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Items: 1 to 50 of 90

1.
2.

MitoFish and MiFish Pipeline: A Mitochondrial Genome Database of Fish with an Analysis Pipeline for Environmental DNA Metabarcoding.

Sato Y, Miya M, Fukunaga T, Sado T, Iwasaki W.

Mol Biol Evol. 2018 Jun 1;35(6):1553-1555. doi: 10.1093/molbev/msy074.

3.

Demonstration of the potential of environmental DNA as a tool for the detection of avian species.

Ushio M, Murata K, Sado T, Nishiumi I, Takeshita M, Iwasaki W, Miya M.

Sci Rep. 2018 Mar 14;8(1):4493. doi: 10.1038/s41598-018-22817-5.

4.

Multilocus phylogenetic analysis of the first molecular data from the rare and monotypic Amarsipidae places the family within the Pelagia and highlights limitations of existing data sets in resolving pelagian interrelationships.

Campbell MA, Sado T, Shinzato C, Koyanagi R, Okamoto M, Miya M.

Mol Phylogenet Evol. 2018 Jul;124:172-180. doi: 10.1016/j.ympev.2018.03.008. Epub 2018 Mar 8.

PMID:
29526805
5.

Molecular systematics of the anchovy genus Encrasicholina in the Northwest Pacific.

Lavoué S, Bertrand JAM, Wang HY, Chen WJ, Ho HC, Motomura H, Hata H, Sado T, Miya M.

PLoS One. 2017 Jul 28;12(7):e0181329. doi: 10.1371/journal.pone.0181329. eCollection 2017.

6.

Phylogenetic classification of bony fishes.

Betancur-R R, Wiley EO, Arratia G, Acero A, Bailly N, Miya M, Lecointre G, Ortí G.

BMC Evol Biol. 2017 Jul 6;17(1):162. doi: 10.1186/s12862-017-0958-3.

7.

Environmental DNA enables detection of terrestrial mammals from forest pond water.

Ushio M, Fukuda H, Inoue T, Makoto K, Kishida O, Sato K, Murata K, Nikaido M, Sado T, Sato Y, Takeshita M, Iwasaki W, Yamanaka H, Kondoh M, Miya M.

Mol Ecol Resour. 2017 Nov;17(6):e63-e75. doi: 10.1111/1755-0998.12690. Epub 2017 Jun 11.

PMID:
28603873
8.

Phylogenetic position of the rainbow sardine Dussumieria (Dussumieriidae) and its bearing on the early evolution of the Clupeoidei.

Lavoué S, Bertrand JAM, Chen WJ, Ho HC, Motomura H, Sado T, Miya M.

Gene. 2017 Aug 5;623:41-47. doi: 10.1016/j.gene.2017.04.032. Epub 2017 Apr 20.

PMID:
28435132
9.

Evolution of bidirectional sex change and gonochorism in fishes of the gobiid genera Trimma, Priolepis, and Trimmatom.

Sunobe T, Sado T, Hagiwara K, Manabe H, Suzuki T, Kobayashi Y, Sakurai M, Dewa SI, Matsuoka M, Shinomiya A, Fukuda K, Miya M.

Naturwissenschaften. 2017 Apr;104(3-4):15. doi: 10.1007/s00114-017-1434-z. Epub 2017 Mar 1.

10.

Evolutionary affinities of the unfathomable Parabrotulidae: Molecular data indicate placement of Parabrotula within the family Bythitidae, Ophidiiformes.

Campbell MA, Nielsen JG, Sado T, Shinzato C, Kanda M, Satoh TP, Miya M.

Mol Phylogenet Evol. 2017 Apr;109:337-342. doi: 10.1016/j.ympev.2017.02.004. Epub 2017 Feb 6.

PMID:
28185947
11.

Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea.

Yamamoto S, Masuda R, Sato Y, Sado T, Araki H, Kondoh M, Minamoto T, Miya M.

Sci Rep. 2017 Jan 12;7:40368. doi: 10.1038/srep40368.

12.

Use of a Filter Cartridge for Filtration of Water Samples and Extraction of Environmental DNA.

Miya M, Minamoto T, Yamanaka H, Oka SI, Sato K, Yamamoto S, Sado T, Doi H.

J Vis Exp. 2016 Nov 25;(117). doi: 10.3791/54741.

13.

Wide distribution range of rhizobial symbionts associated with pantropical sea-dispersed legumes.

Bamba M, Nakata S, Aoki S, Takayama K, Núñez-Farfán J, Ito M, Miya M, Kajita T.

Antonie Van Leeuwenhoek. 2016 Dec;109(12):1605-1614. Epub 2016 Sep 23.

PMID:
27664091
14.

Structure and variation of the mitochondrial genome of fishes.

Satoh TP, Miya M, Mabuchi K, Nishida M.

BMC Genomics. 2016 Sep 7;17:719. doi: 10.1186/s12864-016-3054-y.

15.

Preservation Obscures Pelagic Deep-Sea Fish Diversity: Doubling the Number of Sole-Bearing Opisthoproctids and Resurrection of the Genus Monacoa (Opisthoproctidae, Argentiniformes).

Poulsen JY, Sado T, Hahn C, Byrkjedal I, Moku M, Miya M.

PLoS One. 2016 Aug 10;11(8):e0159762. doi: 10.1371/journal.pone.0159762. eCollection 2016.

16.

Correction: Environmental DNA as a 'Snapshot' of Fish Distribution: A Case Study of Japanese Jack Mackerel in Maizuru Bay, Sea of Japan.

Yamamoto S, Minami K, Fukaya K, Takahashi K, Sawada H, Murakami H, Tsuji S, Hashizume H, Kubonaga S, Horiuchi T, Hongo M, Nishida J, Okugawa Y, Fujiwara A, Fukuda M, Hidaka S, Suzuki KW, Miya M, Araki H, Yamanaka H, Maruyama A, Miyashita K, Masuda R, Minamoto T, Kondoh M.

PLoS One. 2016 Apr 4;11(4):e0153291. doi: 10.1371/journal.pone.0153291. eCollection 2016. No abstract available.

17.

Environmental DNA as a 'Snapshot' of Fish Distribution: A Case Study of Japanese Jack Mackerel in Maizuru Bay, Sea of Japan.

Yamamoto S, Minami K, Fukaya K, Takahashi K, Sawada H, Murakami H, Tsuji S, Hashizume H, Kubonaga S, Horiuchi T, Hongo M, Nishida J, Okugawa Y, Fujiwara A, Fukuda M, Hidaka S, Suzuki KW, Miya M, Araki H, Yamanaka H, Maruyama A, Miyashita K, Masuda R, Minamoto T, Kondoh M.

PLoS One. 2016 Mar 2;11(3):e0149786. doi: 10.1371/journal.pone.0149786. eCollection 2016. Erratum in: PLoS One. 2016;11(4):e0153291.

18.

Composition of glycosaminoglycans in elasmobranchs including several deep-sea sharks: identification of chondroitin/dermatan sulfate from the dried fins of Isurus oxyrinchus and Prionace glauca.

Higashi K, Takeuchi Y, Mukuno A, Tomitori H, Miya M, Linhardt RJ, Toida T.

PLoS One. 2015 Mar 24;10(3):e0120860. doi: 10.1371/journal.pone.0120860. eCollection 2015.

19.

Phylogeny and polyploidy: resolving the classification of cyprinine fishes (Teleostei: Cypriniformes).

Yang L, Sado T, Vincent Hirt M, Pasco-Viel E, Arunachalam M, Li J, Wang X, Freyhof J, Saitoh K, Simons AM, Miya M, He S, Mayden RL.

Mol Phylogenet Evol. 2015 Apr;85:97-116. doi: 10.1016/j.ympev.2015.01.014. Epub 2015 Feb 16.

PMID:
25698355
20.

Phylogenetic relationships of Acheilognathidae (Cypriniformes: Cyprinoidea) as revealed from evidence of both nuclear and mitochondrial gene sequence variation: evidence for necessary taxonomic revision in the family and the identification of cryptic species.

Chang CH, Li F, Shao KT, Lin YS, Morosawa T, Kim S, Koo H, Kim W, Lee JS, He S, Smith C, Reichard M, Miya M, Sado T, Uehara K, Lavoué S, Chen WJ, Mayden RL.

Mol Phylogenet Evol. 2014 Dec;81:182-94. doi: 10.1016/j.ympev.2014.08.026. Epub 2014 Sep 17.

PMID:
25238947
21.

Mitochondrial genomic investigation of flatfish monophyly.

Campbell MA, López JA, Satoh TP, Chen WJ, Miya M.

Gene. 2014 Nov 10;551(2):176-82. doi: 10.1016/j.gene.2014.08.053. Epub 2014 Aug 27.

PMID:
25172210
22.

Mitogenomic phylogeny of the Percichthyidae and Centrarchiformes (Percomorphaceae): comparison with recent nuclear gene-based studies and simultaneous analysis.

Lavoué S, Nakayama K, Jerry DR, Yamanoue Y, Yagishita N, Suzuki N, Nishida M, Miya M.

Gene. 2014 Oct 1;549(1):46-57. doi: 10.1016/j.gene.2014.07.033. Epub 2014 Jul 12.

PMID:
25026502
23.

Mitogenomic circumscription of a novel percomorph fish clade mainly comprising "Syngnathoidei" (Teleostei).

Song HY, Mabuchi K, Satoh TP, Moore JA, Yamanoue Y, Miya M, Nishida M.

Gene. 2014 Jun 1;542(2):146-55. doi: 10.1016/j.gene.2014.03.040. Epub 2014 Mar 25.

PMID:
24680775
24.

Phylogeny of the Elopomorpha (Teleostei): evidence from six nuclear and mitochondrial markers.

Chen JN, López JA, Lavoué S, Miya M, Chen WJ.

Mol Phylogenet Evol. 2014 Jan;70:152-61. doi: 10.1016/j.ympev.2013.09.002. Epub 2013 Sep 13.

PMID:
24041936
25.

Evolutionary origin of the Scombridae (tunas and mackerels): members of a paleogene adaptive radiation with 14 other pelagic fish families.

Miya M, Friedman M, Satoh TP, Takeshima H, Sado T, Iwasaki W, Yamanoue Y, Nakatani M, Mabuchi K, Inoue JG, Poulsen JY, Fukunaga T, Sato Y, Nishida M.

PLoS One. 2013 Sep 4;8(9):e73535. doi: 10.1371/journal.pone.0073535. eCollection 2013.

26.

MitoFish and MitoAnnotator: a mitochondrial genome database of fish with an accurate and automatic annotation pipeline.

Iwasaki W, Fukunaga T, Isagozawa R, Yamada K, Maeda Y, Satoh TP, Sado T, Mabuchi K, Takeshima H, Miya M, Nishida M.

Mol Biol Evol. 2013 Nov;30(11):2531-40. doi: 10.1093/molbev/mst141. Epub 2013 Aug 16.

27.

Pike and salmon as sister taxa: detailed intraclade resolution and divergence time estimation of Esociformes + Salmoniformes based on whole mitochondrial genome sequences.

Campbell MA, López JA, Sado T, Miya M.

Gene. 2013 Nov 1;530(1):57-65. doi: 10.1016/j.gene.2013.07.068. Epub 2013 Aug 15.

PMID:
23954876
28.

Mitogenomic sequences and evidence from unique gene rearrangements corroborate evolutionary relationships of myctophiformes (Neoteleostei).

Poulsen JY, Byrkjedal I, Willassen E, Rees D, Takeshima H, Satoh TP, Shinohara G, Nishida M, Miya M.

BMC Evol Biol. 2013 Jun 3;13:111. doi: 10.1186/1471-2148-13-111.

29.

Mitogenomic evidence for an Indo-West Pacific origin of the Clupeoidei (Teleostei: Clupeiformes).

Lavoué S, Miya M, Musikasinthorn P, Chen WJ, Nishida M.

PLoS One. 2013;8(2):e56485. doi: 10.1371/journal.pone.0056485. Epub 2013 Feb 19.

30.

Limits and phylogenetic relationships of East Asian fishes in the subfamily Oxygastrinae (Teleostei: Cypriniformes: Cyprinidae).

Tang KL, Agnew MK, Hirt MV, Lumbantobing DN, Sado T, Teoh VH, Yang L, Bart HL, Harris PM, He S, Miya M, Saitoh K, Simons AM, Wood RM, Mayden RL.

Zootaxa. 2013;3681:101-35.

PMID:
25232592
31.

Phylogeny and biogeography of highly diverged freshwater fish species (Leuciscinae, Cyprinidae, Teleostei) inferred from mitochondrial genome analysis.

Imoto JM, Saitoh K, Sasaki T, Yonezawa T, Adachi J, Kartavtsev YP, Miya M, Nishida M, Hanzawa N.

Gene. 2013 Feb 10;514(2):112-24. doi: 10.1016/j.gene.2012.10.019. Epub 2012 Nov 19.

PMID:
23174367
32.

Molecular phylogeny of the cyprinid tribe Labeonini (Teleostei: Cypriniformes).

Yang L, Arunachalam M, Sado T, Levin BA, Golubtsov AS, Freyhof J, Friel JP, Chen WJ, Hirt MV, Manickam R, Agnew MK, Simons AM, Saitoh K, Miya M, Mayden RL, He S.

Mol Phylogenet Evol. 2012 Nov;65(2):362-79. doi: 10.1016/j.ympev.2012.06.007. Epub 2012 Jun 21.

PMID:
22728909
33.

Comparable ages for the independent origins of electrogenesis in African and South American weakly electric fishes.

Lavoué S, Miya M, Arnegard ME, Sullivan JP, Hopkins CD, Nishida M.

PLoS One. 2012;7(5):e36287. doi: 10.1371/journal.pone.0036287. Epub 2012 May 14.

34.

Body plan convergence in the evolution of skates and rays (Chondrichthyes: Batoidea).

Aschliman NC, Nishida M, Miya M, Inoue JG, Rosana KM, Naylor GJ.

Mol Phylogenet Evol. 2012 Apr;63(1):28-42. doi: 10.1016/j.ympev.2011.12.012. Epub 2011 Dec 22.

PMID:
22209858
35.

A 'living fossil' eel (Anguilliformes: Protanguillidae, fam. nov.) from an undersea cave in Palau.

Johnson GD, Ida H, Sakaue J, Sado T, Asahida T, Miya M.

Proc Biol Sci. 2012 Mar 7;279(1730):934-43. doi: 10.1098/rspb.2011.1289. Epub 2011 Aug 17.

36.

Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation.

Nakatani M, Miya M, Mabuchi K, Saitoh K, Nishida M.

BMC Evol Biol. 2011 Jun 22;11:177. doi: 10.1186/1471-2148-11-177.

37.

Phylogeny of the gudgeons (Teleostei: Cyprinidae: Gobioninae).

Tang KL, Agnew MK, Chen WJ, Vincent Hirt M, Raley ME, Sado T, Schneider LM, Yang L, Bart HL, He S, Liu H, Miya M, Saitoh K, Simons AM, Wood RM, Mayden RL.

Mol Phylogenet Evol. 2011 Oct;61(1):103-24. doi: 10.1016/j.ympev.2011.05.022. Epub 2011 Jun 6.

PMID:
21672635
38.

Multiple invasions into freshwater by pufferfishes (teleostei: tetraodontidae): a mitogenomic perspective.

Yamanoue Y, Miya M, Doi H, Mabuchi K, Sakai H, Nishida M.

PLoS One. 2011 Feb 25;6(2):e17410. doi: 10.1371/journal.pone.0017410.

39.

Remarkable morphological stasis in an extant vertebrate despite tens of millions of years of divergence.

Lavoué S, Miya M, Arnegard ME, McIntyre PB, Mamonekene V, Nishida M.

Proc Biol Sci. 2011 Apr 7;278(1708):1003-8. doi: 10.1098/rspb.2010.1639. Epub 2010 Sep 29.

40.

Intron-loss evolution of hatching enzyme genes in Teleostei.

Kawaguchi M, Hiroi J, Miya M, Nishida M, Iuchi I, Yasumasu S.

BMC Evol Biol. 2010 Aug 27;10:260. doi: 10.1186/1471-2148-10-260.

41.

Transfer RNA gene arrangement and codon usage in vertebrate mitochondrial genomes: a new insight into gene order conservation.

Satoh TP, Sato Y, Masuyama N, Miya M, Nishida M.

BMC Genomics. 2010 Aug 19;11:479. doi: 10.1186/1471-2164-11-479.

42.

Systematics of the subfamily Danioninae (Teleostei: Cypriniformes: Cyprinidae).

Tang KL, Agnew MK, Hirt MV, Sado T, Schneider LM, Freyhof J, Sulaiman Z, Swartz E, Vidthayanon C, Miya M, Saitoh K, Simons AM, Wood RM, Mayden RL.

Mol Phylogenet Evol. 2010 Oct;57(1):189-214. doi: 10.1016/j.ympev.2010.05.021. Epub 2010 May 27.

PMID:
20553898
43.

Evolutionary origin and phylogeny of the modern holocephalans (Chondrichthyes: Chimaeriformes): a mitogenomic perspective.

Inoue JG, Miya M, Lam K, Tay BH, Danks JA, Bell J, Walker TI, Venkatesh B.

Mol Biol Evol. 2010 Nov;27(11):2576-86. doi: 10.1093/molbev/msq147. Epub 2010 Jun 14.

PMID:
20551041
44.

Intraspecific variation in the mitochondrial genome among local populations of Medaka Oryzias latipes.

Hirayama M, Mukai T, Miya M, Murata Y, Sekiya Y, Yamashita T, Nishida M, Watabe S, Oda S, Mitani H.

Gene. 2010 Jun 1;457(1-2):13-24. doi: 10.1016/j.gene.2010.02.012. Epub 2010 Feb 26.

PMID:
20193748
45.

Evolutionary history of anglerfishes (Teleostei: Lophiiformes): a mitogenomic perspective.

Miya M, Pietsch TW, Orr JW, Arnold RJ, Satoh TP, Shedlock AM, Ho HC, Shimazaki M, Yabe M, Nishida M.

BMC Evol Biol. 2010 Feb 23;10:58. doi: 10.1186/1471-2148-10-58.

46.

Biogeography and evolution of the Carassius auratus-complex in East Asia.

Takada M, Tachihara K, Kon T, Yamamoto G, Iguchi K, Miya M, Nishida M.

BMC Evol Biol. 2010 Jan 12;10:7. doi: 10.1186/1471-2148-10-7.

47.

Deep-ocean origin of the freshwater eels.

Inoue JG, Miya M, Miller MJ, Sado T, Hanel R, Hatooka K, Aoyama J, Minegishi Y, Nishida M, Tsukamoto K.

Biol Lett. 2010 Jun 23;6(3):363-6. doi: 10.1098/rsbl.2009.0989. Epub 2010 Jan 6.

48.

Mitochondrial phylogenomics of anchovies (family Engraulidae) and recurrent origins of pronounced miniaturization in the order Clupeiformes.

Lavoué S, Miya M, Nishida M.

Mol Phylogenet Evol. 2010 Jul;56(1):480-5. doi: 10.1016/j.ympev.2009.11.022. Epub 2009 Nov 26.

PMID:
19944773
49.

Divergence time of the two regional medaka populations in Japan as a new time scale for comparative genomics of vertebrates.

Setiamarga DH, Miya M, Yamanoue Y, Azuma Y, Inoue JG, Ishiguro NB, Mabuchi K, Nishida M.

Biol Lett. 2009 Dec 23;5(6):812-6. doi: 10.1098/rsbl.2009.0419. Epub 2009 Jul 8.

50.

Mitogenomic evaluation of the unique facial nerve pattern as a phylogenetic marker within the percifom fishes (Teleostei: Percomorpha).

Yagishita N, Miya M, Yamanoue Y, Shirai SM, Nakayama K, Suzuki N, Satoh TP, Mabuchi K, Nishida M, Nakabo T.

Mol Phylogenet Evol. 2009 Oct;53(1):258-66. doi: 10.1016/j.ympev.2009.06.009. Epub 2009 Jun 18.

PMID:
19540351

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