; Tam, Aravin et al. 2008; Technau 2008; Wan and Bartolomei 2008; Xie and Qi 2008; Brosnan and Voinnet 2009; Bumgarner, Dowell et al. 2009; Goodrich and Kugel 2009; Harrison, Yazgan et al. 2009; Hirota and Ohta 2009; Hoeppner, White et al. 2009; Khalil, Guttman et al. 2009; Kurokawa, Rosenfeld et al. 2009; Lee 2009; Mattick 2009; Mercer, Dinger et al. 2009; Merchan, Boualem et al. 2009; Morris 2009; Ponjavic, Oliver et al. 2009; Ponting, Oliver et al. 2009; Qureshi and Mehler 2009; Saito, Suzuki et al. 2009; Thomson and Lin 2009; Uchiyama, Fujino et al. 2009; Davis-Dusenbery and Hata 2010; Fujii 2010; Heimberg, Cowper-Sal-lari et al. 2010; Malecova and Morris 2010; Muro and Andrade-Navarro 2010; Valen, Preker et al. 2011; Wen, Zheng et al. 2011; Yang and Lai 2011)

Epigenetic formatting

(Heslop-Harrison 2000; Edwards, Mungall et al. 2008; Royo and Cavaille 2008; Wan and Bartolomei 2008; Wierzbicki, Haag et al. 2008; Huda and Jordan 2009; Huda, Marino-Ramirez et al. 2009; Kurokawa, Rosenfeld et al. 2009; Lee 2009; Morris 2009; Parisod, Salmon et al. 2009; Saito, Suzuki et al. 2009; Wierzbicki, Ream et al. 2009; Zeh, Zeh et al. 2009; Grewal 2010; Habu 2010; Huda, Marino-Ramirez et al. 2010; Malecova and Morris 2010; Rebollo, Horard et al. 2010; Takacs, Banati et al. 2010; Foerster, Dinh et al. 2011; Huda, Bowen et al. 2011; Lisch and Bennetzen 2011; Rebollo, Karimi et al. 2011)

Duplication and amplification of sequence elements and genome segments

(Von Hoff 1991; DeBerardinis, Goodier et al. 1998; Izsvak, Ivics et al. 1999; Brown, Strbuncelj et al. 2002; Lo, Sabatier et al. 2002; Hastings, Slack et al. 2004; Hersh, Ponder et al. 2004; Roth and Andersson 2004; Wong and Choo 2004; Hawkins, Kim et al. 2006; Hoen, Park et al. 2006; Naito, Cho et al. 2006; Neumann, Koblizkova et al. 2006; Slack, Thornton et al. 2006; Alt 2007; Buzdin, Gogvadze et al. 2007; Conrad and Antonarakis 2007; Hastings 2007; Maisonhaute, Ogereau et al. 2007; Pritham and Feschotte 2007; Vitte, Panaud et al. 2007; Wapinski, Pfeffer et al. 2007; Jameson, Georgelis et al. 2008; Nakayama, Yamashita et al. 2008; Powell, Conant et al. 2008; Raman and Stopfer 2008; Andersson and Hughes 2009; Han, Demuth et al. 2009; Hastings, Ira et al. 2009; Macas, Koblizkova et al. 2009; Marcet-Houben, Marceddu et al. 2009; Naamati, Fromer et al. 2009; Naito, Zhang et al. 2009; Pace, Sen et al. 2009; Poteete 2009; Rocchi, Stanyon et al. 2009; Sandegren and Andersson 2009; Sandegren and Andersson 2009; Sun, Berg et al. 2009; Sun, Berg et al. 2009; Tanaka and Yao 2009; Templeton 2009; Ames, Rash et al. 2010; Bhattacharya and Ghosh 2010; Brown, Murray et al. 2010; Domenech, Kolly et al. 2010; Gibson, Lombardo et al. 2010; Hase, Niimura et al. 2010; Heyse, Jonsson et al. 2010; Kugelberg, Kofoid et al. 2010; Libuda and Winston 2010; McGlynn 2010; Nah and Jeffrey Chen 2010; Panchin, Gelfand et al. 2010; Paulander, Andersson et al. 2010; Ragupathy, Banks et al. 2010; Reams, Kofoid et al. 2010; Rosloski, Jali et al. 2010; Schwab and Voinnet 2010; VanderSluis, Bellay et al. 2010; Wapinski, Pfiffner et al. 2010; Yao 2010; Andersson 2011; Brewer, Payen et al. 2011; Galeote, Bigey et al. 2011; Hoffmann, Opazo et al. 2011; Hudson, Puckett et al. 2011; Levasseur and Pontarotti 2011; Magwire, Bayer et al. 2011; Minning, Weatherly et al. 2011; Pramanik, Cui et al. 2011; Smith, Bomblies et al. 2011; Storz, Opazo et al. 2011)

Retroviral involvement in placenta evolution:

(Sawyer, Nachlas et al. 1978; Panem 1979; Nelson, Levy et al. 1981; Jerabek, Mellors et al. 1984; Johnson, Lyden et al. 1990; Harris 1991; Boyd, Bax et al. 1993; Chang-Yeh, Mold et al. 1993; Lyden, Johnson et al. 1994; Blackburn 1995; Venables, Brookes et al. 1995; Villarreal 1997; Harris 1998; Langat, Johnson et al. 1998; Sichangi, Langat et al. 2002; Bonnaud, Bouton et al. 2004; Mallet, Bouton et al. 2004; Prudhomme, Oriol et al. 2004; Rote, Chakrabarti et al. 2004; Aagaard, Villesen et al. 2005; Dupressoir, Marceau et al. 2005; Arimi, Nyachieo et al. 2006; Dunlap, Palmarini et al. 2006; Fowden, Sibley et al. 2006; Huppertz, Bartz et al. 2006; Kriegs, Churakov et al. 2006; Hemberger 2007; Malassine, Blaise et al. 2007; Mess and Carter 2007; Esnault, Priet et al. 2008; Kjeldbjerg, Villesen et al. 2008; Opazo, Hoffmann et al. 2008; Rawn and Cross 2008; Renfree, Ager et al. 2008; Sekita, Wagatsuma et al. 2008; Asher, Bennett et al. 2009; Dupressoir, Vernochet et al. 2009; Gimenez, Montgiraud et al. 2009; Heidmann, Vernochet et al. 2009; Noorali, Rotar et al. 2009; Stoye 2009; Varela, Spencer et al. 2009; Bazer, Wu et al. 2010; Black, Arnaud et al. 2010; Kaneko-Ishino and Ishino 2010; Lynch, Leclerc et al. 2011)

Lineage-specific changes

(von Sternberg, Novick et al. 1992; Wilson 1993; Cardazzo, Bargelloni et al. 2003; Pasyukova, Nuzhdin et al. 2004; Cantrell, Ederer et al. 2005; Grahn, Rinehart et al. 2005; Lenoir, Pelissier et al. 2005; Sternberg RV 2005; Yohn, Jiang et al. 2005; Hawkins, Kim et al. 2006; Jern, Sperber et al. 2006; Tarlinton, Meers et al. 2006; Chung, Bogwitz et al. 2007; Darboux, Charles et al. 2007; Kriegs, Matzke et al. 2007; Pace and Feschotte 2007; Pritham and Feschotte 2007; Cantrell, Scott et al. 2008; Charles, Belcram et al. 2008; Novick, Basta et al. 2009; Piskurek, Nishihara et al. 2009; Gonzalez, Karasov et al. 2010; Kvikstad and Makova 2010; Nowick and Stubbs 2010; Pagan, Smith et al. 2010; Schmidt, Good et al. 2010; Shen, Liang et al. 2010; Wang, Liska et al. 2010; Castoe, Hall et al. 2011; Cerveau, Leclercq et al. 2011; Erickson, Cantrell et al. 2011; Ferreri, Brown et al. 2011; Granzotto, Lopes et al. 2011; Grechko, Kosushkin et al. 2011; Gross and Williamson 2011; Kumari, Sharma et al. 2011; Lee, Kerk et al. 2011; Lerat, Burlet et al. 2011; Perelman, Johnson et al. 2011; Pertea, Pertea et al. 2011; Polavarapu, Arora et al. 2011; Salina, Sergeeva et al. 2011; Tollis and Boissinot 2011; Walters-Conte, Johnson et al. 2011)

Inteins

(Liu 2000; Pietrokovski 2001; Gogarten, Senejani et al. 2002; Perler 2002; Butler, Gray et al. 2006; Gogarten and Hilario 2006; Goodwin, Butler et al. 2006; Raghavan, Hicks et al. 2008; Dassa, London et al. 2009; Raghavan and Minnick 2009; Swithers, Senejani et al. 2009; Elleuche and Poggeler 2010; Barzel, Naor et al. 2011; Rajarajan, Ibrahim et al. 2011)

Changes in genome size

Plant DNA C-values database: http://data.kew.org/cvalues/

Animal Genome Size database: http://www.genomesize.com/

Fungal Genome Size database: http://www.zbi.ee/fungal-genomesize/

Prokaryote Genome Size database: http://www.genomesize.com/prokaryotes/

(Wernegreen, Ochman et al. 2000; Cole, Eiglmeier et al. 2001; Kidwell 2002; Ozkan, Tuna et al. 2003; Greilhuber, Dolezel et al. 2005; Vitte and Panaud 2005; Hawkins, Kim et al. 2006; Neumann, Koblizkova et al. 2006; Gregory, Nicol et al. 2007; Leitch, Beaulieu et al. 2007; Oliver, Petrov et al. 2007; Organ, Shedlock et al. 2007; Zuccolo, Sebastian et al. 2007; Gregory and Johnston 2008; Gregory, Andrews et al. 2009; Hou and Lin 2009; Hou and Lin 2009; Leitch, Kahandawala et al. 2009; Morse, Peterson et al. 2009; Organ and Shedlock 2009; Rho, Zhou et al. 2009; Smith and Gregory 2009; Merhej and Raoult 2010; Arensburger, Hice et al. 2011; Georgiades, Merhej et al. 2011; Kawakami, Dhakal et al. 2011)

Network and pathway evolution

(McClintock 1956; McClintock 1961; Mattick and Gagen 2001; van de Lagemaat, Landry et al. 2003; Amoutzias, Robertson et al. 2004; Kusari, Molina et al. 2004; Lemos, Meiklejohn et al. 2004; Maslov, Sneppen et al. 2004; Teichmann and Babu 2004; Bornberg-Bauer, Beaussart et al. 2005; Hughes and Friedman 2005; Kashtan and Alon 2005; Kaufmann, Melzer et al. 2005; Remenyi, Good et al. 2005; Wilkins 2005; Wuchty and Almaas 2005; Bergman, Quesneville et al. 2006; Gelfand 2006; Madan Babu, Teichmann et al. 2006; Mishra, Tuteja et al. 2006; Balaji and Aravind 2007; Beltrao and Serrano 2007; Evlampiev and Isambert 2007; Hinman, Nguyen et al. 2007; Madan Babu, Balaji et al. 2007; Nardmann and Werr 2007; Pinney, Amoutzias et al. 2007; Ramos, He et al. 2007; Stumpf, Kelly et al. 2007; Veron, Kaufmann et al. 2007; Wilkins 2007; Wilkins 2007; Xiao, Wang et al. 2007; Zhao, Ding et al. 2007; Castro, Dalmolin et al. 2008; Crombach and Hogeweg 2008; Dadon, Wagner et al. 2008; Dagan, Artzy-Randrup et al. 2008; Durek and Walther 2008; Evlampiev and Isambert 2008; Evlampiev and Isambert 2008; Feschotte 2008; Fujimoto, Ishihara et al. 2008; Gonzalez Perez, Gonzalez Gonzalez et al. 2008; Gross and Blasius 2008; Hintze and Adami 2008; Murali and Rivera 2008; Russell and Aloy 2008; Yu, Lin et al. 2008; Zhang, Zmasek et al. 2008; Cui, Purisima et al. 2009; Erten, Li et al. 2009; Erwin and Davidson 2009; Ettensohn 2009; Hinman, Yankura et al. 2009; Johnson, Samuel et al. 2009; Lavoie, Hogues et al. 2009; Li and Davidson 2009; Lin, Liu et al. 2009; Llorens, Munoz-Pomer et al. 2009; Matias Rodrigues and Wagner 2009; Peter and Davidson 2009; Ramos 2009; Ratmann, Wiuf et al. 2009; Robertson and Lovell 2009; Robertson and Lovell 2009; Salazar-Ciudad 2009; Sanderson 2009; Van der Sloot, Kiel et al. 2009; Wang, Bowen et al. 2009; Yamada and Bork 2009; Yuan, Liu et al. 2009; Zhang and Su 2009; Bagowski, Bruins et al. 2010; Bhardwaj, Kim et al. 2010; Cancherini, Franca et al. 2010; Capra, Pollard et al. 2010; Chang, Dilkes et al. 2010; Chipman 2010; Conant 2010; David, Stolovicki et al. 2010; Fusco, Grassi et al. 2010; Hase, Niimura et al. 2010; Hunziker, Tuboly et al. 2010; Kunarso, Chia et al. 2010; Kuo, Licon et al. 2010; Lavoie, Hogues et al. 2010; Lavoie, Hogues et al. 2010; Li and Johnson 2010; Mazurie, Bonchev et al. 2010; McCauley, Weideman et al. 2010; Na, Kim et al. 2010; Nowick and Stubbs 2010; Slot and Rokas 2010; van Dijk and van Ham 2010; Wang, Franzosa et al. 2010; Coate and Doyle 2011; Consortium. 2011; D'Antonio and Ciccarelli 2011; De Smet, Voss et al. 2011; Foss, Radulovic et al. 2011; Kloesges, Popa et al. 2011; Lynch, Leclerc et al. 2011; Mukhtar, Carvunis et al. 2011; Popa, Hazkani-Covo et al. 2011; Portnoy, Bezdan et al. 2011; Shou, Bhardwaj et al. 2011; Shou, Bhardwaj et al. 2011; Siegal-Gaskins, Mejia-Guerra et al. 2011; Wang and Lercher 2011; Wang and Sommer 2011; Finnigan, Hanson-Smith et al. 2012)

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