Molecular evidence from retroposons that whales form a clade within even-toed ungulates
Abstract
The origin of whales and their transition from terrestrial life to a fully aquatic existence has been studied in depth. Palaeontological, morphological and molecular studies suggest that the order Cetacea (whales, dolphins and porpoises) is more closely related to the order Artiodactyla (even-toed ungulates, including cows, camels and pigs) than to other ungulate orders. The traditional view that the order Artiodactyla is monophyletic has been challenged by molecular analyses of variations in mitochondrial and nuclear DNA. We have characterized two families of short interspersed elements (SINEs) that were present exclusively in the genomes of whales, ruminants and hippopotamuses, but not in those of camels and pigs. We made an extensive survey of retropositional events that might have occurred during the divergence of whales and even-toed ungulates. We have characterized nine retropositional events of a SINE unit, each of which provides phylogenetic resolution of the relationships among whales, ruminants, hippopotamuses and pigs. Our data provide evidence that whales, ruminants and hippopotamuses form a monophyletic group.
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Recent molecular phylogenetic studies and comparative morphological analyses support Hippopotamidae and Cetacea as forming a monophyletic group.
“Recent molecular phylogenetic studies and comparative morphological analyses have supported Hippopotamidae and Cetacea as forming a monophyletic group (Shimamura et al. 1997;Nomura et al. 1998;Ursing and Arnason 1998;Nomura and Yasue 1999;Geisler and Uhen 2003;Boisserie 2005;Boisserie et al. 2005;Fisher et al. 2007);”
From Choeropsis liberiensis (Artiodactyla: Hippopotamidae) (2019) · cites this paper as Shimamura et al. 1997
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Repbase update: a database and an electronic journal of repetitive elements.
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Advances in molecular marker techniques and their applications in plant sciences
Agarwal, M., Shrivastava, N., & Padh, H. (2008) · Plant Cell Reports · doi:10.1007/s00299-008-0507-z · Cited by 974 · see citing works
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BackgroundIRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques
Kalendar, R., Grob, T., Regina, M., Suoniemi, A., & Schulman, A. (1999) · Theoretical and Applied Genetics · doi:10.1007/s001220051124 · Cited by 595 · see citing works
“The new insertions may then be detected and used to temporally order insertion events in a lineage, thereby helping to establish phylogenies (Shimamura et al. 1997).”
BackgroundGenomic strategies to identify mammalian regulatory sequences
Pennacchio, L., & Rubin, E. (2001) · Nature reviews genetics · doi:10.1038/35052548 · Cited by 417 · see citing works
Nikaido, M., Rooney, A. P., & Okada, N. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.18.10261 · Cited by 420 · see citing works
Self-citationThe Evolution, Distribution and Diversity of Endogenous Retroviruses
Gifford, R., & Tristem, M. (2003) · Virus genes · doi:10.1023/a:1024455415443 · Cited by 397 · see citing works
Gatesy, J., O'Grady, P., & Baker, R. (1999) · Cladistics · doi:10.1111/j.1096-0031.1999.tb00268.x · Cited by 336 · see citing works
“Copyright q 1999 by The Willi Hennig Society All rights of reproduction in any form reserved once inserted (Shimamura et al., 1997).”
BackgroundMethodResultInfluentialTowards resolving the interordinal relationships of placental mammals.
Waddell, P., Okada, N., & Hasegawa, M. (1999) · Systematic Biology · doi:10.1093/sysbio/48.1.1 · Cited by 335 · see citing works
Self-citationHow good are deep phylogenetic trees?
Philippe, H., & Laurent, J. (1998) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(98)80028-2 · Cited by 324 · see citing works
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Leduc, R., Perrin, W., & Dizon, A. (1999) · Marine Mammal Science · doi:10.1111/j.1748-7692.1999.tb00833.x · Cited by 323 · see citing works
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Gingerich, P. D., Haq, M. U., Zalmout, I. S., Khan, I. H., & Malkani, M. S. (2001) · Science · doi:10.1126/science.1063902 · Cited by 321 · see citing works
Repeats in genomic DNA: mining and meaning.
Jurka, J. (1998) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(98)80067-5 · Cited by 301 · see citing works
The root of the mammalian tree inferred from whole mitochondrial genomes.
Phillips, M., & Penny, D. (2003) · Molecular Phylogenetics and Evolution · doi:10.1016/s1055-7903(03)00057-5 · Cited by 293 · see citing works
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MethodSkeletons of terrestrial cetaceans and the relationship of whales to artiodactyls
Thewissen, J., Williams, E. M., Roe, L., & Hussain, S. (2001) · Nature · doi:10.1038/35095005 · Cited by 287 · see citing works
Polyphyletic origin of cultivated rice: based on the interspersion pattern of SINEs.
Cheng, C.-Y., Motohashi, R., Tsuchimoto, S., Fukuta, Y., Ohtsubo, H., & Ohtsubo, E. (2003) · Molecular biology and evolution · doi:10.1093/molbev/msg004 · Cited by 283 · see citing works
Boore, J., & Fuerstenberg, S. I. (2004) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2007.2234 · Cited by 274 · see citing works
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BackgroundAnalysis of plant diversity with retrotransposon-based molecular markers
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Primate jumping genes elucidate strepsirrhine phylogeny.
Roos, C., Schmitz, J., & Zischler, H. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0403852101 · Cited by 262 · see citing works
Molecular and Morphological Phylogenies of Ruminantia and the Alternative Position of the Moschidae
Hassanin, A., & Douzery, E. (2003) · Systematic Biology · doi:10.1080/10635150390192726 · Cited by 253 · see citing works
“…Tragulina + Pecora, was rooted by one cetacean (Balaenopteridae) and one ancodontan (Hippopotamidae) because these two taxa are considered the closest living relatives of Ruminantia (Irwin and Arnason, 1994; Gatesy et al., 1996; Gatesy, 1997, 1998; Montgelard et al., 1997; Shimamura et al., 1997).”
BackgroundInfluentialHof, P. R., & Van Der Gucht, E. (2007) · The Anatomical Record · doi:10.1002/ar.20407 · Cited by 257 · see citing works
“In fact, a sister-group relationship exists between modern cetaceans and hippopotamids (Nikaido et al., 1996; Shimamura et al., 1997; Gatesy, 1998; Milinkovitch et al., 1998), even though they diverged about 52 million years ago (Gingerich and Uhen, 1998).”
BackgroundConfirming the Phylogeny of Mammals by Use of Large Comparative Sequence Data Sets
Prasad, A., Allard, M., & Green, E. (2008) · Molecular biology and evolution · doi:10.1093/molbev/msn104 · Cited by 250 · see citing works
“…inferences based on genomic characters that change less frequently than individual nucleotides, such as inversions, transposon insertions, and coding insertions/deletions (indels) (Shimamura et al. 1997; Murphy et al. 2004, 2007; Bashir et al. 2005; Chaisson et al. 2006; Kriegs et al. 2006).”
BackgroundShort retroposons in eukaryotic genomes.
Kramerov, D. A., & Vassetzky, N. (2005) · International Review of Cytology · doi:10.1016/s0074-7696(05)47004-7 · Cited by 248 · see citing works
“, 1993) and to demonstrate amazing relations of even‐ toed ungulates to whales rather than to other ungulate orders (Nikaido et al., 1999; Shimamura et al., 1997).”
BackgroundThe repetitive DNA content of eukaryotic genomes.
lóPez-FloreS, I., & Garrido-Ramos, M. (2012) · Genome dynamics · doi:10.1159/000337118 · Cited by 244 · see citing works
Retrotransposon-based insertion polymorphisms (RBIP) for high throughput marker analysis.
Flavell, A. J., Knox, M., Pearce, S. R., & Ellis, T. H. N. (1998) · The Plant Journal · doi:10.1046/j.1365-313x.1998.00334.x · Cited by 243
“© Blackwell Science Ltd, The Plant Journal, (1998), 16, 643–650 but is yet to be applied to plants (Minghetti and Dugaiczyk, 1993; Shimamura et al., 1997)”
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“4) and other multiple sets of molecular evidence (Montgelard, Catzeflis, and Douzery 1997; Shimamura et al. 1997; Gatesy et al. 1999).”
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Price, S. A., Bininda‐Emonds, O. R. P., & Gittleman, J. L. (2005) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1017/s1464793105006743 · Cited by 268 · see citing works
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Nishihara, H., Hasegawa, M., & Okada, N. (2006) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.0603797103 · Cited by 233 · see citing works
Self-citationNikaido, M., Matsuno, F., Hamilton, H., Brownell, R., Cao, Y., Ding, W., Zhu, Z.-Y., Shedlock, A., Fordyce, R., Hasegawa, M., et al. (2001) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.121139198 · Cited by 229 · see citing works
Self-citationMobile elements and the human genome
Prak, E. L. L., & Kazazian, H. (2000) · Nature reviews genetics · doi:10.1038/35038572 · Cited by 225 · see citing works
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Freitag, J., Ludwig, G., Andreini, I., Rössler, P., & Breer, H. (1998) · Journal of Comparative Physiology · doi:10.1007/s003590050287 · Cited by 209 · see citing works
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BackgroundAmrine-Madsen, H., Koepfli, K., Wayne, R., & Springer, M. (2003) · Molecular Phylogenetics and Evolution · doi:10.1016/s1055-7903(03)00118-0 · Cited by 208 · see citing works
“, 1999), Hippopotamidae+Cetacea (Nikaido et al., 1999; Shimamura et al., 1997), tarsiers + anthropoids (Schmitz et al.”
BackgroundTakahashi, K., Terai, Y., Nishida, M., & Okada, N. (2001) · Molecular biology and evolution · doi:10.1093/oxfordjournals.molbev.a003747 · Cited by 204 · see citing works
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Vélez-Zuazo, X., & Agnarsson, I. (2011) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2010.11.018 · Cited by 203
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BackgroundAgnarsson, I., & May-Collado, L. J. (2008) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2008.05.046 · Cited by 195 · see citing works
SINEs of a nearly perfect character.
Ray, D. A., Xing, J.-C., Salem, A.-H., & Batzer, M. (2006) · Systematic Biology · doi:10.1080/10635150600865419 · Cited by 194 · see citing works
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Salem, A., Ray, D. A., Xing, J.-C., Callinan, P. A., Myers, J. S., Hedges, D. J., Garber, R. K., Witherspoon, D., Jorde, L., & Batzer, M. (2003) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.2133766100 · Cited by 193 · see citing works
Morphological Evidence for the Phylogeny of Cetacea
Geisler, J. H., & Sanders, A. E. (2003) · Journal of Mammalian Evolution · doi:10.1023/a:1025552007291 · Cited by 201 · see citing works
Mining the Mammalian Genome for Artiodactyl Systematics
Matthee, C. A., Burzlaff, J. D., Taylor, J. F., & Davis, S. K. (2001) · Systematic Biology · doi:10.1080/10635150119683 · Cited by 171 · see citing works
The biological properties and evolutionary dynamics of mammalian LINE-1 retrotransposons.
Furano, A. (2000) · Progress in Nucleic Acid Research and Molecular Biology · doi:10.1016/s0079-6603(00)64007-2 · Cited by 175 · see citing works
SINEs and LINEs: symbionts of eukaryotic genomes with a common tail
Ohshima, K., & Okada, N. (2005) · Cytogenetic and Genome Research · doi:10.1159/000084981 · Cited by 173 · see citing works
“Bovine signal transduction We previously characterized the CHR-1 SINEs, which are distributed exclusively among cetaceans, ruminants and hippopotamuses (Shimamura et al., 1997, 1999).”
BackgroundSelf-citationNishihara, H., Maruyama, S., & Okada, N. (2009) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.0809297106 · Cited by 172 · see citing works
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Conrath, K., Wernery, U., Muyldermans, S., & Nguyen, V. K. (2003) · Developmental and Comparative Immunology · doi:10.1016/s0145-305x(02)00071-x · Cited by 171 · see citing works
“Tylopoda is classified together with Ruminantia and Suiformes within the order Artiodactyla [1–3].”
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Gatesy, J., Milinkovitch, M. C., Waddell, V. G., & Stanhope, M. J. (1999) · Systematic Biology · doi:10.1080/106351599260409 · Cited by 165 · see citing works
“…1991; Milinkovitch et al., 1993; Irwin and Arnason, 1994; Queralt et al., 1995; Smith et al., 1996; Stanhope et al., 1996; Montgelard et al., 1997; Shimamura et al., 1997) have been added to the casein matrix, but clades A, B, and C have remained intact with the addition of these data (Gatesy,…”
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Sagai, T., Masuya, H., Tamura, M., Shimizu, K., Yada, Y., Wakana, S., Gondo, Y., Noda, T., & Shiroishi, T. (2004) · Mammalian Genome · doi:10.1007/s00335-033-2317-5 · Cited by 163 · see citing works
“The tree is consistent with a previous one constructed based on the sequences of an inserted retroposon (Shimamura et al. 1997).”
MethodMitogenomic relationships of placental mammals and molecular estimates of their divergences.
Árnason, Ú., Adegoke, J. A., Gullberg, A., Harley, E., Janke, A., & Kullberg, M. (2008) · Gene · doi:10.1016/j.gene.2008.05.024 · Cited by 160 · see citing works
SINEs of speciation: tracking lineages with retroposons.
Shedlock, A., Takahashi, K., & Okada, N. (2004) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2004.08.002 · Cited by 156 · see citing works
Self-citationSelective constraints, amino acid composition, and the rate of protein evolution.
Tourasse, N. J., & Li, W.-H. (2000) · Molecular biology and evolution · doi:10.1093/oxfordjournals.molbev.a026344 · Cited by 155
“The relative position of Cetacea within Cetartiodactyla (Cetacea 1 Artiodactyla) has been confirmed by recent analyses of mitochondrial sequence data (Gatesy 1997; Ursing and Arnason 1998) and transposable elements (Shimamura et al. 1997).”
BackgroundSunako, T., Sakuraba, W., Senda, M., Akada, S., Ishikawa, R., Niizeki, M., & Harada, T. (1999) · Plant Physiology · doi:10.1104/pp.119.4.1297 · Cited by 155
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BackgroundBejder, L., & Hall, B. K. (2002) · Evolution & Development · doi:10.1046/j.1525-142x.2002.02033.x · Cited by 152 · see citing works
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BackgroundÁrnason, Ú., Gullberg, A., Grétarsdóttir, S., Ursing, B. M., & Janke, A. (2000) · Journal of Molecular Evolution · doi:10.1007/s002390010060 · Cited by 141 · see citing works
“…the artiodactyls, thereby sug- gesting artiodactyl paraphyly (Beintema et al. 1986; Irwin et al. 1991; Irwin and Arnason 1994; Graur and Higgins 1994; Arnason and Gullberg 1996; Gatesy et al. 1996, 1999; Shimamura et al. 1997; Ursing and Arnason 1998b; Ursing et al. 2000; Kleineidam et al. 1999).”
BackgroundSINEs of the perfect character.
Hillis, D. (1999) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.96.18.9979 · Cited by 148 · see citing works
Rodent evolution: back to the root.
Churakov, G., Sadasivuni, M., Rosenbloom, K., Huchon, D., Brosius, J., & Schmitz, J. (2010) · Molecular biology and evolution · doi:10.1093/molbev/msq019 · Cited by 147 · see citing works
“In the following subsequent years, the Okada group pioneered the usage of presence–absence markers to resolve phylogenetic questions (e.g., Murata et al. 1993; Shimamura et al. 1997).”
BackgroundInfluentialPoxviruses as possible vectors for horizontal transfer of retroposons from reptiles to mammals
Piskurek, O., & Okada, N. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0700531104 · Cited by 149 · see citing works
Self-citationCytochrome b and Bayesian inference of whale phylogeny
May-Collado, L. J., & Agnarsson, I. (2005) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2005.09.019 · Cited by 146 · see citing works
Alu insertion loci and platyrrhine primate phylogeny.
Ray, D. A., Xing, J.-C., Hedges, D. J., Hall, M., Laborde, M. E., Anders, B. A., White, B., Stoilova, N., Fowlkes, J. D., Landry, K. E., et al. (2005) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2004.10.023 · Cited by 137 · see citing works
The application of LTR retrotransposons as molecular markers in plants.
Schulman, A. H., Flavell, A. J., Paux, E., & Ellis, T. H. N. (2012) · Methods in molecular biology · doi:10.1007/978-1-61779-603-6_7 · Cited by 129 · see citing works
Mobile DNA elements in primate and human evolution.
Xing, J.-C., Witherspoon, D., Ray, D. A., Batzer, M., & Jorde, L. (2007) · American Journal of Physical Anthropology · doi:10.1002/ajpa.20722 · Cited by 129 · see citing works
“Before reviewing these applications, we begin with a brief discussion of the basic biology that underlies mobile elements and their behavior in the genome.”
BackgroundMethodStress physiology in marine mammals: how well do they fit the terrestrial model?
Atkinson, S., Crocker, D. E., Houser, D., & Mashburn, K. (2015) · Journal of Comparative Physiology □ B · doi:10.1007/s00360-015-0901-0 · Cited by 126 · see citing works
Cortical complexity in cetacean brains
Hof, P. R., Chanis, R., & Marino, L. (2005) · The Anatomical Record Part A: Discoveries in Molecular, Cellular, and Evolutionary Biology · doi:10.1002/ar.a.20258 · Cited by 124 · see citing works
“…features with that of large terrestrial artiodactyls, consistent with the phylogenetic propinquity of these species (Nikaido et al., 1996; Shimamura et al., 1997; Gatesy, 1998; Gingerich and Uhen, 1998; Milinkovitch et al., 1998; Hof et al., 1999, 2000; Gingerich et al., 2001; Thewissen…”
The position of Hippopotamidae within Cetartiodactyla
Boisserie, J., Lihoreau, F., & Brunet, M. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409518102 · Cited by 124 · see citing works
Families of transposable elements, population structure and the origin of species
Jurka, J., Bao, W.-D., & Kojima, K. (2011) · Biology Direct · doi:10.1186/1745-6150-6-44 · Cited by 121 · see citing works
“The presence of lineage-specific amplification of SINE elements was first observed over a decade ago [63], and successfully used in biological systematics, particularly in mammals [64-73].”
BackgroundTakahashi, K., Terai, Y., Nishida, M., & Okada, N. (1998) · Molecular biology and evolution · doi:10.1093/oxfordjournals.molbev.a025936 · Cited by 119 · see citing works
Self-citationO'Leary, M. A., & Gatesy, J. (2008) · Cladistics · doi:10.1111/j.1096-0031.2007.00187.x · Cited by 118 · see citing works
Myosin superfamily evolutionary history
Thompson, R. F., & Langford, G. (2002) · The Anatomical Record · doi:10.1002/ar.10160 · Cited by 118 · see citing works
“…sometimes referred to as the cladistic approach, has been used by others to infer the phylogenetic relationships of ray-finned fish (Venkatesh et al., 1999), the evolution of vertebrate HOX clusters (Amores et al., 1998), and the historic relationship of SINE genes (Shimamura et al., 1997).”
BackgroundIntegration target site selection by a resurrected human endogenous retrovirus.Preprint
Brady, T. L., Lee, Y. N., Ronen, K., Malani, N., Berry, C., Bieniasz, P., & Bushman, F. (2009) · Genes & Development · doi:10.1101/gad.1762309 · Cited by 117 · see citing works
“638 GENES & DEVELOPMENT These findings support the use of endogenous retroviruses as phylogenetic markers (Shimamura et al. 1997; Takahashi et al. 2001; Salem et al. 2003; Singer et al. 2003).”
BackgroundO’Leary, M. A., & Geisler, J. H. (1999) · Systematic Biology · doi:10.1080/106351599260102 · Cited by 114 · see citing works
Analyses of mitochondrial genomes strongly support a hippopotamus-whale clade
Ursing, B. M., & Arnason, U. (1998) · Proceedings of the Royal Society of London. Series B: Biological Sciences · doi:10.1098/rspb.1998.0567 · Cited by 116 · see citing works
“B (1998) 265, 2251-2255 Received 7 August 1998 Accepted 3 September 1998 positions of SINE (short interspersed elements) insertion sites (Shimamura et al. 1997).”
BackgroundZhou, X., Xu, S., Xu, J., Chen, B., Zhou, K., & Yang, G. (2011) · Systematic Biology · doi:10.1093/sysbio/syr089 · Cited by 108 · see citing works
“…Artiodactyla (i.e., terrestrial artiodactyls) is widely supported by recent phylogenetic analyses of molecular data, regardless if supermatrix or supertree methods are employed (Shimamura et al. 1997; Nikaido et al. 1999; Madsen et al. 2001; Murphy, Eizirik, Johnson, et al. 2001; Beck et al. 2006).”
BackgroundMethodResolution of a Supertree/Supermatrix Paradox
Gatesy, J., Matthee, C. A., DeSalle, R., & Hayashi, C. Y. (2002) · Systematic Biology · doi:10.1080/10635150290102311 · Cited by 206 · see citing works
Genome constitution and classification using retrotransposon-based markers in the orphan crop banana
Teo, C., Tan, S.-H., Ho, C., Faridah, Q., Othman, Y., Heslop-Harrison, J., Kalendar, R., & Schulman, A. (2005) · Journal of Plant Biology · doi:10.1007/bf03030568 · Cited by 106 · see citing works
Morphological support for a close relationship between hippos and whales
Geisler, J. H., & Uhen, M. D. (2003) · Journal of Vertebrate Paleontology · doi:10.1671/32 · Cited by 112 · see citing works
Phylogenetic assessment of molecular and morphological data for eutherian mammals.
Liu, F., & Miyamoto, M. M. (1999) · Systematic Biology · doi:10.1080/106351599260436 · Cited by 104 · see citing works
“Artiodactyl paraphyly, relative to Cetacea, is well supported by many recent molecular studies that include retroposon markers (Shimamura et al., 1997) and complete mtDNA genomes (Ursing and Arnason, 1998).”
BackgroundInfluentialThe visual pigments of the bottlenose dolphin (Tursiops truncatus)
Fasick, J. I., Cronin, T., Hunt, D., & Robinson, P. (1998) · Visual Neuroscience · doi:10.1017/s0952523898154056 · Cited by 104 · see citing works
“This result is in agreement with previous work which has supported cetaceanungulate relationships through both morphological (Fordyce, 1980; Barnes et al., 1985; Novacek, 1994) and molecular (Irwin et al., 1991; Milinkovitch, 1992; Shimamura et al., 1997) investigations.”
ResultFrom the margins of the genome: mobile elements shape primate evolution
Hedges, D. J., & Batzer, M. (2005) · Bioessays · doi:10.1002/bies.20268 · Cited by 103 · see citing works
“Owing largely to the pioneering efforts of Okada and colleagues working on nonprimate taxa,((67,68))”
BackgroundDetermining and dating recent rodent speciation events by using L1 (LINE-1) retrotransposons.
Verneau, O., Catzeflis, F., & Furano, A. (1998) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.95.19.11284 · Cited by 101
A retroposon analysis of Afrotherian phylogeny.
Nishihara, H., Satta, Y., Nikaido, M., Thewissen, J., Stanhope, M. J., & Okada, N. (2005) · Molecular biology and evolution · doi:10.1093/molbev/msi179 · Cited by 100 · see citing works
“…analysis of retroposons has already been used as a powerful marker to resolve phylogenetic relationships of various animals (Murata et al. 1993; Shimamura et al. 1997; Nikaido, Rooney, and Okada 1999; Nikaido et al. 2001; Schmitz et al. 2002; Salem et al. 2003; Roos, Schmitz, and Zischler…”
Self-citationMolecular Evidence for the Major Clades of Placental Mammals
Scally, M., Madsen, O., Douady, C., de Jong, W. D., Stanhope, M., & Springer, M. (2001) · Journal of mammalian evolution · doi:10.1023/a:1014446915393 · Cited by 97 · see citing works
Relationships of Cetacea to Terrestrial Ungulates and the Evolution of Cranial Vasculature in Cete
Geisler, J. H., & Luo, Z. (1998) · Springer eBooks · doi:10.1007/978-1-4899-0159-0_6 · Cited by 97 · see citing works
PETERSON, K. J., SUMMONS, R. E., & DONOGHUE, P. C. J. (2007) · Palaeontology · doi:10.1111/j.1475-4983.2007.00692.x · Cited by 93 · see citing works
“…groups of short interspersed elements (i.e. retroposons that have been amplified and integrated into the genome via retroposi- tion) were present exclusively in the genomes of ruminants, hippos and whales, but not in camels and pigs, nor in any other mammalian group tested (Shimamura et al. 1997).”
BackgroundShimamura, M., Abe, H., Nikaido, M., Ohshima, K., & Okada, N. (1999) · Molecular biology and evolution · doi:10.1093/oxfordjournals.molbev.a026194 · Cited by 93 · see citing works
Self-citationBigot, Y. (2012) · Methods in Molecular Biology · doi:10.1007/978-1-61779-603-6 · Cited by 93
Molecular Systematics and Evolution: Theory and Practice
DeSalle, R., Giribet, G., & Wheeler, W. (2002) · EXS 92 · doi:10.1007/978-3-0348-8114-2 · Cited by 93 · see citing works
Pseudogenization of the tooth gene enamelysin (MMP20) in the common ancestor of extant baleen whales
Meredith, R., Gatesy, J., Cheng, J., & Springer, M. (2011) · Proceedings of the Royal Society of London. Biological Sciences · doi:10.1098/rspb.2010.1280 · Cited by 91
On dynamics of overlapping genes in bacterial genomes.
Fukuda, Y., Nakayama, Y., & Tomita, M. (2003) · Gene · doi:10.1016/j.gene.2003.09.021 · Cited by 91 · see citing works
Gaeth, A., Short, R. V., & Renfree, M. (1999) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.96.10.5555 · Cited by 88
Ecology and evolution of mammalian biodiversity
Jones, K. E., & Safi, K. (2011) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2011.0090 · Cited by 87 · see citing works
Lavoué, S., Sullivan, J., & Hopkins, C. (2003) · doi:10.1046/j.1095-8312.2003.00170.x · Cited by 85
“…INTRONS 15 © 2003 The Linnean Society of London, Biological Journal of the Linnean Society, 2003, 78, ••–•• bij_170.fm have demonstrated the utility of such characters (Shimamura et al., 1997; Qiu et al., 1998, 1999; Gugerli et al., 2001; van Dijk et al., 2001; Venkatesh, Erdmann & Brenner, 2001).”
BackgroundAncient SINEs from African endemic mammals.
Nikaido, M., Nishihara, H., Hukumoto, Y., & Okada, N. (2003) · Molecular biology and evolution · doi:10.1093/molbev/msg052 · Cited by 84
Self-citationHamdi, H., Nishio, H., Zielinski, R., & Dugaiczyk, A. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.2797 · Cited by 84
Spectral-tuning mechanisms of marine mammal rhodopsins and correlations with foraging depth
Fasick, J. I., & Robinson, P. (2000) · Visual Neuroscience · doi:10.1017/s095252380017511x · Cited by 83 · see citing works
“This is in agreement with both morphological (Barnes et al., 1985) and molecular (Graur & Higgins, 1994; Shimamura et al., 1997) data indicating that cetaceans and artiodactyls form a monophyletic group.”
BackgroundResultDNA Banks for Endangered Animal Species
Ryder, O., McLaren, A., Brenner, S., Zhang, Y.-P., & Benirschke, K. (2000) · Science · doi:10.1126/science.288.5464.275 · Cited by 83
Alavi-Kia, S. S., Mohammadi, S., Aharizad, S., & Moghaddam, M. (2008) · doi:10.1080/13102818.2008.10817555 · Cited by 82
Geisler, J. H., & Uhen, M. D. (2005) · Journal of Mammalian Evolution · doi:10.1007/s10914-005-4963-8 · Cited by 92 · see citing works
Evolutionary Cognitive Neuroscience
Platek, S., Keenan, J., & Shackelford, T. (2006) · doi:10.7551/mitpress/2882.003.0029 · Cited by 80
“Molecular evidence shows a sister-taxon relationship between extant cetaceans and the artiodactyl family Hippopotamidae (Gatesy, 1998; Milinkovitch, Berube, & Palsboll, 1998; Nikaido, Rooney, & Okada, 1996; Shimamura et al., 1997) but an early divergence from hippopotamids at least 52mya (Gingerich & Uhen, 1998).”
BackgroundMolecular phylogeny: pitfalls and progress.
Moreira, D., & Philippe, H. (2000) · International Microbiology · doi:10.2436/im.v3i1.9236 · Cited by 79
“events [43].”
Kaiser, V., van Tuinen, M., & Ellegren, H. (2006) · Molecular biology and evolution · doi:10.1093/molbev/msl164 · Cited by 76 · see citing works
“…of transposable elements in phylogenetic reconstruction are available for several vertebrate groups, including salmons (Murata et al. 1993), whales (Shimamura et al. 1997), Lake Malawi cichlids (Takahashi et al. 2001; Terai et al. 2003), turtles (Sasaki et al. 2004), eels (Kajikawa et al. 2005),…”
BackgroundO'Leary, M. (1999) · Cladistics · doi:10.1111/j.1096-0031.1999.tb00269.x · Cited by 76
“This occurred in 80 bases, and for k casein, Camelus was missing 63 and Equus 33 base sequences before they were entered into MALIGN to avoid erroneous Copyright q 1999 by The Willi Hennig Society All rights of reproduction in any form reserved MAUREEN A. O’LEARY and a toothed whale [here Tursiops] (Shimamura et al.,…”
BackgroundInfluential
- Authors
- Shimamura, M., Yasue, H., Ohshima, K., Abe, H., Kato, H., Kishiro, T., Goto, M., Munechika, I., & Okada, N.
- Affiliations
- Tokyo Institute of Technology (JP)
- The Institute of Cetacean Research (JP)
- Corresponding author
- Okada, Norihiro
- Venue
- Nature
- Published
- 1997-08-14
- Volume
- 388
- Issue
- 6643
- Pages
- 666-670
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W1838926299
- Cited by
- 399
- References
- 23
- Citations by year
- 2025: 6 · 2024: 1 · 2023: 3 · 2022: 4 · 2021: 4 · 2020: 4 · 2019: 10 · 2018: 5 · 2017: 9 · 2016: 10 · 2015: 8 · 2014: 9 · 2013: 10 · 2012: 8
- FWCI
- 35.58
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Tokyo Tech Research Repository (Tokyo Institute of Technology) (submittedVersion)
- Topics
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- whale evolution, cetaceans, Artiodactyla, short interspersed nuclear elements, retroposition, monophyly, ruminants, phylogenetic relationships, molecular phylogeny
- MeSH terms
- Animals, Artiodactyla, Base Sequence, DNA, Humans, Molecular Sequence Data, Phylogeny, Whales, Sequence Alignment, Retroelements
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