Cross-species chromosome painting in Cetartiodactyla: Reconstructing the karyotype evolution in key phylogenetic lineages

Chromosome Research

Volumn 17, Issue 3, 2009, Pages 419-436

  Kulemzina, Anastasia I ^a   Trifonov, Vladimir A ^a   Perelman, Polina L ^a,b   Rubtsova, Nadezhda V ^a   Volobuev, Vitaly ^c   Ferguson Smith, Malcolm A ^d   Stanyon, Roscoe ^e   Yang, Fengtang ^f   Graphodatsky, Alexander S ^a  

^a INSTITUTE OF CYTOLOGY AND GENETICS   (Russian Federation)

^b NATIONAL CANCER INSTITUTE   (United States)

^c Sorbonne Universités   (France)

^d Cambridge Resource Centre for Comparative Genomics   (United Kingdom)

^e UNIVERSITY OF FLORENCE   (Italy)

^f WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

Breakpoint reuse; Cetaceans; Chromosome evolution; Hippopotamus; Pecora; Zoo FISH

Indexed keywords

ANIMAL CELL; ARTICLE; ARTIODACTYLA; AUTOSOME; CETACEA; CETARTIODACTYLA; CHROMOSOME 8; CHROMOSOME 9; CHROMOSOME ANALYSIS; CHROMOSOME PAINTING; CHROMOSOME PAIRING; CHROMOSOME REARRANGEMENT; COMPARATIVE GENE MAPPING; DEER; GENE PROBE; GENETIC ASSOCIATION; GENOME ANALYSIS; HOMOPLASY; HUMAN CHROMOSOME; KARYOTYPE EVOLUTION; MOLECULAR EVOLUTION; MOLECULAR GENETICS; MOLECULAR PHYLOGENY; NONHUMAN; PILOT WHALE; PRIORITY JOURNAL; TAXUS;

ANIMALS; CHROMOSOME PAINTING; CHROMOSOMES, MAMMALIAN; EVOLUTION, MOLECULAR; GENE REARRANGEMENT; KARYOTYPING; MAMMALS; PHYLOGENY; SPECIES SPECIFICITY;

ARTIODACTYLA; BOVIDAE; CAMELIDAE; CAMELUS DROMEDARIUS; CERVIDAE; CETACEA; CETARTIODACTYLA; DELPHINIDAE; GIRAFFIDAE; HIPPOPOTAMIDAE; MOSCHIDAE; MOSCHUS MOSCHIFERUS; OKAPIA JOHNSTONI; PECORA; SUIDAE; SUINA;

EID: 67349234211     PISSN: 09673849     EISSN: 15736849     Source Type: Journal    
DOI: 10.1007/s10577-009-9032-3     Document Type: Article

References (85)

1. F Adega R Chaves A Kofler 2006 High-resolution comparative chromosome painting in the Arizona collared peccary (Pecari tajacu, Tayassuidae): a comparison with the karyotype of pig and sheep Chromosome Res 14 243 251
2. MW Allard MM Miyamoto L Jarecki F Kraus MR Tennant 1992 DNA systematics and evolution of the artiodactyl family Bovidae Proc Natl Acad Sci USA 89 3972 3976
3. U Arnason 1972 The role of chromosomal rearrangements in mammalian speciation with special reference to Cetacea and Pinnipedia Hereditas 70 113 118
4. U Arnason 1974 Comparative chromosome studies in Cetacea Heredidas 77 1 36
5. U Arnason A Gullberg 1996 Cytochrome b nucleotide sequences and the identification of five primary lineages of extant cetaceans Mol Biol Evol 13 407 417 (Pubitemid 26035321)
6. U Arnason A Gullberg S Gretarsdottir B Ursing A Janke 2000 The mitochondrial genome of the sperm whale and a new molecular reference for estimating eutherian divergence dates J Mol Evol 50 569 578 (Pubitemid 30429954)
7. JC Avise TJ Robinson 2008 Hemiplasy: a new term in the lexicon of phylogenetics Sys Biol 57 503 507
8. JA Bailey R Baertsch WJ Kent D Haussler EE Eichler 2004 Hotspots of mammalian chromosomal evolution Genome Biology 5 R 23
9. S Bajpai PD Gingerich 1998 A new Eocene archaeocete (Mammalia,Cetacea) from India and the time of origin of whales Proc Natl Acad Sci USA 95 15464 15468 (Pubitemid 29018721)
10. G Balmus VA Trifonov LS Biltueva 2007 Cross species painting among camel, cattle, pig and human: further insights into the putative Cetartiodactyla ancestral karyotype Chromosome Res 15 499 514 (Pubitemid 47025008)
11. RMD Beck ORP Bininda-Emonds M Cardillo FGR Liu A Purvis 2006 A higher-level MRP supertree of placental mammals BMC Evol Biol 6 93
12. AK Behrensmeyer AL Deino A Hill JD Kingston JJ Saunders 2002 Geology and geochronology of the middle Miocene Kipsaramon site complex, Muruyur Beds, Tugen Hills, Kenya J Hum Evol 42 11 38 (Pubitemid 34133489)
13. PE Bielec DS Gallagher JE Womack DL Busbee 1998 Homologies between human and dolphin chromosomes detected by heterologous chromosome painting Cytogenet Cell Genet 81 18 26 (Pubitemid 28380094)
14. LS Biltueva F Yang NV Vorobieva AS Graphodatsky 2004 Comparative map between the domestic pig and dog Mamm Genome 15 809 818 (Pubitemid 40012693)
15. ORP Bininda-Emonds M Cardillo KE Jones 2007 The delayed rise of present-day mammals Nature 446 507 512 (Pubitemid 46514725)
16. JR Boisserie F Lihoreau M Brunet 2005 The position of hippopotamidae within cetartiodactyla Proc Natl Acad Sci USA 102 5 1537 1541
17. JR Boisserie F Lihoreau M Brunet 2005 Origins of Hippopotamidae (Mammalia, Cetartiodactyla): towards resolution Zool Scr 34 2 119 143 (Pubitemid 40335831)
18. A Bonnet-Garnier F Claro S Thevenon M Gantie H Hayes 2003 Identification by R-banding and FISH of chromosome arms involved in Robertsonian translocations in several deer species Chromosome Res 11 649 663 (Pubitemid 37336450)
19. AA Bosma NA Haan GJ Arkesteijn F Yang M Yerle C Zijlstra 2004 Comparative chromosome painting between the domestic pig (Sus scrofa) and two species of peccary, the collared peccary (Tayassu tajacu) and the white-lipped peccary (T. pecari): a phylogenetic perspective Cytogenet Genome Res 105 115 121 (Pubitemid 38823865)
20. TD Bunch WC Foote A Maciulis 1985 Chromosome banding pattern homologies and NORs for the Bactrian camel, guanaco and llama J Hered 76 115 118 (Pubitemid 15148555)
21. R Chaves L Froenicke H Guedes-Pinto J Wienberg 2004 Multidirectional chromosome painting between the Hirola antelope (Damaliscus hunteri, Alcelaphini, Bovidae), sheep and human Chromosome Res 12 495 503
22. J Chi B Fu W Nie J Wang AS Graphodatsky F Yang 2005 New insights into the karyotypic relationships of Chinese muntjac (Muntiacus reevesi), forest musk deer (Moschus berezovskii) and gayal (Bos frontalis) Cytogenet Genome Res 108 310 316 (Pubitemid 40082268)
23. JX Chi L Huang W Nie J Wang B Fu F Yang 2005 Defining the orientation of the tandem fusions that occurred during the evolution of Indian muntjac chromosomes by BAC mapping Chromosoma 114 3 167 172 (Pubitemid 41349175)
24. MA Ferguson-Smith 1997 Genetic analysis by chromosome sorting and painting: phylogenetic and diagnostic applications Eur J Hum Genet 5 253 265 (Pubitemid 27503672)
25. MH Fernandez ES Vrba 2005 A complete estimate of the phylogenetic relationships in Ruminantia: a dated species-level supertree of the extant ruminants Biol Rev 80 269 302 (Pubitemid 40716063)
26. WM Fitch JJ Beintema 1999 Correcting parsimonious trees for unseen nucleotide substitutions: the effect of dense branching as exemplified by ribonuclease Mol Biol Evol 7 5 438 443 (Pubitemid 20291534)
27. F Fontana M Rubini 1990 Chromosome evolution in Cervidae Biosystems 24 157 174
28. L Froenicke J Wienberg 2001 Comparative chromosome painting defines the high rate of karyotype changes between pigs and bovids Mamm Genome 12 442 449 (Pubitemid 32463737)
29. L Froenicke MG Caldés A Graphodatsky 2006 Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes? Genome Res 16 311 313 (Pubitemid 43327498)
30. DS Gallagher JN Derr JE Womack 1994 Chromosome conservation among the advanced pecorans and determination of the primitive bovid karyotype J Hered 85 204 210 (Pubitemid 24188033)
31. J Gatesy 1997 More DNA support for a Cetacea/Hippopotamidae clade: the blood-clotting protein gene gammafibrinogen Mol Biology Evol 14 537 543 (Pubitemid 27200484)
32. AS Graphodatsky OV Sablina MN Meyer 2000 Comparative cytogenetics of hamsters of the genus Calomyscus Cytogenet Cell Genet 88 296 304 (Pubitemid 30311610)
33. AS Graphodatsky F Yang PCM O'Brien 2001 Phylogenetic implications of the 38 putative ancestral chromosome segments for four canid species Cytogenet Cell Genet 92 243 247 (Pubitemid 32642002)
34. S Guha SP Goyal VK Kashyap 2007 Molecular phylogeny of musk deer: a genomic view with mitochondrial 16S rRNA and cytochrome b gene Mol Phylogenet Evol 42 3 585 597 (Pubitemid 46330800)
35. M Hasegawa J Adachi 1996 Phylogenetic position of cetaceans relative to artiodactyls: reanalysis of mitochondrial and nuclear sequences Mol Biol Evol 13 710 717 (Pubitemid 26131893)
36. A Hassanin EJP Douzery 2003 Molecular and morphological phylogenies of Ruminantia and the alternative position of the Moschidae Syst Biol 52 2 206 228 (Pubitemid 36594678)
37. L Huang W Nie J Wang W Su F Yang 2005 Phylogenomic study of the subfamily Caprinae by cross-species chromosome painting with Chinese muntjac paints Chromosome Res 13 389 399 (Pubitemid 40853833)
38. L Huang J Chi W Nie J Wang F Yang 2006 Phylogenomics of several deer species revealed by comparative chromosome painting with Chinese muntjac paints Genetica 127 25 33 (Pubitemid 44087050)
39. L Huang A Nesterenko W Nie 2008 Karyotypic evolution of giraffes (Giraffa camelopardalis) revealed by cross-species chromosome painting with Chinese muntjac (Muntiacus reevesi) and human (Homo sapiens) paints Cytogenet Genome Res 122 132 138
40. Hsu TC, Benirschke K (1967) An atlas of mammalian chromosomes. Springer-Verlag, New York
41. L Iannuzzi GP Di Meo A Perucatti T Bardaro 1998 ZOO-FISH and R-banding reveal extensive conservation of human chromosome regions in euchromatic regions of river buffalo chromosomes Cytogenet Cell Genet 82 210 214 (Pubitemid 29002466)
42. CM Janis 1993 Tertiary mammal evolution in the context of changing climates, vegetation, and tectonic events Annu Rev Ecol Syst 24 467 500 (Pubitemid 2022120)
43. Janis CM, Scott KM, Jacobs LL (1998) Evolution of tertiary mammals of north America. terrestrial carnivores, ungulates, and ungulatelike mammals. Cambridge University Press, Cambridge
44. RG Kleineidam G Pesole HJ Breukelman JJ Beintema RA Kastelein 1999 Inclusion of £r Artiodactyla based on phylogenetic analysis of pancreatic ribonuclease genes J Mol Evol 48 360 368 (Pubitemid 29116082)
45. MV Kuznetsova MV Kholodova AA Luschekina 2002 Phylogenetic analysis of sequences of the 12S and 16S rRNA mitochondrial genes in the family Bovidae: new evidence Russ J Genet 38 942 950 (Pubitemid 135705100)
46. P Langer 2001 Evidence from the digestive tract on phylogenetic relationships in ungulates and whales J Zool Syst Evol Res 39 77 90 (Pubitemid 32320031)
47. JK Lum M Nikaido M Shimamura 2000 Consistency of SINE insertion topology and flanking sequence tree: quantifying relationships among cetartiodactyls Mol Biol Evol 17 1417 1424
48. Mahon A (2004) A molecular supertree of the Artiodactyla. In: Bininda-Emonds ORP (ed) Phylogenetic supertrees: Combining information to reveal the tree of life. Kluwer Academic Publishers, Dordrecht, pp 411-437
49. Z Maniou OC Wallis M Wallis 2003 Episodic molecular evolution of pituitary growth hormone in Cetartiodactyla J Mol Evol 58 743 753
50. Marcot JD (2007) Molecular phylogeny of terrestrial artiodactyls. In: Prothero DR, Foss SE (eds) The evolution of artiodactyls. The John Hopkins University Press, Baltimore, pp 4-18
51. CA Matthee JD Burzlaff JF Taylor SK Davis 2001 Mining the mammalian genome for artiodactyl systematics Syst Biol 50 367 390 (Pubitemid 33578222)
52. CA Matthee G Eick S Willows-Munro C Montgelard AT Pardini TJ Robinson 2007 Indel evolution of mammalian introns and the utility of non-coding nuclear markers in eutherian phylogenetics Mol Phylogenet Evol 42 827 837 (Pubitemid 46350739)
53. C Montgelard MF Catzejfis E Douzery 1997 Phylogenetic relationships of artiodactyls and cetaceans as deduced from the comparison of cytochrome b and 12s rRNA mitochondrial sequences Mol Biol Evol 14 5 550 559 (Pubitemid 27200486)
54. WJ Murphy E Eizirik WE Johnson YP Zhang OA Ryder SJ O'Brien 2001 Molecular phylogenetics and the origins of placental mammals Nature 409 614 618 (Pubitemid 32154812)
55. WJ Murphy TH Pringle A Tess TA Crider MS Springer W Miller 2007 Using genomic data to unravel the root of the placental mammal phylogeny Genome Res 17 413 421 (Pubitemid 46556445)
56. M Nikaido AP Rooney N Okada 1999 Phylogenetic relationships among cetartiodactyls based on insertions of short and long interpersed elements: Hippopotamuses are the closest extant relatives of whales Proc Natl Acad Sci USA 96 10261 10266 (Pubitemid 29422546)
57. H Nishihara M Hasegawa N Okada 2006 Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions Proc Natl Acad Sci USA 103 9929 9934 (Pubitemid 43993600)
58. Nowak RM (1999) Order artiodactyla. In: Walker's mammals of the world. John Hopkins University Press, London
59. MA O'Leary JH Geisler 1999 The position of Cetecea within Mammalia: Phylogenetic analysis of morphological data from extinct and extant taxa Syst Biol 48 455 490 (Pubitemid 129479559)
60. P Pevzner G Tesler 2003 Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution Proc Natl Acad Sci USA 100 7672 7677 (Pubitemid 36760028)
61. P Pinton L Schibler E Cribiu J Gellin M Yerle 2000 Localization of 113 anchor loci in pigs: improvement of the comparative map for humans, pigs, and goats Mamm Genome 11 306 315 (Pubitemid 30171663)
62. SA Price ORP Bininda-Emonds JL Gittleman 2005 A complete phylogeny of the whales, dolphins and even-toed hoofed mammals (Cetartiodactyla) Biol Rev 80 445 473 (Pubitemid 41081467)
63. TJ Robinson A Ruiz-Herrera JC Avise 2008 Hemiplasy and homoplasy in the karyotypic phylogenies of mammals Proc Natl Acad Sci USA 105 14477 14481
64. KD Rose 1996 On the origin of the order Artiodactyla Proc Natl Acad Sci USA 93 1705 1709 (Pubitemid 26075189)
65. Ryder OA (2006a) A G-stained karyotype of Massai giraffe (Giraffa camelopardalis tippelskirchi). In: O'Brien SJ, Menninger JC, Nash WG (eds) Atlas of mammalian chromosomes. Wiley-Liss, Hoboken, NJ, p 577
66. Ryder OA (2006b) A G- stained karyotype of okapi (Okapia johnstoni). In: O'Brien SJ, Menninger JC, Nash WG (eds) Atlas of mammalian chromosomes, Wiley-Liss, Hoboken, NJ, p 577
67. M Seabright 1971 A rapid banding technique for human chromosomes Lancet 2 971 972
68. M Shimamura H Yasue K Ohshima H Abe H Kato T Kishiro I Munechikak N Okada 1997 Molecular evidence from retroposons that whales form a clade within even toed ungulates Nature 12 241 249
69. Simpson CD (1984) Artiodactyls. In: Anderson S, Jones JK (eds) Orders and Families of Recent Mammals of the World. Wiley, New York, pp 563-588
70. J Slate TCV Stijn RM Anderson 2002 A deer (Subfamily Cervinae) genetic linkage map and the evolution of ruminant genomes Genetics 160 1587 1597 (Pubitemid 34454380)
71. HF Stanley M Kadwell JC Wheeler 1994 Molecular evolution of the family Camelidae: a mitochondrial study Proc R Soc Lond B 256 1 6 (Pubitemid 24132907)
72. Stanyon R (2006) A G- stained karyotype of hippopotamus (Hippopotamus amphibius). In: O'Brien SJ, Menninger JC, Nash WG (eds) Atlas of Mammalian Chromosomes. Wiley-Liss, Hoboken, NJ, p 573
73. B Su YX Wang H Lan W Wang Y Zhang 1999 Phylogenetic study of complete cytochrome b genes in musk deer (genus Moschus) using museum samples Mol Phylogenet Evol 12 241 249 (Pubitemid 129499305)
74. H Telenius NP Carter CE Bebb M Nordenskjold BA Ponder A Tunnacliffe 1992 Degenerate oligonucleotide-primed PCR: general amplification of target DNA by a single degenerate primer Genomics 13 718 725
75. JM Theodor 2004 Molecular clock divergence estimates and the fossil record of Cetartiodactyla J Paleontol 78 39 44 (Pubitemid 38092724)
76. VA Trifonov R Stanyon AI Nesterenko 2008 Multidirectional cross-species painting illuminates the history of karyotypic evolution in Perissodactyla Chromosome Res 16 89 107
77. BM Ursing U Arnason 1998 Analyses of mitochondrial genomes strongly support a hippopotamus-whale clade Proc R Soc Lond B 265 2251 2255 (Pubitemid 28561165)
78. M Volleth KG Heller RA Pfeiffer H Hameister 2002 A comparative ZOO-FISH analysis in bats elucidates the phylogenetic relationships between Megachiroptera and five microchiropteran families Chromosome Res 10 477 497 (Pubitemid 35402069)
79. DH Wurster K Benirschke 1968 Chromosome studies in the superfamily Bovoidea Chromosoma 25 152 171
80. F Yang PC O'Brien J Wienberg MA Ferguson-Smith 1997 A reappraisal of the tandem fusion theory of karyotype evolution in the Indian muntjac using chromosome painting Chromosome Res 5 109 117 (Pubitemid 27182804)
81. F Yang PC O'Brien J Wienberg H Neitzel CC Lin MA Ferguson-Smith 1997 Chromosomal evolution of the Chinese muntjac (Muntiacus reevesi) Chromosoma 106 37 43 (Pubitemid 27399624)
82. F Yang PC O'Brien J Wienberg MA Ferguson-Smith 1997 Evolution of the black muntjac (Muntiacus crinifrons) karyotype revealed by comparative chromosome painting Cytogenet Cell Genet 76 159 163 (Pubitemid 27239160)
83. F Yang PC O'Brien BS Milne 1999 A complete comparative chromosome map for the dog, red fox, and human and its integration with canine genetic maps Genomics 62 189 202 (Pubitemid 30053934)
84. F Yang B Fu PC O'Brien TJ Robinson OA Ryder MA Ferguson-Smith 2003 Karyotypic relationships of horses and zebras: results of cross-species chromosome painting Cytogenet Genome Res 102 235 343 (Pubitemid 38280903)
85. F Yang B Fu PC O'Brien W Nie OA Ryder MA Ferguson-Smith 2004 Refined genome-wide comparative map of the domestic horse, donkey and human based on cross-species chromosome painting: insight into the occasional fertility of mules Chromosome Res 12 65 76 (Pubitemid 38187086)