Positive selection for the male functionality of a co-retroposed gene in the hominoids

BMC Evolutionary Biology

Volumn 9, Issue 1, 2009, Pages

  Zhang, Yong ^a,b   Lu, Shujuan ^a   Zhao, Shuqi ^a   Zheng, Xiaofeng ^a   Long, Manyuan ^a,b   Wei, Liping ^a  

^a PEKING UNIVERSITY   (China)

^b UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; 1-PHOSPHATIDYLINOSITOL-4-PHOSPHATE 5-KINASE; CARRIER PROTEIN; PHOSPHATIDYLINOSITOL 4 PHOSPHATE KINASE; PHOSPHOTRANSFERASE; PIPSL PROTEIN, HUMAN; PROTEASOME; PSMD4 PROTEIN, HUMAN;

ANALYSIS; ANIMAL GENETICS; ARTICLE; CONTROLLED STUDY; FEMALE; GENDER; GENE; GENE CONTROL; GENE DELETION; GENE INSERTION; GENE SEQUENCE; GENE STRUCTURE; GENETIC TRANSCRIPTION; HOMINOID; MALE; METHYLATION; MOLECULAR EVOLUTION; NONHUMAN; PIPSL GENE; PRIMATE; PSMD4 GENE; RELATIVE; RETROPOSON; SPECIES; TESTIS; ANIMAL; DNA SEQUENCE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC SELECTION; GENETICS; HUMAN; INDEL MUTATION; METABOLISM; PAN TROGLODYTES; POPULATION GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES DIFFERENCE;

HOMINOIDEA; HOMO; MAMMALIA;

ANIMALS; CARRIER PROTEINS; EVOLUTION, MOLECULAR; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS, POPULATION; HUMANS; INDEL MUTATION; MALE; METHYLATION; PAN TROGLODYTES; PHOSPHOTRANSFERASES (ALCOHOL GROUP ACCEPTOR); POLYMORPHISM, SINGLE NUCLEOTIDE; PRIMATES; PROTEASOME ENDOPEPTIDASE COMPLEX; RETROELEMENTS; SELECTION, GENETIC; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; TESTIS; TRANSCRIPTION, GENETIC;

EID: 72049113083     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-9-252     Document Type: Article

References (49)

1. The origin of new genes: glimpses from the young and old. M Long E Betran K Thornton W Wang, Nat Rev Genet 2003 4 11 865 875 10.1038/nrg1204 14634634
2. Molecular Evolution. W-H Li, Sunderland: Sinauer Associates Inc 1997
3. Retroposed new genes out of the X in Drosophila. E Betran K Thornton M Long, Genome Res 2002 12 12 1854 1859 12466289 10.1101/gr.6049 (Pubitemid 35469934)
4. Emergence of young human genes after a burst of retroposition in primates. AC Marques I Dupanloup N Vinckenbosch A Reymond H Kaessmann, PLoS Biol 2005 3 11 357 16201836 10.1371/journal.pbio.0030357 (Pubitemid 41652449)
5. The evolution of courtship behaviors through the origination of a new gene in Drosophila. H Dai Y Chen S Chen Q Mao D Kennedy P Landback A Eyre-Walker W Du M Long, Proceedings of the National Academy of Sciences 2008 105 21 7478 7483 10.1073/pnas.0800693105 (Pubitemid 351830043)
6. Comparative genomics reveals a constant rate of origination and convergent acquisition of functional retrogenes in Drosophila. Y Bai C Casola C Feschotte E Betran, Genome Biol 2007 8 1 11 17233920 10.1186/gb-2007-8-1-r11 (Pubitemid 351910991)
7. Evolving protein functional diversity in new genes of Drosophila. J Zhang AM Dean F Brunet M Long, Proc Natl Acad Sci USA 2004 101 46 16246 16250 15534206 10.1073/pnas.0407066101 (Pubitemid 39552830)
8. Evolutionary fate of retroposed gene copies in the human genome. N Vinckenbosch I Dupanloup H Kaessmann, Proceedings of the National Academy of Sciences 2006 103 9 3220 3225 10.1073/pnas.0511307103 (Pubitemid 43346451)
9. Transcription-mediated gene fusion in the human genome. P Akiva A Toporik S Edelheit Y Peretz A Diber R Shemesh A Novik R Sorek, Genome Res 2006 16 1 30 36 16344562 10.1101/gr.4137606 (Pubitemid 43048931)
10. Type I phosphatidylinositol-4-phosphate 5-Kinases are distinct members of this Novel Lipid Kinase Family. JC Loijens RA Anderson, J Biol Chem 1996 271 51 32937 32943 10.1074/jbc.271.51.32937 8955136
11. A conspicuous connection: structure defines function for the phosphatidylinositol-phosphate kinase family. JN Heck DL Mellman K Ling Y Sun MP Wagoner NJ Schill RA Anderson, Crit Rev Biochem Mol Biol 2007 42 1 15 39 10.1080/10409230601162752 17364683
12. Structure of S5a bound to monoubiquitin provides a model for polyubiquitin recognition. Q Wang P Young KJ Walters, J Mol Biol 2005 348 3 727 739 10.1016/j.jmb.2005.03.007 15826667
13. A novel testis ubiquitin-binding protein gene arose by exon shuffling in hominoids. DV Babushok K Ohshima EM Ostertag X Chen Y Wang PK Mandal N Okada CS Abrams HH Kazazian Jr, Genome Res 2007 17 8 1129 1138 17623810 10.1101/gr.6252107 (Pubitemid 47204856)
14. A high-resolution map of active promoters in the human genome. TH Kim LO Barrera M Zheng C Qu MA Singer TA Richmond Y Wu RD Green B Ren, Nature 2005 436 7052 876 15988478 10.1038/nature03877 (Pubitemid 41160649)
15. Human population genetics. DL Hartl AG Clark, Principles of population genetics Sinauer Associates, Inc. Publishers Fourth 2007
16. Gene genealogies and the coalescent process. RR Hudson, Oxford Surveys in Evolutionary Biology 7. Oxford 1990 1 44
17. Population Genetics: A Concise Guide. JH Gillespie, Baltimore: The Johns Hopkins University Press 2004
18. Evolutionary simulations to detect functional lineage-specific genes. I Dupanloup H Kaessmann, Bioinformatics 2006 22 15 1815 1822 10.1093/ bioinformatics/btl280 16766551
19. Evolutionary deterioration of the vomeronasal pheromone transduction pathway in catarrhine primates. J Zhang DM Webb, Proceedings of the National Academy of Sciences 2003 100 14 8337 8341 10.1073/pnas.1331721100 (Pubitemid 36842546)
20. PAML 4: phylogenetic analysis by maximum likelihood. Z Yang, Mol Biol Evol 2007 24 8 1586 1591 10.1093/molbev/msm088 17483113
21. Epsin 1 is a polyubiquitin-selective clathrin-associated sorting protein. MJ Hawryluk PA Keyel SK Mishra SC Watkins JE Heuser LM Traub, Traffic 2006 7 3 262 281 10.1111/j.1600-0854.2006.00383.x 16497222
22. Transcriptional promiscuity in testes. EE Schmidt, Curr Biol 1996 6 7 768 769 10.1016/S0960-9822(02)00589-4 8805310
23. PseudoPipe: an automated pseudogene identification pipeline. Z Zhang N Carriero D Zheng J Karro PM Harrison M Gerstein, Bioinformatics 2006 22 12 1437 1439 10.1093/bioinformatics/btl116 16574694
24. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. M Weber I Hellmann MB Stadler L Ramos S Paabo M Rebhan D Schubeler, Nature Genetics 2007 39 4 457 466 10.1038/ng1990 17334365
25. Nucleotide diversity in Gorillas. N Yu MI Jensen-Seaman L Chemnick O Ryder WH Li, Genetics 2004 166 3 1375 1383 15082556 10.1534/genetics.166.3.1375 (Pubitemid 38507056)
26. Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. FC Chen WH Li, Am J Hum Genet 2001 68 2 444 456 11170892 10.1086/318206 (Pubitemid 32147813)
27. Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model. A Hobolth OF Christensen T Mailund MH Schierup, PLoS Genet 2007 3 2 7 17319744 10.1371/journal.pgen. 0030007 (Pubitemid 46318408)
28. Demographic history and genetic differentiation in apes. A Fischer J Pollack O Thalmann B Nickel S Paabo, Curr Biol 2006 16 11 1133 1138 10.1016/j.cub.2006.04.033 16753568
29. Neutral Theory of Molecular Evolution. M Kimura, Cambridge: Cambridge University Press 1985
30. The Origins of Genome Architecture. M Lynch, Sunderland (MA): Sinauer Associates 2007
31. Origination of an X-linked testes chimeric gene by illegitimate recombination in Drosophila. JR Arguello Y Chen S Yang W Wang M Long, PLoS Genet 2006 2 5 77 16715176 10.1371/journal.pgen.0020077 (Pubitemid 43794323)
32. Defining how ubiquitin receptors hHR23a and S5a bind polyubiquitin. Y Kang X Chen JW Lary JL Cole KJ Walters, J Mol Biol 2007 369 1 168 176 10.1016/j.jmb.2007.03.008 17408689
33. Human Exon Array 1.0 ST Panel. http://www.affymetrix.com/products- services/arrays/specific/exon.affx
34. Guide to Probe Logarithmic Intensity Error (PLIER) Estimation. http://www.affymetrix.com/support/technical/technotes/plier-technote.pdf
35. Base-calling of automated sequencer traces using phred. II. Error probabilities. B Ewing P Green, Genome Res 1998 8 3 186 194 9521922 (Pubitemid 28177230)
36. Consed: a graphical tool for sequence finishing. D Gordon C Abajian P Green, Genome Res 1998 8 3 195 202 9521923
37. PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing. DA Nickerson VO Tobe SL Taylor, Nucleic Acids Res 1997 25 14 2745 2751 9207020 10.1093/nar/25.14.2745 (Pubitemid 27299787)
38. PolyScan: an automatic indel and SNP detection approach to the analysis of human resequencing data. K Chen MD McLellan L Ding MC Wendl Y Kasai RK Wilson ER Mardis, Genome Res 2007 17 5 659 666 17416743 10.1101/gr.6151507 (Pubitemid 46715517)
39. DnaSP, DNA polymorphism analyses by the coalescent and other methods. J Rozas JC Sanchez-DelBarrio X Messeguer R Rozas, Bioinformatics 2003 19 18 2496 2497 10.1093/bioinformatics/btg359 14668244
40. A test of neutral molecular evolution based on nucleotide data. RR Hudson M Kreitman M Aguade, Genetics 1987 116 1 153 159 3110004
41. Tracembler-software for in-silico chromosome walking in unassembled genomes. Q Dong MD Wilkerson V Brendel, BMC Bioinformatics 2007 8 151 17490482 10.1186/1471-2105-8-151 (Pubitemid 46785163)
42. BLAT-the BLAST-like alignment tool. WJ Kent, Genome Res 2002 12 4 656 664 11932250
43. MUSCLE: multiple sequence alignment with high accuracy and high throughput. RC Edgar, Nucleic Acids Res 2004 32 5 1792 1797 15034147 10.1093/nar/gkh340 (Pubitemid 38832724)
44. GeneDoc: analysis and visualization of genetic variation. KB Nicholas HB Nicholas DW Deerfield, EMBNEW NEWS 1997 4 14
45. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. M Suyama D Torrents P Bork, Nucleic Acids Res 2006 34 Web Server 609 612 16845082 10.1093/nar/gkl315 (Pubitemid 44529842)
46. Phylogenetic analysis using PHYLIP. JD Retief, Methods Mol Biol 2000 132 243 258 10547839
47. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Z Yang R Nielsen, Mol Biol Evol 2002 19 6 908 917 12032247
48. Evaluation of an Improved Branch-Site Likelihood Method for Detecting Positive Selection at the Molecular Level. J Zhang R Nielsen Z Yang, Mol Biol Evol 2005 22 12 2472 2479 10.1093/molbev/msi237 16107592
49. HyPhy: hypothesis testing using phylogenies. SL Pond SD Frost SV Muse, Bioinformatics 2005 21 5 676 679 10.1093/bioinformatics/bti079 15509596