mesopelagic crenarchaeote reveals multiple horizontal gene
transfers. Environ Microbiol 6:19–34
Lorenz MG, Wackernagel W (1994) Bacterial gene transfer by natural
genetic transformation in the environment. Microbiol Rev
58:563–602
Makarova KS, Sorokin AV, Novichkov PS, Wolf YI, Koonin EV
(2007) Clusters of orthologous genes for 41 archaeal genomes and
implications for evolutionary genomics of archaea. Biol Direct 2:33
Martin W et al (2002) Evolutionary analysis of Arabidopsis,
cyanobacterial, and chloroplast genomes reveals plastid phylogeny
and thousands of cyanobacterial genes in the nucleus. Proc Natl
Acad Sci U S A 99:12246–12251
Maughan H, Redfield RJ (2009) Extensive variation in natural competence in Haemophilus Influenzae. Evolution 63:1852–1866
Millen RS et al (2001) Many parallel losses of infA from chloroplast
DNA during angiosperm evolution with multiple independent
transfers to the nucleus. Plant Cell 13:645–658
Mongodin EF et al (2005) The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic Bacteria and
Archaea. Proc Natl Acad Sci U S A 102:18147–18152
Murray NE (2000) Type I restriction systems: sophisticated molecular
machines (a legacy of Bertani and Weigle). Microbiol Mol Biol Rev
64:412–434
Nakamura Y, Itoh T, Matsuda H, Gojobori T (2004) Biased biological
functions of horizontally transferred genes in prokaryotic genomes.
Nat Genet 36:760–766
Nelson KE et al (1999) Evidence for lateral gene transfer between
Archaea and Bacteria from genome sequence of Thermotoga
maritima. Nature 399:323–329
Nesbo CL, L’Haridon S, Stetter KO, Doolittle WF (2001) Phylogenetic
analyses of two “archaeal” genes in Thermotoga maritima reveal
multiple transfers between archaea and bacteria. Mol Biol Evol
18:362–375
Nikoh N, Tanaka K, Shibata F, Kondo N, Hizume M, Shimada M,
Fukatsu T (2008) Wolbachia genome integrated in an insect chromosome: evolution and fate of laterally transferred endosymbiont
genes. Genome Res 18:272–280
Normand P et al (2007) Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography. Genome Res 17:7–15
Novick RP (1987) Plasmid incompatibility. Microbiol Rev 51:381–395
Ochman H, Lawrence JG, Groisman EA (2000) Lateral gene transfer
and the nature of bacterial innovation. Nature 405:299–304
Philippe H, Germot A, Moreira D (2000) The new phylogeny of
eukaryotes. Curr Opin Genet Dev 10:596–601
Podell S, Gaasterland T (2007) DarkHorse: a method for genome-wide
prediction of horizontal gene transfer. Genome Biol 8:R16
Ragan MA (2001) On surrogate methods for detecting lateral gene
transfer. FEMS Microbiol Lett 201:187–191
Ramirez-Arcos S, Fernandez-Herrero LA, Marin I, Berenguer J (1998)
Anaerobic growth, a property horizontally transferred by an
Hfr-like mechanism among extreme thermophiles. J Bacteriol
180:3137–3143
Ricard G et al (2006) Horizontal gene transfer from Bacteria to rumen
Ciliates indicates adaptation to their anaerobic, carbohydrates-rich
environment. BMC Genomics 7:22
Richards TA, Dacks JB, Jenkinson JM, Thornton CR, Talbot NJ (2006)
Evolution of filamentous plant pathogens: gene exchange across
eukaryotic kingdoms. Curr Biol 16:1857–1864
Rocha EP, Viari A, Danchin A (1998) Oligonucleotide bias in Bacillus
subtilis: general trends and taxonomic comparisons. Nucleic Acids
Res 26:2971–2980
Roger AJ (1999) Reconstructing Early events in eukaryotic evolution.
Am Nat 154:S146–S163
Ruepp A et al (2000) The genome sequence of the thermoacidophilic
scavenger Thermoplasma acidophilum. Nature 407:508–513
Simpson AG, Perley TA, Lara E (2008) Lateral transfer of the gene for
a widely used marker, alpha-tubulin, indicated by a multi-protein
study of the phylogenetic position of Andalucia (Excavata). Mol
Phylogenet Evol 47:366–377
Slot JC, Hibbett DS (2007) Horizontal transfer of a nitrate assimilation
gene cluster and ecological transitions in fungi: a phylogenetic
study. PLoS One 2:e1097
Smith HO, Tomb JF, Dougherty BA, Fleischmann RD, Venter JC (1995)
Frequency and distribution of DNA uptake signal sequences in the
Haemophilus influenzae Rd genome. Science 269:538–540
Suttle CA (2007) Marine viruses – major players in the global ecosystem. Nat Rev Microbiol 5:801–812
Szollosi GJ, Boussau B, Abby SS, Tannier E, Daubin V (2012) Phylogenetic modeling of lateral gene transfer reconstructs the pattern
and relative timing of speciations. Proc Natl Acad Sci U S A
109:17513–17518
Taddei F, Matic I, Radman M (1996) Du nouveau sur l’origine des
especes. La recherche 291:52–59
Tatum EL, Lederberg J (1947) Gene recombination in the bacterium
Escherichia coli. J Bacteriol 53:673–684
Tettelin H et al (2005) Genome analysis of multiple pathogenic isolates
of Streptococcus agalactiae: implications for the microbial “pangenome”. Proc Natl Acad Sci U S A 102:13950–13955
Thomas CM, Nielsen KM (2005) Mechanisms of, and barriers to,
horizontal gene transfer between bacteria. Nat Rev Microbiol
3:711–721
Timmis JN, Ayliffe MA, Huang CY, Martin W (2004) Endosymbiotic
gene transfer: organelle genomes forge eukaryotic chromosomes.
Nat Rev Genet 5:123–135
Touchon M et al (2009) Organised genome dynamics in the Escherichia
coli species results in highly diverse adaptive paths. PLoS Genet 5:
e1000344
Twort FW (1915) An investigation on the nature of ultra-microscopic
viruses. Lancet 2:1241–1243
Zeldovich KB, Berezovsky IN, Shakhnovich EI (2007) Protein and
DNA sequence determinants of thermophilic adaptation. PLoS
Comput Biol 3:e5
Zhaxybayeva O (2009) Detection and quantitative assessment of horizontal gene transfer. Methods Mol Biol 532:195–213
Zhaxybayeva O, Gogarten JP, Charlebois RL, Doolittle WF, Papke RT
(2006) Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events. Genome Res 16:1099–1108
Zhaxybayeva O, Nesbo CL, Doolittle WF (2007) Systematic overestimation of gene gain through false diagnosis of gene absence.
Genome Biol 8:402
Zhaxybayeva O et al (2009) On the chimeric nature, thermophilic
origin, and phylogenetic placement of the Thermotogales. Proc
Natl Acad Sci U S A 106:5865–5870
Zinder ND (1992) Forty years ago: the discovery of bacterial transduction. Genetics 132:291–294
Zinder ND, Lederberg J (1952) Genetic exchange in Salmonella.
J Bacteriol 64:679–699. 512 512
12 Horizontal Gene Transfer in Microbial Ecosystems
481
transfers. Environ Microbiol 6:19–34
Lorenz MG, Wackernagel W (1994) Bacterial gene transfer by natural
genetic transformation in the environment. Microbiol Rev
58:563–602
Makarova KS, Sorokin AV, Novichkov PS, Wolf YI, Koonin EV
(2007) Clusters of orthologous genes for 41 archaeal genomes and
implications for evolutionary genomics of archaea. Biol Direct 2:33
Martin W et al (2002) Evolutionary analysis of Arabidopsis,
cyanobacterial, and chloroplast genomes reveals plastid phylogeny
and thousands of cyanobacterial genes in the nucleus. Proc Natl
Acad Sci U S A 99:12246–12251
Maughan H, Redfield RJ (2009) Extensive variation in natural competence in Haemophilus Influenzae. Evolution 63:1852–1866
Millen RS et al (2001) Many parallel losses of infA from chloroplast
DNA during angiosperm evolution with multiple independent
transfers to the nucleus. Plant Cell 13:645–658
Mongodin EF et al (2005) The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic Bacteria and
Archaea. Proc Natl Acad Sci U S A 102:18147–18152
Murray NE (2000) Type I restriction systems: sophisticated molecular
machines (a legacy of Bertani and Weigle). Microbiol Mol Biol Rev
64:412–434
Nakamura Y, Itoh T, Matsuda H, Gojobori T (2004) Biased biological
functions of horizontally transferred genes in prokaryotic genomes.
Nat Genet 36:760–766
Nelson KE et al (1999) Evidence for lateral gene transfer between
Archaea and Bacteria from genome sequence of Thermotoga
maritima. Nature 399:323–329
Nesbo CL, L’Haridon S, Stetter KO, Doolittle WF (2001) Phylogenetic
analyses of two “archaeal” genes in Thermotoga maritima reveal
multiple transfers between archaea and bacteria. Mol Biol Evol
18:362–375
Nikoh N, Tanaka K, Shibata F, Kondo N, Hizume M, Shimada M,
Fukatsu T (2008) Wolbachia genome integrated in an insect chromosome: evolution and fate of laterally transferred endosymbiont
genes. Genome Res 18:272–280
Normand P et al (2007) Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography. Genome Res 17:7–15
Novick RP (1987) Plasmid incompatibility. Microbiol Rev 51:381–395
Ochman H, Lawrence JG, Groisman EA (2000) Lateral gene transfer
and the nature of bacterial innovation. Nature 405:299–304
Philippe H, Germot A, Moreira D (2000) The new phylogeny of
eukaryotes. Curr Opin Genet Dev 10:596–601
Podell S, Gaasterland T (2007) DarkHorse: a method for genome-wide
prediction of horizontal gene transfer. Genome Biol 8:R16
Ragan MA (2001) On surrogate methods for detecting lateral gene
transfer. FEMS Microbiol Lett 201:187–191
Ramirez-Arcos S, Fernandez-Herrero LA, Marin I, Berenguer J (1998)
Anaerobic growth, a property horizontally transferred by an
Hfr-like mechanism among extreme thermophiles. J Bacteriol
180:3137–3143
Ricard G et al (2006) Horizontal gene transfer from Bacteria to rumen
Ciliates indicates adaptation to their anaerobic, carbohydrates-rich
environment. BMC Genomics 7:22
Richards TA, Dacks JB, Jenkinson JM, Thornton CR, Talbot NJ (2006)
Evolution of filamentous plant pathogens: gene exchange across
eukaryotic kingdoms. Curr Biol 16:1857–1864
Rocha EP, Viari A, Danchin A (1998) Oligonucleotide bias in Bacillus
subtilis: general trends and taxonomic comparisons. Nucleic Acids
Res 26:2971–2980
Roger AJ (1999) Reconstructing Early events in eukaryotic evolution.
Am Nat 154:S146–S163
Ruepp A et al (2000) The genome sequence of the thermoacidophilic
scavenger Thermoplasma acidophilum. Nature 407:508–513
Simpson AG, Perley TA, Lara E (2008) Lateral transfer of the gene for
a widely used marker, alpha-tubulin, indicated by a multi-protein
study of the phylogenetic position of Andalucia (Excavata). Mol
Phylogenet Evol 47:366–377
Slot JC, Hibbett DS (2007) Horizontal transfer of a nitrate assimilation
gene cluster and ecological transitions in fungi: a phylogenetic
study. PLoS One 2:e1097
Smith HO, Tomb JF, Dougherty BA, Fleischmann RD, Venter JC (1995)
Frequency and distribution of DNA uptake signal sequences in the
Haemophilus influenzae Rd genome. Science 269:538–540
Suttle CA (2007) Marine viruses – major players in the global ecosystem. Nat Rev Microbiol 5:801–812
Szollosi GJ, Boussau B, Abby SS, Tannier E, Daubin V (2012) Phylogenetic modeling of lateral gene transfer reconstructs the pattern
and relative timing of speciations. Proc Natl Acad Sci U S A
109:17513–17518
Taddei F, Matic I, Radman M (1996) Du nouveau sur l’origine des
especes. La recherche 291:52–59
Tatum EL, Lederberg J (1947) Gene recombination in the bacterium
Escherichia coli. J Bacteriol 53:673–684
Tettelin H et al (2005) Genome analysis of multiple pathogenic isolates
of Streptococcus agalactiae: implications for the microbial “pangenome”. Proc Natl Acad Sci U S A 102:13950–13955
Thomas CM, Nielsen KM (2005) Mechanisms of, and barriers to,
horizontal gene transfer between bacteria. Nat Rev Microbiol
3:711–721
Timmis JN, Ayliffe MA, Huang CY, Martin W (2004) Endosymbiotic
gene transfer: organelle genomes forge eukaryotic chromosomes.
Nat Rev Genet 5:123–135
Touchon M et al (2009) Organised genome dynamics in the Escherichia
coli species results in highly diverse adaptive paths. PLoS Genet 5:
e1000344
Twort FW (1915) An investigation on the nature of ultra-microscopic
viruses. Lancet 2:1241–1243
Zeldovich KB, Berezovsky IN, Shakhnovich EI (2007) Protein and
DNA sequence determinants of thermophilic adaptation. PLoS
Comput Biol 3:e5
Zhaxybayeva O (2009) Detection and quantitative assessment of horizontal gene transfer. Methods Mol Biol 532:195–213
Zhaxybayeva O, Gogarten JP, Charlebois RL, Doolittle WF, Papke RT
(2006) Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events. Genome Res 16:1099–1108
Zhaxybayeva O, Nesbo CL, Doolittle WF (2007) Systematic overestimation of gene gain through false diagnosis of gene absence.
Genome Biol 8:402
Zhaxybayeva O et al (2009) On the chimeric nature, thermophilic
origin, and phylogenetic placement of the Thermotogales. Proc
Natl Acad Sci U S A 106:5865–5870
Zinder ND (1992) Forty years ago: the discovery of bacterial transduction. Genetics 132:291–294
Zinder ND, Lederberg J (1952) Genetic exchange in Salmonella.
J Bacteriol 64:679–699. 512 512
12 Horizontal Gene Transfer in Microbial Ecosystems
481