Molecular evidence from retroposons that whales form a clade within even-toed ungulates

Cited by (354)

Items 101–200 of 354

1. Coevolution of immunoglobulin heavy- and light-chain variable-region gene families.
   T. Sitnikova, C. Su · 1998 · Molecular biology and evolution
2. Lungworms of Marine Mammals
   L. Measures · 2008
3. Effects of age and sex on clinicopathologic reference ranges in a healthy managed Atlantic bottlenose dolphin population.
   S. Venn-Watson, E. Jensen, S. Ridgway · 2007 · Journal of the American Veterinary Medical Association
4. Primate phylogeny: molecular evidence from retroposons
   Jürgen Schmitz, C. Roos, H. Zischler · 2004 · Cytogenetic and Genome Research
5. Molecular cladistic markers in New World monkey phylogeny (Platyrrhini, Primates)
   Silke S. Singer, Jürgen Schmitz, Claudia Schwiegk, Hans Zischler · 2003 · Molecular Phylogenetics and Evolution
6. Molecular Evidence for the Phylogenetic Affinities of Cetacea
   John Gatesy · 1998 · Springer eBooks
7. Evolutionary relationships among rice species with AA genome based on SINE insertion analysis.
   Chao-Yang Cheng, S. Tsuchimoto, H. Ohtsubo, E. Ohtsubo · 2002 · Genes & Genetic Systems
8. Forelimb myology of the pygmy hippopotamus (<i>Choeropsis liberiensis</i>)
   Fisher, Rebecca E., Scott, Kathleen M., Naples, Virginia L. · 2007 · The Anatomical Record
9. SINEs of progress: Mobile element applications to molecular ecology
   David A. Ray · 2006 · Molecular Ecology
10. A New Protocetid Whale (Cetacea: Archaeoceti) from the Late Middle Eocene of South Carolina
    J. Geisler, A. Sanders, Z. Luo · 2005 · American Museum Novitates
11. Retropositional events consolidate the branching order among New World monkey genera.
    Martin Osterholz, L. Walter, C. Roos · 2009 · Molecular Phylogenetics and Evolution
12. Retroelement insertional polymorphisms, diversity and phylogeography within diploid, D-genome Aegilops tauschii (Triticeae, Poaceae) sub-taxa in Iran.
    H. Saeidi, M. Rahiminejad, J. Heslop-Harrison · 2008 · Annals of Botany
13. Retrotransposons and their Role in Plant—Genome Evolution
    E. Todorovska · 2007
14. Characterization of the bovine pseudoautosomal boundary: Documenting the evolutionary history of mammalian sex chromosomes.
    A. Van Laere, W. Coppieters, M. Georges · 2008 · Genome Research
15. B1 and related SINEs in mammalian genomes.
    N. Vassetzky, O. Ten, D. A. Kramerov · 2003 · Gene
16. The time of origin of whales and the role of behavioral changes in the terrestrial-aquatic transition
    M. O'Leary, M. Uhen · 1999 · Paleobiology
17. Structure, functionality, and evolution of the BARE-1 retrotransposon of barley
    C. Vicient, R. Kalendar, K. Anamthawat-Jónsson, Annu Suoniemi, A. Schulman · 2004 · Genetica
18. New Morphological Evidence for the Phylogeny of Artiodactyla, Cetacea, and Mesonychidae
    Jonathan H. Geisler · 2001 · American Museum Novitates
19. Comparative studies on mammalian Hoxc8 early enhancer sequence reveal a baleen whale-specific deletion of a cis-acting element
    Cooduvalli S. Shashikant, Chang B. Kim, Marc A. Borbély, Wayne C. H. Wang, Frank H. Ruddle · 1998 · Proceedings of the National Academy of Sciences
20. Retrotransposon-based molecular markers for grapevine species and cultivars identification
    C. d'Onofrio, G. De Lorenzis, T. Giordani, L. Natali, A. Cavallini, G. Scalabrelli · 2010 · Tree Genetics & Genomes
21. Wide distribution of short interspersed elements among eukaryotic genomes
    Olga R. Borodulina, D. Kramerov · 1999 · FEBS Letters
22. Sauria SINEs: Novel Short Interspersed Retroposable Elements That Are Widespread in Reptile Genomes
    Oliver Piskurek, Christopher C. Austin, Norihiro Okada · 2006 · Journal of Molecular Evolution
23. A brief history of human autosomes.
    David Haig · 1999 · Philosophical transactions of the Royal Society of London. Series B, Biological sciences
24. Phylogeny of mysticete whales based on mitochondrial and nuclear data.
    Amanda L. Rychel, T. Reeder, A. Berta · 2004 · Molecular Phylogenetics and Evolution
25. SINE Insertions as Clade Markers for Wild Crucifer Species
    C. Tatout, S. Warwick, A. Lenoir, J. Deragon · 1999
26. Incomplete Lineage Sorting and Hybridization Statistics for Large-Scale Retroposon Insertion Data
    A. Kuritzin, Tabea G. Kischka, J. Schmitz, G. Churakov · 2016 · PLoS Comput. Biol.
27. SINE evolution, missing data, and the origin of whales.
    A. Shedlock, M. Milinkovitch, N. Okada · 2000 · Systematic Biology
28. First application of the SINE (short interspersed repetitive element) method to infer phylogenetic relationships in reptiles: an example from the turtle superfamily Testudinoidea.
    Takeshi Sasaki, Kazuhiko Takahashi, M. Nikaido, Seiko Miura, Y. Yasukawa, N. Okada · 2004 · Molecular biology and evolution
29. Unique Functions of Repetitive Transcriptomes
    Gerald G. Schumann, Elena V. Gogvadze, Mizuko Osanai-Futahashi, Azusa Kuroki, Carsten Münk, Haruko Fujiwara, Zoltán Ivics, Anton A. Buzdin · 2010 · International review of cytology
30. CAN—a pan-carnivore SINE family
    N. Vassetzky, D. A. Kramerov · 2001 · Mammalian Genome
31. Cross-species chromosome painting in Cetartiodactyla: Reconstructing the karyotype evolution in key phylogenetic lineages
    Anastasia I. Kulemzina, Vladimir A. Trifonov, Polina L. Perelman, Nadezhda V. Rubtsova, Vitaly Volobuev, Malcolm Andrew Ferguson-Smith, Roscoe Stanyon, Fengtang Yang, Alexander S. Graphodatsky · 2009 · Chromosome Research
32. Birth of a gene: locus of neuronal BC200 snmRNA in three prosimians and human BC200 pseudogenes as archives of change in the Anthropoidea lineage.
    V. Kuryshev, B. V. Skryabin, Joachim Kremerskothen, J. Jurka, Juergen Brosius · 2001 · Journal of Molecular Biology
33. Gene duplication and mobile genetic elements in the morning glories.
    Atsushi Hoshino, Yasuyo Johzuka-Hisatomi, S. Iida · 2001 · Gene
34. Phylogenetic affinities of tarsier in the context of primate Alu repeats.
    E. Ziętkiewicz, Chantal Richer, D. Labuda · 1999 · Molecular Phylogenetics and Evolution
35. Mobile element biology – new possibilities with high-throughput sequencing
    Jin-Chuan Xing, D. Witherspoon, L. Jorde · 2013 · Trends in Genetics
36. Ankle morphology of the earliest Cetaceans and its implications for the phylogenetic relations among ungulates.
    J. Thewissen, S. Madar · 1999 · Systematic Biology
37. The Cerebral Cortex of the Pygmy Hippopotamus, Hexaprotodon liberiensis (Cetartiodactyla, Hippopotamidae): MRI, Cytoarchitecture, and Neuronal Morphology
    Camilla Butti, R. Ewan Fordyce, Mary Ann Raghanti, Xiaosi Gu, Christopher J. Bonar, Bridget A. Wicinski, Edmund W. Wong, Jessica Roman, Alanna Brake, Emily L. Eaves et al. · 2014 · The Anatomical Record
38. Opening Darwin's black box: teaching evolution through developmental genetics
    S. Gilbert · 2003 · Nature reviews genetics
39. Reconstructing cetacean brain evolution using computed tomography.
    L. Marino, M. Uhen, N. Pyenson, B. Frohlich · 2003 · The Anatomical Record Part B The New Anatomist
40. Cetaceans Are Highly Derived Artiodactyls
    Michel C. Milinkovitch, Martine Bérubé, Per Jakob Palsbøll · 1998 · Springer eBooks
41. Speciation network in Laurasiatheria: retrophylogenomic signals
    L. Doronina, G. Churakov, A. Kuritzin, Jingjing Shi, R. Baertsch, H. Clawson, J. Schmitz · 2017 · Genome Research
42. The use of retrotransposon-based molecular markers to analyze genetic diversity
    R. Kalendar · 2011 · Ratarstvo i povrtarstvo
43. A novel abundant family of retroposed elements (DAS-SINEs) in the nine-banded armadillo (Dasypus novemcinctus).
    G. Churakov, A. Smit, J. Brosius, J. Schmitz · 2005 · Molecular biology and evolution
44. SINE cousins: the 3'-end tails of the two oldest and distantly related families of SINEs are descended from the 3' ends of LINEs with the same genealogical origin.
    Y. Terai, K. Takahashi, N. Okada · 1998 · Molecular biology and evolution
45. Genetic variability of Old Portuguese bread wheat cultivars assayed by IRAP and REMAP markers
    A. Carvalho, H. Guedes-Pinto, P. Martins-Lopes, J. Lima-Brito · 2010
46. Adaptive evolution of 5'HoxD genes in the origin and diversification of the cetacean flipper.
    Zhe Wang, Li-Hong Yuan, S. Rossiter, Xueguo Zuo, Bi Ru, H. Zhong, Naijian Han, Gareth Jones, P. Jepson, Shu-Yi Zhang · 2008 · Molecular biology and evolution
47. Amphibious communication with sound in hippos, Hippopotamus amphibius
    William E. Barklow · 2004 · Animal Behaviour
48. Molecules remodel the mammalian tree
    Wilfried W. DE JONG · 1998 · Trends in Ecology & Evolution
49. Genomic and anatomical comparisons of skin support independent adaptation to life in water by cetaceans and hippos
    M. Springer, C. Guerrero-Juarez, Matthias Huelsmann, Matthew A. Collin, K. Danil, M. McGowen, J. Oh, Raul Ramos, Michael Hiller, M. Plikus et al. · 2020 · bioRxiv
50. Inactivation of C4orf26 in toothless placental mammals.
    M. Springer, James Starrett, P. Morin, A. Lanzetti, C. Hayashi, J. Gatesy · 2016 · Molecular Phylogenetics and Evolution
51. Phylogeny of Nolana (Solanaceae) of the Atacama and Peruvian deserts inferred from sequences of four plastid markers and the nuclear LEAFY second intron.
    T. Tu, M. Dillon, Hang Sun, Jun Wen · 2008 · Molecular Phylogenetics and Evolution
52. Genomic and evolutionary analysis of Feilai, a diverse family of highly reiterated SINEs in the yellow fever mosquito, Aedes aegypti.
    Z. Tu · 1999 · Molecular biology and evolution
53. Orthologous repeats and mammalian phylogenetic inference.
    A. Bashir, Chun Jimmie Ye, Alkes L. Price, V. Bafna · 2005 · Genome Research
54. Toothed whale monophyly reassessed by SINE insertion analysis: the absence of lineage sorting effects suggests a small population of a common ancestral species.
    M. Nikaido, O. Piskurek, N. Okada · 2007 · Molecular Phylogenetics and Evolution
55. Plasma and Urine Levels of Electrolytes, Urea and Steroid Hormones Involved in Osmoregulation of Cetaceans
    N. Birukawa, H. Ando, M. Goto, N. Kanda, L. Pastene, H. Nakatsuji, H. Hata, A. Urano · 2005 · Zoological Science
56. Additional holotype remains of Ambulocetus natans (Cetacea, Ambulocetidae), and their implications for locomotion in early whales
    S. Madar, J. Thewissen, S. Hussain · 2002 · Journal of Vertebrate Paleontology
57. Genetic mosaics in the massive persisting rhizosphere colony “shiro” of the ectomycorrhizal basidiomycete Tricholoma matsutake
    H. Murata, A. Ohta, A. Yamada, M. Narimatsu, Norihiro Futamura · 2005 · Mycorrhiza
58. Human genetic disorders, a phylogenetic perspective.
    J. Martinez, Lars J. Dugaiczyk, R. Zielinski, Achilles Dugaiczyk · 2001 · Journal of Molecular Biology
59. Comprehensive Analysis of Two Alu Yd Subfamilies
    Jinchuan Xing, Abdel Halim Salem, Dale J. Hedges, Gail E. Kilroy, W. Scott Watkins, John E. Schienman, Caro‐Beth Stewart, Jerzy Jurka, Lynn B. Jorde, Mark A. Batzer · 2003 · Journal of Molecular Evolution
60. The ethmoid and presphenoid of cetaceans
    Hiroto Ichishima · 2016 · Journal of Morphology
61. PCR-based approach to SINE isolation: simple and complex SINEs.
    O. Borodulina, D. A. Kramerov · 2005 · Gene
62. Tracking Alu evolution in New World primates
    David A. Ray, Mark A. Batzer · 2005 · BMC Evolutionary Biology
63. Phylogenetic Relationships Among East African Haplochromine Fish as Revealed by Short Interspersed Elements (SINEs)
    Y. Terai, N. Takezaki, W. Mayer, H. Tichy, N. Takahata, J. Klein, N. Okada · 2003 · Journal of Molecular Evolution
64. The rise and fall of the CR1 subfamily in the lineage leading to penguins
    Maiko Watanabe, Masato Nikaido, Tomi T. Tsuda, Hidetoshi Inoko, David P. Mindell, Koichi Murata, Norihiro Okada · 2005 · Gene
65. Consistency of SINE insertion topology and flanking sequence tree: quantifying relationships among cetartiodactyls.
    J. Lum, M. Nikaido, M. Shimamura, Hidetoshi Shimodaira, A. Shedlock, N. Okada, M. Hasegawa · 2000 · Molecular biology and evolution
66. Fast Evolution of Interleukin-2 in Mammals and Positive Selection in Ruminants
    D. Zelus, M. Robinson-Rechavi, M. Delacre, C. Auriault, V. Laudet · 2000 · Journal of Molecular Evolution
67. Patterns of diversity among SINE elements isolated from three Y-chromosome genes in carnivores.
    J. Slattery, W. J. Murphy, S. O'Brien · 2000 · Molecular biology and evolution
68. Phylogenetic Relationships Between the Orders Artiodactyla and Cetacea: A Combined Assessment of Morphological and Molecular Evidence
    W. Patrick Luckett, Nancy Hong · 1998 · Journal of Mammalian Evolution
69. Hind limb myology of the common hippopotamus, Hippopotamus amphibius (Artiodactyla: Hippopotamidae)
    R. E. Fisher, K. Scott, Brent Adrian · 2010
70. Disentangling the Relationship of the Australian Marsupial Orders Using Retrotransposon and Evolutionary Network Analyses
    Susanne Gallus, A. Janke, Vikas Kumar, M. Nilsson · 2015 · Genome Biology and Evolution
71. Organization and number of orexinergic neurons in the hypothalamus of two species of Cetartiodactyla: A comparison of giraffe (Giraffa camelopardalis) and harbour porpoise (Phocoena phocoena)
    L. Dell, N. Patzke, A. Bhagwandin, F. Bux, K. Fuxe, Grace Barber, J. Siegel, P. Manger · 2012 · Journal of Chemical Neuroanatomy
72. Inclusion of Cetaceans Within the Order Artiodactyla Based on Phylogenetic Analysis of Pancreatic Ribonuclease Genes
    Reinhard G. Kleineidam, Graziano Pesole, Heleen J. Breukelman, Jaap J. Beintema, Ronald A. Kastelein · 1999 · Journal of Molecular Evolution
73. The mouth, the anus, and the blastopore—open questions about questionable openings
    Hejnol, Andreas, Martindale, Mark Q. · 2009 · Animal Evolution
74. Unique mammalian tRNA-derived repetitive elements in dermopterans: the t-SINE family and its retrotransposition through multiple sources.
    O. Piskurek, M. Nikaido, Boeadi, M. Baba, N. Okada · 2003 · Molecular biology and evolution
75. Feeding strategy of an Early Miocene cetothere from the Toyama and Akeyo Formations, central Japan
    T. Kimura · 2002 · Paleontological Research
76. Evolution of CHR-2 SINEs in cetartiodactyl genomes: possible evidence for the monophyletic origin of toothed whales
    M. Nikaido, F. Matsuno, Hideaki Abe, M. Shimamura, H. Hamilton, H. Matsubayashi, N. Okada · 2001 · Mammalian Genome
77. Molecular phylogenetics of ‘river dolphins’ and the baiji mitochondrial genome
    Jie Yan, Kaiya Zhou, Guang Yang · 2005 · Molecular Phylogenetics and Evolution
78. The Phylogenetic Position of Cetaceans: Further Combined Data Analyses, Comparisons with the Stratigraphic Record and a Discussion of Character Optimization1
    M. O'Leary · 2001
79. The evolutionary position of dormice (Gliridae) in Rodentia determined by a novel short retroposon.
    D. Kramerov, N. Vassetzky, Irina Serdobova · 1999 · Molecular biology and evolution
80. Phylogenomics
    C. Bleidorn · 2017 · Cambridge International Law Journal
81. ILS-Aware Analysis of Low-Homoplasy Retroelement Insertions: Inference of Species Trees and Introgression Using Quartets.
    M. Springer, E. Molloy, Daniel B. Sloan, Mark P. Simmons, J. Gatesy · 2019 · Journal of Heredity
82. Retroposition of the AFC Family of SINEs (Short Interspersed Repetitive Elements) Before and During the Adaptive Radiation of Cichlid Fishes in Lake Malawi and Related Inferences About Phylogeny
    Kazuhiko Takahashi, M. Nishida, M. Yuma, N. Okada · 2001 · Journal of Molecular Evolution
83. The myth of the hippo-like anthracothere: The eternal problem of homology and convergence
    Martin H. L. Pickford · 2021 · Spanish Journal of Palaeontology
84. Extensive morphological convergence and rapid radiation in the evolutionary history of the family Geoemydidae (old world pond turtles) revealed by SINE insertion analysis.
    Takeshi Sasaki, Y. Yasukawa, Kazuhiko Takahashi, Seiko Miura, A. Shedlock, N. Okada · 2006 · Systematic Biology
85. Highly polymorphic DNA markers to specify strains of the ectomycorrhizal basidiomycete Tricholoma matsutake based on σmarY1, the long terminal repeat of gypsy-type retroelement marY1
    H. Murata, K. Babasaki, A. Yamada · 2005 · Mycorrhiza
86. The neocortex of cetartiodactyls: I. A comparative Golgi analysis of neuronal morphology in the bottlenose dolphin (Tursiops truncatus), the minke whale (Balaenoptera acutorostrata), and the humpback whale (Megaptera novaeangliae)
    Camilla Butti, Caroline M. Janeway, C. Townshend, B. Wicinski, J. Reidenberg, S. Ridgway, C. Sherwood, P. Hof, Bob Jacobs · 2015 · Brain Structure and Function
87. SINE Retrotransposition During the Evolution of the Pecoran Ruminants
    I. Nijman, Patrick van Tessel, J. Lenstra · 2002 · Journal of Molecular Evolution
88. True Homoplasy of Retrotransposon Insertions in Primates
    L. Doronina, Olga Reising, H. Clawson, David A. Ray, J. Schmitz · 2018 · Systematic Biology
89. Interspecies Somatic Cell Nuclear Transfer for In Vitro Production of Antarctic Minke Whale (Balaenoptera bonaerensis) Embryos
    Sachiko Ikumi, K. Sawai, Yurika Takeuchi, H. Iwayama, H. Ishikawa, S. Ohsumi, Y. Fukui · 2004 · Cloning and Stem Cells
90. Reconstructing the Organization of Neocortex of the First Mammals and Subsequent Modifications
    J. Kaas · 2007 · Evolution of Nervous Systems
91. A genomic landscape of mitochondrial DNA insertions in the pig nuclear genome provides evolutionary signatures of interspecies admixture
    Giuseppina Schiavo, Orsolya Ivett Hoffmann, Anisa Ribani, Valerio Joe Utzeri, Marco Ciro Ghionda, Francesca Bertolini, Claudia Geraci, Samuele Bovo, Luca Fontanesi · 2017 · DNA Research
92. Rice retroposon p-SINE1 and origin of cultivated rice
    H. Ohtsubo, Chao-Yang Cheng, Isaku Ohsawa, S. Tsuchimoto, E. Ohtsubo · 2004 · Ikushugaku zasshi
93. Subordinal artiodactyl relationships in the light of phylogenetic analysis of 12 mitochondrial protein‐coding genes
    Björn M. Ursing, Kerryn E. Slack, Úlfur Árnason · 2000 · Zoologica Scripta
94. Applications of Molecular Data in Cetacean Taxonomy and Population Genetics with Special Emphasis on Defining Species Boundaries
    M. Milinkovitch, R. Leduc, R. Tiedemann, A. Dizon · 2002
95. Phylogenetic Relationships Among Cetaceans Revealed by Y-Chromosome Sequences
    Shin Nishida, Mutsuo Goto, Luis A. Pastene, Naohisa Kanda, Hiroko Koike · 2007 · ZOOLOGICAL SCIENCE
96. Whale ankles and evolutionary relationships
    J. Thewissen, S. Madar, S. Hussain · 1998 · Nature
97. Effects of fresh and seawater ingestion on osmoregulation in Atlantic bottlenose dolphins (Tursiops truncatus)
    S. Ridgway, S. Venn-Watson · 2009 · Journal of Comparative Physiology □ B
98. Organization of retrotransposons and microsatellites in cereal genomes
    A. Schulman, P. Gupta, R. Varshney · 2004 · Kluwer Academic Publishers eBooks
99. Use of SSR and Retrotransposon-Based Markers to Interpret the Population Structure of Native Grapevines from Southern Italy
    C. Villano, D. Carputo, L. Frusciante, Xenia Santoro, R. Aversano · 2014 · Molecular Biotechnology
100. A memetic-aided approach to hierarchical clustering from distance matrices: application to gene expression clustering and phylogeny.
     C. Cotta, P. Moscato · 2003 · Bio Systems