Endangered species hold clues to human evolution

Journal of Heredity

Volumn 101, Issue 4, 2010, Pages 437-447

  Lowe, Craig B ^a   Bejerano, Gill ^b,c   Salama, Sofie R ^a,d   Haussler, David ^a,d  

^a University of California Santa Cruz   (United States)

^b STANFORD UNIVERSITY   (United States)

^c Stanford University   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

conservation biology; endangered species; exaptation; retroposons; transposons; tuatara

Indexed keywords

TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR ASXL3; UNCLASSIFIED DRUG; ASXL3 PROTEIN, HUMAN; RETROPOSON;

ARTICLE; CONTROLLED STUDY; ENDANGERED SPECIES; EVOLUTION; EXON; GENE EXPRESSION REGULATION; GENE INSERTION; HUMAN; HUMAN GENETICS; NONHUMAN; PRIORITY JOURNAL; PURIFICATION; REPTILE; RETROPOSON; RNA SPLICING; ANIMAL; GENETICS; HUMAN GENOME; MAMMAL; MOLECULAR EVOLUTION;

MAMMALIA; SPHENODON PUNCTATUS;

ANIMALS; ENDANGERED SPECIES; EVOLUTION, MOLECULAR; GENOME, HUMAN; HUMANS; MAMMALS; RETROELEMENTS; TRANSCRIPTION FACTORS;

EID: 77953867045     PISSN: 00221503     EISSN: 14657333     Source Type: Journal    
DOI: 10.1093/jhered/esq016     Document Type: Article

References (54)

1. Albert EM, San Mauro D, García-París M, Rüber L, Zardoya R. 2009. Effect of taxon sampling on recovering the phylogeny of squamate reptiles based on complete mitochondrial genome and nuclear gene sequence data. Gene. 441:12-21.
2. Augustin L, Barbante C, Barnes PRF, Barnola JM, Bigler M, Castellano E, Cattani O, Chappellaz J, Dahl-Jensen D, Delmonte B, et al. 2004. Eight glacial cycles from an Antarctic ice core. Nature. 429:623-628.
3. Baskind HA, Na L, Ma Q, Patel MP, Geenen DL, Wang QT. 2009. Functional conservation of asxl2, a murine homolog for the Drosophila enhancer of trithorax and polycomb group gene asx. PLoS ONE. 4:e4750.
4. Beard C, Hochedlinger K, Plath K, Wutz A, Jaenisch R. 2006. Efficient method to generate single-copy transgenic mice by site-specific integration in embryonic stem cells. Genesis. 44:23-28.
5. Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, Salama SR, Rubin EM, Kent WJ, Haussler D. 2006. A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature. 441:87-90.
6. Boutz PL, Stoilov P, Li Q, Lin CH, Chawla G, Ostrow K, Shiue L, Ares M, Black DL. 2007. A post-transcriptional regulatory switch in polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons. Genes Dev. 21:1636-1652.
7. Brosius J. 1999. RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene. 238:115-134.
8. Campbell L. 2003. Endangered and threatened animals of Texas. Austin (TX): Texas Parks and Wildlife Department.
9. Chiaromonte F, Yap V, Miller W. 2001. Scoring pairwise genomic sequence alignments. In: Altman RB, Dunker AK, Hunter L, Lauderdale K, Klein T, editors. Pacific Symposium on Biocomputing. 2002 Jan 3-7. Singapore: World Scientific. p. 115-126.
10. Cordaux R, Batzer MA. 2009. The impact of retrotransposons on human genome evolution. Nat Rev Genet. 10:691-703.
11. Daugherty CH, Cree A, Hay JM, Thompson MB. 1990. Neglected taxonomy and continuing extinctions of tuatara (Sphenodon). Nature. 347:177-179.
12. Dawkins R, Krebs JR. 1979. Arms races between and within species. Proc R Soc Lond B Biol Sci. 205:489-511.
13. Deininger PL, Moran JV, Batzer MA, Kazazian HHJ. 2003. Mobile elements and mammalian genome evolution. Curr Opin Genet Dev. 13:651-658.
14. Feschotte C. 2008. Transposable elements and the evolution of regulatory networks. Nat Rev Genet. 9:397-405.
15. Gish W. 2006 May. Wu-blast 2.0. [Internet]. [cited 2008 Sep 3] Available from: URL http://blast.wustl.edu/.
16. Genome 10K Community of Scientists. 2009. Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species. J Hered. 100:659-674.
17. Gould SJ, Vrba ES. 1982. Exaptation-a missing term in the science of form. Paleobiology. 8:4-15.
18. Graur D, Li WH. 2000. Fundamentals of molecular evolution. Sunderland (MA): Sinauer.
19. Harris R. 2007. Improved pairwise alignment of genomic DNA. State College (PA): Pennsylvania State University.
20. Houle D, Nuzhdin SV. 2004. Mutation accumulation and the effect of copia insertions in Drosophila melanogaster. Genet Res. 83:7-18.
21. IUCN. 2009 Nov. IUCN red list of threatened species. Version 2009.1 [Internet]. [cited 2009 Jun 2] Available from: URL http://www.iucnredlist .org/.
22. Jones MEH, Tennyson AJD, Worthy JP, Evans SE, Worthy TH. 2009. A sphenodontine (Rhynchocephalia) from the Miocene of New Zealand and palaeobiogeography of the tuatara (Sphenodon). Proc R Soc Lond B Biol Sci. 276:1385-1390.
23. Jurka J, Kapitonov VV, Kohany O, Jurka MV. 2007. Repetitive sequences in complex genomes: structure and evolution. Annu Rev Genomics Hum Genet. 8:241-259.
24. Kajikawa M, Ohshima K, Okada N. 1997. Determination of the entire sequence of turtle CR1: the first open reading frame of the turtle CR1 element encodes a protein with a novel zinc finger motif. Mol Biol Evol. 14:1206-1217.
25. Kapitonov VV, Jurka J. 2003. The esterase and PHD domains in CR1-like non-LTR retrotransposons. Mol Biol Evol. 20:38-46.
26. Kazazian HH. 2004. Mobile elements: drivers of genome evolution. Science. 303:1626-1632.
27. Kimura M. 1962. On the probability of fixation of mutant genes in a population. Genetics. 47:713-719.
28. Kuhn RM, Karolchik D, Zweig AS, Wang T, Smith KE, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pheasant M, et al. 2009. The UCSC Genome Browser Database: update 2009. Nucleic Acids Res. 37:D755-D761.
29. Lareau LF, Inada M, Green RE, Wengrod JC, Brenner SE. 2007. Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements. Nature. 446:926-929.
30. Le M, Raxworthy CJ, McCord WP, Mertz L. 2006. A molecular phylogeny of tortoises (Testudines: Testudinidae) based on mitochondrial and nuclear genes. Mol Phylogenet Evol. 40:517-531.
31. Lev-Maor G, Sorek R, Shomron N, Ast G. 2003. The birth of an alternatively spliced exon: 3' splice-site selection in Alu exons. Science. 300:1288-1291.
32. Lowe CB, Bejerano G, Haussler D. 2007. Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proc Natl Acad Sci USA. 104:8005-8010.
33. Lynch M, Conery JS. 2003. The origins of genome complexity. Science. 302:1401-1404.
34. Maquat LE. 2005. Nonsense-mediated mRNA decay in mammals. J Cell Sci. 118:1773-1776.
35. Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A, et al. 2007. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature. 447:167-177.
36. Miller W, Rosenbloom K, Hardison RC, Hou M, Taylor J, Raney B, Burhans R, King DC, Baertsch R, Blankenberg D, et al. 2007. 28-Way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Res. 17:1797-1808.
37. Mitchell NJ, Kearney MR, Nelson NJ, Porter WP. 2008. Predicting the fate of a living fossil: how will global warming affect sex determination and hatching phenology in tuatara? Proc Biol Sci. 275:2185-2193.
38. Moore JA, Nelson NJ, Keall SN, Daugherty CH. 2008. Implications for social dominance and multiple paternity for the genetic diversity of a captive-bred reptile population (tuatara). Conserv Genet. 9:1243-1251.
39. Ni JZ, Grate L, Donohue JP, Preston C, Nobida N, O'Brien G, Shiue L, Clark TA, Blume JE, Ares M. 2007. Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay. Genes Dev. 21:708-718.
40. Nicholls H. Aug 2009. Time to sequence the red and the dead [Internet]. [cited 2009 Apr 15] Available from: URL http://www.nature.com/news /2009/090414/full/458812a.html.
41. Nishihara H, Smit AF, Okada N. 2006. Functional noncoding sequences derived from SINEs in the mammalian genome. Genome Res. 16: 864-874.
42. Olmo E. 1981. Evolution of genome size and DNA base composition in reptiles. Genetica. 57:39-50.
43. Ostertag EM, DeBerardinis RJ, Goodier JL, Zhang Y, Yang N, Gerton GL, Kazazian HH. 2002. A mouse model of human L1 retrotransposition. Nat Genet. 32:655-660.
44. Purvis A, Agapow PM, Gittleman JL, Mace GM. 2000. Nonrandom extinction and the loss of evolutionary history. Science. 288:328-330.
45. Sasaki T, Nishihara H, Hirakawa M, Fujimura K, Tanaka M, Kokubo N, Kimura-Yoshida C, Matsuo I, Sumiyama K, Saitou N, et al. 2008. Possible involvement of SINEs in mammalian-specific brain formation. Proc Natl Acad Sci USA. 105:4220-4225.
46. Shedlock A, Edwards S. 2009. Amniotes (Amniota). In: Hedges SB, Kumar S, editors. The timetree of life. New York: Oxford University Press. p. 375-379.
47. Siepel AC, Pollard KS, Haussler D. 2006. New methods for detecting lineage-specific selection. In: RECOMB. 2006 Apr 2-5. Berlin: Springer. p. 190-205.
48. Smit A, Hubley R, Green P. 2009. Repeatmasker open-3.27 [Internet]. [cited 2009 Feb 1] Available from: URL http://www.repeatmasker.org/.
49. Vinogradov AE. 2004. Genome size and extinction risk in vertebrates. Proc Biol Sci. 271:1701-1705.
50. Volff JN. 2006. Turning junk into gold: domestication of transposable elements and the creation of new genes in eukaryotes. Bioessays. 28:913-922.
51. Wang T, Zeng J, Lowe CB, Sellers RG, Salama SR, Yang M, Burgess SM, Brachmann RK, Haussler D. 2007. Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53. Proc Natl Acad Sci USA. 104:18613-18618.
52. Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F, Belov K, Miller W, Clarke L, Chinwalla AT, et al. 2008. Genome analysis of the platypus reveals unique signatures of evolution. Nature. 453:175-183.
53. Wright S. 1938. Size of population and breeding structure in relation to evolution. Science. 87:430-431.
54. Ying QL, Smith AG. 2003. Defined conditions for neural commitment and differentiation. Methods Enzymol. 365:327-341.