Cited by 399Evolution and Paleontology StudiesChromosomal and Genetic VariationsGenomics and Phylogenetic Studies

The DOI matches its Crossref record.

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

Shimamura, Mitsuru, Yasue, Hiroshi, Ohshima, Kazuhiko, Abe, Hideaki, Kato, Hidehiro, Kishiro, Toshiya, Goto, Mutsuo, Munechika, Isao, Okada, Norihiro·1997·Nature

DOI 10.1038/41759

Open this paper in CoChat — free account

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.

Integrity signals

Registry

Crossref · 10.1038/41759

Cites

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

No references could be resolved yet.

Research works printed but not linked: 25

Gingerich, P. D., Smith, B. H. & Simons, E. L. Hind limbs of Eocene Basilosaurus: evidence of feet in whales. Science 249, 154–157 (1990). · DOI
Thewissen, J. G. M. & Hussain, S. T. Origin of underwater hearing in whales. Nature 361, 444–445 (1993). · DOI
Novacek, M. J. Mammalian phylogeny: shaking the tree. Nature 356, 121–125 (1992). · DOI
Milinkovitch, M. C., Ortí, G. & Meyer, A. Revised phylogeny of whales suggested by mitochondrial ribosomal DNA sequences. Nature 361, 346–348 (1993). · DOI
Graur, D. & Higgins, D. G. Molecular evidence for the inclusion of cetaceans within the order Artiodactyla. Mol. Biol. Evol. 11, 357–364 (1994).
Irwin, D. M. & Arnason, U. Cytochrome b gene of marine mammals: Phylogeny and evolution. J. Mamm. Evol. 2, 37–55 (1994). · DOI
Gatesy, J., Hayashi, C., Cronin, M. A. & Arctander, P. Evidence from milk casein genes that cetaceans are close relatives of hippopotamid artiodactyls. Mol. Biol. Evol. 13, 954–963 (1996). · DOI
Weiner, A. M., Deininger, P. L. & Efstratiadiss, A. Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. Annu. Rev. Biochem. 55, 631–661 (1986). · DOI
Schmid, C. & Maraia, R. Transcriptional regulation and transpositional selection of active SINE sequences. Curr. Opin. Genet. Dev. 2, 874–882 (1992). · DOI
Okada, N. SINEs: Short interspersed repeated elements of the eukaryotic genome. Trends Ecol. Evol. 6, 358–361 (1991). · DOI
Okada, N. & Ohshima, K. in The Impact of Short Interspersed Elements (SINEs) on the Host Genome (ed. Maraia, R. J.) 61–79 (Landes, Austin, TX, 1995).
Murata, S., Takasaki, N., Saitoh, M. & Okada, N. Determination of the phylogenetic relationships among Pacific salmonids by using short interspersed elements (SINEs) as temporal landmarks of evolution. Proc. Natl Acad. Sci. USA 90, 6995–6999 (1993). · DOI
Murata, S., Takasaki, N., Saitoh, M., Tachida, H. & Okada, N. Details of retropositional genome dynamics that provide a rationale for a generic division: The distinct branching of all the Pacific salmon and trout (Oncorhynchus) from the Atlantic salmon and trout (Salmo). Genetics 142, 915–926 (1996). · DOI
Takahashi, H., Awata, T. & Yasue, H. Characterization of swine short interspersed repetitive sequences. Anim. Genet. 23, 443–448 (1992). · DOI
Lenstra, J. A., van Boxtel, J. A. F., Zwaagstra, K. A. & Schwerin, M. Short interspersed nuclear element (SINE) sequences of the Bovidae. Anim. Genet. 24, 33–39 (1993). · DOI
Gentry, A. W. n & Hooker, J. J. in The Phylogeny and Classification of the Tetrapods Vol. 2 Mammals (ed. Benton, M. J.) 235–272 (Clarendon, Oxford, 1988).
Adachi, J. & Hasegawa, M. Instability of quartet analyses of molecular sequence data by the maximum likelihood method: The Cetacea/Artiodactyla relationships. Mol. Phyl. Evol. 6, 72–76 (1996). · DOI
Hasegawa, M. & Adachi, J. Phylogenetic position of cetaceans relative to artiodactyls: Reanalysis of mitochondrial and nuclear sequences. Mol. Biol. Evol. 13, 710–717 (1996). · DOI
Philippe, H. & Douzery, E. The pitfalls of molecular phylogeny based on four species, as illustrated by the Cetacea/Artiodactyla relationships. J. Mamm. Evol. 2, 133–152 (1994). · DOI
Thewissen, J. G. M. Phylogenetic aspects of cetacean origins: a morphological perspective. J. Mamm. Evol. 2, 157–184 (1994). · DOI
Prothero, D. R., Manning, E. M. & Fischer, M. in The Phylogeny and Classification of the Tetrapods Vol. 2 Mammals (ed. Benton, M. J.) 201–234 (Clarendon, Oxford, 1988).
Fordyce, R. E. & Barnes, L. G. The evolutionary history of whales and dolphins. Annu. Rev. Earth Planet. Sci. 22, 419–455 (1994). · DOI
Rose, K. D. Skeleton of Diacodexis, oldest known artiodactyl. Science 216, 621–623 (1982). · DOI
Golz, D. J. Eocene Artiodactyla of southern California. Nat. Hist. Mus. Los Angeles County, Sci. Bull. 26, 1–85 (1976).
Hedges, S. B., Parker, P. H., Sibley, C. G. & Kumar, S. Continental breakup and the ordinal diversification of birds and mammals. Nature 381, 226–229 (1996). · DOI

Sorted by citations

Items 201–300 of 354

The neocortex of cetartiodactyls. II. Neuronal morphology of the visual and motor cortices in the giraffe (Giraffa camelopardalis)
Jacobs, B., Harland, T., Kennedy, D., Schall, M., Wicinski, B. A., Butti, C., Hof, P. R., Sherwood, C. C., & Manger, P. R. (2014) · Brain Structure and Function · doi:10.1007/s00429-014-0830-9 · Cited by 29
“It should be noted that the Artiodactyla suborder Ruminantia appears to be most closely related to hippopotami and cetaceans, and composes a clade referred to as Cetruminantia (Graur and Higgins 1994; Shimamura et al. 1997).”
Background
Phylogenetic analysis of Oryza rufipogon strains and their relations to Oryza sativa strains by insertion polymorphism of rice SINEs.
Xu, J.-H., Cheng, C.-Y., Tsuchimoto, S., Ohtsubo, H., & Ohtsubo, E. (2007) · Genes & Genetic Systems · doi:10.1266/ggs.82.217 · Cited by 27
Non-thermal signals govern selective brain cooling in pigs
Fuller, A., Mitchell, G., & Mitchell, D. (1999) · Journal of Comparative Physiology □ B · doi:10.1007/s003600050261 · Cited by 27
“artiodactyls (Shimamura et al. 1997), so they probably did not originally evolve for the purposes of thermoregulation.”
Background
A SINE that acquired a role in signal transduction during evolution.
Shimamura, M., Nikaido, M., Ohshima, K., & Okada, N. (1998) · Molecular biology and evolution · doi:10.1093/oxfordjournals.molbev.a025997 · Cited by 27
“We recently characterized the CHR-1 SINEs, which are distributed exclusively among whales, cows, and hippopotamuses (Shimamura et al. 1997).”
BackgroundSelf-citation
Distinct groups of repetitive families preserved in mammals correspond to different periods of regulatory innovations in vertebrates
Jurka, J., Bao, W.-D., Kojima, K., Kohany, O., & Yurka, M. G. (2012) · Biology Direct · doi:10.1186/1745-6150-7-36 · Cited by 26
“Outbreaks of new TE families are often lineage and species-specific [15-24], which suggests a potential involvement of TEs in speciation.”
Background
Information theory reveals large-scale synchronisation of statistical correlations in eukaryote genomes.
Dehnert, M., Helm, W., & Hütt, M.-T. (2005) · Gene · doi:10.1016/j.gene.2004.11.026 · Cited by 26
Primate genus Miopithecus: evidence for the existence of species and subspecies of dwarf guenons based on cellular and endogenous viral sequences.
van der Kuyl, A. C., Dekker, J. T., & Goudsmit, J. (2000) · Molecular Phylogenetics and Evolution · doi:10.1006/mpev.1999.0721 · Cited by 26
Taxonomic revision of the dolphin genusLagenorhynchus
Vollmer, N. L., Ashe, E., Brownell, R. L., Cipriano, F., Mead, J. G., Reeves, R. R., Soldevilla, M. S., & Williams, R. (2019) · Marine Mammal Science · doi:10.1111/mms.12573 · Cited by 36
Disparity, adaptation, exaptation, bookkeeping, and contingency at the genome level
Brosius, J. (2005) · Paleobiology · doi:10.1666/0094-8373(2005)031[0001:daebac]2.0.co;2 · Cited by 23
Episodic Molecular Evolution of Pituitary Growth Hormone in Cetartiodactyla
Maniou, Z., Wallis, O. C., & Wallis, M. (2004) · Journal of Molecular Evolution · doi:10.1007/s00239-004-2595-x · Cited by 24
“This analysis takes into account recent molecular evidence suggesting that cetaceans are nested within the artiodactyl phylogenetic tree (Arnason et al. 2000; Gatesy et al. 1996; Graur and Higgins 1994; Kleineidam et al. 1999; Liu et al. 2001a; Madsen et al. 2001; Murphy et al. 2001; Nikaido et al. 1999; Shimamura et…”
Background
Short interspersed elements (SINEs) from insectivores. Two classes of mammalian SINEs distinguished by A-rich tail structure
Borodulina, O., & Kramerov, D. A. (2001) · Mammalian Genome · doi:10.1007/s003350020029 · Cited by 25
“The presence or absence of CHR-1 and CHR-2 SINEs at particular orthologous loci prove that whales form a clade within even-toed ungulates (Shimamura et al. 1997).”
Background
Major mammalian clades: a review under consideration of molecular and palaeontological evidence
Helgen, K. M. (2003) · Mammalian Biology · doi:10.1078/1616-5047-1610057 · Cited by 15
Genomic, phylogenetic, and cell biological insights into metazoan origins
Nichols, S. A., Dayel, M. J., & King, N. (2009) · Animal Evolution · doi:10.1093/acprof:oso/9780199549429.003.0003 · Cited by 24
Evolutionary Histories of Transposable Elements in the Genome of the Largest Living Marsupial Carnivore, the Tasmanian Devil
Gallus, S., Hallström, B. M., Kumar, V., Dodt, W. G., Janke, A., Schumann, G. G., & Nilsson, M. A. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv017 · Cited by 27
“Previously, retrotransposons have been successfully utilized as phylogenetic markers to resolve relationships among several mammalian groups (e.g., Shimamura et al. 1997; Kriegs et al. 2006; Nilsson et al. 2010).”
Background
Tracking ancient polyploids: a retroposon insertion reveals an extinct diploid ancestor in the polyploid origin of belladonna.
Yuan, Y.-W., Zhang, Z.-Y., Chen, Z.-D., & Olmstead, R. (2006) · Molecular biology and evolution · doi:10.1093/molbev/msl099 · Cited by 24
“…interspersed element) families, have been employed as a powerful tool to complement DNA sequence data for addressing phylogenetic questions in a number of animal groups (Murata et al. 1993; Shimamura et al. 1997; Nikaido et al. 1999; Terai et al. 2003; Sasaki et al. 2004; Nikaido et al. 2006).”
Method
Genetic distinction of American and European mink (Mustela vison and M. lutreola) and European polecat (M. putorius) hair samples by detection of a species-specific SINE and a RFLP assay
López-Giráldez, F., Gómez-Moliner, B., Marmi, J., & Domingo-Roura, X. (2005) · doi:10.1017/s0952836905006497 · Cited by 24
Using Inter-SINE–PCR to Study Mammalian Phylogeny
Bannikova, A., Matveev, V., & Kramerov, D. A. (2002) · Russian Journal of Genetics · doi:10.1023/a:1016056304555 · Cited by 23
Retroposons: Genetic Footprints on the Evolutionary Paths of Life
Nishihara, H., & Okada, N. (2008) · Methods in molecular biology · doi:10.1007/978-1-59745-581-7_13 · Cited by 21
Self-citation
Alu elements and the phylogeny of capuchin (Cebus and Sapajus) monkeys
Martins, A. M., Amorim, N., Carneiro, J., Affonso, P. R. A. D. M., Sampaio, I., & Schneider, H. (2015) · American Journal of Primatology · doi:10.1002/ajp.22352 · Cited by 22
SRY gene structure and phylogeny in the cetacean species
Nishida, S., Pastene, L. A., Goto, M., & Koike, H. (2003) · Mammal Study · doi:10.3106/mammalstudy.28.57 · Cited by 22
“…ribonuclease genes (Kleineidam et al. 1999), IRBP (Smith et al. 1996), vWF and protamine P1 (Gatesy et al. 1999) in the nuclear DNA, and SINE data (Shimamura et al. 1997; Nikaido et al. 2001) were applied to study the cetacean phylogeny (Graur and Higgins 1994; Adachi and Hasegawa 1995;…”
MethodSelf-citation
Marine Morbilliviruses: Diversity and Interaction with Signaling Lymphocyte Activation Molecules
Ohishi, K., Maruyama, T., Seki, F., & Takeda, M. (2019) · Viruses · doi:10.3390/v11070606 · Cited by 21
Development of crop-specific transposable element (SINE) markers for studying gene flow from oilseed rape to wild radish
Prieto, J., Pouilly, N., Jenczewski, E., Deragon, J., & Chèvre, A. (2005) · Theoretical and Applied Genetics · doi:10.1007/s00122-005-2017-5 · Cited by 21
“Consequently, SINE insertions have often been used to retrace phylogenetic relationships in animals (Murata et al. 1993; Batzer et al. 1994; Shimamura et al. 1997; Salem et al. 2003) and plants (Tatout et al. 1999; Cheng et al. 2003).”
Background
Characterizationof Murine Leukemia Virus Restriction inMammals
Besnier, C., Ylinen, L., Strange, B., Lister, A., Takeuchi, Y., Goff, S., & Towers, G. (2003) · Journal of Virology · doi:10.1128/jvi.77.24.13403-13406.2003 · Cited by 21
Bones, molecules…or both?
Gura, T. (2000) · Nature · doi:10.1038/35018729 · Cited by 21
Whale Hageman factor (factor XII): prevented production due to pseudogene conversion.
Semba, U., Shibuya, Y., Okabe, H., & Yamamoto, T. (1998) · Thrombosis Research · doi:10.1016/s0049-3848(97)00307-1 · Cited by 21
megB1, a Novel Macroevolutionary Genomic Marker of the Fungal Phylum Basidiomycota
Babasaki, K., Neda, H., & Murata, H. (2007) · Bioscience, biotechnology and biochemistry · doi:10.1271/bbb.70144 · Cited by 20
Specific chicken repeat 1 (CR1) retrotransposon insertion suggests phylogenetic affinity of rockfowls (genus Picathartes) to crows and ravens (Corvidae).
Treplin, S., & Tiedemann, R. (2007) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2006.10.020 · Cited by 20
Comparative evolution history of SINEs in Arabidopsis thaliana and Brassica oleracea: evidence for a high rate of SINE loss
Lenoir, A., Pélissier, T., Bousquet-Antonelli, C., & Deragon, J. (2005) · Cytogenetic and Genome Research · doi:10.1159/000084976 · Cited by 20
“They have been used as molecular markers over long evolutionary periods (F60 million years; Shimamura et al., 1997; Gilbert and Labuda, 1999, 2000; Lum et al., 2000) and even older elements are rarely found with 5) or 3) deletions.”
Retrophylogenomics in rorquals indicate large ancestral population sizes and a rapid radiation
Lammers, F., Blumer, M., Rücklé, C., & Nilsson, M. A. (2019) · Mobile DNA · doi:10.1186/s13100-018-0143-2 · Cited by 20
Amino acid sequence variations of signaling lymphocyte activation molecule and mortality caused by morbillivirus infection in cetaceans
Shimizu, Y., Ohishi, K., Suzuki, R., Tajima, Y., Yamada, T., Kakizoe, Y., Bando, T., Fujise, Y., Taru, H., Murayama, T., et al. (2013) · Microbiology and immunology · doi:10.1111/1348-0421.12078 · Cited by 19
Occurrence of Can-SINEs and intron sequence evolution supports robust phylogeny of pinniped carnivores and their terrestrial relatives.
Schröder, C., Bleidorn, C., Hartmann, S., & Tiedemann, R. (2009) · Gene · doi:10.1016/j.gene.2009.06.012 · Cited by 19
Parasite histories and novel phylogenetic tools: alternative approaches to inferring parasite evolution from molecular markers.
Hypša, V. (2006) · International Journal of Parasitology · doi:10.1016/j.ijpara.2005.10.010 · Cited by 19
Molecular Cladistic Markers and the Infraordinal Phylogenetic Relationships of Primates
Schmitz, J., & Zischler, H. (2004) · Springer eBooks · doi:10.1007/978-1-4419-8873-7_3 · Cited by 21
The Nasal Complex of a Semiaquatic Artiodactyl, the Moose (Alces alces): Is it a Good Evolutionary Model for the Ancestors of Cetaceans?
Márquez, S., Pagano, A., Mongle, C., Albertine, K., & Laitman, J. (2018) · The Anatomical Record · doi:10.1002/ar.24022 · Cited by 18
Retraction Note to: Potential Start Codon Targeted (SCoT) and Interretrotransposon Amplified Polymorphism (IRAP) Markers for Evaluation of Genetic Diversity and Conservation of Wild Pistacia Species Population
Sorkheh, K., Amirbakhtiar, N., & Ercişli, S. (2016) · Biochemical Genetics · doi:10.1007/s10528-017-9830-9 · Cited by 18
Genomic distribution of SINEs in Entamoeba histolytica strains: implication for genotyping
Kumari, V., Iyer, L., Roy, R., Bhargava, V., Panda, S., Paul, J., Verweij, J., Clark, C., Bhattacharya, A., & Bhattacharya, S. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-432 · Cited by 18
“The probability of independent insertions at the same locus is exceedingly low, which links SINE-containing loci as related by descent [16,17].”
Background
Mobile DNA distributions refine the phylogeny of “matsutake” mushrooms, Tricholoma sect. Caligata
Murata, H., Ota, Y., Yamaguchi, M., Yamada, A., Katahata, S., Otsuka, Y., Babasaki, K., & Neda, H. (2013) · Mycorrhiza · doi:10.1007/s00572-013-0487-x · Cited by 18
“…are well-characterized genetic elements with evolutionary footprints, are often associated with evolutionary traits, and are distributed across taxa, unlike microsatellite DNA and SNPs, which are limited to population analyses (Nikaido et al. 2007; Shedlock et al. 2004; Shimamura et al. 1997).”
Background
Characterization of a SINE species from vicuna and its distribution in animal species including the family Camelidae
Lin, Z., Nomura, O., Hayashi, T., Wada, Y., & Yasue, H. (2001) · Mammalian Genome · doi:10.1007/s003350010272 · Cited by 18
“Based on insertion analysis using a cetacean SINE, Shimamura et al. (1997) demonstrated that ruminants and hippopotamus form a monophyletic group together with cetaceans, and that swine form a group independent of the hippopotamus.”
BackgroundMethodSelf-citation
Genetic relationships among hippopotamus, whales, and bovine based on SINE insertion analysis
Nomura, O., & Yasue, H. (1999) · Mammalian Genome · doi:10.1007/s003359901035 · Cited by 18
“More recently, Shimamura et al. (1997) clearly demonstrated that cetaceans formed a clade with ruminants and hippopotamus, by analyzing insertion of a cetacean SINE, CHR-1, into the genomes of ruminants and hippopotamus.”
BackgroundSelf-citation
Anatomy of the eye of the sperm whale ( Physeter macrocephalus L.)
Bjerager, P., Heegaard, S., & Tougaard, J. (2003) · doi:10.1578/016754203101024059 · Cited by 18
“The presence of the same tapetum in an artiodactyle suggests that this type of tapetum is a synapomorphy of the artiodactyle-cetacean clade (Shimamura et al., 1997) and not an aquatic specialization unique to whales.”
Background
Elucidate Genetic Diversity and Population Structure of Bread Wheat (Triticum Aestivum L.) Cultivars Using IRAP and REMAP Markers
Holasou, H. A., Rahmati, F., Rahmani, F., Imani, M., & Talebzadeh, Z. (2019) · Journal of Crop Science and Biotechnology · doi:10.1007/s12892-018-0211-0 · Cited by 17
Phylogenetic Conflict in Bears Identified by Automated Discovery of Transposable Element Insertions in Low-Coverage Genomes
Lammers, F., Gallus, S., Janke, A., & Nilsson, M. (2017) · bioRxiv · doi:10.1093/gbe/evx170 · Cited by 17
RETRACTED ARTICLE: Potential Start Codon Targeted (SCoT) and Inter-retrotransposon Amplified Polymorphism (IRAP) Markers for Evaluation of Genetic Diversity and Conservation of Wild Pistacia Species Population
Sorkheh, K., Amirbakhtiar, N., & Ercişli, S. (2016) · Biochemical Genetics · doi:10.1007/s10528-016-9725-1 · Cited by 17
“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; Alavi-Kia et al. 2008; Talebi et al. 2012).”
Retracted
What is a Suiforme (Artiodactyla)?
Montgelard, C., Ducrocq, S., & Douzery, E. (1998) · Molecular Phylogenetics and Evolution · doi:10.1006/mpev.1998.0499 · Cited by 16
Resolving kangaroo phylogeny and overcoming retrotransposon ascertainment bias
Dodt, W. G., Gallus, S., Phillips, M., & Nilsson, M. (2017) · Scientific Reports · doi:10.1038/s41598-017-16148-0 · Cited by 16
AMYLOIDOSIS IN TWO STEJNEGER'S BEAKED WHALES (MESOPLODON STEJNEGERI) STRANDED AT THE SEA OF JAPAN
Tajima, Y., Shimada, A., Yamada, T., & Cowan, D. (2007) · Journal of zoo and wildlife medicine · doi:10.1638/05-108.1 · Cited by 16
Alu elements support independent origin of prosimian, platyrrhine, and catarrhine Mhc-DRB genes.
Kriener, K., O'hUigin, C., & Klein, J. (2000) · Genome Research · doi:10.1101/gr.10.5.634 · Cited by 16
A SINE species from hippopotamus and its distribution among animal species
Nomura, O., Lin, Z.-H., Muladno, Wada, Y., & Yasue, H. (1998) · Mammalian Genome · doi:10.1007/s003359900817 · Cited by 16
“In addition, the consensus sequence of the hippopotamus SINE had 93% homology with the consensus sequence of a whale SINE, CHR-2 (Shimamura et al. 1997) and 73% homology with mouse tRNA Glu gene (Looney and Harding 1983).”
MethodInfluentialSelf-citation
Phoronid genome supports a monophyletic Lophophorata
Lewin, T. D., Sakagami, T., Kao, L.-J., Liao, I. J.-Y., Chiu, Y., Piñón-González, V. M., Li, J.-Y., Tin, K.-X., Lu, M. J., Endo, K., et al. (2025) · Current Biology · doi:10.1016/j.cub.2025.10.020 · Cited by 22
Estimating phylogenies from genomes: A beginners review of commonly used genomic data in vertebrate phylogenomics
Carter, J. K., Kimball, R. T., Funk, E. R., Kane, N. C., Schield, D. R., Spellman, G. M., & Safran, R. J. (2023) · Journal of Heredity · doi:10.1093/jhered/esac061 · Cited by 24
Comparative Chromosome Map and Heterochromatin Features of the Gray Whale Karyotype (Cetacea)
Kulemzina, A., Proskuryakova, A. A., Beklemisheva, V., Lemskaya, N. A., Perelman, P., & Graphodatsky, A. (2016) · Cytogenetic and Genome Research · doi:10.1159/000445459 · Cited by 15
Determining the Position of Storks on the Phylogenetic Tree of Waterbirds by Retroposon Insertion Analysis
Kuramoto, T., Nishihara, H., Watanabe, M., & Okada, N. (2015) · Genome Biology and Evolution · doi:10.1093/gbe/evv213 · Cited by 15
“…to resolve difficult phylogenetic issues for various species, for example, fish (Murata et al. 1993), turtles (Sasaki et al. 2004), mammals (Shimamura et al. 1997; Nikaido et al. 1999, 2001; Kriegs et al. 2006; Nishihara et al. 2006, 2009; Churakov et al. 2009), and birds (Watanabe,…”
BackgroundSelf-citation
Activity of ancient RTE retroposons during the evolution of cows, spiral-horned antelopes, and Nilgais (Bovinae).
Nilsson, M., Klassert, D., Bertelsen, M. F., Hallström, B., & Janke, A. (2012) · Molecular biology and evolution · doi:10.1093/molbev/mss158 · Cited by 15
“In Artiodactyla, one prominent SINE type is the Cetacea, Hippopotamidae, and Ruminantia (CHR) SINE (Shimamura et al. 1997).”
Background
Description of Ruehmaphelenchus formosanus n. sp. (Tylenchina: Aphelenchoididae) isolated from Euwallacea fornicates from Taiwan
Kanzaki, N., Masuya, H., Taki, H., Okabe, K., & Chen, C. (2013) · doi:10.1163/15685411-00002728 · Cited by 15
Phylogeny of the order rodentia inferred from structural analysis of short retroposon B1
Veniaminova, N., Vassetzky, N., Lavrenchenko, L., Popov, S. V., & Kramerov, D. A. (2007) · Russian Journal of Genetics · doi:10.1134/s1022795407070071 · Cited by 14
Comparative anatomical study on the relationships between the vestigial pelvic bones and the surrounding structures of finless porpoises (Neophocaena phocaenoides).
Tajima, Y., Hayashi, Y., & Yamada, T. (2004) · Journal of Veterinary Medical Science · doi:10.1292/jvms.66.761 · Cited by 14
Whale high-molecular-weight and low-molecular-weight kininogens.
Semba, U., Shibuya, Y., Okabe, H., Hayashi, I., & Yamamoto, T. (2000) · Thrombosis Research · doi:10.1016/s0049-3848(99)00199-1 · Cited by 14
Comparative genomics and evolutionary biology.
Kondrashov, A. (1999) · Current Opinion in Genetics and Development · doi:10.1016/s0959-437x(99)00027-1 · Cited by 14
Model dependence of the phylogenetic inference: Relationship among Carnivores, Perissodactyls and Cetartiodactyls as inferred from mitochondrial genome sequences.
Cao, Y., Kim, K. S., Ha, J., & Hasegawa, M. (1999) · Genes & Genetic Systems · doi:10.1266/ggs.74.211 · Cited by 46
“…existence of the clade formed by Cetartiodactyla (Cetacea + Artiodactyla; e.g., Cao et al., 1994; Stanhope et al., 1996; Gatesy et al., 1996, 1999; Shimamura et al., 1997; Graur et al., 1997; Ursing and Arnason, 1998), Perissodactyla, and Carnivora (e.g., Krettek et al., 1995; de Jong, 1998; Cao…”
BackgroundResultInfluential
The pygmy hippopotamus Choeropsis liberiensis (Morton, 1849): bringing to light research priorities for the largely forgotten, smaller hippo species
Flacke, G. L., Chambers, B. K., Martin, G. B., & Paris, M. C. J. (2015) · Der Zoologische Garten · doi:10.1016/j.zoolgart.2015.07.006 · Cited by 13
On the origin of Cetartiodactyla: Comparison of data on evolutionary morphology and Molecular biology
Вислобокова, И. А. (2013) · Paleontological Journal · doi:10.1134/s003103011303012x · Cited by 14
Production of Sei whale (Balaenoptera borealis) cloned embryos by inter- and intra-species somatic cell nuclear transfer.
Bhuiyan, M. U., Suzuki, Y., Watanabe, H., Lee, E., Hirayama, H., Matsuoka, K., Fujise, Y., Ishikawa, H., Ohsumi, S., & Fukui, Y. (2010) · Journal of reproduction and development · doi:10.1262/jrd.09-158a · Cited by 13
“This can be explained by the fact that bovine oocytes as recipient cytoplasm are considered not very evolutionally distant from whales [25].”
Background
Short interspersed elements (SINEs) of the Geomyoidea superfamily rodents.
Gogolevsky, K. P., & Kramerov, D. A. (2006) · Gene · doi:10.1016/j.gene.2006.01.007 · Cited by 13
Life history, growth, and form
George, J. C., Thewissen, J. G. M., Duyke, A. L. V., Breed, G. A., SUYDAM, R. S., Sformo, T. L., Person, B. T., & Brower, H. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-818969-6.00007-8 · Cited by 26
A Molecular Supertree of the Artiodactyla
Mahon, A. S. (2004) · Computational biology · doi:10.1007/978-1-4020-2330-9_20 · Cited by 10
Pathological findings and probable causes of the death of Stejneger’s beaked whales (Mesoplodon stejnegeri) stranded in Japan from 1999 and 2011
Tajima, Y., Maeda, K., & Yamada, T. (2014) · Journal of Veterinary Medical Science · doi:10.1292/jvms.13-0454 · Cited by 12
“A comparison of amyloidosis in the Stejneger’s beaked whale and that of cattle revealed similar findings as well as findings based on molecular [36] and morphological [42] likenesses.”
Result
Identification and Molecular Variations of CAN-SINEs from the ZFY Gene Final Intron of the Eurasian Badgers (Genus Meles)
Tashima, S., Kaneko, Y., Anezaki, T., Baba, M., Yachimori, S., Abramov, A., Saveljev, A., & Masuda, R. (2011) · doi:10.3106/041.036.0105 · Cited by 12
“The phylogenetic relationships by SINE markers were reconstructed in many mammalian taxa such as cetaceans (Shimamura et al. 1997), vespertilionids (Kawai et al.”
Influential
Transposable Element Dynamics in Rice and Its Wild Relatives
Jiang, N., & Panaud, O. (2013) · Springer eBooks · doi:10.1007/978-1-4614-7903-1_5 · Cited by 12
Cetacean Evolution and Systematics
Berta, A., Sumich, J., Kovacs, K., Folkens, P., & Adam, P. (2006) · doi:10.1016/b978-012088552-7/50005-9 · Cited by 12
Tempo and mode of evolution in an orthologous Can SINE
Zehr, S., Nedbal, M. A., & Flynn, J. J. (2001) · Mammalian Genome · doi:10.1007/s003350010224 · Cited by 12
“…evidence that SINEs have a preference for integration into genomic regions (Korenberg and Rykowski 1988) possessing Arich sequences (Batzer et al. 1990), it has been suggested that SINEs do not insert independently at orthologous loci within different evolutionary lineages (Shimamura et al. 1997).”
Background
A genome survey sequencing of the Java mouse deer (Tragulus javanicus) adds new aspects to the evolution of lineage specific retrotransposons in Ruminantia (Cetartiodactyla)
Gallus, S., Kumar, V., Bertelsen, M. F., Janke, A., & Nilsson, M. A. (2015) · Gene · doi:10.1016/j.gene.2015.06.064 · Cited by 10
MyrSINEs: a novel SINE family in the anteater genomes.
Nishihara, H., Kuno, S., Nikaido, M., & Okada, N. (2007) · Gene · doi:10.1016/j.gene.2007.06.003 · Cited by 11
Self-citation
Genomic expansion of the Bov-A2 retroposon relating to phylogeny and breed management
Onami, J.-I., Nikaido, M., Mannen, H., & Okada, N. (2007) · Mammalian Genome · doi:10.1007/s00335-007-9000-1 · Cited by 11
“…2002; Hassanin and Ropiquet 2004; Hassanin et al. 2006), Arabian oryx, which are included in the Bovidae subfamily (Gatesy et al. 1992; Groves and Shields 1996; Hassanin and Douzery 1999), axis deer, reticulated giraffe, and pronghorn (Shimamura et al. 1997; Hassanin and Douzery 2003) (Table 1).”
Self-citation
Cloning and characterisation of the GH gene from the common dolphin (Delphinus delphis)
Maniou, Z., Wallis, O. C., & Wallis, M. (2002) · General and Comparative Endocrinology · doi:10.1016/s0016-6480(02)00058-8 · Cited by 10
Use of IRAP and REMAP markers to interpret the population structure of Linum usitatissimum from Iran
Holasou, H. A., Abdollahi-Mandoulakani, B., Jafari, M., & Bernousi, I. (2016) · Biologia · doi:10.1515/biolog-2016-0042 · Cited by 10
“The advantage of application of these marker systems consists in the ability to track an insertion event and its subsequent vertical radiation through a pedigree or phylogeny (Shimamura et al. 1997).”
Background
Cetacean Origins: Evolutionary Turmoil during the Invasion of the Oceans
Thewissen, J. (1998) · Springer eBooks · doi:10.1007/978-1-4899-0159-0_16 · Cited by 10
Choeropsis liberiensis (Artiodactyla: Hippopotamidae)
Flacke, G. L., & Decher, J. (2019) · Mammalian Species · doi:10.1093/mspecies/sez017 · Cited by 9
Linkage disequilibrium and functional analysis of PRE1 insertion together with SNPs in the promoter region of IGFBP7 gene in different pig breeds
Wu, Q., Yu, H., Wei, W., Cheng, Y., Huang, S., Shi, H., Liu, S., Xia, J., Jia, H., & Hao, L. (2018) · Journal of Applied Genetics · doi:10.1007/s13353-018-0430-0 · Cited by 18
The wide expansion of hepatitis delta virus-like ribozymes throughout trypanosomatid genomes is linked to the spreading of L1Tc/ingi clade mobile elements
Sanchez-Luque, F. J., López, M. C., Carreira, P. E., Alonso‐Moreno, C., & Thomas, M. C. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-340 · Cited by 12
“coincide with those of previous studies involving other molecular markers [39,40] and support the idea that mobile elements as well as the extensive survey of retropositional events that might have occurred during the divergence among some eukaryotes may be used as a powerful method for making phylogenetic inferences…”
Result
Laterality of Eye Use by Bottlenose (Tursiops truncatus) and Rough-Toothed (Steno bredanensis) Dolphins While Viewing Predictable and Unpredictable Stimuli
Lilley, M. K., de Vere, A. J., & Yeater, D. (2020) · International Journal of Comparative Psychology · doi:10.46867/ijcp.2020.33.03.01 · Cited by 9
“Ungulates, including elk and cows, are distant evolutionary relatives of cetaceans (Shimamura et al., 1997), thus increasing the likelihood that this trend may be preserved across species and also observed in dolphins.”
Background
Molecular Markers in Salvia L.: Past, Present and Future
Karaca, M., & İnce, A. G. (2017) · Springer eBooks · doi:10.1007/978-3-319-73900-7_9 · Cited by 7
Chapter 5 – Aquatic Olfaction
Korsching, S. (2016) · Elsevier eBooks · doi:10.1016/b978-0-12-801694-7.00005-6 · Cited by 9
SINEs as Credible Signs to Prove Common Ancestry in the Tree of Life: A Brief Review of Pioneering Case Studies in Retroposon Systematics
Nikaido, M., Nishihara, H., & Okada, N. (2022) · Genes · doi:10.3390/genes13060989 · Cited by 8
“We used these SINEs to resolve the Cetacea–Artiodactyla issue and clearly demonstrate that three SINE loci are shared among cetaceans, ruminants, and hippopotamuses but not among camels and pigs, thus strongly suggesting the paraphyly of the order Artiodactyla (Figure 3) [23].”
MethodSelf-citation
Molecular cloning of urea transporters from the kidneys of baleen and toothed whales.
Birukawa, N., Ando, H., Goto, M., Kanda, N., Pastene, L., & Urano, A. (2008) · Comparative Biochemistry and Physiology Part B Comparative Biochemistry · doi:10.1016/j.cbpb.2006.11.033 · Cited by 8
Self-citation
Walking with whales
de MUIZON, C. (2001) · Nature · doi:10.1038/35095137 · Cited by 5
Identification of a non‐LTR retrotransposon from the gypsy moth
Field, L., James, A., Garner, K., & Slavicek, J. (1999) · Insect molecular biology (Print) · doi:10.1046/j.1365-2583.1999.820231.x · Cited by 8
“Such polymorph isms may be useful as phylogenetic or population markers (Batzer et al., 1994; Shimamura et al., 1997).”
Background
Evolutionary applications of MIRs and SINEs.
Buchanan, F., Crawford, A., Strobeck, C., Palsbøll, P., & Plante, Y. (1999) · Animal Genetics · doi:10.1046/j.1365-2052.1999.00388.x · Cited by 8
USAGE OPTIMIZATION OF UNEVENLY SAMPLED DATA THROUGH THE COMBINATION OF QUARTET TREES: A EUTHERIAN DRAFT PHYLOGENY BASED ON 640 NUCLEAR AND MITOCHONDRIAL PROTEINS
Robinson-Rechavi, M., & Graur, D. (2001) · doi:10.1560/w1g1-bdtw-hj3x-fjpw · Cited by 8
Characterization of Olive (Olea Europaea L.) Genetic Resources via PCR-Based Molecular Marker Systems
Galatali, S., Ghafoor, N. A., & Kaya, E. (2021) · doi:10.24018/ejbio.2021.2.1.146 · Cited by 7
Short interspersed elements (SINEs) of squamate reptiles (Squam1 and Squam2): structure and phylogenetic significance.
Grechko, V., Kosushkin, S. A., Borodulina, O., Butaeva, F., & Darevsky, I. (2011) · Journal of Experimental Zoology Part B: Molecular and Developmental Evolution · doi:10.1002/jez.b.21391 · Cited by 7
Short interspersed repetitive sequences as a phylogenetic tool
Kramerov, D. A., & Vasetskiĭ, N. (2009) · Molecular Biology · doi:10.1134/s0026893309050057 · Cited by 7
Investigating Evolutionary Questions Using Online Molecular Databases
Puterbaugh, M. N., & Burleigh, J. G. (2001) · The American Biology Teacher · doi:10.1662/0002-7685(2001)063[0422:iequom]2.0.co;2 · Cited by 4
Comparative Genomics of Thermophilic Bacteria and Archaea
Akanuma, S., Yokobori, S., & Yamagishi, A. (2013) · Springer eBooks · doi:10.1007/978-94-007-5899-5_12 · Cited by 8
Genetic diversity of growth hormone receptor gene in cattle.
Lin, B.-Z., Sasazaki, S., Lee, J.-H.-O., & Mannen, H. (2009) · Animal science journal = Nihon chikusan Gakkaiho · doi:10.1111/j.1740-0929.2009.00676.x · Cited by 6
Genome constitution for Musa beccarii (Musaceae) varieties
Häkkinen, M., Teo, C., & Othman, Y. (2007) · doi:10.1360/aps06020 · Cited by 6
Phylogenetic analysis of a retroposon family as represented on the human X chromosome.
Kim, H.-S., Hyun, B.-H., Choi, J., & Crow, T. (2000) · Genes & Genetic Systems · doi:10.1266/ggs.75.197 · Cited by 6
“Thus the CHR1 SINEs are distributed in cetaceans, hippopotamus and ruminants but not in other mammals (Shimamura et al., 1997) and Hpa1 SINEs are distributed specifically in the Salmonidae but not in other fishes (Kido et al.”
Background
Insect Transposable Elements
Tu, Z. J. (2011) · Elsevier eBooks · doi:10.1016/b978-0-12-384747-8.10003-0 · Cited by 9
Instabilité génomique associée à la rétrotransposition du LINE-1 humain : Structure et évolution des éléments transposables
Gilbert, N., Doucet, A., & Bucheton, A. (2004) · doi:10.1051/jbio/2004198040419 · Cited by 6
“Ils sont couramment utilisés comme marqueurs de polymorphisme entre les espèces ou au sein d’une même espèce (Salem et al., 2003 ; Shimamura et al., 1997).”
Background
IRAP: An efficient retrotransposon‐based electrophoretic technique for studying genetic variability among geographical isolates of Schistosoma japonicum
Li, J., Zhao, G.-H., Li, X.-Y., Chen, F., Chen, J.-B., Zou, F.-C., Yang, J.-F., Lin, R., Weng, Y.-B., & Zhu, X.-Q. (2011) · Electrophoresis · doi:10.1002/elps.201100044 · Cited by 5
Development of primers for detection of heat-treated cetacean materials in porcine meat and bone meal.
Shinoda, N., Yoshida, T., Kusama, T., Takagi, M., Onodera, T., & Sugiura, K. (2009) · Journal of Food Protection · doi:10.4315/0362-028x-72.7.1496 · Cited by 5

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
ORCID: Ohshima, Kazuhiko
Abe, Hideaki
Goto, Mutsuo
Okada, Norihiro
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 1997-08-14
Volume: 388
Issue: 6643
Pages: 666-670
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/41759
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: www.springernature.com/gp/researchers/text-and-data-mining (tdm)
www.springernature.com/gp/researchers/text-and-data-mining (vor)
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 › Biochemistry, Genetics and Molecular Biology › Genetics › 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

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

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

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Citations

Cites

Cited by

Metadata

Record

About these checks