Gene family evolution and homology: Genomics meets phylogenetics

Annual Review of Genomics and Human Genetics

Volumn 1, Issue 2000, 2000, Pages 41-73

  Thornton, Joseph W ^a   DeSalle, Rob ^b  

^a Och Spine at New York Presbyterian Hospitals   (United States)

^b DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

Author keywords

Concerted evolution; Evolution of novelty; Exon shuffling; Gene duplication; Lateral gene transfer; Maximum likelihood; Molecular evolution; Orthology; Parsimony

Indexed keywords

PROTEIN;

ANIMAL; BIOLOGICAL MODEL; EVOLUTION; GENE DUPLICATION; GENETIC VARIABILITY; GENETICS; GENOMICS; HUMAN; MULTIGENE FAMILY; PHYLOGENY; REVIEW; STATISTICAL MODEL;

ANIMALS; EVOLUTION; GENE DUPLICATION; GENOMICS; HUMANS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MULTIGENE FAMILY; PHYLOGENY; PROTEINS; VARIATION (GENETICS);

EID: 0034578465     PISSN: 15278204     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.genom.1.1.41     Document Type: Article

References (130)

1. Abouheif E, Akam M, Dickinson WJ, Holland PWH, Meyer A, et al. 1997. Homology and developmental trends. Trends Genet. 13:432-33
2. Agosti D, Jacobs D, DeSalle R. 1996. On combining protein sequences and nucleic acid sequences in phylogenetic analysis: the homeobox protein case. Cladistics 12: 65-82
3. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-10
4. Amero, SA, Kretsinger RH, Moncrief ND, Yamamoto KR, Pearson WR. 1992. The origin of nuclear receptor proteins: a single precursor distinct from other transcription factors. Mol. Endocrinol. 6:3-7
5. Applebury ML. 1994. Relationships of G-protein-coupled receptors: a survey with the photoreceptor opsin subfamily. See Ref. 28a, pp. 235-48
6. Aravind LA, Tatusov RI, Wolf YT, Walker R, Koonin EV. 1998. Evidence for massive gene exchange between archael and bacterial hyperthermophiles. Trends Genet. 14:442-44
7. Atchley WR, Fitch WM. 1997. A natural classification of the basic helix-loop-helix class of transcription factors. Proc. Natl. Acad. Sci. USA 94:5172-76
8. Baker ME. 1997. Steroid receptor phylogeny and vertebrate origins. Mol. Cell Endocrinol. 135:101-7
9. Bonci A, Chiesurin A, Muscas P, Rossolini GM. 1997. Relatedness and phylogeny within the family of periplasmic chaperones involved in the assembly of pilli or capsule-like structures of gram-negative bacteria. J. Mol. Evol. 44:299-309
10. Bremer K. 1995. Branch support and tree stability. Cladistics 10:295-304
11. Brendel V, Brocchieri L, Sandier SJ, Clark AJ, Karlin S. 1997. Evolutionary comparisons of RecA-like proteins across all major kingdoms of living organisms. J. Mol. Evol. 44:528-41
12. Brower AVZ, Schawaroch V. 1996. Three steps of homology assessment. Cladistics 12:265-72
13. Brown JR, Doolittle WF. 1999. Gene descent, duplication, and horizontal transfer in the evolution of glutamyI- and glutaminyI-tRNA synthetases. J. Mol. Evol. 49:485-95
14. Brown JR, Robb FT, Weiss R, Doolittle WF. 1997. Evidence of the early divergence of tryptophanyI- and tyrosyI-tRNA synthetases. J. Mol. Evol 45:9-16
15. Burt DW, Bruley C, Dunn IC, Jones CT, Ramage A, et al. 1999. The dynamics of chromosome evolution in birds and mammals. Nature 402:411-13
16. Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, et al. 1998. Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science 282:2022-28
17. Chiu J, DeSalle R, Lam HM, Meisel L, Coruzzi G. 1999. Molecular evolution of glutamate receptors: a primitive signaling mechanism that existed before plants and animals diverged. Mol. Biol. Evol. 16: 826-38
18. Coulier F, Pontarotti P, Roubin R, Hartun G, Goldfarb M, Birnbaum D. 1997. Of worms and men: an evolutionary perspective on the fibroblast growth factor (FGF) and FGF receptor families. J. Mol. Evol. 44:43-56
19. Crandall KA, Templeton AR. 1999. Statistical approaches to detecting recombination. In The Evolution of HIV, ed. KA Crandall, pp. 153-76. Baltimore, MD: Johns Hopkins Univ. Press
20. De Pinna MCC. 1991. Concepts and tests of homology in the cladistic paradigm. Cladistics 7:367-94
21. de Rosa R, Grenier JK, Andreeva T, Cook CE, Adoutte A, et al. 1999. Hox genes in brachiopods and priapulids and protostome evolution. Nature 399:772-76
22. Doolittle RF, 1995. The multiplicity of domains in proteins. Annu. Rev. Biochem. 64:287-314
23. Doolittle RF, Bork P. 1993. Evolutionarily mobile modules in proteins. Sci. Am. 269(4):50-56
24. Dover GA, Linares AR, Bowen T, Hancock HM. 1993. Detection and quantification of concerted evolution and molecular drive. Methods Enzymol. 224: 525-41
25. Ebendal T. 1992. Function and evolution in the NGF family and its receptors. J. Neurosci. Res. 32:461-70
26. Enright AJ, Illiopoulos I, Kyrpides, Ouzounis CA. 1999. Protein interaction maps for complete genomes based on gene fusion events. Nature 402:86-90
27. Eriksson T. 1996. Auto-Decay, version 2.9.5 (software). Stockholm, Swed: Stockholm Univ.
28. Escriva H, Safi R, Hanni C, Langlois MC, Saumitou-Laprade P. 1997. Ligand binding was acquired during evolution of nuclear receptors. Proc. Natl. Acad. Sci. USA 94(13):6803-8
29. Fambrough DM, ed. 1994. Molecular Evolution of Physiological Processes. New York: Rockefeller Univ. Press
30. Farris JS. 1982. Distance data in phylogenetic analysis. Adv. Cladistics 1:3-23
31. Farris JS. 1983. The logical basis of phylogenetic analysis. Adv. Cladistics 2:7-36
32. Farris JS, Kallersjo M, Kluge AG, Bult C. 1995. Constructing a significance test for incongruence. Syst. Biol. 44:570-72
33. Felsenstein J. 1978. Cases in which parsimony and compatibility methods will be positively misleading. Syst. Zool. 27: 401-10
34. Felsenstein J. 1978. The number of evolutionary trees. Syst. Zool. 27:27-33
35. Felsenstein J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-76
36. Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-91
37. Fitch WM. 1970. Distinguishing homologous from analogous proteins. Syst. Zool. 19:99-113
38. Fitch WM. 1979. Cautionary remarks on using gene expression events in parsimony procedures. Syst. Zool. 28:375-79
39. Fitch WM, Upper K. 1987. The phylogeny of tRNA sequences provides evidence for ambiguity reduction in the origin of the genetic code. Cold Spring Harbor Symp. Quant. Biol. 52:759-67
40. Force A, Lynch M, Pickett FB, Amores A, Yan Y-L, Postlethwaite JH. 1996. Preservation of duplicate genes by complementary degenerative mutations. Genetics 151:1531-45
41. Fryxell KJ. 1996. The coevolution of gene family trees. Trends Genet. 12:364-69
42. Gatesy J, DeSalle R, Wheeler W. 1993. Alignment-ambiguous nucleotide sites and the exclusion of systematic data. Mol. Phylogenet. Evol. 2:152-57
43. Gatesy JC, Hayashi C, DeSalle R, Vrba E. 1994. Rate limits for mispairing and compensatory change: the mitochondrial ribosomal DNA of antelopes. Evolution 48:188-96
44. Gaudieri S, Leelayuwat C, Townsend DC, Kulski JK, Dawkins RL. 1997. Genomic characterization of the region between HLA-B and TNF: implications for the evolution of multicopy gene families. J. Mol. Evol. 44(Suppl. 1):S147-54
45. Gellon G, McGinnis W. 1998. Shaping animal body plans in development and evolution: modulation of Hox expression patterns. BioEssays 20:116-25
46. Gibson TJ, Spring J. 1998. Genetic redundancy in vertebrates: polyploidy and persistence of genes encoding multidomain proteins. Trends Genet. 14:46-49
47. Golding GB, Dean AM. 1998. The structural basis of molecular adaptation. Mol. Biol. Evol. 15:355-69
48. Goodman M, Czelusniak J, Moore GW, Matsuda G. 1979. Fitting the gene lineage into its species lineage: a parsimony strategy illustrated by cladograms constructed from globin sequences. Syst. Zool. 28: 132-63
49. Graur D, Li WH. 1999. Fundamentals of Molecular Evolution. Sunderland, MA: Sinauer. 2nd ed. 481 pp.
50. Harvey PH, Pagel MD. 1991. The Comparative Method in Evolutionary Biology. Oxford, UK: Oxford Univ. Press
51. Hein J. 1990. Unified approach to alignment and phylogenies. Methods Enzymol. 183;626-44
52. Hendy MD, Penny D. 1989. A framework for the quantitative study of evolutionary trees. Syst. Zool. 38:297-309
53. Hennig W. 1963. Phylogenetic systematics. Annu. Rev. Entomol. 10:97-116
54. Holland PWH, Garcia-Femandez J, Williams NA, Sidow A. 1994. Gene duplications and the origins of vertebrate development. Development (Suppl.) pp. 125-33
55. Holm L. 1998. Unification of protein families. Curr. Opin. Struct. Biol. 8:372-79
56. Huelsenbeck JP, Bull JJ. 1996. A likelihood ratio test for detection of conflicting phylogenetic signal. Syst. Biol. 42: 247-64
57. Huelsenbeck JP, Crandall KA. 1997. Phylogeny estimation and hypothesis testing using maximum likelihood. Annu. Rev. Ecol. Syst. 28:437-66
58. Hughes AL. 1999. Phylogenies of developmentally important proteins do not support the hypothesis of two rounds of genome duplication early in vertebrate history. J. Mol. Evol. 48:565-76
59. Hull DL. 1988. Science as a Process: An Evolutionary Account of the Social and Conceptual Development of Science. Chicago, IL: Univ. Chicago Press
60. Iwabe N, Kuma K, Hasegawa M, Osawa S, Miyata T. 1989. Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc. Natl. Acad. Sci. USA 86:9355-59
61. Jain R, Rivera MC, Lake JA. 1999. Horizontal gene transfer among genomes: the complexity hypothesis. Proc. Natl. Acad. Sci. USA 96:3801-6
62. Kissinger JC, Hahn J-H, Raff RA. 1997. Rapid evolution in a conserved gene family: evolution of the actin gene family in the sea urchin genus Heliocidaris and related genera. Mol. Biol. Evol. 14:654-65
63. Koonin EV, Muhegian AR, Bork P. 1996. Non-orthologous gene displacement. Trends Genet. 12:334-36
64. Koonin EV, Tatusov RL, Galperin MY. 1998. Beyond complete genomes: from sequence to structure and function. Curr. Opin. Struct. Biol. 8:355-63
65. Koonin EV, Tatusov RL Rudd KE. 1996. Protein sequence comparison at genome scale. Methods Enzymol. 266:295-323
66. Kornegay JR, Schilling JW, Wilson AC. 1994. Molecular adaptation of a leaf-eating bird: stomach lysozyme of the hoatzin. Mol. Biol. Evol. 11:921-28
67. Kyripides N, Overbeek R, Ouzonis C. 1999. Universal protein families and the functional content of the last universal common ancestor. J. Mol. Evol. 49: 413-23
68. Labedan B, Boyen A, Baetens M, Charlier D, Chen P, et al. 1999. The evolutionary history of carbamoyltransferases: A complex set of paralogous genes was already present in the last universal common ancestor. J. Mol. Evol. 49:461-73
69. Lahn BT, Page DC. 1999. Retrotransposition of autosomal mRNA yielded testisspecific gene family on human Y chromosome. Nat. Genet. 21:429-33
70. Laudet V. 1997. Evolution of the nuclear receptor superfamily: early diversification from an ancestral orphan receptor. J. Mol. Endocrinol. 19:207-26
71. Laudet V, Hanni C, Coll J, Catzeflis F, Stehelin D. 1992. Evolution of the nuclear receptor gene superfamily. EMBO J. 11:1003-13
72. Leape DD. 1996. Biodiversity, genomes, and DNA sequence databases. Curr. Opin. Genet. Dev. 6:686-91
73. Lewis DFV. 1996. Cytochromes P450: Structure, Function and Mechanism. London: Taylor & Francis. 348 pp.
74. Li WH. 1985. Accelerated evolution following gene duplication and its implications for the neutralist-selection controversy. In Population Genetics and Molecular Evolution, ed. T Ohta, pp. 335-52. Berlin: Springer-Verlag
75. Li WH. 1997. Molecular Evolution. Sunderland, MA: Sinauer. 487 pp.
76. Maddison WP, Maddison DR. 1997. MacClade 3.07 (software). Sunderland, MA: Sinauer
77. Marcotte EM, Pellegrini M, Ng H-L, Rice DW, Yeates TO, Eisenberg D. 1999. Detecting protein function and protein interactions from genome sequences. Science 285:751-53
78. Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D. 1999. A combined algorithm for genome-wide prediction of protein function. Nature 402:83-86
79. Mayr E. 1982. The Growth of Biological Thought. New York: Belknap Press
80. Meyer A. 1998. Hox gene variation and evolution. Nature 391:225-27
81. Meyer A, Malaga-Trillo E. 1999. Vertebrate genomics: more fishy tales about Hox genes. Curr. Biol. 9:R210-13
82. Murzin AG. 1998. How far divergent evolution goes in proteins. Curr. Opin. Struct. Biol. 8:380-87
83. Muse SV. 1999. Modeling the molecular evolution of HIV sequences. In The Evolution of HIV, ed. KA Crandall. pp. 122-52. Baltimore, MD: Johns Hopkins Univ. Press
84. Mushegian AR, Garey JR, Martin J, Liu LX. 1998. Large-scale taxonomic profiling of eukaryotic model organisms: a comparison of orthologous proteins encoded by the human, fly, nematode and yeast genomes. Genome Res. 8:590-98
85. Nadeau JH, Sankoff D. 1998. Counting on comparative maps. Trends Genet. 14:495-501
86. Nelson G. 1994. Homology and systematics. In Homology: The Hierarchical Basis of Comparative Biology, ed. BK Hall, pp. 102-38. New York: Academic
87. Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, et al. 1999. Evidence for lateral gene transfer between archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399: 323-29
88. Newfeld SJ, Wisotzkey RG, Kumar S. 1999. Molecular evolution of a developmental pathway: phylogenetic analyses of transforming growth factor-β family ligands, receptors, and Smad signal transducers. Genetics 152:783-95
89. Nixon KC, Davis JL, Goloboff PA. 1998. Search strategies for large dataset: an example using rbcL. Am. J. Bot. 85:148-53
90. Ohno S. 1970. Evolution by Gene Duplication. Berlin: Springer-Verlag. 160 pp.
91. Ono K, Suga H, Iwabe N, Kuma K, Miyata T. 1999. Multiple protein tyrosine phosphatases in sponges and explosive gene duplication in the early evolution of animals before the parazoan-eumetazoan split. J. Mol. Evol. 48:654-62
92. Page RDM. 1993. Component 2.0 (software). London: Nat. Hist. Mus.
93. Page RDM. 1993. Genes, organisms, and areas: the problem of multiple lineages. Syst. Biol. 42:77-84
94. Page RDM. 1994. Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas. Syst. Biol. 43:58-77
95. Page RDM. 1998. Genetree 1.0 (software). Glasgow, Scotland: Univ. Glasgow
96. Page RDM, Charleston MA. 1997. From gene to organismal phylogeny: reconciled trees and the gene tree/species tree problem. Mol. Phylogenet. Evol. 7:231-40
97. Patterson C. 1988. Homology in classical and molecular biology. Mol. Biol. Evol. 5:603-25
98. Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO. 1999. Assigning protein function by comparative genome analysis: protein phylogenetic profiles. Proc. Natl. Acad. Sci. USA 96: 4285-88
99. Phillippe H, Forterre P. 1999. The rooting of the universal tree of life is not reliable. J. Mol. Evol. 49:509-23
100. Raymond CS, Shamu CE, Shen MM, Seifert KJ, Hirsch B, et al. 1998. Evidence for evolutionary conservation of sex-determining genes. Nature 391:691-95
101. Reeck GR, de Haen C, Teller DC, Doolittle RF, Fitch WM, et al. 1987. Homology in proteins and nucleic acids: a terminology muddle and a way out of it. Cell 50:667
102. Rice KA, Donoghue MJ, Olmstead R. 1997. Analyzing large data sets: rbcL 500 revisited. Syst. Biol. 46:554-63
103. Sanderson MJ. 1994. Reconstructing the history of evolutionary processes using maximum likelihood. See Ref. 28a, pp. 13-26
104. Sanderson MJ. 1995. Objections to bootstrapping phytogenies: a critique. Syst. Biol. 44:299-320
105. Sanderson MJ, Doyle JJ. 1992. Reconstruction of organismal and gene phytogenies from data on multigene families: concerted evolution, homoplasy and confidence. Syst. Biol. 41:4-17
106. Sawyer S. 1989. Statistical tests for detecting gene conversion. Mol. Biol. Evol. 6:526-38
107. Schledzewski K, Brinkmann H, Mendel RR. 1999. Phylogenetic analysis of components of the eukaryotic vesicle transport system reveals a common origin of adaptor protein complexes 1, 2 and 3 and the F subcomplex of the coatomer COPI. J. Mol. Evol. 48:770-78
108. Schwanz JH. 1999. Homeobox genes, fossils and the origin of species. Anat. Rec. 257:15-31
109. Semple C, Wolfe KH. 1999. Gene duplication and gene conversion in the Caenorhabditis elegans genome. J. Mol. Evol. 48:555-64
110. Siddall ME, Kluge AG. 1997. Probabilism and phylogenetic inference. Cladistics 13:313-36
111. Sidow A. 1992. Diversification of the Wnt gene family on the ancestral lineage of vertebrates. Proc. Natl. Acad. Sci. USA 89:5098-102
112. Sidow A. 1996. Genome duplications in the evolution of early vertebrates. Curr. Opin. Genet. Dev. 6:715-22
113. Smith NGC, Knight R, Hurst LD. 1999. Vertebrate genome evolution: a slow shuffle or a big bang? BioEssays 21:697-703
114. Soltis PS, Soltis DE, Chase M. 1999. Angiosperm phytogeny inferred from multiple genes as a tool for comparative biology. Nature 402: 402-4
115. Song Y, Fambrough D. 1994. Molecular evolution of the calcium-transporting ATPases analyzed by the maximum parsimony method. See Ref. 28a, pp. 271-83
116. Soullier S, Jay P, Poulat F, Vanacker J-M, Berta P, Laudet V. 1999. Diversification patterns of the HMG and SOX family members during evolution. J. Mol. Evol. 48:517-27
117. Spring J. 1997. Vertebrate evolution by interspecific hybridisation: are we polyploid? FEBS Lett. 400:2-8
118. Suga H, Koyanagi M, Hoshiyama D, Ono K, Iwabe N, et al. 1999. Extensive gene duplication in the early evolution of animals before the parazoan-eumetazoan split demonstrated by G proteins and protein tyrosine kinases from sponge and hydra. J. Mol. Evol. 48:646-53
119. Swofford DL. 1999. PAUP*: Phylogenetic Analysis Using Parsimony (* and Other Methods) (software). Sunderland, MA: Sinauer
120. Swofford DL, Olsen GJ, Waddell PJ, Hillis DM. 1996. Phylogenetic inference. In Molecular Systematics, ed. DM Hillis, C Moritz, BK Mable, pp. 407-509. Sunderland, MA: Sinauer. 2nd ed.
121. Tannenbaum DM, Wang Y, Williams SP, Sigler PB. 1998. Crystallographic comparisons of the estrogen and progesterone receptor's ligand binding domains. Proc. Natl. Acad. Sci. USA 95:5998-6003
122. Tatusov RL, Koonin EV, Lipman DJ. 1997. A genomic perspective on protein families. Science 278:631-37
123. Tautz D. 1998. Evolutionary biology: debatable homologies. Nature 395:17-19
124. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-80
125. Thornton JW, DeSalle R. 2000. A new method to localize and test the significance of incongruence: detecting domainshuffling in the nuclear receptor super-family. Syst. Biol. 49(2):183-201
126. Thornton JW, Kelly DB. 1998. Evolution of the androgen receptor: structurefunction implications. BioEssays 20:860-68
127. Wheeler WC, Gatesy J, DeSalle R. 1995. Elision: a method for accommodating multiple molecular sequence alignments with alignment-ambiguous sites. Mol. Phylogenet. Evol 4:1-9
128. Wheeler WC, Gladstein DS. 1995. Malign 2.7 (software). New York: Am. Mus. Nat. Hist.
129. Wilkie TM, Gilvert DJ, Olsen AS, Chen XN, Amatruda TT, et al. 1992. Evolution of the mammalian G protein alphasubunit multigene family. Nat. Genet. 1:85-92
130. Yokoyama S, Radlwimmer FB. 1999. The molecular genetics of red and green color vision in mammals. Genetics 153: 919-32