Families of transposable elements, population structure and the origin of species

Biology Direct

Volumn 6, Issue , 2011, Pages

  Jurka, Jerzy ^a   Bao, Weidong ^a   Kojima, Kenji K ^a  

^a Genetic Information Research Institute   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EUKARYOTA; MAMMALIA;

ALU SEQUENCE; ANIMAL; ARTICLE; CLASSIFICATION; GENE FLOW; GENETIC DRIFT; GENETICS; HUMAN; HYBRIDIZATION; LONG TERMINAL REPEAT; MAMMAL; MOLECULAR EVOLUTION; MUTATION; PHYLOGENY; SPECIES DIFFERENCE; SPECIES DIFFERENTIATION; TRANSPOSON;

ALU ELEMENTS; ANIMALS; DNA TRANSPOSABLE ELEMENTS; EVOLUTION, MOLECULAR; GENE FLOW; GENETIC DRIFT; GENETIC SPECIATION; HUMANS; HYBRIDIZATION, GENETIC; MAMMALS; MUTATION; PHYLOGENY; SPECIES SPECIFICITY; TERMINAL REPEAT SEQUENCES;

EID: 80052854314     PISSN: None     EISSN: 17456150     Source Type: Journal    
DOI: 10.1186/1745-6150-6-44     Document Type: Article

References (98)

1. Weiner AM, Deininger PL, Efstratiadis A. Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. Annu Rev Biochem 1986, 55:631-661. 10.1146/annurev.bi.55.070186.003215, 2427017.
2. Brosius J. Retroposons--seeds of evolution. Science 1991, 251:753. 10.1126/science.1990437, 1990437.
3. Kidwell MG, Lisch D. Transposable elements as sources of variation in animals and plants. Proc Natl Acad Sci USA 1997, 94:7704-7711. 10.1073/pnas.94.15.7704, 33680, 9223252.
4. Kidwell MG, Lisch DR. Transposable elements and host genome evolution. TREE 2000, 15:95-99.
5. Kidwell MG, Lisch DR. Perspective: transposable elements, parasitic DNA, and genome evolution. Evolution Int J Org Evolution 2001, 55:1-24.
6. Kazazian HH. Mobile elements: drivers of genome evolution. Science 2004, 303:1626-1632. 10.1126/science.1089670, 15016989.
7. Bohne A, Brunet F, Galiana-Arnoux D, Schultheis C, Volff JN. Transposable elements as drivers of genomic and biological diversity in vertebrates. Chromosome Res 2008, 16:203-215. 10.1007/s10577-007-1202-6, 18293113.
8. Oliver KR, Greene WK. Transposable elements: powerful facilitators of evolution. Bioessays 2009, 31:703-714. 10.1002/bies.200800219, 19415638.
9. Oliver KR, Greene WK. Mobile DNA and the TE-Thrust hypothesis: supporting evidence from the primates. Mob DNA 2011, 2:8. 10.1186/1759-8753-2-8, 3123540, 21627776.
10. Slagel V, Flemington E, Traina-Dorge V, Bradshaw H, Deininger PL. Clustering and subfamily relationships of the Alu family in the human genome. Mol Biol Evol 1987, 4:19-29.
11. Willard C, Nguyen HT, Schmid CW. Existence of at least three distinct Alu subfamilies. J Mol Evol 1987, 26:180-186. 10.1007/BF02099850, 3129565.
12. Britten RJ, Baron WF, Stout DB, Davidson EH. Sources and evolution of human Alu repeated sequences. Proc Natl Acad Sci USA 1988, 85:4770-4774. 10.1073/pnas.85.13.4770, 280517, 3387437.
13. Jurka J, Smith T. A fundamental division in the Alu family of repeated sequences. Proc Natl Acad Sci USA 1988, 85:4775-4778. 10.1073/pnas.85.13.4775, 280518, 3387438.
14. Quentin Y. The Alu family developed through successive waves of fixation closely connected with primate lineage history. J Mol Evol 1988, 27:194-202. 10.1007/BF02100074, 3138422.
15. Shen MR, Batzer MA, Deininger PL. Evolution of the master Alu gene(s). J Mol Evol 1991, 33:311-320. 10.1007/BF02102862, 1774786.
16. Venner S, Feschotte C, Biemont C. Dynamics of transposable elements: towards a community ecology of the genome. Trends Genet 2009, 25:317-323. 10.1016/j.tig.2009.05.003, 2945704, 19540613.
17. Charlesworth B, Charlesworth D. The population dynamics of transposable elements. Genet Res Camb 1983, 42:1-27.
18. Langley CH, Brookfield JF, Kaplan N. Transposable elements in mendelian populations. I. A theory. Genetics 1983, 104:457-471. 1202088, 17246142.
19. Brookfield JF, Badge RM. Population genetics models of transposable elements. Genetica 1997, 100:281-294. 10.1023/A:1018310418744, 9440281.
20. Le Rouzic A, Capy P. The first steps of transposable elements invasion: parasitic strategy vs. genetic drift. Genetics 2005, 169:1033-1043. 10.1534/genetics.104.031211, 1449084, 15731520.
21. Lynch M, Conery JS. The origins of genome complexity. Science 2003, 302:1401-1404. 10.1126/science.1089370, 14631042.
22. Lynch M. The frailty of adaptive hypotheses for the origins of organismal complexity. Proc Natl Acad Sci USA 2007, 104(Suppl 1):8597-8604. 1876435, 17494740.
23. Lynch M. The Origins of Genome Archiecture 2007, Sunderland MA: Sinauer Associates, Inc.
24. Jurka J, Kapitonov VV, Kohany O, Jurka MV. Repetitive sequences in complex genomes: structure and evolution. Annu Rev Genomics Hum Genet 2007, 8:241-259. 10.1146/annurev.genom.8.080706.092416, 17506661.
25. Wright S. Evolution in Mendelian Populations. Genetics 1931, 16:97-159. 1201091, 17246615.
26. Provine WB. Ernst Mayr: Genetics and speciation. Genetics 2004, 167:1041-1046. 1470966, 15280221.
27. Kimura M. On the probability of fixation of mutant genes in a population. Genetics 1962, 47:713-719. 1210364, 14456043.
28. Ohta T. Slightly deleterious mutant substitutions in evolution. Nature 1973, 246:96-98. 10.1038/246096a0, 4585855.
29. Ohta T, Gillespie JH. Development of Neutral and Nearly Neutral Theories. Theor Popul Biol 1996, 49:128-142. 10.1006/tpbi.1996.0007, 8813019.
30. Slatkin M. Gene flow in natural populations. Ann Rev Ecol Syst 1985, 16:393-430.
31. Vieira C, Biemont C. Geographical variation in insertion site number of retrotransposon 412 in Drosophila simulans. J Mol Evol 1996, 42:443-451. 10.1007/BF02498638, 8642613.
32. Kalendar R, Tanskanen J, Immonen S, Nevo E, Schulman AH. Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. Proc Natl Acad Sci USA 2000, 97:6603-6607. 10.1073/pnas.110587497, 18673, 10823912.
33. Capy P, Gasperi G, Biemont C, Bazin C. Stress and transposable elements: co-evolution or useful parasites?. Heredity 2000, 85(Pt 2):101-106.
34. Lonnig WE, Saedler H. Chromosome rearrangements and transposable elements. Annu Rev Genet 2002, 36:389-410. 10.1146/annurev.genet.36.040202.092802, 12429698.
35. Kidwell MG, Kidwell JF, Sved JA. Hybrid dysgenesis in Drosophila melanogaster: a syndrome of aberrant traits including mutation, sterility and male recombination. Genetics 1977, 86:813-833. 1213713, 17248751.
36. Bingham PM, Kidwell MG, Rubin GM. The molecular basis of P-M hybrid dysgenesis: the role of the P element, a P-strain-specific transposon family. Cell 1982, 29:995-1004. 10.1016/0092-8674(82)90463-9, 6295641.
37. Coyne JA. Meiotic segregation and male recombination in interspecific hybrids of Drosophila. Genetics 1986, 114:485-494. 1202952, 3021573.
38. Coyne JA. A test of the role of meiotic drive in fixing a pericentric inversion. Genetics 1989, 123:241-243. 1203787, 2806886.
39. O'Neill RJ, O'Neill MJ, Graves JA. Undermethylation associated with retroelement activation and chromosome remodelling in an interspecific mammalian hybrid. Nature 1998, 393:68-72. 10.1038/29985, 9590690.
40. Labrador M, Farre M, Utzet F, Fontdevila A. Interspecific hybridization increases transposition rates of Osvaldo. Mol Biol Evol 1999, 16:931-937.
41. Ungerer MC, Strakosh SC, Zhen Y. Genome expansion in three hybrid sunflower species is associated with retrotransposon proliferation. Curr Biol 2006, 16:R872-873. 10.1016/j.cub.2006.09.020, 17055967.
42. Kawakami T, Strakosh SC, Zhen Y, Ungerer MC. Different scales of Ty1/copia-like retrotransposon proliferation in the genomes of three diploid hybrid sunflower species. Heredity 2010, 104:341-350. 10.1038/hdy.2009.182, 20068588.
43. Noor MA, Chang AS. Evolutionary genetics: jumping into a new species. Curr Biol 2006, 16:R890-892. 10.1016/j.cub.2006.09.022, 17055974.
44. Michalak P. An eruption of mobile elements in genomes of hybrid sunflowers. Heredity 2010, 104:329-330. 10.1038/hdy.2009.187, 20068587.
45. Rose MR, Doolittle WF. Molecular biological mechanisms of speciation. Science 1983, 220:157-162. 10.1126/science.220.4593.157, 17795801.
46. Michalak P. Epigenetic, transposon and small RNA determinants of hybrid dysfunctions. Heredity 2009, 102:45-50. 10.1038/hdy.2008.48, 18545265.
47. Brookfield JF, Johnson LJ. The evolution of mobile DNAs: when will transposons create phylogenies that look as if there is a master gene?. Genetics 2006, 173:1115-1123. 10.1534/genetics.104.027219, 1526530, 16790583.
48. Johnson LJ, Brookfield JF. A test of the master gene hypothesis for interspersed repetitive DNA sequences. Mol Biol Evol 2006, 23:235-239.
49. Jurka J. Repbase Update: a database and an electronic journal of repetitive elements. Trends Genet 2000, 16:418-420. 10.1016/S0168-9525(00)02093-X, 10973072.
50. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 2005, 110:462-467. 10.1159/000084979, 16093699.
51. Kapitonov VV, Jurka J. A universal classification of eukaryotic transposable elements implemented in Repbase. Nat Rev Genet 2008, 9:411-412. author reply 414.
52. Mousson L, Dauga C, Garrigues T, Schaffner F, Vazeille M, Failloux AB. Phylogeography of Aedes (Stegomyia) aegypti (L.) and Aedes (Stegomyia) albopictus (Skuse) (Diptera: Culicidae) based on mitochondrial DNA variations. Genet Res 2005, 86:1-11. 10.1017/S0016672305007627, 16181519.
53. Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S, et al. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 2002, 419:498-511. 10.1038/nature01097, 12368864.
54. Hua-Van A, Le Rouzic A, Boutin TS, Filee J, Capy P. The struggle for life of the genome's selfish architects. Biol Direct 2011, 6:19. 10.1186/1745-6150-6-19, 3072357, 21414203.
55. Pace JK, Gilbert C, Clark MS, Feschotte C. Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods. Proc Natl Acad Sci USA 2008, 105:17023-17028. 10.1073/pnas.0806548105, 2579371, 18936483.
56. Kojima KK, Kapitonov VV, Jurka J. Recent expansion of a new Ingi-related clade of Vingi non-LTR retrotransposons in hedgehogs. Mol Biol Evol 2011, 28:17-20. 10.1093/molbev/msq220, 20716533.
57. Zupunski V, Gubensek F, Kordis D. Evolutionary dynamics and evolutionary history in the RTE clade of non-LTR retrotransposons. Mol Biol Evol 2001, 18:1849-1863.
58. Larsen PA, Marchan-Rivadeneira MR, Baker RJ. Natural hybridization generates mammalian lineage with species characteristics. Proc Natl Acad Sci USA 2010, 107:11447-11452. 10.1073/pnas.1000133107, 2895066, 20534512.
59. Jurka J, Krnjajic M, Kapitonov VV, Stenger JE, Kohkanyy O. Active Alu elements are passed primarily through paternal germlines. Theor Popul Biol 2002, 61:519-530. 10.1006/tpbi.2002.1602, 12167372.
60. Kvikstad EM, Makova KD. The (r)evolution of SINE versus LINE distributions in primate genomes: sex chromosomes are important. Genome Res 2010, 20:600-613. 10.1101/gr.099044.109, 2860162, 20219940.
61. Jurka J, Kohany O, Pavlicek A, Kapitonov VV, Jurka MV. Duplication, coclustering, and selection of human Alu retrotransposons. Proc Natl Acad Sci USA 2004, 101:1268-1272. 10.1073/pnas.0308084100, 337042, 14736919.
62. Brosius J. Genomes were forged by massive bombardments with retroelements and retrosequences. Genetica 1999, 107:209-238. 10.1023/A:1004018519722, 10952214.
63. Shimamura M, Yasue H, Ohshima K, Abe H, kato H, Kishiro T, Goto M, Munechika I, Okada N. Molecular evidence from retroposons that whales form a clade within even-toed ungulates. Nature 1997, 388:666-670. 10.1038/41759, 9262399.
64. Shedlock AM, Okada N. SINE insertions: powerful tools for molecular systematics. Bioessays 2000, 22:148-160. 10.1002/(SICI)1521-1878(200002)22:2<148::AID-BIES6>3.0.CO;2-Z, 10655034.
65. Shedlock AM, Takahashi K, Okada N. SINEs of speciation: tracking lineages with retroposons. Trends Ecol Evol 2004, 19:545-553. 10.1016/j.tree.2004.08.002, 16701320.
66. Okada N, Shedlock AM, Nikaido M. Retroposon mapping in molecular systematics. Methods Mol Biol 2004, 260:189-226.
67. Kriegs JO, Churakov G, Kiefmann M, Jordan U, Brosius J, Schmitz J. Retroposed elements as archives for the evolutionary history of placental mammals. PLoS Biol 2006, 4:e91. 10.1371/journal.pbio.0040091, 1395351, 16515367.
68. Kriegs JO, Churakov G, Jurka J, Brosius J, Schmitz J. Evolutionary history of 7SL RNA-derived SINEs in Supraprimates. Trends Genet 2007, 23:158-161. 10.1016/j.tig.2007.02.002, 17307271.
69. Nishihara H, Maruyama S, Okada N. Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals. Proc Natl Acad Sci USA 2009, 106:5235-5240. 10.1073/pnas.0809297106, 2655268, 19286970.
70. Kriegs JO, Zemann A, Churakov G, Matzke A, Ohme M, Zischler H, Brosius J, Kryger U, Schmitz J. Retroposon insertions provide insights into deep lagomorph evolution. Mol Biol Evol 2010, 27:2678-2681. 10.1093/molbev/msq162, 20584773.
71. Moller-Krull M, Delsuc F, Churakov G, Marker C, Superina M, Brosius J, Douzery EJ, Schmitz J. Retroposed elements and their flanking regions resolve the evolutionary history of xenarthran mammals (armadillos, anteaters, and sloths). Mol Biol Evol 2007, 24:2573-2582. 10.1093/molbev/msm201, 17884827.
72. Nishihara H, Satta Y, Nikaido M, Thewissen JG, Stanhope MJ, Okada N. A retroposon analysis of Afrotherian phylogeny. Mol Biol Evol 2005, 22:1823-1833. 10.1093/molbev/msi179, 15930154.
73. Shim WB, Dunkle LD. Malazy, a degenerate, species-specific transposable element in Cercospora zeae-maydis. Mycologia 2005, 97:349-355. 10.3852/mycologia.97.2.349, 16396343.
74. Churakov G, Smit AF, Brosius J, Schmitz J. A novel abundant family of retroposed elements (DAS-SINEs) in the nine-banded armadillo (Dasypus novemcinctus). Mol Biol Evol 2005, 22:886-893. 10.1093/molbev/msi071, 15616140.
75. Nishihara H, Kuno S, Nikaido M, Okada N. MyrSINEs: a novel SINE family in the anteater genomes. Gene 2007, 400:98-103. 10.1016/j.gene.2007.06.003, 17628355.
76. Hawkins JS, Kim H, Nason JD, Wing RA, Wendel JF. Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium. Genome Res 2006, 16:1252-1261. 10.1101/gr.5282906, 1581434, 16954538.
77. Yang HP, Barbash DA. Abundant and species-specific DINE-1 transposable elements in 12 Drosophila genomes. Genome Biol 2008, 9:R39. 10.1186/gb-2008-9-2-r39, 2374699, 18291035.
78. Gogolevsky KP, Vassetzky NS, Kramerov DA. 5S rRNA-derived and tRNA-derived SINEs in fruit bats. Genomics 2009, 93:494-500. 10.1016/j.ygeno.2009.02.001, 19442632.
79. Venancio TM, Wilson RA, Verjovski-Almeida S, DeMarco R. Bursts of transposition from non-long terminal repeat retrotransposon families of the RTE clade in Schistosoma mansoni. Int J Parasitol 2010, 40:743-749. 10.1016/j.ijpara.2009.11.013, 20018191.
80. Devor EJ, Moffat-Wilson KA. Molecular and temporal characteristics of human retropseudogenes. Hum Biol 2003, 75:661-672. 10.1353/hub.2003.0075, 14763603.
81. Ereshefsky M, Matthen M. Taxonomy, Polymorphism, and History: An Introduction to Population Structure Theory. Philosophy of Science 2005, 72:1-21.
82. Jurka J. Conserved eukaryotic transposable elements and the evolution of gene regulation. Cell Mol Life Sci 2008, 65:201-204. 10.1007/s00018-007-7369-3, 18030428.
83. Lowe CB, Bejerano G, Haussler D. Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proc Natl Acad Sci USA 2007, 104:8005-8010. 10.1073/pnas.0611223104, 1876562, 17463089.
84. Kidwell MG. Transposable elements and the evolution of genome size in eukaryotes. Genetica 2002, 115:49-63. 10.1023/A:1016072014259, 12188048.
85. Vieira C, Nardon C, Arpin C, Lepetit D, Biemont C. Evolution of genome size in Drosophila. is the invader's genome being invaded by transposable elements?. Mol Biol Evol 2002, 19:1154-1161.
86. Koonin EV. Evolution of genome architecture. Int J Biochem Cell Biol 2009, 41:298-306. 10.1016/j.biocel.2008.09.015, 18929678.
87. Whitney KD, Garland T. Did genetic drift drive increases in genome complexity?. PLoS Genet 2010, 6.
88. Lynch M. Statistical inference on the mechanisms of genome evolution. PLoS Genet 2011, 7:e1001389. 10.1371/journal.pgen.1001389, 3111481, 21695228.
89. Whitney KD, Boussau B, Baack EJ, Garland T. Drift and genome complexity revisited. PLoS Genet 2011, 7:e1002092. 10.1371/journal.pgen.1002092, 3111538, 21695239.
90. Jones G, Teeling EC. The evolution of echolocation in bats. Trends Ecol Evol 2006, 21:149-156. 10.1016/j.tree.2006.01.001, 16701491.
91. Kapitonov VV, Jurka J. RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons. PLoS Biol 2005, 3:e181. 10.1371/journal.pbio.0030181, 1131882, 15898832.
92. Gould SJ, Eldredge N. Punctuated equilibria: the tempo and mode of evolution reconsidered. Paleobiology 1977, 3:115-151.
93. Casavant NC, Scott L, Cantrell MA, Wiggins LE, Baker RJ, Wichman HA. The end of the LINE?: lack of recent L1 activity in a group of South American rodents. Genetics 2000, 154:1809-1817. 1461046, 10747071.
94. Lima M, Marquet PA, Jaksic FA. Extinction and colonization processes in subpopulations of five neotropical species. Oecologia 1996, 107:197-202.
95. Hunt JJ, Bonsall MB. The effects of colonization, extinction and competition on co-existence in metacommunities. J Anim Ecol 2009, 78:866-879. 10.1111/j.1365-2656.2009.01532.x, 19302319.
96. Cadotte MW, Strauss SY. Phylogenetic patterns of colonization and extinction in experimentally assembled plant communities. PLoS One 2011, 6:e19363. 10.1371/journal.pone.0019363, 3089622, 21573117.
97. Baskett ML, Gomulkiewicz R. Introgressive hybridization as a mechanism for species rescue. Theor Ecol 2011, 4:223-239.
98. Flegr J. Elastic, not plastic species: frozen plasticity theory and the origin of adaptive evolution in sexually reproducing organisms. Biol Direct 2010, 5:2. 10.1186/1745-6150-5-2, 2823622, 20067646.