The evolution of eutherian chromosomes

Current Opinion in Genetics and Development

Volumn 14, Issue 6, 2004, Pages 657-666

  Wienberg, Johannes ^a  

^a INSTITUTE OF EPIDEMIOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMOSOME; CHROMOSOME ARM; CHROMOSOME NUMBER; CHROMOSOME TRANSLOCATION; CYTOGENETICS; GENOME; HUMAN; KARYOTYPE; NONHUMAN; PHYLOGENY; PLACENTAL MAMMALS; PRIORITY JOURNAL; REVIEW;

ANIMALS; CHROMOSOMES; EVOLUTION, MOLECULAR; GENE REARRANGEMENT; KARYOTYPING; MAMMALS;

EUTHERIA; MAMMALIA;

EID: 8644290092     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gde.2004.10.001     Document Type: Review

References (65)

1. Q. Ji, Z.X. Luo, C.X. Yuan, J.R. Wible, J.P. Zhang, and J.A. Georgi The earliest known eutherian mammal Nature 416 2002 816 822
2. Z.X. Luo, Q. Ji, J.R. Wible, and C.X. Yuan An Early Cretaceous tribosphenic mammal and metatherian evolution Science 302 2003 1934 1940
3. W.J. Murphy, E. Eizirik, W.E. Johnson, Y.P. Zhang, O.A. Ryder, and S.J. O'Brien Molecular phylogenetics and the origins of placental mammals Nature 409 2001 614 618
4. W.J. Murphy, E. Eizirik, S.J. O'Brien, O. Madsen, M. Scally, C.J. Douady, E. Teeling, O.A. Ryder, M.J. Stanhope, and W.W. de Jong Resolution of the early placental mammal radiation using Bayesian phylogenetics Science 294 2001 2348 2351
5. M.S. Springer, W.J. Murphy, E. Eizirik, and S.J. O'Brien Placental mammal diversification and the Cretaceous-Tertiary boundary Proc Natl Acad Sci USA 100 2003 1056 1061
6. J.D. Archibald Timing and biogeography of the eutherian radiation: fossils and molecules compared Mol Phylogenet Evol 28 2003 350 359
7. A. Rokas, and P.W. Holland Rare genomic changes as a tool for phylogenetics Trends Ecol Evol 15 2000 454 459
8. J. Wienberg, A. Jauch, R. Stanyon, and T. Cremer Molecular cytotaxonomy of primates by chromosomal in situ suppression hybridization Genomics 8 1990 347 350
9. A. Jauch, J. Wienberg, R. Stanyon, N. Arnold, S. Tofanelli, T. Ishida, and T. Cremer Reconstruction of genomic rearrangements in great apes and gibbons by chromosome painting Proc Natl Acad Sci USA 89 1992 8611 8615
10. H. Scherthan, T. Cremer, U. Arnason, H.U. Weier, A. Lima-de-Faria, and L. Fronicke Comparative chromosome painting discloses homologous segments in distantly related mammals Nat Genet 6 1994 342 347
11. F. Yang, E.Z. Alkalaeva, P.L. Perelman, A.T. Pardini, W.R. Harrison, P.C. O'Brien, B. Fu, A.S. Graphodatsky, M.A. Ferguson-Smith, and T.J. Robinson Reciprocal chromosome painting among human, aardvark, and elephant (superorder Afrotheria) reveals the likely eutherian ancestral karyotype Proc Natl Acad Sci USA 100 2003 1062 1066 The authors present chromosome painting results for representatives of two of the six suggested Afrotherian orders: the Tubulidentata (aardvark) and Proboscidea (elephant). This is the first molecular cytogenetic analysis of a complete karyotype of members of the assumed oldest clade of placental mammals. From these data the authors derive an ancestral karyotype which is supposed to be the ancestor for all modern-day placental mammals with 2n = 4, and in which various chromosomes and chromosome segments homologous to humans are already conserved.
12. ••] with only slightly different interpretation of the ancestral karyotype (2n = 46) that is the basis of Figure 1 of the present paper. The African elephant shows a moderately rearranged chromosome complement when compared to humans. Two chromosome rearrangements - the associations of human homologous segments to chromosomes 1/19 and 5/21 - were observed that should be considered as common derived markers for both the Tubulidentata and Proboscidea.
13. M. Svartman, G. Stone, J.E. Page, and R. Stanyon A chromosome painting test of the basal eutherian karyotype Chromosome Res 12 2004 45 53 A member of the Macroscelidea, the short-eared elephant shrew (Macroscelides proboscideus), was analyzed by chromosome painting - the third species of the Afrotheria studied by this approach up to now. Similar to Tubulidentata and Proboscidea, the elephant shrew showed associations of human homologous segments to chromosomes 1/19 and 5/21. Additional rearrangements (associations 2/8, 3/20 and 10/17) strongly link aardvarks and elephant shrews after the divergence of the line leading to elephants. In this paper, the authors suggest a most likely ancestral eutherian karyotype of 2n = 48 chromosomes. There are three more Afrotheria orders that have not yet been analyzed by chromosome painting.
14. S. Müller, R. Stanyon, P.C. O'Brien, M.A. Ferguson-Smith, R. Plesker, and J. Wienberg Defining the ancestral karyotype of all primates by multidirectional chromosome painting between tree shrews, lemurs and humans Chromosoma 108 1999 393 400
15. D. Haig A brief history of human autosomes Philos Trans R Soc Lond B Biol Sci 354 1999 1447 1470
16. R. Stanyon, G. Stone, M. Garcia, and L. Froenicke Reciprocal chromosome painting shows that squirrels, unlike murid rodents, have a highly conserved genome organization Genomics 82 2003 245 249 This is the first report of chromosome painting between humans and rodents (in this case, the Eastern gray squirrel Sciurus carolinensis). Whereas early gene mapping and sequencing data lead to the generalization that rodent genomes are highly rearranged, the chromosome painting between humans and squirrels demonstrate a conserved pattern that is similar to most other placental mammals. The authors also propose some evolutionarily derived rearrangements that may be cladistic markers for the cohort Glires, linking rodents and lagomorphs (see also Update).
17. P.E. Bielec, D.S. Gallagher, J.E. Womack, and D.L. Busbee Homologies between human and dolphin chromosomes detected by heterologous chromosome painting Cytogenet Cell Genet 81 1998 18 25
18. Froenicke L: Origins of primate chromosomes - as delineated by Zoo-FISH and alignments of human and mouse draft genome sequences. Cytogenet Genome Res 2004, in press.
19. M. Volleth, K.G. Heller, R.A. Pfeiffer, and H. Hameister A comparative ZOO-FISH analysis in bats elucidates the phylogenetic relationships between Megachiroptera and five microchiropteran families Chromosome Res 10 2002 477 497
20. M. Volleth, G. Bronner, M.C. Gopfert, K.G. Heller, K. von Helversen, and H.S. Yong Karyotype comparison and phylogenetic relationships of Pipistrellus-like bats (Vespertilionidae; Chiroptera; Mammalia) Chromosome Res 9 2001 25 46
21. E.C. Teeling, O. Madsen, R.A. Van den Bussche, W.W. de Jong, M.J. Stanhope, and M.S. Springer Microbat paraphyly and the convergent evolution of a key innovation in Old World rhinolophoid microbats Proc Natl Acad Sci USA 99 2002 1431 1436
22. K.E. Jones, A. Purvis, A. MacLarnon, O.R. Bininda-Emonds, and N.B. Simmons A phylogenetic supertree of the bats (Mammalia: Chiroptera) Biol Rev Camb Philos Soc 77 2002 223 259
23. S. Müller, M. Hollatz, and J. Wienberg Chromosomal phylogeny and evolution of gibbons (Hylobatidae) Hum Genet 113 2003 493 501 Although closely related to humans, gibbons have karyotypes that differ dramatically from that of other primates. Furthermore, highly variant chromosome sets can be observed within the group. In this paper, a phylogeny of extant gibbon species is suggested on the basis of multicolor chromosome painting.
24. F. Bigoni, M.L. Houck, O.A. Ryder, J. Wienberg, and R. Stanyon Chromosome painting shows that Pygathrix nemaeus has the most basal karyotype among Asian Colobinae Intern J of Primatol 25 2004 679 688
25. F. Bigoni, R. Stanyon, R. Wimmer, and W. Schempp Chromosome painting shows that the proboscis monkey (Nasalis larvatus) has a derived karyotype and is phylogenetically nested within Asian Colobines Am J Primatol 60 2003 85 93
26. R. Stanyon, U. Koehler, and S. Consigliere Chromosome painting reveals that galagos have highly derived karyotypes Am J Phys Anthropol 117 2002 319 326
27. E.H. de Oliveira, M. Neusser, W.B. Figueiredo, C. Nagamachi, J.C. Pieczarka, I.J. Sbalqueiro, J. Wienberg, and S. Müller The phylogeny of howler monkeys (Alouatta, Platyrrhini): reconstruction by multicolor cross-species chromosome painting Chromosome Res 10 2002 669 683
28. R. Stanyon, S. Consigliere, F. Bigoni, M. Ferguson-Smith, P.C. O'Brien, and J. Wienberg Reciprocal chromosome painting between a New World primate, the woolly monkey, and humans Chromosome Res 9 2001 97 106
29. F. Garcia, A. Ruiz-Herrera, J. Egozcue, M. Ponsa, and M. Garcia Chromosomal homologies between Cebus and Ateles (primates) based on ZOO-FISH and G-banding comparisons Am J Primatol 57 2002 177 188
30. M. Neusser, R. Stanyon, F. Bigoni, J. Wienberg, and S. Müller Molecular cytotaxonomy of New World monkeys (Platyrrhini) - comparative analysis of five species by multi-color chromosome painting gives evidence for a classification of Callimico goeldii within the family of Callitrichidae Cytogenet Cell Genet 94 2001 206 215
31. R. Stanyon, C.R. Bonvicino, M. Svartman, and H.N. Seuanez Chromosome painting in Callicebus lugens, the species with the lowest diploid number (2n = 16) known in primates Chromosoma 112 2003 201 206
32. de Oliveira EH, Neusser M, Pieczarka JC, Nagamachi C, Sbalqueiro IJ, Müller S: Phylogenetic inferences of Atelinae (Platyrrhini) based on multi-directional chromosome painting in Brachyteles arachnoides, Ateles paniscus paniscus and Ateles b. marginatus. Cytogenet Genome Res 2004, in press.
33. P. Cavagna, A. Menotti, and R. Stanyon Genomic homology of the domestic ferret with cats and humans Mamm Genome 11 2000 866 870
34. W.G. Nash, J.C. Menninger, J. Wienberg, H.M. Padilla-Nash, and S.J. O'Brien The pattern of phylogenomic evolution of the Canidae Cytogenet Cell Genet 95 2001 210 224
35. W.G. Nash, J. Wienberg, M.A. Ferguson-Smith, J.C. Menninger, and S.J. O'Brien Comparative genomics: tracking chromosome evolution in the family Ursidae using reciprocal chromosome painting Cytogenet Cell Genet 83 1998 182 192
36. A.S. Graphodatsky, F. Yang, P.C. O'Brien, P. Perelman, B.S. Milne, N. Serdukova, S.I. Kawada, and M.A. Ferguson-Smith Phylogenetic implications of the 38 putative ancestral chromosome segments for four canid species Cytogenet Cell Genet 92 2001 243 247
37. A.S. Graphodatsky, F. Yang, P.C. O'Brien, N. Serdukova, B.S. Milne, V. Trifonov, and M.A. Ferguson-Smith A comparative chromosome map of the Arctic fox, red fox and dog defined by chromosome painting and high resolution G-banding Chromosome Res 8 2000 253 263
38. F. Yang, P.C. O'Brien, B.S. Milne, A.S. Graphodatsky, N. Solanky, V. Trifonov, W. Rens, D. Sargan, and M.A. Ferguson-Smith A complete comparative chromosome map for the dog, red fox, and human and its integration with canine genetic maps Genomics 62 1999 189 202
39. P. Finelli, R. Stanyon, R. Plesker, M.A. Ferguson-Smith, P.C. O'Brien, and J. Wienberg Reciprocal chromosome painting shows that the great difference in diploid number between human and African green monkey is mostly due to non-Robertsonian fissions Mamm Genome 10 1999 713 718
40. W.J. Murphy, S. Sun, Z. Chen, N. Yuhki, D. Hirschmann, M. Menotti-Raymond, and S.J. O'Brien A radiation hybrid map of the cat genome: implications for comparative mapping Genome Res 10 2000 691 702
41. M.F. Cardone, M. Ventura, S. Tempesta, M. Rocchi, and N. Archidiacono Analysis of chromosome conservation in Lemur catta studied by chromosome paints and BAC/PAC probes Chromosoma 111 2002 348 356
42. K. Mrasek, A. Heller, N. Rubtsov, V. Trifonov, H. Starke, M. Rocchi, U. Claussen, and T. Liehr Reconstruction of the female Gorilla gorilla karyotype using 25-color FISH and multicolor banding (MCB) Cytogenet Cell Genet 93 2001 242 248
43. S. Müller, R. Stanyon, P. Finelli, N. Archidiacono, and J. Wienberg Molecular cytogenetic dissection of human chromosomes 3 and 21 evolution Proc Natl Acad Sci USA 97 2000 206 211
44. Y. Tian, W. Nie, J. Wang, M.A. Ferguson-Smith, and F. Yang Chromosome evolution in bears: reconstructing phylogenetic relationships by cross-species chromosome painting Chromosome Res 12 2004 55 63
45. L. Froenicke, and J. Wienberg Comparative chromosome painting defines the high rate of karyotype changes between pigs and bovids Mamm Genome 12 2001 442 449
46. A. Goureau, A. Garrigues, G. Tosser-Klopp, Y. Lahbib-Mansais, P. Chardon, and M. Yerle Conserved synteny and gene order difference between human chromosome 12 and pig chromosome 5 Cytogenet Cell Genet 94 2001 49 54
47. M. Ventura, J.M. Mudge, V. Palumbo, S. Burn, E. Blennow, M. Pierluigi, R. Giorda, O. Zuffardi, N. Archidiacono, and M.S. Jackson Neocentromeres in 15q24-26 map to duplicons which flanked an ancestral centromere in 15q25 Genome Res 13 2003 2059 2068 The fission point of the ancestral eutherian chromosomes homologous to human chromosome 15 and 14 was analyzed by FISH with a panel of human BAC clones. The ancestral centromere - as found in Old World primates - was found to be silenced, and two new centromeres had evolved on the 'new' chromosome 14- and 15-homologs in hominoids. The site of the ancestral centromere is found in a region homologous to human chromosomal 15q24-26, which is also known as a hot spot for neocentromere formation in human genetic pathology.
48. V. Eder, M. Ventura, M. Ianigro, M. Teti, M. Rocchi, and N. Archidiacono Chromosome 6 phylogeny in primates and centromere repositioning Mol Biol Evol 20 2003 1506 1512 The position of the centromere of the human chromosome 6 homolog was found to be located in three distinct regions in different primates, without any evidence for chromosomal rearrangement that would account for its movement.
49. J.A. Bailey, Z. Gu, R.A. Clark, K. Reinert, R.V. Samonte, S. Schwartz, M.D. Adams, E.W. Myers, P.W. Li, and E.E. Eichler Recent segmental duplications in the human genome Science 297 2002 1003 1007
50. E.E. Eichler, and D. Sankoff Structural dynamics of eukaryotic chromosome evolution Science 301 2003 793 797
51. H.C. Mefford, and B.J. Trask The complex structure and dynamic evolution of human subtelomeres Nat Rev Genet 3 2002 91 102
52. A. Fujiyama, H. Watanabe, A. Toyoda, T.D. Taylor, T. Itoh, S.F. Tsai, H.S. Park, M.L. Yaspo, H. Lehrach, and Z. Chen Construction and analysis of a human-chimpanzee comparative clone map Science 295 2002 131 134
53. S.M. Gribble, H. Fiegler, D.C. Burford, E. Prigmore, F. Yang, P. Carr, B.L. Ng, T. Sun, E.S. Kamberov, and V.L. Makarov Applications of combined DNA microarray and chromosome sorting technologies Chromosome Res 12 2004 35 43 A technique, called 'array painting' was used with gibbon chromosome-specific probes hybridized on human BAC arrays. The hybridization pattern allowed the identification of various breakpoint-spanning clones within a single experiment.
54. Y. Fan, E. Linardopoulou, C. Friedman, E. Williams, and B.J. Trask Genomic structure and evolution of the ancestral chromosome fusion site in 2q13-2q14.1 and paralogous regions on other human chromosomes Genome Res 12 2002 1651 1662
55. Y. Fan, T. Newman, E. Linardopoulou, and B.J. Trask Gene content and function of the ancestral chromosome fusion site in human chromosome 2q13-2q14.1 and paralogous regions Genome Res 12 2002 1663 1672
56. C.L. Martin, A. Wong, A. Gross, J. Chung, J.A. Fantes, and D.H. Ledbetter The evolutionary origin of human subtelomeric homologies - or where the ends begin Am J Hum Genet 70 2002 972 984
57. S. Müller, P. Finelli, M. Neusser, and J. Wienberg The evolutionary history of human chromosome 7 Genomics 84 2004 458 467 In addition to considerable changes during mammalian evolution (see Figure 1 and Figure 2), the human chromosome 7 homolog experienced two further inversions: the pericentric inversion in the human/African-ape ancestor and the paracentric inversion in the common ancestor of human and chimpanzees. All four breakpoints were flanked by large segmental duplications. The authors propose a scenario by which segmental duplications may have been the cause rather than the result of these chromosome rearrangements.
58. P. Stankiewicz, S.S. Park, K. Inoue, and J.R. Lupski The evolutionary chromosome translocation 4;19 in Gorilla gorilla is associated with microduplication of the chromosome fragment syntenic to sequences surrounding the human proximal CMT1A-REP Genome Res 11 2001 1205 1210
59. H. Kehrer-Sawatzki, B. Schreiner, S. Tanzer, M. Platzer, S. Müller, and H. Hameister Molecular characterization of the pericentric inversion that causes differences between chimpanzee chromosome 19 and human chromosome 17 Am J Hum Genet 71 2002 375 388
60. D.P. Locke, N. Archidiacono, D. Misceo, M.F. Cardone, S. Deschamps, B. Roe, M. Rocchi, and E.E. Eichler Refinement of a chimpanzee pericentric inversion breakpoint to a segmental duplication cluster Genome Biol 4 2003 R50 Human chromosome 15 differs from the homolog in the chimpanzee by a pericentric inversion that should have occurred in chimpanzees after the divergence from humans. The breakpoint region in human 15q11-q13 of this rearrangement was assigned to a region consisting of entirely duplicated segments in a 600 kb interval of the homologous human sequences.
61. B.K. Dennehey, D.G. Gutches, E.H. McConkey, and K.S. Krauter Inversion, duplication, and changes in gene context are associated with human chromosome 18 evolution Genomics 83 2004 493 501
62. G.P. Holmquist Chromosome bands, their chromatin flavors, and their functional features Am J Hum Genet 51 1992 17 37
63. H. Tanabe, S. Müller, M. Neusser, J. von Hase, E. Calcagno, M. Cremer, I. Solovei, C. Cremer, and T. Cremer Evolutionary conservation of chromosome territory arrangements in cell nuclei from higher primates Proc Natl Acad Sci USA 99 2002 4424 4429
64. T.J. Robinson, B. Fu, M.A. Ferguson-Smith, and F. Yang Cross-species chromosome painting in the golden mole and elephant-shrew: support for the mammalian clades Afrotheria and Afroinsectiphillia but not Afroinsectivora Proc R Soc Lond B Biol Sci 271 2004 1477 1484 See update.
65. Richard F, Messaoudi C, Bonnet-Garnier A, Lombard M, Dutrillaux B: Highly conserved chromosomes in an Asian squirrel (Menetes berdmorei, Rodentia: Sciuridae) as demonstrated by ZOO-FISH with human probes. Chromosome Res, 11:597-603. See update.