Accelerated rate of gene gain and loss in primates

Genetics

Volumn 177, Issue 3, 2007, Pages 1941-1949

  Hahn, Matthew W ^a   Demuth, Jeffery P ^a   Han, Sang Gook ^a  

^a INDIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHIMPANZEE; CONTROLLED STUDY; GENE DUPLICATION; GENE LOSS; GENE MUTATION; GENE STRUCTURE; GENETIC GAIN; GENETIC HETEROGENEITY; GENETIC LINKAGE; GENOME; HUMAN; HUMAN VERSUS ANIMAL COMPARISON; MAMMAL; MOLECULAR EVOLUTION; MOUSE; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PRIMATE; PRIORITY JOURNAL; RAT; RHESUS MONKEY; SPECIES COMPARISON;

ANIMALS; DOGS; EVOLUTION, MOLECULAR; GENE DOSAGE; GENE DUPLICATION; HUMANS; LIKELIHOOD FUNCTIONS; MACACA MULATTA; MAMMALS; MICE; MULTIGENE FAMILY; PAN TROGLODYTES; PRIMATES; RATS; SELECTION (GENETICS);

MACACA MULATTA; MAMMALIA; PAN; PRIMATES;

EID: 37249061101     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.107.080077     Document Type: Article

References (53)

1. ADKINS, R. M., A. H. WALTON and R. L. HONEYCUTT, 2003 Higher-level systematics of rodents and divergence time estimates based on two congruent nuclear genes. Mol. Phylogenet. Evol. 26: 409-420.
2. BAILEY, J. A., Z. P. GU, R. A. CLARK, K. REINERT, R. V. SAMONTE et al., 2002 Recent segmental duplications in the human genome. Science 297: 1003-1007.
3. BAILEY, J. A., G. LIU and E. E. EICHLER, 2003 An Alu transposition model for the origin and expansion of human segmental duplications. Am. J. Hum. Genet. 73: 823-834.
4. BAILEY, J. A., A. M. YAVOR, H. F. MASSA, B. J. TRASK and E. E. EICHLER, 2001 Segmental duplications: Organization and impact within the current Human Genome Project assembly. Genome Res. 11: 1005-1017.
5. BIRTLE, Z., L. GOODSTADT and C. P. PONTING, 2005 Duplication and positive selection among hominin-specific PRAME genes. BMC Genomics 6: 120.
6. BURNHAM, K. P., and D. R. ANDERSON, 2002 Model Selection and Multimodel Inference: A Practical Information-Theoretic Approach. Springer-Verlag, New York.
7. CARROLL, S. B., 2005 Evolution at two levels: on genes and form. PLoS Biol. 3: e245.
8. CHEN, K., D. DURAND and M. FARACH-COLTON, 2000 NOTUNG: A program for dating gene duplications and optimizing gene family trees. J. Comput. Biol. 7: 429-447.
9. CHENG, Z., M. VENTURA, X. SHE, P. KHAITOVICH, T. GRAVES et al., 2005 A genome-wide comparison of recent chimpanzee and human segmental duplications. Nature 437: 88-93.
10. DAUBIN, V., N. A. MORAN and H. OCHMAN, 2003 Phylogenetics and the cohesion of bacterial genomes. Science 301: 829-832.
11. DE BIE, T., J. P. DEMUTH, N. CRISTIANINI and M. W. HAHN, 2006 CAFE: a computational tool for the study of gene family evolution. Bioinformatics 22: 1269-1271.
12. DEMUTH, J. P., T. DE BIE, J. E. STAJICH, N. CRISTIANINI and M. W. HAHN, 2006 The evolution of mammalian gene families. PLoS ONE 1: e85.
13. DOUZERY, E. J. P., F. DELSUC, M. J. STANHOPE and D. HUCHON, 2003 Local molecular clocks in three nuclear genes: Divergence times for rodents and other mammals and incompatibility among fossil calibrations. J. Mol. Evol. 57: S201-S213.
14. DURAND, D., B. V. HALLDORSSON and B. VERNOT, 2005 A hybrid micro-macroevolutionary approach to gene tree reconstruction. J. Comput. Biol. 13: 320-335.
15. ELANGO, N., J. W. THOMAS and S. V. YI, 2006 Variable molecular clocks in hominoids. Proc. Natl. Acad. Sci. USA 103: 1370-1375.
16. FELSENSTEIN, J., 1989 PHYLIP-hylogeny Inference Package (Version 3.2). Cladistics 5: 164-166.
17. FORTNA, A., Y. KIM, E. MACLAREN, K. MARSHALL, G. HAHN et al., 2004 Lineage-specific gene duplication and loss in human and great ape evolution. PLoS Biol. 2: e207.
18. GIBBS, R., J. ROGERS, M. KATZE, R. BUMGARNER, G. WEINSTOCK et al., 2007 Evolutionary and biomedical insights from the rhesus macaque genome. Science 316: 222-234.
19. GIBBS, R. A., G. M. WEINSTOCK, M. L. METZKER, D. M. MUZNY, E. J. SODERGREN et al., 2004 Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428: 493-521.
20. GOODSTADT, L., and C. P. PONTING, 2006 Phylogenetic reconstruction of orthology, paralogy, and conserved synteny for dog and human. PLoS Comput. Biol. 2: e133.
21. HAHN, M. W., 2007a Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution. Genome Biol. 8:R141.
22. HAHN, M. W., 2007b Detecting natural selection on cis-regulatory DNA. Genetica 129: 7-18.
23. HAHN, M. W., T. DE BIE, J. E. STAJICH, C. NGUYEN and N. CRISTIANINI, 2005 Estimating the tempo and mode of gene family evolution from comparative genomic data. Genome Res. 15: 1153-1160.
24. HOEKSTRA, H. E., and J. A. COYNE, 2007 The locus of evolution: evo devo and the genetics of adaptation. Evolution 61: 995-1016.
25. HUGHES, A. L., 1994 The evolution of functionally novel proteins after gene duplication. Proc. R. Soc. Lond. B Biol. Sci. 256: 119-124.
26. KAREV, G. P., Y. I. WOLF, A. Y. RZHETSKY, F. S. BEREZOVSKAYA and E. V. KOONIN, 2002 Birth and death of protein domains: A simple model of evolution explains power law behavior. BMC Evol. Biol. 2: 18.
27. KING, M.-C., and A. C. WILSON, 1975 Evolution at two levels in humans and chimpanzees. Science 188: 107-116.
28. KUMAR, S., A. FILIPSKI, V. SWARNA, A. WALKER and S. B. HEDGES, 2005 Placing confidence limits on the molecular age of the human-chimpanzee divergence. Proc. Natl. Acad. Sci. USA 102: 18842-18847.
29. LI, W.-H., 1997 Molecular Evolution. Sinaur Associates, Sunderland, MA.
30. LYNCH, M., and J. S. CONERY, 2003 The evolutionary demography of duplicate genes. J. Struct. Funct. Genomics 3: 35-44.
31. LYNCH, M., M. O'HELY, B. WALSH and A. FORCE, 2001 The probability of preservation of a newly arisen gene duplicate. Genetics 159: 1789-1804.
32. MCLYSAGHT, A., P. F. BALDI and B. S. GAUT, 2003 Extensive gene gain associated with adaptive evolution of poxviruses. Proc. Natl. Acad. Sci. USA 100: 15655-15660.
33. NEI, M., and G. V. GLAZKO, 2002 Estimation of divergence times for a few mammalian and several primate species. J. Hered. 93: 157-164.
34. NEI, M., X. GU and T. SITNIKOVA, 1997 Evolution by the birth-and-death process in multigene families of the vertebrate immune system. Proc. Natl. Acad. Sci. USA 94: 7799-7806.
35. OLSON, M. V., 1999 When less is more: gene loss as an engine of evolutionary change. Amer. J. Hum. Genet. 64: 18-23.
36. PATTERSON, N., D. J. RICHTER, S. GNERRE, E. S. LANDER and D. REICH, 2006 Genetic evidence for complex speciation of humans and chimpanzees. Nature 441: 1103-1108.
37. POPESCO, M. C., E. J. MACLAREN, J. HOPKINS, L. DUMAS, M. COX et al., 2006 Human lineage-specific amplification, selection, and neuronal expression of DUF1220 domains. Science 313: 1304-1307.
38. PRABHAKAR, S., J. P. NOONAN, S. PAABO and E. M. RUBIN, 2006 Accelerated evolution of conserved noncoding sequences in humans. Science 315: 786.
39. SEBAT, J., B. LAKSHMI, D. MALHOTRA, J. TROGE, C. LESE-MARTIN et al., 2007 Strong association of de novo copy number mutations with autism. Science 316: 445-449.
40. SHANNON, M., A. T. HAMILTON, L. GORDON, E. BRANSCOMB and L. STUBBS, 2003 Differential expansion of zinc-finger transcription factor loci in homologous human and mouse gene clusters. Genome Res. 13: 1097-1110.
41. SHE, X., G. LIU, M. VENTURA, S. ZHAO, D. MISCEO et al., 2006 A preliminary comparative analysis of primate segmental duplications shows elevated substitution rates and a great-ape expansion of intrachromosomal duplications. Genome Res. 16: 576-583.
42. SHEN, M. R., M. A. BATZER and P. L. DEININGER, 1991 Evolution of the master Alu gene(s). J. Mol. Evol. 33: 311-320.
43. SPOFFORD, J. B., 1969 Heterosis and evolution of duplications. Am. Nat. 103: 407-432.
44. SPRINGER, M. S., W. J. MURPHY, E. EIZIRIK and S. J. O'BRIEN, 2003 Placental mammal diversification and the cretaceous-tertiary boundary. Proc. Natl. Acad. Sci. USA 100: 1056-1061.
45. STEPPAN, S. J., R. M. ADKINS and J. ANDERSON, 2004 Phylogeny and divergence-date estimates of rapid radiations in muroid rodents based on multiple nuclear genes. Syst. Biol. 53: 533-553.
46. WANG, X., W. E. GRUS and J. ZHANG, 2006 Gene losses during human origins. PLoS Biol. 4: e52.
47. WASSINK, T. H., J. PIVEN, V. J. VIELAND, L. JENKINS, R. FRANTZ et al., 2005 Evaluation of the chromosome 2q37.3 gene CENTG2 as an autism susceptibility gene. Am. J. Med. Genet. B Neuropsychiatr. Genet. 136B: 36-44.
48. WATERSTON, R. H., K. LINDBLAD-TOH, E. BIRNEY, J. ROGERS, J. F. ABRIL et al., 2002 Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
49. WONG, W. S. W., Z. YANG, N. GOLDMAN and R. NIELSEN, 2004 Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics 168: 1041-1051.
50. WU, C. I., and W. H. LI, 1985 Evidence for higher rates of nucleotide substitution in rodents than in man. Proc. Natl. Acad. Sci. USA 82: 1741-1745.
51. YANG, Z., 1997 PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13: 555-556.
52. YI, S. J., D. L. ELLSWORTH and W. H. LI, 2002 Slow molecular clocks in Old World monkeys, apes, and humans. Mol. Biol. Evol. 19: 2191-2198.
53. ZMASEK, C. M., and S. R. EDDY, 2001 A simple algorithm to infer gene duplication and speciation events on a gene tree. Bioinformatics 17: 821-828.