Additional References

 

Section 2. Parsing the Fundamental Question in Evolution: How do Heritable Adaptive Novelties and New Groups of Organisms Arise? [1-13]


Section 3. Biomath: One + One = One [14, 15]; Ubiquitous Cell Mergers in Reproduction and Evolution

3.1. Symbiogenetic Origins of Eukaryotic Cells and Their Photosynthetic Lineages [16-72]


3.2. Symbiosis as an Adaptive and Evolutionary Stimulus; Speciation by Endosymbiosis and Mating Incompatibility [73-135]

       Symbiont effects on complex host phenotypes: [86, 91-101, 136-148]


3.3. Holobiont Evolution: Lamarckian Acquisition and Inheritance of Novel Traits [1-5, 125, 149-160]


Section 4.1. Abundant Examples of Speciation and Adaptive Radiations by Interspecific Hybridization and Whole Genome Duplications (WGDs) in Plants and Animals

Genome duplications in vertebrate origins [161]
 

Cichlids: [162-169]


Section 5. Widespread Horizontal DNA Sequence Mobility between Organisms [170-172].


            5.2. Lessons on Rapid Evolution from the Smallest Living Cells [106, 173-193]


            5.3.
Horizontal DNA Transfer across Large Taxonomic Boundaries [194-199]


Section 6
Genome Writing by Natural Genetic Engineering—Protein Evolution by Natural Genetic Engineering, Exon Rearrangements and Exon Originations

            6.1. The Modular Domain-Based Structure of Proteins [200-217]


            6.2.
Protein Evolution by Exon Shuffling and Exon Accumulation, Changes to Alternative Splicing Patterns, and Insertion of
                   Reverse-Transcribed Coding Sequences
[218-241]

·     
       
Chimeric proteins from trans-splicing plus retroposition and from NHEJ [242-256].

            6.3. Protein Evolution by Domain/Exon Origination [257-280]

·    
 
Synthesis of novel coding sequences without a template: Terminal transferase enzymes synthesize nucleic acids without a template determining sequence [281-283]. Terminal deoxyribonucleotidyltransferase (TdT) is utilized to generate novel DNA-coding segments (“N region diversity”) in formation of antibody heavy chains and other immune system receptor proteins [284-286]. X family DNA polymerases, including TdT, insert untemplated nucleotides at NHEJ joining of broken DNA molecules, a process which also generates DNA sequences that did not previously exist in the genome [287-291]. In cancer cells, there is evidence that error-prone trans-lesion DNA polymerases are important in microhomology-mediated chromosome rearrangements [292]. RNA-templated DNA can also participate in NHEJ DS break repair to introduce novel sequences at the repair junction [293-297]. TdT action has also been identified in cancer cells [298, 299].

RNA-templated DNA synthesis is more error-prone than DNA replication because reverse transcriptases lacks the exonuclease-proofreading domains of replicative DNA polymerases [300, 301]. Thus, many retroposed DNAs inserted into the genome have altered sequences from the original DNA template. Significant post-transcriptional processing of RNAs, including cis- and trans-splicing and chemical modifications to individual nucleotides, such as RNA editing by cytidine deamination to uracil [302, 303] and adenosine deamination to inosine (which base-pairs like guanosine) [304-306]. So RNA templates can be significantly modified prior to reverse transcription, and there is even a report of template-independent DNA synthesis by a retrotransposon-encoded reverse transcriptase [307]. Furthermore, retroposed DNA sequences come from non-coding as well as protein-coding RNA molecules, and non-coding retroelements can contribute completely novel coding exons if their transcripts can be spliced into mRNAs [308]. As with other mutagenic processes [309-312], retroposition of cellular RNAs has been observed to occur in real time in cancer origins and progression [313].

Section 7. Genome Writing by Natural Genetic Engineering: Mobile and Repetitive DNA Elements Actively Contributing to Genome Organization, Organismal Complexity and Genome Regulation

            7.1. Regulatory Studies Led to Recognizing the Syntactical Organization of Genomes. [314-319]


            7.2.
Repetitive DNA Elements Provide Distributed Copies of Each Class of Regulatory Site [318, 320-323]


            7.3.
How Do Organisms Use Repetitive DNA for Genome Rewriting in Evolution? Dispersed Mobile DNA Elements [324-337]


            7.4.
Rewiring Transcriptional Regulatory Networks in Evolution of Complex Organisms [338-346]


            7.5.
Mobile DNA Elements Are Major Contributors to “Non-Coding” Regulatory RNA Molecules [347-355]


Section 8.
Ecological Disruption and Read-Write Genome Modifications

            8.2. Regulated Biochemistry at the Basis of Point Mutations, Deletions, Translocations and Mutational “Storms”[356-358]


Section 9.
Further Reflections on Genome Rewriting by NGE As a Core Biological Capability

            9.1.8. Trypanosome Antigenic Variation [359-361]


            9.2.
Lessons on the Real Time Potential of Natural Genetic Engineering from Cancer Genomes [362-365]

Cancer genome changes are tumor specific:
(1) L1 retrotransposition
repeatedly observed in three epithelial cancers (colorectal, prostate, and ovarian), no insertions found in blood and brain cancers [366].
(2) Chromothripsis prevalence vary from 0 in basal type breast cancer and ovarian cancer to 100% in “Sonic Hedgehog (
SHH) medulloblastoma with mutant TP53,” twelve other tumor types show chromothripsis prevalence above 30%  [367].
(3)Chromothripsis alters different chromosome regions in distinct tumor types
[368]. In SHH meduloblastomas, amplified regions typically contain medulloblastoma oncogenes, such as SHH pathway members MYCN, GLI2 and BOC [369].
(4)
Complex indels display strong tissue specificity (VHL in kidney cancer, GATA3 in breast cancer) [370].
(5) Certain cancers display repeat changes, such as “Philadelphia chromosome” translocation in
chronic myeloid leukemias but not other tumors [371].


    9.3. What Factors May Bias Genome Rewriting to Generate Selectively Positive Outcomes? [372-378]

 

REFERENCES

 

1.         Guerrero, R., L. Margulis, and M. Berlanga, Symbiogenesis: the holobiont as a unit of evolution. Int Microbiol, 2013. 16(3): p. 133-43. http://www.ncbi.nlm.nih.gov/pubmed/24568029.

2.         Salvucci, E., Microbiome, holobiont and the net of life. Crit Rev Microbiol, 2014: p. 1-10. http://www.ncbi.nlm.nih.gov/pubmed/25430522.

3.         Vandenkoornhuyse, P., et al., The importance of the microbiome of the plant holobiont. New Phytol, 2015. 206(4): p. 1196-206. http://www.ncbi.nlm.nih.gov/pubmed/25655016.

4.         Bordenstein, S.R. and K.R. Theis, Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes. PLoS Biol, 2015. 13(8): p. e1002226. http://www.ncbi.nlm.nih.gov/pubmed/26284777.

5.         Zilber-Rosenberg, I. and E. Rosenberg, Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution. FEMS Microbiol Rev, 2008. 32(5): p. 723-35. http://www.ncbi.nlm.nih.gov/pubmed/18549407.

6.         Mallet, J., Hybridization as an invasion of the genome. Trends Ecol Evol, 2005. 20(5): p. 229-37. http://www.ncbi.nlm.nih.gov/pubmed/16701374.

7.         Chaffron, S., et al., A global network of coexisting microbes from environmental and whole-genome sequence data. Genome Res, 2010. 20(7): p. 947-59. http://www.ncbi.nlm.nih.gov/pubmed/20458099.

8.         Grassi, L., J. Grilli, and M.C. Lagomarsino, Large-scale dynamics of horizontal transfers. Mob Genet Elements, 2012. 2(3): p. 163-167. http://www.ncbi.nlm.nih.gov/pubmed/23061026.

9.         Koonin, E.V., Horizontal gene transfer: essentiality and evolvability in prokaryotes, and roles in evolutionary transitions. F1000Res, 2016. 5. http://www.ncbi.nlm.nih.gov/pubmed/27508073.

10.       Lacroix, B. and V. Citovsky, Transfer of DNA from Bacteria to Eukaryotes. MBio, 2016. 7(4). http://www.ncbi.nlm.nih.gov/pubmed/27406565.

11.       Soucy, S.M., J. Huang, and J.P. Gogarten, Horizontal gene transfer: building the web of life. Nat Rev Genet, 2015. 16(8): p. 472-82. http://www.ncbi.nlm.nih.gov/pubmed/26184597.

12.       Gao, C., et al., Horizontal gene transfer in plants. Funct Integr Genomics, 2013. http://www.ncbi.nlm.nih.gov/pubmed/24132513.

13.       Rosenzweig, B.K., et al., Powerful methods for detecting introgressed regions from population genomic data. Mol Ecol, 2016. 25(11): p. 2387-97. http://www.ncbi.nlm.nih.gov/pubmed/26945783.

14.       Margulis, L. and Symbiogenesis. A new principle of evolution rediscovery of Boris Mikhaylovich Kozo-Polyansky (1890–1957). Paleontological Journal, 2010. 44(12): p. 1525–1539. .

15.       Kozo-Polyansky, B.M., Symbiogenesis: A New Principle of Evolution (1924), ed. E.a.t.b.V. Fet and E.b.L. Margulis2010, Cambridge, MA: Harvard University Press. .

16.       Martin, W.F., S. Garg, and V. Zimorski, Endosymbiotic theories for eukaryote origin. Philos Trans R Soc Lond B Biol Sci, 2015. 370(1678): p. 20140330. http://www.ncbi.nlm.nih.gov/pubmed/26323761.

17.       Ku, C., et al., Endosymbiotic origin and differential loss of eukaryotic genes. Nature, 2015. 524(7566): p. 427-32. http://www.ncbi.nlm.nih.gov/pubmed/26287458.

18.       Meheust, R., P. Lopez, and E. Bapteste, Metabolic bacterial genes and the construction of high-level composite lineages of life. Trends Ecol Evol, 2015. 30(3): p. 127-9. http://www.ncbi.nlm.nih.gov/pubmed/25601290.

19.       Lane, C.E. and J.M. Archibald, The eukaryotic tree of life: endosymbiosis takes its TOL. Trends Ecol Evol, 2008. 23(5): p. 268-75. http://www.ncbi.nlm.nih.gov/pubmed/18378040.

20.       Meheust, R., et al., Protein networks identify novel symbiogenetic genes resulting from plastid endosymbiosis. Proc Natl Acad Sci U S A, 2016. 113(13): p. 3579-84. http://www.ncbi.nlm.nih.gov/pubmed/26976593.

21.       Nasir, A., et al., Arguments Reinforcing the Three-Domain View of Diversified Cellular Life. Archaea, 2016. 2016: p. 1851865. http://www.ncbi.nlm.nih.gov/pubmed/28050162.

22.       Burki, F., The eukaryotic tree of life from a global phylogenomic perspective. Cold Spring Harb Perspect Biol, 2014. 6(5): p. a016147. http://www.ncbi.nlm.nih.gov/pubmed/24789819.

23.       Burki, F., K. Shalchian-Tabrizi, and J. Pawlowski, Phylogenomics reveals a new 'megagroup' including most photosynthetic eukaryotes. Biol Lett, 2008. 4(4): p. 366-9. http://www.ncbi.nlm.nih.gov/pubmed/18522922.

24.       Lane, N., Plastids, genomes, and the probability of gene transfer. Genome Biol Evol, 2011. 3: p. 372-4. http://www.ncbi.nlm.nih.gov/pubmed/21292628.

25.       Sousa, F.L., et al., Early bioenergetic evolution. Philos Trans R Soc Lond B Biol Sci, 2013. 368(1622): p. 20130088. http://www.ncbi.nlm.nih.gov/pubmed/23754820.

26.       Lane, N., Energetics and genetics across the prokaryote-eukaryote divide. Biol Direct, 2011. 6: p. 35. http://www.ncbi.nlm.nih.gov/pubmed/21714941.

27.       Lane, N. and W. Martin, The energetics of genome complexity. Nature, 2010. 467(7318): p. 929-34. http://www.ncbi.nlm.nih.gov/pubmed/20962839.

28.       Price, D.C., et al., Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants. Science, 2012. 335(6070): p. 843-7. http://www.ncbi.nlm.nih.gov/pubmed/22344442.

29.       Spring, J., Major transitions in evolution by genome fusions: from prokaryotes to eukaryotes, metazoans, bilaterians and vertebrates. J Struct Funct Genomics, 2003. 3(1-4): p. 19-25. http://www.ncbi.nlm.nih.gov/pubmed/12836681.

30.       van der Giezen, M. and J. Tovar, Degenerate mitochondria. EMBO Rep., 2005. 6: p. 525-530. .

31.       van der Giezen, M., Endosymbiosis: past and present. Heredity, 2005. 95(5): p. 335-6. http://www.ncbi.nlm.nih.gov/pubmed/15931237.

32.       Koumandou, V.L., et al., Molecular paleontology and complexity in the last eukaryotic common ancestor. Crit Rev Biochem Mol Biol, 2013. 48(4): p. 373-96. http://www.ncbi.nlm.nih.gov/pubmed/23895660.

33.       Hackstein, J.H., J. Tjaden, and M. Huynen, Mitochondria, hydrogenosomes and mitosomes: products of evolutionary tinkering! Curr Genet, 2006. 50(4): p. 225-45. http://www.ncbi.nlm.nih.gov/pubmed/16897087.

34.       Lithgow, T. and A. Schneider, Evolution of macromolecular import pathways in mitochondria, hydrogenosomes and mitosomes. Philos Trans R Soc Lond B Biol Sci, 2010. 365(1541): p. 799-817. http://www.ncbi.nlm.nih.gov/pubmed/20124346.

35.       Dolezal, P., et al., Evolution of the molecular machines for protein import into mitochondria. Science, 2006. 313(5785): p. 314-8. http://www.ncbi.nlm.nih.gov/pubmed/16857931.

36.       Rotte, C., et al., Origins of hydrogenosomes and mitochondria. Curr Opin Microbiol, 2000. 3(5): p. 481-6. http://www.ncbi.nlm.nih.gov/pubmed/11050446.

37.       Hjort, K., et al., Diversity and reductive evolution of mitochondria among microbial eukaryotes. Philos Trans R Soc Lond B Biol Sci, 2010. 365(1541): p. 713-27. http://www.ncbi.nlm.nih.gov/pubmed/20124340\.

38.       Gray, M.W., B.F. Lang, and G. Burger, Mitochondria of protists. Annu Rev Genet, 2004. 38: p. 477-524. http://www.ncbi.nlm.nih.gov/pubmed/15568984.

39.       Gray, M.W., G. Burger, and B.F. Lang, Mitochondrial evolution. Science, 1999. 283(5407): p. 1476-81. http://www.ncbi.nlm.nih.gov/pubmed/10066161.

40.       Lang, B.F., M.W. Gray, and G. Burger, Mitochondrial genome evolution and the origin of eukaryotes. Annu Rev Genet, 1999. 33: p. 351-97. http://www.ncbi.nlm.nih.gov/pubmed/10690412.

41.       Bhattacharya, D., H.S. Yoon, and J.D. Hackett, Photosynthetic eukaryotes unite: endosymbiosis connects the dots. Bioessays, 2004. 26(1): p. 50-60. http://www.ncbi.nlm.nih.gov/pubmed/14696040.

42.       Rockwell, N.C., J.C. Lagarias, and D. Bhattacharya, Primary endosymbiosis and the evolution of light and oxygen sensing in photosynthetic eukaryotes. Front Ecol Evol, 2014. 2(66). http://www.ncbi.nlm.nih.gov/pubmed/25729749.

43.       Gross, J. and D. Bhattacharya, Endosymbiont or host: who drove mitochondrial and plastid evolution? Biol Direct, 2011. 6: p. 12. http://www.ncbi.nlm.nih.gov/pubmed/21333023.

44.       Reyes-Prieto, A., et al., Differential gene retention in plastids of common recent origin. Mol Biol Evol, 2010. 27(7): p. 1530-7. http://www.ncbi.nlm.nih.gov/pubmed/20123796.

45.       Nosenko, T., et al., Chimeric plastid proteome in the Florida "red tide" dinoflagellate Karenia brevis. Mol Biol Evol, 2006. 23(11): p. 2026-38. http://www.ncbi.nlm.nih.gov/pubmed/16877498.

46.       Moreira, D., L. Ranjard, and P. Lopez-Garcia, The nucleolar proteome and the (endosymbiotic) origin of the nucleus. Bioessays, 2004. 26(10): p. 1144-5; author reply 1145-7. http://www.ncbi.nlm.nih.gov/pubmed/15382131.

47.       Deschamps, P. and D. Moreira, Signal conflicts in the phylogeny of the primary photosynthetic eukaryotes. Mol Biol Evol, 2009. 26(12): p. 2745-53. http://www.ncbi.nlm.nih.gov/pubmed/19706725.

48.       Moreira, D. and P. Lopez-Garcia, Symbiosis between methanogenic archaea and delta-proteobacteria as the origin of  eukaryotes: the syntrophic hypothesis. J Mol Evol, 1998. 47(5): p. 517-30. http://www.ncbi.nlm.nih.gov/pubmed/9797402.

49.       Moreira, D. and P. Deschamps, What was the real contribution of endosymbionts to the eukaryotic nucleus? Insights from photosynthetic eukaryotes. Cold Spring Harb Perspect Biol, 2014. 6(7): p. a016014. http://www.ncbi.nlm.nih.gov/pubmed/24984774.

50.       Gomez, F., P. Lopez-Garcia, and D. Moreira, Molecular phylogeny of the ocelloid-bearing dinoflagellates erythropsidinium and warnowia (warnowiaceae, dinophyceae). J Eukaryot Microbiol, 2009. 56(5): p. 440-5. http://www.ncbi.nlm.nih.gov/pubmed/19737196.

51.       Deschamps, P., et al., Metabolic symbiosis and the birth of the plant kingdom. Mol Biol Evol, 2008. 25(3): p. 536-48. http://www.ncbi.nlm.nih.gov/pubmed/18093994.

52.       Reyes-Prieto, A., A.P. Weber, and D. Bhattacharya, The origin and establishment of the plastid in algae and plants. Annu Rev Genet, 2007. 41: p. 147-68. http://www.ncbi.nlm.nih.gov/pubmed/17600460.

53.       Bhattacharya, D., et al., Genome of the red alga Porphyridium purpureum. Nat Commun, 2013. 4: p. 1941. http://www.ncbi.nlm.nih.gov/pubmed/23770768.

54.       Hackett, J., Anderson, DM, Erdner, DL, Bhattacharya, D, Dinoflagellates: A remarkable evolutionary experiment. Am J Bot, 2004. 91: p. 1523–1534. .

55.       Nowack, E.C. and M. Melkonian, Endosymbiotic associations within protists. Philos Trans R Soc Lond B Biol Sci\, 2010. 365\(1541\): p. 699-712\. http://www.ncbi.nlm.nih.gov/pubmed/20124339\.

56.       Nowack, E.C. and A.R. Grossman, Trafficking of protein into the recently established photosynthetic organelles of Paulinella chromatophora. Proc Natl Acad Sci U S A, 2012. 109(14): p. 5340-5. http://www.ncbi.nlm.nih.gov/pubmed/22371600.

57.       Mackiewicz, P., A. Bodyl, and P. Gagat, Possible import routes of proteins into the cyanobacterial endosymbionts/plastids of Paulinella chromatophora. Theory Biosci, 2012. 131(1): p. 1-18. http://www.ncbi.nlm.nih.gov/pubmed/22209953.

58.       Dorrell, R.G. and A.G. Smith, Do red and green make brown?: perspectives on plastid acquisitions within chromalveolates. Eukaryot Cell, 2011. 10(7): p. 856-68. http://www.ncbi.nlm.nih.gov/pubmed/21622904.

59.       Dorrell, R.G., et al., Evolution of chloroplast transcript processing in Plasmodium and its chromerid algal relatives. PLoS Genet, 2014. 10(1): p. e1004008. http://www.ncbi.nlm.nih.gov/pubmed/24453981.

60.       Dorrell, R.G. and C.J. Howe, Integration of plastids with their hosts: Lessons learned from dinoflagellates. Proc Natl Acad Sci U S A, 2015. 112(33): p. 10247-54. http://www.ncbi.nlm.nih.gov/pubmed/25995366.

61.       Chan, C.X., et al., Red and green algal monophyly and extensive gene sharing found in a rich repertoire of red algal genes. Curr Biol, 2011. 21(4): p. 328-33. http://www.ncbi.nlm.nih.gov/pubmed/21315598.

62.       Yoon, H.S., et al., Tertiary endosymbiosis driven genome evolution in dinoflagellate algae. Mol Biol Evol, 2005. 22(5): p. 1299-308. http://www.ncbi.nlm.nih.gov/pubmed/15746017.

63.       Hayakawa, S., et al., Function and evolutionary origin of unicellular camera-type eye structure. PLoS One, 2015. 10(3): p. e0118415. http://www.ncbi.nlm.nih.gov/pubmed/25734540.

64.       Adams, K.L., et al., Punctuated evolution of mitochondrial gene content: high and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution. Proc Natl Acad Sci U S A, 2002. 99(15): p. 9905-12. http://www.ncbi.nlm.nih.gov/pubmed/12119382.

65.       Adams, K.L., et al., Repeated, recent and diverse transfers of a mitochondrial gene to the nucleus in flowering plants. Nature, 2000. 408(6810): p. 354-7. http://www.ncbi.nlm.nih.gov/pubmed/11099041.

66.       Adams, K.L. and J.D. Palmer, Evolution of mitochondrial gene content: gene loss and transfer to the nucleus. Mol Phylogenet Evol, 2003. 29(3): p. 380-95. http://www.ncbi.nlm.nih.gov/pubmed/14615181.

67.       Gandini, C.L. and M.V. Sanchez-Puerta, Foreign Plastid Sequences in Plant Mitochondria are Frequently Acquired Via Mitochondrion-to-Mitochondrion Horizontal Transfer. Sci Rep, 2017. 7: p. 43402. http://www.ncbi.nlm.nih.gov/pubmed/28262720.

68.       Lang, B.F., et al., An ancestral mitochondrial DNA resembling a eubacterial genome in miniature. Nature, 1997. 387(6632): p. 493-7. http://www.ncbi.nlm.nih.gov/pubmed/9168110.

69.       Gray, M.W., et al., Genome structure and gene content in protist mitochondrial DNAs. Nucleic Acids Res, 1998. 26(4): p. 865-78. http://www.ncbi.nlm.nih.gov/pubmed/9461442.

70.       Boussau, B., et al., Computational inference of scenarios for alpha-proteobacterial genome evolution. Proc Natl Acad Sci U S A, 2004. 101(26): p. 9722-7. http://www.ncbi.nlm.nih.gov/pubmed/15210995.

71.       Howe, C.J., et al., The origin of plastids. Philos Trans R Soc Lond B Biol Sci, 2008. 363(1504): p. 2675-85. http://www.ncbi.nlm.nih.gov/pubmed/18468982.

72.       Bhattacharya, D., et al., Single cell genome analysis supports a link between phagotrophy and primary plastid endosymbiosis. Sci Rep, 2012. 2: p. 356. http://www.ncbi.nlm.nih.gov/pubmed/22493757.

73.       Bucher, M., et al., Development and Symbiosis Establishment in the Cnidarian Endosymbiosis Model Aiptasia sp. Sci Rep, 2016. 6: p. 19867. http://www.ncbi.nlm.nih.gov/pubmed/26804034.

74.       Hoogenboom, M.O., et al., Effects of light, food availability and temperature stress on the function of photosystem II and photosystem I of coral symbionts. PLoS One, 2012. 7(1): p. e30167. http://www.ncbi.nlm.nih.gov/pubmed/22253915.

75.       Stefano, G.B., C. Snyder, and R.M. Kream, Mitochondria, Chloroplasts in Animal and Plant Cells: Significance of Conformational Matching. Med Sci Monit, 2015. 21: p. 2073-8. http://www.ncbi.nlm.nih.gov/pubmed/26184462.

76.       Qiu, H., H.S. Yoon, and D. Bhattacharya, Algal endosymbionts as vectors of horizontal gene transfer in photosynthetic eukaryotes. Front Plant Sci, 2013. 4: p. 366. http://www.ncbi.nlm.nih.gov/pubmed/24065973.

77.       Dearnaley, J.D., Further advances in orchid mycorrhizal research. Mycorrhiza, 2007. 17(6): p. 475-86. http://www.ncbi.nlm.nih.gov/pubmed/17582535.

78.       Bonnardeaux, Y., et al., Diversity of mycorrhizal fungi of terrestrial orchids: compatibility webs, brief encounters, lasting relationships and alien invasions. Mycol Res, 2007. 111(Pt 1): p. 51-61. http://www.ncbi.nlm.nih.gov/pubmed/17289365.

79.       Cameron, D.D., J.R. Leake, and D.J. Read, Mutualistic mycorrhiza in orchids: evidence from plant-fungus carbon and nitrogen transfers in the green-leaved terrestrial orchid Goodyera repens. New Phytol, 2006. 171(2): p. 405-16. http://www.ncbi.nlm.nih.gov/pubmed/16866946.

80.       Bucher, M., S. Wegmuller, and D. Drissner, Chasing the structures of small molecules in arbuscular mycorrhizal signaling. Curr Opin Plant Biol, 2009. 12(4): p. 500-7. http://www.ncbi.nlm.nih.gov/pubmed/19576840.

81.       Neish, A.S., Microbes in gastrointestinal health and disease. Gastroenterology, 2009. 136(1): p. 65-80. http://www.ncbi.nlm.nih.gov/pubmed/19026645.

82.       Hoffmeister, M. and W. Martin, Interspecific evolution: microbial symbiosis, endosymbiosis and gene transfer. Environ Microbiol, 2003. 5(8): p. 641-9. http://www.ncbi.nlm.nih.gov/pubmed/12871231.

83.       Ohkuma, M., Termite symbiotic systems: efficient bio-recycling of lignocellulose. Appl Microbiol Biotechnol, 2003. 61(1): p. 1-9. http://www.ncbi.nlm.nih.gov/pubmed/12658509.

84.       Venkatesh, M., et al., Symbiotic Bacterial Metabolites Regulate Gastrointestinal Barrier Function via the Xenobiotic Sensor PXR and Toll-like Receptor 4. Immunity, 2014. http://www.ncbi.nlm.nih.gov/pubmed/25065623.

85.       Li, M., et al., Symbiotic gut microbes modulate human metabolic phenotypes. Proc Natl Acad Sci U S A\, 2008. 105\(6\): p. 2117-22\. http://www.ncbi.nlm.nih.gov/pubmed/18252821\.

86.       Fast, E.M., et al., Wolbachia Enhance Drosophila Stem Cell Proliferation and Target the Germline Stem Cell Niche. Science, 2011. http://www.ncbi.nlm.nih.gov/pubmed/22021671.

87.       Liang, Y., et al., Nonlegumes respond to rhizobial Nod factors by suppressing the innate immune response. Science, 2013. 341(6152): p. 1384-7. http://www.ncbi.nlm.nih.gov/pubmed/24009356.

88.       Zook, D., Symbiosis—Evolution’s Co-Author, in Reticulate Evolution, Interdisciplinary Evolution Research 3, N. Gontier, Editor 2015, Soringer: Heidelberg. .

89.       Frugier, F., et al., Cytokinin: secret agent of symbiosis. Trends Plant Sci\, 2008. 13\(3\): p. 115-20\. http://www.ncbi.nlm.nih.gov/pubmed/18296104\.

90.       Crespi, M. and F. Frugier, De novo organ formation from differentiated cells: root nodule organogenesis. Sci Signal, 2008. 1(49): p. re11. http://www.ncbi.nlm.nih.gov/pubmed/19066400.

91.       Walker, T., et al., The wMel Wolbachia strain blocks dengue and invades caged Aedes aegypti populations. Nature, 2011. 476(7361): p. 450-3. http://www.ncbi.nlm.nih.gov/pubmed/21866159.

92.       Kambris, Z., et al., Wolbachia stimulates immune gene expression and inhibits plasmodium development in Anopheles gambiae. PLoS Pathog, 2010. 6(10). http://www.ncbi.nlm.nih.gov/pubmed/20949079.

93.       Frentiu, F.D., et al., Wolbachia-mediated resistance to dengue virus infection and death at the cellular level. PLoS One, 2010. 5(10): p. e13398. http://www.ncbi.nlm.nih.gov/pubmed/20976219.

94.       Mousson, L., et al., Wolbachia modulates Chikungunya replication in Aedes albopictus. Mol Ecol, 2010. http://www.ncbi.nlm.nih.gov/pubmed/20345686.

95.       Osborne, S.E., et al., Variation in antiviral protection mediated by different Wolbachia strains in Drosophila simulans. PLoS Pathog, 2009. 5(11): p. e1000656. http://www.ncbi.nlm.nih.gov/pubmed/19911047.

96.       Teixeira, L., A. Ferreira, and M. Ashburner, The bacterial symbiont Wolbachia induces resistance to RNA viral infections in Drosophila melanogaster. PLoS Biol, 2008. 6(12): p. e2. http://www.ncbi.nlm.nih.gov/pubmed/19222304.

97.       Pfeiffer, J.K. and J.L. Sonnenburg, The intestinal microbiota and viral susceptibility. Front Microbiol, 2011. 2: p. 92. http://www.ncbi.nlm.nih.gov/pubmed/21833331.

98.       Kuss, S.K., et al., Intestinal microbiota promote enteric virus replication and systemic pathogenesis. Science, 2011. 334(6053): p. 249-52. http://www.ncbi.nlm.nih.gov/pubmed/21998395.

99.       Cash, H.L., et al., Symbiotic bacteria direct expression of an intestinal bactericidal lectin. Science, 2006. 313(5790): p. 1126-30. http://www.ncbi.nlm.nih.gov/pubmed/16931762.

100.     Dash, S., et al., The gut microbiome and diet in psychiatry: focus on depression. Curr Opin Psychiatry, 2015. 28(1): p. 1-6. http://www.ncbi.nlm.nih.gov/pubmed/25415497.

101.     Cryan, J.F. and S.M. O'Mahony, The microbiome-gut-brain axis: from bowel to behavior. Neurogastroenterol Motil, 2011. 23(3): p. 187-92. http://www.ncbi.nlm.nih.gov/pubmed/21303428.

102.     Masson-Boivin, C., et al., Establishing nitrogen-fixing symbiosis with legumes: how many rhizobium recipes? Trends Microbiol, 2009. 17(10): p. 458-66. http://www.ncbi.nlm.nih.gov/pubmed/19766492.

103.     Marchetti, M., et al., Experimental evolution of a plant pathogen into a legume symbiont. PLoS Biol, 2010. 8(1): p. e1000280. http://www.ncbi.nlm.nih.gov/pubmed/20084095.

104.     Guan, S.H., et al., Experimental evolution of nodule intracellular infection in legume symbionts. Isme J, 2013. 7(7): p. 1367-77. http://www.ncbi.nlm.nih.gov/pubmed/23426010.

105.     Marchetti, M., et al., Shaping bacterial symbiosis with legumes by experimental evolution. Mol Plant Microbe Interact, 2014. 27(9): p. 956-64. http://www.ncbi.nlm.nih.gov/pubmed/25105803.

106.     Remigi, P., et al., Transient Hypermutagenesis Accelerates the Evolution of Legume Endosymbionts following Horizontal Gene Transfer. PLoS Biol, 2014. 12(9): p. e1001942. http://www.ncbi.nlm.nih.gov/pubmed/25181317.

107.     Cairney, J.W., Evolution of mycorrhiza systems. Naturwissenschaften, 2000. 87(11): p. 467-75. http://www.ncbi.nlm.nih.gov/pubmed/11151665.

108.     Finlay, R.D., Ecological aspects of mycorrhizal symbiosis: with special emphasis on the functional diversity of interactions involving the extraradical mycelium. J Exp Bot, 2008. 59(5): p. 1115-26. http://www.ncbi.nlm.nih.gov/pubmed/18349054.

109.     Willing, B.P., S.L. Russell, and B.B. Finlay, Shifting the balance: antibiotic effects on host-microbiota mutualism. Nat Rev Microbiol, 2011. 9(4): p. 233-43. http://www.ncbi.nlm.nih.gov/pubmed/21358670.

110.     Bonfante, P. and N. Requena, Dating in the dark: how roots respond to fungal signals to establish arbuscular mycorrhizal symbiosis. Curr Opin Plant Biol, 2011. 14(4): p. 451-7. http://www.ncbi.nlm.nih.gov/pubmed/21489861.

111.     Navazio, L., et al., A diffusible signal from arbuscular mycorrhizal fungi elicits a transient cytosolic calcium elevation in host plant cells. Plant Physiol, 2007. 144(2): p. 673-81. http://www.ncbi.nlm.nih.gov/pubmed/17142489.

112.     Salvioli, A., et al., Endobacteria affect the metabolic profile of their host Gigaspora margarita, an arbuscular mycorrhizal fungus. Environ Microbiol, 2010. http://www.ncbi.nlm.nih.gov/pubmed/20545745.

113.     Tisserant, E., et al., Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis. Proc Natl Acad Sci U S A, 2013. http://www.ncbi.nlm.nih.gov/pubmed/24277808.

114.     Ghignone, S., et al., The genome of the obligate endobacterium of an AM fungus reveals an interphylum network of nutritional interactions. Isme J, 2011. http://www.ncbi.nlm.nih.gov/pubmed/21866182.

115.     Ghignone, S., et al., The genome of the obligate endobacterium of an AM fungus reveals an interphylum network of nutritional interactions. Isme J, 2012. 6(1): p. 136-45. http://www.ncbi.nlm.nih.gov/pubmed/21866182.

116.     Torres-Cortes, G., et al., Mosaic genome of endobacteria in arbuscular mycorrhizal fungi: Transkingdom gene transfer in an ancient mycoplasma-fungus association. Proc Natl Acad Sci U S A, 2015. 112(112): p. 7785-90. http://www.ncbi.nlm.nih.gov/pubmed/25964335.

117.     Martin, F., et al., Perigord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis. Nature, 2010. http://www.ncbi.nlm.nih.gov/pubmed/20348908.

118.     Bonfante, P., Plants, mycorrhizal fungi and endobacteria: a dialog among cells and genomes. Biol Bull, 2003. 204(2): p. 215-20. http://www.ncbi.nlm.nih.gov/pubmed/12700157.

119.     Bonfante, P. and I.A. Anca, Plants, mycorrhizal fungi, and bacteria: a network of interactions. Annu Rev Microbiol, 2009. 63: p. 363-83. http://www.ncbi.nlm.nih.gov/pubmed/19514845.

120.     Ohkuma, M., et al., Acetogenesis from H2 plus CO2 and nitrogen fixation by an endosymbiotic spirochete of a termite-gut cellulolytic protist. Proc Natl Acad Sci U S A, 2015. http://www.ncbi.nlm.nih.gov/pubmed/25979941.

121.     Noda, S., et al., Complex coevolutionary history of symbiotic Bacteroidales bacteria of various protists in the gut of termites. BMC Evol Biol, 2009. 9: p. 158. http://www.ncbi.nlm.nih.gov/pubmed/19586555.

122.     Hongoh, Y., et al., The motility symbiont of the termite gut flagellate Caduceia versatilis is a member of the "Synergistes" group. Appl Environ Microbiol, 2007. 73(19): p. 6270-6. http://www.ncbi.nlm.nih.gov/pubmed/17675420.

123.     Ohkuma, M., Symbioses of flagellates and prokaryotes in the gut of lower termites. Trends Microbiol, 2008. 16(7): p. 345-52. http://www.ncbi.nlm.nih.gov/pubmed/18513972.

124.     Kudo, T., Termite-microbe symbiotic system and its efficient degradation of lignocellulose. Biosci Biotechnol Biochem, 2009. 73(12): p. 2561-7. http://www.ncbi.nlm.nih.gov/pubmed/19966490.

125.     Balmand, S., et al., Tissue distribution and transmission routes for the tsetse fly endosymbionts. J Invertebr Pathol, 2013. 112 Suppl: p. S116-22. http://www.ncbi.nlm.nih.gov/pubmed/22537833.

126.     Fenn, K., et al., Phylogenetic relationships of the Wolbachia of nematodes and arthropods. PLoS Pathog\, 2006. 2\(10\): p. e94\. http://www.ncbi.nlm.nih.gov/pubmed/17040125\.

127.     Zouache, K., et al., Persistent Wolbachia and cultivable bacteria infection in the reproductive and somatic tissues of the mosquito vector Aedes albopictus. PLoS One, 2009. 4(7): p. e6388. http://www.ncbi.nlm.nih.gov/pubmed/19633721.

128.     Raychoudhury, R., et al., Modes of acquisition of Wolbachia: horizontal transfer, hybrid introgression, and codivergence in the Nasonia species complex. Evolution, 2009. 63(1): p. 165-83. http://www.ncbi.nlm.nih.gov/pubmed/18826448.

129.     Hughes, G.L., et al., Invasion of Wolbachia into Anopheles and other insect germlines in an ex vivo organ culture system. PLoS One, 2012. 7(4): p. e36277. http://www.ncbi.nlm.nih.gov/pubmed/22558418.

130.     Narita, S., et al., Unexpected mechanism of symbiont-induced reversal of insect sex: feminizing Wolbachia continuously acts on the butterfly Eurema hecabe during larval development. Appl Environ Microbiol, 2007. 73(13): p. 4332-41. http://www.ncbi.nlm.nih.gov/pubmed/17496135.

131.     Gazla, I.N. and M.C. Carracedo, Effect of intracellular Wolbachia on interspecific crosses between Drosophila melanogaster and Drosophila simulans. Genet Mol Res, 2009. 8(3): p. 861-9. http://www.ncbi.nlm.nih.gov/pubmed/19731208.

132.     Landmann, F., et al., Wolbachia-mediated cytoplasmic incompatibility is associated with impaired histone deposition in the male pronucleus. PLoS Pathog, 2009. 5(3): p. e1000343. http://www.ncbi.nlm.nih.gov/pubmed/19300496.

133.     Kutschera, U. and K.J. Niklas, Endosymbiosis, cell evolution, and speciation. Theory Biosci, 2005. 124(1): p. 1-24. http://www.ncbi.nlm.nih.gov/pubmed/17046345.

134.     Taylor, F.J., Symbionticism revisited: a discussion of the evolutionary impact of intracellular symbioses. Proc R Soc Lond B Biol Sci, 1979. 204(1155): p. 267-86. http://www.ncbi.nlm.nih.gov/pubmed/36627.

135.     Brucker, R.M. and S.R. Bordenstein, Speciation by symbiosis. Trends Ecol Evol, 2012. 27(8): p. 443-51. http://www.ncbi.nlm.nih.gov/pubmed/22541872.

136.     Round, J.L., R.M. O'Connell, and S.K. Mazmanian, Coordination of tolerogenic immune responses by the commensal microbiota. J Autoimmun, 2010. 34(3): p. J220-5. http://www.ncbi.nlm.nih.gov/pubmed/19963349.

137.     Petersen, C. and J.L. Round, Defining dysbiosis and its influence on host immunity and disease. Cell Microbiol, 2014. 16(7): p. 1024-33. http://www.ncbi.nlm.nih.gov/pubmed/24798552.

138.     Round, J.L. and S.K. Mazmanian, The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol, 2009. 9(5): p. 313-23. http://www.ncbi.nlm.nih.gov/pubmed/19343057.

139.     Round, J.L. and S.K. Mazmanian, Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota. Proc Natl Acad Sci U S A, 2010. 107(27): p. 12204-9. http://www.ncbi.nlm.nih.gov/pubmed/20566854.

140.     Molloy, M.J., N. Bouladoux, and Y. Belkaid, Intestinal microbiota: shaping local and systemic immune responses. Semin Immunol, 2012. 24(1): p. 58-66. http://www.ncbi.nlm.nih.gov/pubmed/22178452.

141.     Kaplan, J.L., H. Ning Shi, and W.A. Walker, The Role of Microbes in Developmental Immunologic Programming. Pediatr Res, 2011. http://www.ncbi.nlm.nih.gov/pubmed/21364495.

142.     Chrostek, E., et al., Wolbachia Variants Induce Differential Protection to Viruses in Drosophila melanogaster: A Phenotypic and Phylogenomic Analysis. PLoS Genet, 2013. 9(12): p. e1003896. http://www.ncbi.nlm.nih.gov/pubmed/24348259.

143.     Borre, Y.E., et al., The impact of microbiota on brain and behavior: mechanisms & therapeutic potential. Adv Exp Med Biol, 2014. 817: p. 373-403. http://www.ncbi.nlm.nih.gov/pubmed/24997043.

144.     Bravo, J.A., et al., Ingestion of Lactobacillus strain regulates emotional behavior and central GABA receptor expression in a mouse via the vagus nerve. Proc Natl Acad Sci U S A, 2011. http://www.ncbi.nlm.nih.gov/pubmed/21876150.

145.     Dinan, T.G. and J.F. Cryan, Melancholic microbes: a link between gut microbiota and depression? Neurogastroenterol Motil, 2013. 25(9): p. 713-9. http://www.ncbi.nlm.nih.gov/pubmed/23910373.

146.     Cryan, J.F. and T.G. Dinan, Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour. Nat Rev Neurosci, 2012. 13(10): p. 701-12. http://www.ncbi.nlm.nih.gov/pubmed/22968153.

147.     O'Mahony, S.M., et al., Serotonin, tryptophan metabolism and the brain-gut-microbiome axis. Behav Brain Res, 2015. 277: p. 32-48. http://www.ncbi.nlm.nih.gov/pubmed/25078296.

148.     Shin, S.C., et al., Drosophila microbiome modulates host developmental and metabolic homeostasis via insulin signaling. Science, 2011. 334(6056): p. 670-4. http://www.ncbi.nlm.nih.gov/pubmed/22053049.

149.     Hongoh, Y., Diversity and genomes of uncultured microbial symbionts in the termite gut. Biosci Biotechnol Biochem, 2010. 74(6): p. 1145-51. http://www.ncbi.nlm.nih.gov/pubmed/20530908.

150.     Aanen, D.K., et al., High symbiont relatedness stabilizes mutualistic cooperation in fungus-growing termites. Science, 2009. 326(5956): p. 1103-6. http://www.ncbi.nlm.nih.gov/pubmed/19965427.

151.     Serbus, L.R. and W. Sullivan, A cellular basis for Wolbachia recruitment to the host germline. PLoS Pathog, 2007. 3(12): p. e190. http://www.ncbi.nlm.nih.gov/pubmed/18085821.

152.     Aksoy, S., X. Chen, and V. Hypsa, Phylogeny and potential transmission routes of midgut-associated endosymbionts of tsetse (Diptera:Glossinidae). Insect Mol Biol, 1997. 6(2): p. 183-90. http://www.ncbi.nlm.nih.gov/pubmed/9099582.

153.     Koga, R., et al., Cellular mechanism for selective vertical transmission of an obligate insect symbiont at the bacteriocyte-embryo interface. Proc Natl Acad Sci U S A, 2012. 109(20): p. E1230-7. http://www.ncbi.nlm.nih.gov/pubmed/22517738.

154.     Webster, N.S., et al., Deep sequencing reveals exceptional diversity and modes of transmission for bacterial sponge symbionts. Environ Microbiol, 2010. 12(8): p. 2070-82. http://www.ncbi.nlm.nih.gov/pubmed/21966903.

155.     Bright, M. and S. Bulgheresi, A complex journey: transmission of microbial symbionts. Nat Rev Microbiol, 2010. 8(3): p. 218-30. http://www.ncbi.nlm.nih.gov/pubmed/20157340.

156.     Schmitt, S., et al., Vertical transmission of a phylogenetically complex microbial consortium in the viviparous sponge Ircinia felix. Appl Environ Microbiol, 2007. 73(7): p. 2067-78. http://www.ncbi.nlm.nih.gov/pubmed/17277226.

157.     Schneider, D., et al., Phylogenetic analysis of a microbialite-forming microbial mat from a hypersaline lake of the Kiritimati atoll, Central Pacific. PLoS One, 2013. 8(6): p. e66662. http://www.ncbi.nlm.nih.gov/pubmed/23762495.

158.     Baumgartner, L.K., et al., Microbial diversity in modern marine stromatolites, Highborne Cay, Bahamas. Environ Microbiol, 2009. 11(10): p. 2710-9. http://www.ncbi.nlm.nih.gov/pubmed/19601956.

159.     Papineau, D., et al., Composition and structure of microbial communities from stromatolites of Hamelin Pool in Shark Bay, Western Australia. Appl Environ Microbiol, 2005. 71(8): p. 4822-32. http://www.ncbi.nlm.nih.gov/pubmed/16085880.

160.     Reid, R.P., et al., The role of microbes in accretion, lamination and early lithification of modern marine stromatolites. Nature, 2000. 406(6799): p. 989-92. http://www.ncbi.nlm.nih.gov/pubmed/10984051.

161.     Robinson-Rechavi, M., B. Boussau, and V. Laudet, Phylogenetic dating and characterization of gene duplications in vertebrates: the cartilaginous fish reference. Mol Biol Evol, 2004. 21(3): p. 580-6. http://www.ncbi.nlm.nih.gov/pubmed/14694077.

162.     Hulsey, C.D. and F.J. Garcia-de-Leon, Introgressive hybridization in a trophically polymorphic cichlid. Ecol Evol, 2013. 3(13): p. 4536-47. http://www.ncbi.nlm.nih.gov/pubmed/24340193.

163.     Magalhaes, I.S., et al., Untangling the evolutionary history of a highly polymorphic species: introgressive hybridization and high genetic structure in the desert cichlid fish Herichtys minckleyi. Mol Ecol, 2015. 24(17): p. 4505-20. http://www.ncbi.nlm.nih.gov/pubmed/26175313.

164.     Keller, I., et al., Population genomic signatures of divergent adaptation, gene flow and hybrid speciation in the rapid radiation of Lake Victoria cichlid fishes. Mol Ecol, 2013. 22(11): p. 2848-63. http://www.ncbi.nlm.nih.gov/pubmed/23121191.

165.     Smith, P.F., A. Konings, and I. Kornfield, Hybrid origin of a cichlid population in Lake Malawi: implications for genetic variation and species diversity. Mol Ecol, 2003. 12(9): p. 2497-504. http://www.ncbi.nlm.nih.gov/pubmed/12919487.

166.     Joyce, D.A., et al., Repeated colonization and hybridization in Lake Malawi cichlids. Curr Biol, 2011. 21(3): p. R108-9. http://www.ncbi.nlm.nih.gov/pubmed/21300271.

167.     Loh, Y.H., et al., Origins of shared genetic variation in African cichlids. Mol Biol Evol, 2013. 30(4): p. 906-17. http://www.ncbi.nlm.nih.gov/pubmed/23275489.

168.     Seehausen, O., Process and pattern in cichlid radiations - inferences for understanding unusually high rates of evolutionary diversification. New Phytol, 2015. 207(2): p. 304-12. http://www.ncbi.nlm.nih.gov/pubmed/25983053.

169.     Seehausen, O., African cichlid fish: a model system in adaptive radiation research. Proc Biol Sci, 2006. 273(1597): p. 1987-98. http://www.ncbi.nlm.nih.gov/pubmed/16846905.

170.     Syvanen, M. and C.I. Kado, Horizontal Gene Transfer 2nd Ed2002, London: Academic Press. .

171.     Syvanen, M., Cross-species gene transfer; implications for a new theory of evolution. J Theor Biol, 1985. 112(2): p. 333-43. http://www.ncbi.nlm.nih.gov/pubmed/2984477.

172.     Katz, L.A., Recent events dominate interdomain lateral gene transfers between prokaryotes and eukaryotes and, with the exception of endosymbiotic gene transfers, few ancient transfer events persist. Philos Trans R Soc Lond B Biol Sci, 2015. 370(1678): p. 20140324. http://www.ncbi.nlm.nih.gov/pubmed/26323756.

173.     Benveniste, R. and J. Davies, Mechanisms of antibiotic resistance in bacteria. Annu Rev Biochem, 1973. 42: p. 471-506. http://www.ncbi.nlm.nih.gov/pubmed/4581231.

174.     Watanabe, T., Selected Methods of Genetic Study of Episome-Mediated Drug Resistance in Bacteria. Methods Med Res, 1964. 10: p. 202-20. http://www.ncbi.nlm.nih.gov/pubmed/14284923.

175.     Watanabe, T., Episome-Mediated Transfer of Drug Resistance in Enterobacteriaceae. Vi. High-Frequency Resistance Transfer System in Escherichia Coli. J Bacteriol, 1963. 85: p. 788-94. http://www.ncbi.nlm.nih.gov/pubmed/14044944.

176.     Svara, F. and D.J. Rankin, The evolution of plasmid-carried antibiotic resistance. BMC Evol Biol, 2011. 11(1): p. 130. http://www.ncbi.nlm.nih.gov/pubmed/21595903.

177.     Domingues, S., K.M. Nielsen, and G.J. da Silva, Various pathways leading to the acquisition of antibiotic resistance by natural transformation. Mob Genet Elements, 2012. 2(6): p. 257-260. http://www.ncbi.nlm.nih.gov/pubmed/23482877.

178.     Stalder, T., et al., Integron involvement in environmental spread of antibiotic resistance. Front Microbiol, 2012. 3: p. 119. http://www.ncbi.nlm.nih.gov/pubmed/22509175.

179.     Norman, A., L.H. Hansen, and S.J. Sorensen, Conjugative plasmids: vessels of the communal gene pool. Philos Trans R Soc Lond B Biol Sci, 2009. 364(1527): p. 2275-89. http://www.ncbi.nlm.nih.gov/pubmed/19571247.

180.     Faguy, D.M. and W.F. Doolittle, Horizontal transfer of catalase-peroxidase genes between archaea and pathogenic bacteria. Trends Genet, 2000. 16(5): p. 196-7. http://www.ncbi.nlm.nih.gov/pubmed/10782109.

181.     Nesbo, C.L., et al., Phylogenetic analyses of two "archaeal" genes in thermotoga maritima reveal multiple transfers between archaea and bacteria. Mol Biol Evol, 2001. 18(3): p. 362-75. http://www.ncbi.nlm.nih.gov/pubmed/11230537.

182.     Chen, J., et al., Pathogenicity island-directed transfer of unlinked chromosomal virulence genes. Mol Cell, 2015. 57(1): p. 138-49. http://www.ncbi.nlm.nih.gov/pubmed/25498143.

183.     Maiques, E., et al., Beta-lactam antibiotics induce the SOS response and horizontal transfer of virulence factors in Staphylococcus aureus. J Bacteriol, 2006. 188(7): p. 2726-9. http://www.ncbi.nlm.nih.gov/pubmed/16547063.

184.     Saisongkorh, W., et al., Evidence of transfer by conjugation of type IV secretion system genes between Bartonella species and Rhizobium radiobacter in amoeba. PLoS One, 2010. 5(9): p. e12666. http://www.ncbi.nlm.nih.gov/pubmed/20856925.

185.     Venner, S., et al., Ecological networks to unravel the routes to horizontal transposon transfers. PLoS Biol, 2017. 15(2): p. e2001536. http://www.ncbi.nlm.nih.gov/pubmed/28199335.

186.     Guglielmini, J., et al., The Repertoire of ICE in Prokaryotes Underscores the Unity, Diversity, and Ubiquity of Conjugation. PLoS Genet, 2011. 7(8): p. e1002222. http://www.ncbi.nlm.nih.gov/pubmed/21876676.

187.     Burrus, V., J. Marrero, and M.K. Waldor, The current ICE age: biology and evolution of SXT-related integrating conjugative elements. Plasmid, 2006. 55(3): p. 173-83. http://www.ncbi.nlm.nih.gov/pubmed/16530834.

188.     Wozniak, R.A., et al., Comparative ICE genomics: insights into the evolution of the SXT/R391 family of ICEs. PLoS Genet, 2009. 5(12): p. e1000786. http://www.ncbi.nlm.nih.gov/pubmed/20041216.

189.     Burrus, V. and M.K. Waldor, Shaping bacterial genomes with integrative and conjugative elements. Res Microbiol, 2004. 155(5): p. 376-86. http://www.ncbi.nlm.nih.gov/pubmed/15207870.

190.     Burrus, V., et al., Conjugative transposons: the tip of the iceberg. Mol Microbiol, 2002. 46(3): p. 601-10. http://www.ncbi.nlm.nih.gov/pubmed/12410819.

191.     Lautner, M., et al., Regulation, integrase-dependent excision, and horizontal transfer of genomic islands in Legionella pneumophila. J Bacteriol, 2013. 195(7): p. 1583-97. http://www.ncbi.nlm.nih.gov/pubmed/23354744.

192.     Gal-Mor, O. and B.B. Finlay, Pathogenicity islands: a molecular toolbox for bacterial virulence. Cell Microbiol, 2006. 8(11): p. 1707-19. http://www.ncbi.nlm.nih.gov/pubmed/16939533.

193.     Kers, J.A., et al., A large, mobile pathogenicity island confers plant pathogenicity on Streptomyces species. Mol Microbiol, 2005. 55(4): p. 1025-33. http://www.ncbi.nlm.nih.gov/pubmed/15686551.

194.     Haggerty, L.S., et al., A pluralistic account of homology: adapting the models to the data. Mol Biol Evol, 2014. 31(3): p. 501-16. http://www.ncbi.nlm.nih.gov/pubmed/24273322.

195.     Fournier, G.P., C.P. Andam, and J.P. Gogarten, Ancient horizontal gene transfer and the last common ancestors. BMC Evol Biol, 2015. 15: p. 70. http://www.ncbi.nlm.nih.gov/pubmed/25897759.

196.     Filee, J., Lateral gene transfer, lineage-specific gene expansion and the evolution of Nucleo Cytoplasmic Large DNA viruses. J Invertebr Pathol, 2009. 101(3): p. 169-71. http://www.ncbi.nlm.nih.gov/pubmed/19457437.

197.     Filee, J. and M. Chandler, Gene exchange and the origin of giant viruses. Intervirology, 2010. 53(5): p. 354-61. http://www.ncbi.nlm.nih.gov/pubmed/20551687.

198.     Filee, J., N. Pouget, and M. Chandler, Phylogenetic evidence for extensive lateral acquisition of cellular genes by Nucleocytoplasmic large DNA viruses. BMC Evol Biol, 2008. 8: p. 320. http://www.ncbi.nlm.nih.gov/pubmed/19036122.

199.     Boyer, M., et al., Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms. Proc Natl Acad Sci U S A, 2009. 106(51): p. 21848-53. http://www.ncbi.nlm.nih.gov/pubmed/20007369.

200.     Forslund, K. and E.L. Sonnhammer, Evolution of protein domain architectures. Methods Mol Biol, 2012. 856: p. 187-216. http://www.ncbi.nlm.nih.gov/pubmed/22399460.

201.     Doolittle, R.F. and P. Bork, Evolutionarily mobile modules in proteins. Sci Am, 1993. 269(4): p. 50-6. http://www.ncbi.nlm.nih.gov/pubmed/8235550.

202.     Itzhaki, Z. and H. Margalit, Reduced polymorphism in domains involved in protein-protein interactions. PLoS One, 2012. 7(4): p. e34503. http://www.ncbi.nlm.nih.gov/pubmed/22509312.

203.     Kanaan, S.P., et al., Inferring protein-protein interactions from multiple protein domain combinations. Methods Mol Biol, 2009. 541: p. 43-59. http://www.ncbi.nlm.nih.gov/pubmed/19381530.

204.     Bondos, S.E. and X.X. Tan, Combinatorial transcriptional regulation: the interaction of transcription factors and cell signaling molecules with homeodomain proteins in Drosophila development. Crit Rev Eukaryot Gene Expr, 2001. 11(1-3): p. 145-71. http://www.ncbi.nlm.nih.gov/pubmed/11693959.

205.     Sanselicio, S. and P.H. Viollier, Convergence of alarmone and cell cycle signaling from trans-encoded sensory domains. MBio, 2015. 6(5): p. e01415-15. http://www.ncbi.nlm.nih.gov/pubmed/26489861.

206.     Wuchty, S. and E. Almaas, Evolutionary cores of domain co-occurrence networks. BMC Evol Biol, 2005. 5(1): p. 24. http://www.ncbi.nlm.nih.gov/pubmed/15788102.

207.     Weiner, J., 3rd, A.D. Moore, and E. Bornberg-Bauer, Just how versatile are domains? BMC Evol Biol, 2008. 8: p. 285. http://www.ncbi.nlm.nih.gov/pubmed/18854028.

208.     Kummerfeld, S.K. and S.A. Teichmann, Protein domain organisation: adding order. BMC Bioinformatics, 2009. 10: p. 39. http://www.ncbi.nlm.nih.gov/pubmed/19178743.

209.     Bornberg-Bauer, E., et al., The evolution of domain arrangements in proteins and interaction networks. Cell Mol Life Sci, 2005. 62(4): p. 435-45. http://www.ncbi.nlm.nih.gov/pubmed/15719170.

210.     Wang, Z., et al., A protein domain co-occurrence network approach for predicting protein function and inferring species phylogeny. PLoS One, 2011. 6(3): p. e17906. http://www.ncbi.nlm.nih.gov/pubmed/21455299.

211.     Buljan, M., A. Frankish, and A. Bateman, Quantifying the mechanisms of domain gain in animal proteins. Genome Biol, 2010. 11(7): p. R74. http://www.ncbi.nlm.nih.gov/pubmed/20633280\.

212.     Da Lage, J.L., G. Feller, and S. Janecek, Horizontal gene transfer from Eukarya to bacteria and domain shuffling: the alpha-amylase model. Cell Mol Life Sci, 2004. 61(1): p. 97-109. http://www.ncbi.nlm.nih.gov/pubmed/14704857.

213.     Ponting, C.P. and R.R. Russell, The natural history of protein domains. Annu Rev Biophys Biomol Struct, 2002. 31: p. 45-71. http://www.ncbi.nlm.nih.gov/pubmed/11988462.

214.     Basu, M.K., et al., Evolution of protein domain promiscuity in eukaryotes. Genome Res, 2008. 18(3): p. 449-61. http://www.ncbi.nlm.nih.gov/pubmed/18230802.

215.     Bjorklund, A.K., et al., Domain rearrangements in protein evolution. J Mol Biol, 2005. 353(4): p. 911-23. http://www.ncbi.nlm.nih.gov/pubmed/16198373.

216.     Kosak, S.T. and M. Groudine, Gene order and dynamic domains. Science, 2004. 306(5696): p. 644-7. http://www.ncbi.nlm.nih.gov/pubmed/15499009.

217.     Deeds, E.J., H. Hennessey, and E.I. Shakhnovich, Prokaryotic phylogenies inferred from protein structural domains. Genome Res, 2005. 15(3): p. 393-402. http://www.ncbi.nlm.nih.gov/pubmed/15741510.

218.     Liu, M., et al., Significant expansion of exon-bordering protein domains during animal proteome evolution. Nucleic Acids Res, 2005. 33(1): p. 95-105. http://www.ncbi.nlm.nih.gov/pubmed/15640447.

219.     Sammeth, M., S. Foissac, and R. Guigo, A general definition and nomenclature for alternative splicing events. PLoS Comput Biol, 2008. 4(8): p. e1000147. http://www.ncbi.nlm.nih.gov/pubmed/18688268.

220.     Carvalho, R.F., C.V. Feijao, and P. Duque, On the physiological significance of alternative splicing events in higher plants. Protoplasma, 2013. 250(3): p. 639-50. http://www.ncbi.nlm.nih.gov/pubmed/22961303.

221.     Kelemen, O., et al., Function of alternative splicing. Gene, 2013. 514(1): p. 1-30. http://www.ncbi.nlm.nih.gov/pubmed/22909801.

222.     Kalsotra, A. and T.A. Cooper, Functional consequences of developmentally regulated alternative splicing. Nat Rev Genet, 2011. 12(10): p. 715-29. http://www.ncbi.nlm.nih.gov/pubmed/21921927.

223.     Venables, J.P., J. Tazi, and F. Juge, Regulated functional alternative splicing in Drosophila. Nucleic Acids Res, 2012. 40(1): p. 1-10. http://www.ncbi.nlm.nih.gov/pubmed/21908400.

224.     Chen, M. and J.L. Manley, Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. Nat Rev Mol Cell Biol, 2009. 10(11): p. 741-54. http://www.ncbi.nlm.nih.gov/pubmed/19773805.

225.     House, A.E., Lynch, K.W., Regulation of Alternative Splicing: More than Just the ABCs. J Biol Chem, 2008. 283(3): p. 1217 - 1221. .

226.     Tarn, W., Cellular signals modulate alternative splicing. J Biomed Sci, 2007. 14: p. 517-522. .

227.     Fedor, M.J., Alternative Splicing Minireview Series: Combinatorial Control Facilitates Splicing Regulation of Gene Expression and Enhances Genome Diversity. J Biol Chem, 2008. 283(3): p. 1209 - 1210. .

228.     Chen, T.W., et al., Interrogation of alternative splicing events in duplicated genes during evolution. BMC Genomics, 2011. 12 Suppl 3: p. S16. http://www.ncbi.nlm.nih.gov/pubmed/22369477.

229.     Zhang, P.G., et al., Extensive divergence in alternative splicing patterns after gene and genome duplication during the evolutionary history of Arabidopsis. Mol Biol Evol, 2010. 27(7): p. 1686-97. http://www.ncbi.nlm.nih.gov/pubmed/20185454.

230.     Evlampiev, K. and H. Isambert, Modeling protein network evolution under genome duplication and domain shuffling. BMC Syst Biol, 2007. 1: p. 49. http://www.ncbi.nlm.nih.gov/pubmed/17999763.

231.     Barbosa-Morais, N.L., et al., The evolutionary landscape of alternative splicing in vertebrate species. Science, 2012. 338(6114): p. 1587-93. http://www.ncbi.nlm.nih.gov/pubmed/23258890.

232.     Mudge, J.M., et al., The origins, evolution, and functional potential of alternative splicing in vertebrates. Mol Biol Evol, 2011. 28(10): p. 2949-59. http://www.ncbi.nlm.nih.gov/pubmed/21551269.

233.     Furuta, Y., et al., Domain movement within a gene: a novel evolutionary mechanism for protein diversification. PLoS One, 2011. 6(4): p. e18819. http://www.ncbi.nlm.nih.gov/pubmed/21533192.

234.     Paulding, C.A., M. Ruvolo, and D.A. Haber, The Tre2 (USP6) oncogene is a hominoid-specific gene. Proc Natl Acad Sci U S A, 2003. 100(5): p. 2507-11. http://www.ncbi.nlm.nih.gov/pubmed/12604796.

235.     Ciccarelli, F.D., et al., Complex genomic rearrangements lead to novel primate gene function. Genome Res, 2005. 15(3): p. 343-51. http://www.ncbi.nlm.nih.gov/pubmed/15710750.

236.     She, X., et al., The structure and evolution of centromeric transition regions within the human genome. Nature, 2004. 430(7002): p. 857-64. http://www.ncbi.nlm.nih.gov/pubmed/15318213.

237.     Babushok, D.V., et al., A novel testis ubiquitin-binding protein gene arose by exon shuffling in hominoids. Genome Res, 2007. 17(8): p. 1129-38. http://www.ncbi.nlm.nih.gov/pubmed/17623810.

238.     Williams, G.J., et al., Structural insights into NHEJ: building up an integrated picture of the dynamic DSB repair super complex, one component and interaction at a time. DNA Repair (Amst), 2014. 17: p. 110-20. http://www.ncbi.nlm.nih.gov/pubmed/24656613.

239.     Sisu, C., et al., Comparative analysis of pseudogenes across three phyla. Proc Natl Acad Sci U S A, 2014. 111(37): p. 13361-6. http://www.ncbi.nlm.nih.gov/pubmed/25157146.

240.     Xing, J., et al., Emergence of primate genes by retrotransposon-mediated sequence transduction. Proc Natl Acad Sci U S A, 2006. 103(47): p. 17608-13. http://www.ncbi.nlm.nih.gov/pubmed/17101974.

241.     Cordaux, R. and M.A. Batzer, The impact of retrotransposons on human genome evolution. Nat Rev Genet, 2009. 10(10): p. 691-703. http://www.ncbi.nlm.nih.gov/pubmed/19763152.

242.     Jividen, K. and H. Li, Chimeric RNAs generated by intergenic splicing in normal and cancer cells. Genes Chromosomes Cancer, 2014. 53(12): p. 963-71. http://www.ncbi.nlm.nih.gov/pubmed/25131334.

243.     Okonechnikov, K., et al., InFusion: Advancing Discovery of Fusion Genes and Chimeric Transcripts from Deep RNA-Sequencing Data. PLoS One, 2016. 11(12): p. e0167417. http://www.ncbi.nlm.nih.gov/pubmed/27907167.

244.     Kozlov, A.P., Expression of evolutionarily novel genes in tumors. Infect Agent Cancer, 2016. 11: p. 34. http://www.ncbi.nlm.nih.gov/pubmed/27437030.

245.     Narsing, S., et al., Genes that contribute to cancer fusion genes are large and evolutionarily conserved. Cancer Genet Cytogenet, 2009. 191(2): p. 78-84. http://www.ncbi.nlm.nih.gov/pubmed/19446742.

246.     Kumar-Sinha, C., S. Kalyana-Sundaram, and A.M. Chinnaiyan, Landscape of gene fusions in epithelial cancers: seq and ye shall find. Genome Med, 2015. 7: p. 129. http://www.ncbi.nlm.nih.gov/pubmed/26684754.

247.     Annala, M.J., et al., Fusion genes and their discovery using high throughput sequencing. Cancer Lett, 2013. 340(2): p. 192-200. http://www.ncbi.nlm.nih.gov/pubmed/23376639.

248.     Saleem, M. and N.M. Yusoff, Fusion genes in malignant neoplastic disorders of haematopoietic system. Hematology, 2016. 21(9): p. 501-12. http://www.ncbi.nlm.nih.gov/pubmed/26871368.

249.     Mertens, F., C.R. Antonescu, and F. Mitelman, Gene fusions in soft tissue tumors: Recurrent and overlapping pathogenetic themes. Genes Chromosomes Cancer, 2016. 55(4): p. 291-310. http://www.ncbi.nlm.nih.gov/pubmed/26684580.

250.     Qi, M., et al., Morphologic features of carcinomas with recurrent gene fusions. Adv Anat Pathol, 2012. 19(6): p. 417-24. http://www.ncbi.nlm.nih.gov/pubmed/23060067.

251.     Latysheva, N.S. and M.M. Babu, Discovering and understanding oncogenic gene fusions through data intensive computational approaches. Nucleic Acids Res, 2016. 44(10): p. 4487-503. http://www.ncbi.nlm.nih.gov/pubmed/27105842.

252.     Mertens, F., et al., The emerging complexity of gene fusions in cancer. Nat Rev Cancer, 2015. 15(6): p. 371-81. http://www.ncbi.nlm.nih.gov/pubmed/25998716.

253.     Jia, Y., Z. Xie, and H. Li, Intergenically Spliced Chimeric RNAs in Cancer. Trends Cancer, 2016. 2(9): p. 475-484. http://www.ncbi.nlm.nih.gov/pubmed/28210711.

254.     Li, H., et al., Gene fusions and RNA trans-splicing in normal and neoplastic human cells. Cell Cycle, 2009. 8(2): p. 218-22. http://www.ncbi.nlm.nih.gov/pubmed/19158498.

255.     Seki, Y., T. Mizukami, and T. Kohno, Molecular Process Producing Oncogene Fusion in Lung Cancer Cells by Illegitimate Repair of DNA Double-Strand Breaks. Biomolecules, 2015. 5(4): p. 2464-76. http://www.ncbi.nlm.nih.gov/pubmed/26437441.

256.     Lawson, A.R., et al., RAF gene fusion breakpoints in pediatric brain tumors are characterized by significant enrichment of sequence microhomology. Genome Res, 2011. 21(4): p. 505-14. http://www.ncbi.nlm.nih.gov/pubmed/21393386.

257.     Khalturin, K., et al., More than just orphans: are taxonomically-restricted genes important in evolution? Trends Genet, 2009. 25(9): p. 404-13. http://www.ncbi.nlm.nih.gov/pubmed/19716618.

258.     Zhou, K., A. Kuo, and I.V. Grigoriev, Reverse transcriptase and intron number evolution. Stem Cell Investig, 2014. 1: p. 17. http://www.ncbi.nlm.nih.gov/pubmed/27358863.

259.     Pavesi, A., G. Magiorkinis, and D.G. Karlin, Viral proteins originated de novo by overprinting can be identified by codon usage: application to the "gene nursery" of Deltaretroviruses. PLoS Comput Biol, 2013. 9(8): p. e1003162. http://www.ncbi.nlm.nih.gov/pubmed/23966842.

260.     Delaye, L., et al., The origin of a novel gene through overprinting in Escherichia coli. BMC Evol Biol, 2008. 8: p. 31. http://www.ncbi.nlm.nih.gov/pubmed/18226237.

261.     Murphy, D.N. and A. McLysaght, De novo origin of protein-coding genes in murine rodents. PLoS One, 2012. 7(11): p. e48650. http://www.ncbi.nlm.nih.gov/pubmed/23185269.

262.     Reinhardt, J.A., et al., De novo ORFs in Drosophila are important to organismal fitness and evolved rapidly from previously non-coding sequences. PLoS Genet, 2013. 9(10): p. e1003860. http://www.ncbi.nlm.nih.gov/pubmed/24146629.

263.     Donoghue, M.T., et al., Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana. BMC Evol Biol, 2011. 11: p. 47. http://www.ncbi.nlm.nih.gov/pubmed/21332978.

264.     Wu, D.D., et al., "Out of pollen" hypothesis for origin of new genes in flowering plants: study from Arabidopsis thaliana. Genome Biol Evol, 2014. 6(10): p. 2822-9. http://www.ncbi.nlm.nih.gov/pubmed/25237051.

265.     Li, C.Y., et al., A human-specific de novo protein-coding gene associated with human brain functions. PLoS Comput Biol, 2010. 6(3): p. e1000734. http://www.ncbi.nlm.nih.gov/pubmed/20376170.

266.     Betran, E., K. Thornton, and M. Long, Retroposed new genes out of the X in Drosophila. Genome Res, 2002. 12(12): p. 1854-9. http://www.ncbi.nlm.nih.gov/pubmed/12466289.

267.     Schmidt, E.E. and C.J. Davies, The origins of polypeptide domains. Bioessays, 2007. 29(3): p. 262-70. http://www.ncbi.nlm.nih.gov/pubmed/17295290.

268.     Tajnik, M., et al., Intergenic Alu exonisation facilitates the evolution of tissue-specific transcript ends. Nucleic Acids Res, 2015. 43(21): p. 10492-505. http://www.ncbi.nlm.nih.gov/pubmed/26400176.

269.     Kwon, Y.J., et al., Structure and Expression Analyses of SVA Elements in Relation to Functional Genes. Genomics Inform, 2013. 11(3): p. 142-8. http://www.ncbi.nlm.nih.gov/pubmed/24124410.

270.     Park, S.J., et al., Gain of a New Exon by a Lineage-Specific Alu Element-Integration Event in the BCS1L Gene during Primate Evolution. Mol Cells, 2015. 38(11): p. 950-8. http://www.ncbi.nlm.nih.gov/pubmed/26537194.

271.     Mandal, A.K., et al., Transcriptome-wide expansion of non-coding regulatory switches: evidence from co-occurrence of Alu exonization, antisense and editing. Nucleic Acids Res, 2013. 41(4): p. 2121-37. http://www.ncbi.nlm.nih.gov/pubmed/23303787.

272.     Zarnack, K., et al., Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements. Cell, 2013. 152(3): p. 453-66. http://www.ncbi.nlm.nih.gov/pubmed/23374342.

273.     Moller-Krull, M., et al., Beyond DNA: RNA editing and steps toward Alu exonization in primates. J Mol Biol, 2008. 382(3): p. 601-9. http://www.ncbi.nlm.nih.gov/pubmed/18680752.

274.     Grover, D., et al., Alu repeat analysis in the complete human genome: trends and variations with respect to genomic composition. Bioinformatics, 2004. 20(6): p. 813-7. http://www.ncbi.nlm.nih.gov/pubmed/14751968.

275.     Hormozdiari, F., et al., Alu repeat discovery and characterization within human genomes. Genome Res, 2011. 21(6): p. 840-9. http://www.ncbi.nlm.nih.gov/pubmed/21131385.

276.     Corvelo, A. and E. Eyras, Exon creation and establishment in human genes. Genome Biol, 2008. 9(9): p. R141. http://www.ncbi.nlm.nih.gov/pubmed/18811936.

277.     Wu, M., L. Li, and Z. Sun, Transposable element fragments in protein-coding regions and their contributions to human functional proteins. Gene, 2007. 401(1-2): p. 165-71. http://www.ncbi.nlm.nih.gov/pubmed/17716834.

278.     Schwartz, S., et al., Alu exonization events reveal features required for precise recognition of exons by the splicing machinery. PLoS Comput Biol, 2009. 5(3): p. e1000300. http://www.ncbi.nlm.nih.gov/pubmed/19266014.

279.     Lev-Maor, G., et al., RNA-editing-mediated exon evolution. Genome Biol, 2007. 8(2): p. R29. http://www.ncbi.nlm.nih.gov/pubmed/17326827.

280.     Neme, R. and D. Tautz, Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution. BMC Genomics, 2013. 14: p. 117. http://www.ncbi.nlm.nih.gov/pubmed/23433480.

281.     Wu, W., et al., Flock house virus RNA polymerase initiates RNA synthesis de novo and possesses a terminal nucleotidyl transferase activity. PLoS One, 2014. 9(1): p. e86876. http://www.ncbi.nlm.nih.gov/pubmed/24466277.

282.     Troshchynsky, A., et al., Functional analyses of polymorphic variants of human terminal deoxynucleotidyl transferase. Genes Immun, 2015. 16(6): p. 388-98. http://www.ncbi.nlm.nih.gov/pubmed/26043173.

283.     Motea, E.A. and A.J. Berdis, Terminal deoxynucleotidyl transferase: the story of a misguided DNA polymerase. Biochim Biophys Acta, 2010. 1804(5): p. 1151-66. http://www.ncbi.nlm.nih.gov/pubmed/19596089.

284.     Thai, T.H. and J.F. Kearney, Isoforms of terminal deoxynucleotidyltransferase: developmental aspects and function. Adv Immunol, 2005. 86: p. 113-36. http://www.ncbi.nlm.nih.gov/pubmed/15705420.

285.     Bentolila, L.A., et al., Constitutive expression of terminal deoxynucleotidyl transferase in transgenic mice is sufficient for N region diversity to occur at any Ig locus throughout B cell differentiation. J Immunol, 1997. 158(2): p. 715-23. http://www.ncbi.nlm.nih.gov/pubmed/8992987.

286.     Komori, T., et al., Lack of N regions in antigen receptor variable region genes of TdT-deficient lymphocytes. Science, 1993. 261(5125): p. 1171-5. http://www.ncbi.nlm.nih.gov/pubmed/8356451.

287.     Nick McElhinny, S.A. and D.A. Ramsden, Sibling rivalry: competition between Pol X family members in V(D)J recombination and general double strand break repair. Immunol Rev, 2004. 200: p. 156-64. http://www.ncbi.nlm.nih.gov/pubmed/15242403.

288.     Yamtich, J. and J.B. Sweasy, DNA polymerase family X: function, structure, and cellular roles. Biochim Biophys Acta, 2010. 1804(5): p. 1136-50. http://www.ncbi.nlm.nih.gov/pubmed/19631767.

289.     Gouge, J., et al., Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair. Embo J, 2015. 34(8): p. 1126-42. http://www.ncbi.nlm.nih.gov/pubmed/25762590.

290.     Black, S.J., et al., DNA Polymerase theta: A Unique Multifunctional End-Joining Machine. Genes (Basel), 2016. 7(9). http://www.ncbi.nlm.nih.gov/pubmed/27657134.

291.     Wyatt, D.W., et al., Essential Roles for Polymerase theta-Mediated End Joining in the Repair of Chromosome Breaks. Mol Cell, 2016. 63(4): p. 662-73. http://www.ncbi.nlm.nih.gov/pubmed/27453047.

292.     Sakofsky, C.J., et al., Translesion Polymerases Drive Microhomology-Mediated Break-Induced Replication Leading to Complex Chromosomal Rearrangements. Mol Cell, 2015. 60(6): p. 860-72. http://www.ncbi.nlm.nih.gov/pubmed/26669261.

293.     Morrish, T.A., et al., DNA repair mediated by endonuclease-independent LINE-1 retrotransposition. Nat Genet, 2002. 31(2): p. 159-65. http://www.ncbi.nlm.nih.gov/pubmed/12006980.

294.     Storici, F., et al., RNA-templated DNA repair. Nature, 2007. 447(7142): p. 338-41. http://www.ncbi.nlm.nih.gov/pubmed/17429354.

295.     Meers, C., H. Keskin, and F. Storici, DNA repair by RNA: Templated, or not templated, that is the question. DNA Repair (Amst), 2016. 44: p. 17-21. http://www.ncbi.nlm.nih.gov/pubmed/27237587.

296.     Keskin, H., et al., Transcript-RNA-templated DNA recombination and repair. Nature, 2014. 515(7527): p. 436-9. http://www.ncbi.nlm.nih.gov/pubmed/25186730.

297.     Ono, R., et al., Double strand break repair by capture of retrotransposon sequences and reverse-transcribed spliced mRNA sequences in mouse zygotes. Sci Rep, 2015. 5: p. 12281. http://www.ncbi.nlm.nih.gov/pubmed/26216318.

298.     Kung, P.C., et al., Terminal deoxynucleotidyl transferase in the diagnosis of leukemia and malignant lymphoma. Am J Med, 1978. 64(5): p. 788-94. http://www.ncbi.nlm.nih.gov/pubmed/347933.

299.     Munsch, N., et al., Evolution of DNA polymerase alpha, beta and terminal deoxynucleotidyl transferase in hamster lymphoid populations during the development of different types of tumors. Biomed Pharmacother, 1982. 36(10): p. 440-4. http://www.ncbi.nlm.nih.gov/pubmed/7184515.

300.     Ji, J.P. and L.A. Loeb, Fidelity of HIV-1 reverse transcriptase copying RNA in vitro. Biochemistry, 1992. 31(4): p. 954-8. http://www.ncbi.nlm.nih.gov/pubmed/1370910.

301.     Menendez-Arias, L., Molecular basis of fidelity of DNA synthesis and nucleotide specificity of retroviral reverse transcriptases. Prog Nucleic Acid Res Mol Biol, 2002. 71: p. 91-147. http://www.ncbi.nlm.nih.gov/pubmed/12102562.

302.     Smith, H.C., RNA binding to APOBEC deaminases; Not simply a substrate for C to U editing. RNA Biol, 2016: p. 1-13. http://www.ncbi.nlm.nih.gov/pubmed/27869537.

303.     Salter, J.D., R.P. Bennett, and H.C. Smith, The APOBEC Protein Family: United by Structure, Divergent in Function. Trends Biochem Sci, 2016. 41(7): p. 578-94. http://www.ncbi.nlm.nih.gov/pubmed/27283515.

304.     Bass, B.L., RNA editing and hypermutation by adenosine deamination. Trends Biochem Sci, 1997. 22(5): p. 157-62. http://www.ncbi.nlm.nih.gov/pubmed/9175473.

305.     Wheeler, E.C., et al., Noncoding regions of C. elegans mRNA undergo selective adenosine to inosine deamination and contain a small number of editing sites per transcript. RNA Biol, 2015. 12(2): p. 162-74. http://www.ncbi.nlm.nih.gov/pubmed/25826568.

306.     Sakurai, M., et al., Inosine cyanoethylation identifies A-to-I RNA editing sites in the human transcriptome. Nat Chem Biol, 2010. 6(10): p. 733-40. http://www.ncbi.nlm.nih.gov/pubmed/20835228.

307.     Oz-Gleenberg, I., E. Herzig, and A. Hizi, Template-independent DNA synthesis activity associated with the reverse transcriptase of the long terminal repeat retrotransposon Tf1. FEBS J, 2012. 279(1): p. 142-53. http://www.ncbi.nlm.nih.gov/pubmed/22035236.

308.     Brosius, J., RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene, 1999. 238: p. 115–134. http://www.ncbi.nlm.nih.gov/pubmed/10570990.

309.     Loeb, L.A., C.F. Springgate, and N. Battula, Errors in DNA replication as a basis of malignant changes. Cancer Res, 1974. 34(9): p. 2311-21. http://www.ncbi.nlm.nih.gov/pubmed/4136142.

310.     Venkatesan, R.N. and L.A. Loeb, The multiplicity of mutations in human cancers. Adv Exp Med Biol, 2005. 570: p. 3-17. http://www.ncbi.nlm.nih.gov/pubmed/18727496.

311.     Loeb, L.A., Mutator phenotype may be required for multistage carcinogenesis. Cancer Res, 1991. 51(12): p. 3075-9. http://www.ncbi.nlm.nih.gov/pubmed/2039987.

312.     Kaer, K. and M. Speek, Retroelements in human disease. Gene, 2013. 518(2): p. 231-41. http://www.ncbi.nlm.nih.gov/pubmed/23333607.

313.     Sinibaldi-Vallebona, P., C. Matteucci, and C. Spadafora, Retrotransposon-encoded reverse transcriptase in the genesis, progression and cellular plasticity of human cancer. Cancers (Basel), 2011. 3(1): p. 1141-57. http://www.ncbi.nlm.nih.gov/pubmed/24212657.

314.     Fraser, J., et al., Chromatin conformation signatures of cellular differentiation. Genome Biol, 2009. 10(4): p. R37. http://www.ncbi.nlm.nih.gov/pubmed/19374771.

315.     Dekker, J., et al., Capturing chromosome conformation. Science, 2002. 295(5558): p. 1306-11. http://www.ncbi.nlm.nih.gov/pubmed/11847345.

316.     Cao, R. and J. Cheng, Deciphering the association between gene function and spatial gene-gene interactions in 3D human genome conformation. BMC Genomics, 2015. 16: p. 880. http://www.ncbi.nlm.nih.gov/pubmed/26511362.

317.     Phillips-Cremins, J.E., et al., Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment. Cell, 2013. 153(6): p. 1281-95. http://www.ncbi.nlm.nih.gov/pubmed/23706625.

318.     Sanyal, A., et al., The long-range interaction landscape of gene promoters. Nature, 2012. 489(7414): p. 109-13. http://www.ncbi.nlm.nih.gov/pubmed/22955621.

319.     Thurman, R.E., et al., The accessible chromatin landscape of the human genome. Nature, 2012. 489(7414): p. 75-82. http://www.ncbi.nlm.nih.gov/pubmed/22955617.

320.     Zedek, F., et al., Correlated evolution of LTR retrotransposons and genome size in the genus Eleocharis. BMC Plant Biol, 2010. 10: p. 265. http://www.ncbi.nlm.nih.gov/pubmed/21118487.

321.     Ecker, J.R., et al., Genomics: ENCODE explained. Nature, 2012. 489(7414): p. 52-5. http://www.ncbi.nlm.nih.gov/pubmed/22955614.

322.     Birney, E., The making of ENCODE: Lessons for big-data projects. Nature, 2012. 489(7414): p. 49-51. http://www.ncbi.nlm.nih.gov/pubmed/22955613.

323.     Skipper, M., R. Dhand, and P. Campbell, Presenting ENCODE. Nature, 2012. 489(7414): p. 45. http://www.ncbi.nlm.nih.gov/pubmed/22955612.

324.     Piriyapongsa, J., L. Marino-Ramirez, and I.K. Jordan, Origin and evolution of human microRNAs from transposable elements. Genetics, 2007. 176(2): p. 1323-37. http://www.ncbi.nlm.nih.gov/pubmed/17435244.

325.     Qin, S., et al., The Role of Transposable Elements in the Origin and Evolution of MicroRNAs in Human. PLoS One, 2015. 10(6): p. e0131365. http://www.ncbi.nlm.nih.gov/pubmed/26115450.

326.     Biemont, C. and C. Vieira, Genetics: junk DNA as an evolutionary force. Nature, 2006. 443(7111): p. 521-4. http://www.ncbi.nlm.nih.gov/pubmed/17024082.

327.     Brunet, T.D. and W.F. Doolittle, Multilevel Selection Theory and the Evolutionary Functions of Transposable Elements. Genome Biol Evol, 2015. 7(8): p. 2445-57. http://www.ncbi.nlm.nih.gov/pubmed/26253318.

328.     Wang, K., G. Huang, and Y. Zhu, Transposable elements play an important role during cotton genome evolution and fiber cell development. Sci China Life Sci, 2016. 59(2): p. 112-21. http://www.ncbi.nlm.nih.gov/pubmed/26687725.

329.     Polavarapu, N., et al., Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA. BMC Genomics, 2008. 9: p. 226. http://www.ncbi.nlm.nih.gov/pubmed/18485226.

330.     Huda, A., et al., Prediction of transposable element derived enhancers using chromatin modification profiles. PLoS One, 2011. 6(11): p. e27513. http://www.ncbi.nlm.nih.gov/pubmed/22087331.

331.     Xie, M., et al., DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape. Nat Genet, 2013. 45(7): p. 836-41. http://www.ncbi.nlm.nih.gov/pubmed/23708189.

332.     Huda, A., et al., Epigenetic regulation of transposable element derived human gene promoters. Gene, 2011. 475(1): p. 39-48. http://www.ncbi.nlm.nih.gov/pubmed/21215797.

333.     Miller, W.J. and P. Capy, Mobile genetic elements as natural tools for genome evolution. Methods Mol Biol, 2004. 260: p. 1-20. http://www.ncbi.nlm.nih.gov/pubmed/15020798.

334.     Biemont, C., A brief history of the status of transposable elements: from junk DNA to major players in evolution. Genetics, 2010. 186(4): p. 1085-93. http://www.ncbi.nlm.nih.gov/pubmed/21156958.

335.     Oliver, K.R. and W.K. Greene, Transposable elements: powerful facilitators of evolution. Bioessays, 2009. 31(7): p. 703-14. http://www.ncbi.nlm.nih.gov/pubmed/19415638.

336.     Hedges, D.J. and M.A. Batzer, From the margins of the genome: mobile elements shape primate evolution. Bioessays, 2005. 27(8): p. 785-94. http://www.ncbi.nlm.nih.gov/pubmed/16015599.

337.     Belyayev, A., Bursts of transposable elements as an evolutionary driving force. J Evol Biol, 2014. 27(12): p. 2573-84. http://www.ncbi.nlm.nih.gov/pubmed/25290698.

338.     Dimitri, P. and N. Junakovic, Revising the selfish DNA hypothesis: new evidence on accumulation of transposable elements in heterochromatin. Trends Genet, 1999. 15(4): p. 123-4. http://www.ncbi.nlm.nih.gov/pubmed/10203812.

339.     Matharu, N.K. and S.H. Ahanger, Chromatin Insulators and Topological Domains: Adding New Dimensions to 3D Genome Architecture. Genes (Basel), 2015. 6(3): p. 790-811. http://www.ncbi.nlm.nih.gov/pubmed/26340639.

340.     Feschotte, C., Transposable elements and the evolution of regulatory networks. Nat Rev Genet, 2008. 9(5): p. 397-405. http://www.ncbi.nlm.nih.gov/pubmed/18368054.

341.     Rebollo, R., M.T. Romanish, and D.L. Mager, Transposable elements: an abundant and natural source of regulatory sequences for host genes. Annu Rev Genet, 2012. 46: p. 21-42. http://www.ncbi.nlm.nih.gov/pubmed/22905872.

342.     Cowley, M. and R.J. Oakey, Transposable elements re-wire and fine-tune the transcriptome. PLoS Genet, 2013. 9(1): p. e1003234. http://www.ncbi.nlm.nih.gov/pubmed/23358118.

343.     van de Lagemaat, L.N., et al., Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions. Trends Genet, 2003. 19(10): p. 530-6. http://www.ncbi.nlm.nih.gov/pubmed/14550626.

344.     Castanera, R., et al., Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles. PLoS Genet, 2016. 12(6): p. e1006108. http://www.ncbi.nlm.nih.gov/pubmed/27294409.

345.     Bennetzen, J.L. and H. Wang, The contributions of transposable elements to the structure, function, and evolution of plant genomes. Annu Rev Plant Biol, 2014. 65: p. 505-30. http://www.ncbi.nlm.nih.gov/pubmed/24579996.

346.     Shapiro, J.A., Exploring the read-write genome: mobile DNA and mammalian adaptation. Crit Rev Biochem Mol Biol, 2016: p. 1-17. http://www.ncbi.nlm.nih.gov/pubmed/27599542.

347.     Bartel, D.P., MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 2004. 116(2): p. 281-97. http://www.ncbi.nlm.nih.gov/pubmed/14744438.

348.     Smalheiser, N.R. and V.I. Torvik, Mammalian microRNAs derived from genomic repeats. Trends Genet, 2005. 21(6): p. 322-6. http://www.ncbi.nlm.nih.gov/pubmed/15922829.

349.     Sun, J., et al., Characterization and evolution of microRNA genes derived from repetitive elements and duplication events in plants. PLoS One, 2012. 7(4): p. e34092. http://www.ncbi.nlm.nih.gov/pubmed/22523544.

350.     Yuan, Z., et al., MicroRNA genes derived from repetitive elements and expanded by segmental duplication events in mammalian genomes. PLoS One, 2011. 6(3): p. e17666. http://www.ncbi.nlm.nih.gov/pubmed/21436881.

351.     Borchert, G.M., et al., Comprehensive analysis of microRNA genomic loci identifies pervasive repetitive-element origins. Mob Genet Elements, 2011. 1(1): p. 8-17. http://www.ncbi.nlm.nih.gov/pubmed/22016841.

352.     Hezroni, H., et al., Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species. Cell Rep, 2015. 11(7): p. 1110-22. http://www.ncbi.nlm.nih.gov/pubmed/25959816.

353.     Gaiti, F., et al., Dynamic and Widespread lncRNA Expression in a Sponge and the Origin of Animal Complexity. Mol Biol Evol, 2015. 32(9): p. 2367-82. http://www.ncbi.nlm.nih.gov/pubmed/25976353.

354.     Kannan, S., et al., Transposable Element Insertions in Long Intergenic Non-Coding RNA Genes. Front Bioeng Biotechnol, 2015. 3: p. 71. http://www.ncbi.nlm.nih.gov/pubmed/26106594.

355.     Campo-Paysaa, F., et al., microRNA complements in deuterostomes: origin and evolution of microRNAs. Evol Dev, 2011. 13(1): p. 15-27. http://www.ncbi.nlm.nih.gov/pubmed/21210939.

356.     Witkin, E.M., Nuclear segregation and the delayed appearance of induced mutants in Escherichia coli. Cold Spring Harb Symp Quant Biol, 1951. 16: p. 357-72. http://www.ncbi.nlm.nih.gov/pubmed/14942750.

357.     Witkin, E.M., Effects of Temperature on Spontaneous and Induced Mutations in Escherichia Coli. Proc Natl Acad Sci U S A, 1953. 39(5): p. 427-33. http://www.ncbi.nlm.nih.gov/pubmed/16589286.

358.     Witkin, E.M., The use of sodium nucleate in the study of the mutagenic activity of acriflavine in Escherichia coli. Proc Natl Acad Sci U S A, 1950. 36(12): p. 724-31. http://www.ncbi.nlm.nih.gov/pubmed/14808162.

359.     Al-Khedery, B. and D.R. Allred, Antigenic variation in Babesia bovis occurs through segmental gene conversion of  the ves multigene family, within a bidirectional locus of active transcription. Mol Microbiol, 2006. 59(2): p. 402-14. http://www.ncbi.nlm.nih.gov/pubmed/16390438.

360.     Stringer, J.R., Antigenic variation in pneumocystis. J Eukaryot Microbiol, 2007. 54(1): p. 8-13. http://www.ncbi.nlm.nih.gov/pubmed/17300510.

361.     Vink, C., G. Rudenko, and H.S. Seifert, Microbial antigenic variation mediated by homologous DNA recombination. FEMS Microbiol Rev, 2012. 36(5): p. 917-48. http://www.ncbi.nlm.nih.gov/pubmed/22212019.

362.     Hardianti, M.S., et al., Activation-induced cytidine deaminase expression in follicular lymphoma: association between AID expression and ongoing mutation in FL. Leukemia, 2004. 18(4): p. 826-31. http://www.ncbi.nlm.nih.gov/pubmed/14990977.

363.     Papaemmanuil, E., et al., RAG-mediated recombination is the predominant driver of oncogenic rearrangement in ETV6-RUNX1 acute lymphoblastic leukemia. Nat Genet, 2014. 46(2): p. 116-25. http://www.ncbi.nlm.nih.gov/pubmed/24413735.

364.     Robbiani, D.F. and M.C. Nussenzweig, Chromosome translocation, B cell lymphoma, and activation-induced cytidine deaminase. Annu Rev Pathol, 2013. 8: p. 79-103. http://www.ncbi.nlm.nih.gov/pubmed/22974238.

365.     Halper-Stromberg, E., et al., Fine mapping of V(D)J recombinase mediated rearrangements in human lymphoid malignancies. BMC Genomics, 2013. 14: p. 565. http://www.ncbi.nlm.nih.gov/pubmed/23957733.

366.     Lee, E., et al., Landscape of somatic retrotransposition in human cancers. Science, 2012. 337(6097): p. 967-71. http://www.ncbi.nlm.nih.gov/pubmed/22745252.

367.     Rode, A., et al., Chromothripsis in cancer cells: An update. Int J Cancer, 2016. 138(10): p. 2322-33. http://www.ncbi.nlm.nih.gov/pubmed/26455580.

368.     de Pagter, M.S. and W.P. Kloosterman, The Diverse Effects of Complex Chromosome Rearrangements and Chromothripsis in Cancer Development. Recent Results Cancer Res, 2015. 200: p. 165-93. http://www.ncbi.nlm.nih.gov/pubmed/26376877.

369.     Rausch, T., et al., Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations. Cell, 2012. 148(1-2): p. 59-71. http://www.ncbi.nlm.nih.gov/pubmed/22265402.

370.     Ye, K., et al., Systematic discovery of complex insertions and deletions in human cancers. Nat Med, 2015. http://www.ncbi.nlm.nih.gov/pubmed/26657142.

371.     Chandra, H.S., et al., Philadelphia Chromosome Symposium: commemoration of the 50th anniversary of the discovery of the Ph chromosome. Cancer Genet, 2011. 204(4): p. 171-9. http://www.ncbi.nlm.nih.gov/pubmed/21536234.

372.     Caporale, L.H., Overview of the creative genome: effects of genome structure and sequence on the generation of variation and evolution. Ann N Y Acad Sci, 2012. 1267(1): p. 1-10. http://www.ncbi.nlm.nih.gov/pubmed/22954209.

373.     Damiani, G., The Yin and Yang of anti-Darwinian epigenetics and Darwinian genetics. Riv Biol, 2007. 100(3): p. 361-402. http://www.ncbi.nlm.nih.gov/pubmed/18278738.

374.     Ploeger, A. and F. Galis, Evo Devo and cognitive science. Wiley Interdiscip Rev Cogn Sci, 2011. 2(4): p. 429-40. http://www.ncbi.nlm.nih.gov/pubmed/26302202.

375.     Affifi, R., The Semiosis of "Side Effects" in Genetic Interventions. Biosemiotics, 2016. 9(3): p. 345-364. http://www.ncbi.nlm.nih.gov/pubmed/28066514.

376.     Liu, S., et al., Mu transposon insertion sites and meiotic recombination events co-localize with epigenetic marks for open chromatin across the maize genome. PLoS Genet, 2009. 5(11): p. e1000733. http://www.ncbi.nlm.nih.gov/pubmed/19936291.

377.     Baller, J.A., J. Gao, and D.F. Voytas, Access to DNA establishes a secondary target site bias for the yeast retrotransposon Ty5. Proc Natl Acad Sci U S A, 2011. 108(51): p. 20351-6. http://www.ncbi.nlm.nih.gov/pubmed/21788500.

378.     Gangadharan, S., et al., DNA transposon Hermes inserts into DNA in nucleosome-free regions in vivo. Proc Natl Acad Sci U S A, 2010. 107(51): p. 21966-72. http://www.ncbi.nlm.nih.gov/pubmed/21131571.