메뉴 건너뛰기




Volumn 5, Issue 1, 2013, Pages 113-129

Low diversity in the mitogenome of sperm whales revealed by Next-Generation Sequencing

Author keywords

Bayesian phylogenetics; Cetacean; Mitochondrial genome; MtDNA; Nucleotide diversity; Physeter macrocephalus; Population genetics; Substitution rates

Indexed keywords

CETACEA; PHYSETER CATODON; PHYSETERIDAE;

EID: 84876578461     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evs126     Document Type: Article
Times cited : (36)

References (112)
  • 1
    • 0029974748 scopus 로고    scopus 로고
    • Model of amino acid substitution in proteins encoded by mitochondrial DNA
    • Adachi J, Hasegawa M. 1996. Model of amino acid substitution in proteins encoded by mitochondrial DNA. J Mol Evol. 42:459-468.
    • (1996) J Mol Evol. , vol.42 , pp. 459-468
    • Adachi, J.1    Hasegawa, M.2
  • 2
    • 29044448930 scopus 로고    scopus 로고
    • Population differentiation of the Atlantic spotted dolphin (Stenella frontalis) in the western North Atlantic, including the Gulf of Mexico
    • Adams L, Rosel P. 2006. Population differentiation of the Atlantic spotted dolphin (Stenella frontalis) in the western North Atlantic, including the Gulf of Mexico. Mar Biol. 148:671-681.
    • (2006) Mar Biol. , vol.148 , pp. 671-681
    • Adams, L.1    Rosel, P.2
  • 3
    • 35448951703 scopus 로고    scopus 로고
    • DNA evidence for historic population size and past ecosystem impacts of gray whales
    • Alter SE, Rynes E, Palumbi SR. 2007. DNA evidence for historic population size and past ecosystem impacts of gray whales. Proc Natl Acad Sci U S A. 104:15162-15167.
    • (2007) Proc Natl Acad Sci U S A. , vol.104 , pp. 15162-15167
    • Alter, S.E.1    Rynes, E.2    Palumbi, S.R.3
  • 4
    • 0033937019 scopus 로고    scopus 로고
    • The mitochondrial genome of the sperm whale and a new molecular reference for estimating Eutherian divergence dates
    • Arnason U, Gullberg A, Gretarsdottir S, Ursing B, Janke A. 2000. The mitochondrial genome of the sperm whale and a new molecular reference for estimating Eutherian divergence dates. J Mol Evol. 50: 569-578.
    • (2000) J Mol Evol. , vol.50 , pp. 569-578
    • Arnason, U.1    Gullberg, A.2    Gretarsdottir, S.3    Ursing, B.4    Janke, A.5
  • 5
    • 2942529014 scopus 로고    scopus 로고
    • Mitogenomic analyses provide new insights into cetacean origin and evolution
    • Arnason U, Gullberg A, Janke A. 2004. Mitogenomic analyses provide new insights into cetacean origin and evolution. Gene 333:27-34.
    • (2004) Gene , vol.333 , pp. 27-34
    • Arnason, U.1    Gullberg, A.2    Janke, A.3
  • 6
    • 0027296884 scopus 로고
    • Abundant mitochondrial DNA variation and world-wide population structure in humpback whales
    • Baker CS, et al. 1993. Abundant mitochondrial DNA variation and world-wide population structure in humpback whales. Proc Natl Acad Sci U S A. 90:8239-8243.
    • (1993) Proc Natl Acad Sci U S A. , vol.90 , pp. 8239-8243
    • Baker, C.S.1
  • 7
    • 0028483255 scopus 로고
    • Hierarchical structure of mitochondrial DNA gene flow among humpback whales Megaptera novaeangliae, world-wide
    • Baker CS, et al. 1994. Hierarchical structure of mitochondrial DNA gene flow among humpback whales Megaptera novaeangliae, world-wide. Mol Ecol. 3:313-327.
    • (1994) Mol Ecol. , vol.3 , pp. 313-327
    • Baker, C.S.1
  • 8
    • 7144229374 scopus 로고    scopus 로고
    • Population structure of nuclear and mitochondrial DNA variation among humpback whales in the North Pacific
    • Baker CS, et al. 1998. Population structure of nuclear and mitochondrial DNA variation among humpback whales in the North Pacific. Mol Ecol. 7:695-707.
    • (1998) Mol Ecol. , vol.7 , pp. 695-707
    • Baker, C.S.1
  • 9
    • 0035546158 scopus 로고    scopus 로고
    • The mitochondrial genome: Mutation, selection and recombination
    • Ballard JWO, Dean MD. 2001. The mitochondrial genome: mutation, selection and recombination. Curr Opin Genet Dev. 11:667-672.
    • (2001) Curr Opin Genet Dev. , vol.11 , pp. 667-672
    • Ballard, J.W.O.1    Dean, M.D.2
  • 10
    • 77956874630 scopus 로고    scopus 로고
    • The influence of glacial epochs and habitat dependence on the diversity and phylogeography of a coastal dolphin species: Lagenorhynchus albirostris
    • Banguera-Hinestroza E, Bjørge A, Reid R, Jepson P, Hoelzel A. 2010. The influence of glacial epochs and habitat dependence on the diversity and phylogeography of a coastal dolphin species: Lagenorhynchus albirostris. Conserv Genet. 11:1823-1836.
    • (2010) Conserv Genet. , vol.11 , pp. 1823-1836
    • Banguera-Hinestroza, E.1    Bjørge, A.2    Reid, R.3    Jepson, P.4    Hoelzel, A.5
  • 11
    • 0032078735 scopus 로고    scopus 로고
    • Population genetic structure of North Atlantic, Mediterranean Sea and Sea of Cortez fin whales, Balaenoptera physalus (Linnaeus 1758): Analysis of mitochondrial and nuclear loci
    • Bérubé M, et al. 1998. Population genetic structure of North Atlantic, Mediterranean Sea and Sea of Cortez fin whales, Balaenoptera physalus (Linnaeus 1758): analysis of mitochondrial and nuclear loci. Mol Ecol. 7:585-599.
    • (1998) Mol Ecol. , vol.7 , pp. 585-599
    • Bérubé, M.1
  • 12
    • 0001727722 scopus 로고
    • Chapter 7: Social organization in sperm whales, Physeter macrocephalus
    • Winn HE, Olla BL, editors. New York: Plenum Press
    • Best PB. 1979. Chapter 7: Social organization in sperm whales, Physeter macrocephalus. In: Winn HE, Olla BL, editors. Behavior of marine animals, Vol. 3. Cetaceans. New York: Plenum Press.
    • (1979) Behavior of Marine Animals, Vol. 3. Cetaceans
    • Best, P.B.1
  • 13
    • 0033921801 scopus 로고    scopus 로고
    • The power of relative rates tests depends on the data
    • Bromham L, Penny D, Rambaut A, Hendy MD. 2000. The power of relative rates tests depends on the data. J Mol Evol. 50:296-301.
    • (2000) J Mol Evol. , vol.50 , pp. 296-301
    • Bromham, L.1    Penny, D.2    Rambaut, A.3    Hendy, M.D.4
  • 15
    • 79959697688 scopus 로고    scopus 로고
    • Population structure and individual movement of southern right whales around New Zealand and Australia
    • Carroll E, et al. 2011. Population structure and individual movement of southern right whales around New Zealand and Australia. Mar Ecol Prog Ser. 432:257-268.
    • (2011) Mar Ecol Prog Ser. , vol.432 , pp. 257-268
    • Carroll, E.1
  • 16
    • 12444340887 scopus 로고    scopus 로고
    • Evidence for male dispersal along the coasts but no migration in pelagic waters in dusky dolphins (Lagenorhynchus obscurus)
    • Cassens I, et al. 2005. Evidence for male dispersal along the coasts but no migration in pelagic waters in dusky dolphins (Lagenorhynchus obscurus). Mol Ecol. 14:107-121.
    • (2005) Mol Ecol. , vol.14 , pp. 107-121
    • Cassens, I.1
  • 18
    • 33846084077 scopus 로고    scopus 로고
    • Small-scale population structure of eastern North Pacific harbour porpoises (Phocoena phocoena) indicated by molecular genetic analyses
    • Chivers SJ, Dizon AE, Gearin PJ, Robertson KM. 2002. Small-scale population structure of eastern North Pacific harbour porpoises (Phocoena phocoena) indicated by molecular genetic analyses. J Cetacean Res Manage. 4:111-122.
    • (2002) J Cetacean Res Manage. , vol.4 , pp. 111-122
    • Chivers, S.J.1    Dizon, A.E.2    Gearin, P.J.3    Robertson, K.M.4
  • 19
    • 25844475165 scopus 로고    scopus 로고
    • Genetic variation of Kogia spp. with preliminary evidence for two species of Kogia sima
    • Chivers SJ, Leduc RG, Robertson KM, Barros NB, Dizon AE. 2005. Genetic variation of Kogia spp. with preliminary evidence for two species of Kogia sima. Mar Mammal Sci. 21:619-634.
    • (2005) Mar Mammal Sci. , vol.21 , pp. 619-634
    • Chivers, S.J.1    Leduc, R.G.2    Robertson, K.M.3    Barros, N.B.4    Dizon, A.E.5
  • 20
    • 35348834906 scopus 로고    scopus 로고
    • Genetic variation and evidence for population structure in eastern North Pacific false killer whales (Pseudorca crassidens)
    • Chivers SJ, et al. 2007. Genetic variation and evidence for population structure in eastern North Pacific false killer whales (Pseudorca crassidens). Can J Zoolog. 85:783-794.
    • (2007) Can J Zoolog. , vol.85 , pp. 783-794
    • Chivers, S.J.1
  • 21
    • 56149096455 scopus 로고    scopus 로고
    • Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology
    • Cronn R, et al. 2008. Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Res. 36:e122.
    • (2008) Nucleic Acids Res. , vol.36
    • Cronn, R.1
  • 22
    • 84876540591 scopus 로고    scopus 로고
    • last accessed January 8, 2012
    • Davies RM. 2009. Custom PERL script [Internet]. Available from: http://seqanswers.com/forums/showthread.php?s= 361b236c525031c8219a97238f053b06&t=5192 (last accessed January 8, 2012).
    • (2009) Custom PERL Script
    • Davies, R.M.1
  • 23
    • 84855870606 scopus 로고    scopus 로고
    • Relaxed clocks and inferences of heterogeneous patterns of nucleotide substitution and divergence time estimates across whales and dolphins (Mammalia: Cetacea)
    • Dornburg A, Brandley MC, McGowen MR, Near TJ. 2012. Relaxed clocks and inferences of heterogeneous patterns of nucleotide substitution and divergence time estimates across whales and dolphins (Mammalia: Cetacea). Mol Biol Evol. 29:721-736.
    • (2012) Mol Biol Evol. , vol.29 , pp. 721-736
    • Dornburg, A.1    Brandley, M.C.2    McGowen, M.R.3    Near, T.J.4
  • 24
    • 38649110663 scopus 로고    scopus 로고
    • BEAST: Bayesian evolutionary analysis by sampling trees
    • Drummond A, Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 7:214.
    • (2007) BMC Evol Biol. , vol.7 , pp. 214
    • Drummond, A.1    Rambaut, A.2
  • 26
    • 17744381574 scopus 로고    scopus 로고
    • Bayesian coalescent inference of past population dynamics frommolecular sequences
    • Drummond AJ, Rambaut A, Shapiro B, Pybus OG. 2005. Bayesian coalescent inference of past population dynamics frommolecular sequences. Mol Biol Evol. 22:1185-1192.
    • (2005) Mol Biol Evol. , vol.22 , pp. 1185-1192
    • Drummond, A.J.1    Rambaut, A.2    Shapiro, B.3    Pybus, O.G.4
  • 27
    • 84858778486 scopus 로고    scopus 로고
    • Mitogenome phylogenetics: The impact of using single regions and partitioning schemes on topology, substitution rate and divergence time estimation
    • Duchêne S, Archer FI, Vilstrup J, Caballero S, Morin PA. 2011. Mitogenome phylogenetics: the impact of using single regions and partitioning schemes on topology, substitution rate and divergence time estimation. PLoS One 6:e27138.
    • (2011) PLoS One , vol.6
    • Duchêne, S.1    Archer, F.I.2    Vilstrup, J.3    Caballero, S.4    Morin, P.A.5
  • 28
    • 43749084099 scopus 로고    scopus 로고
    • Pseudogenes and DNA-based diet analyses: A cautionary tale from a relatively well sampled predator-prey system
    • Dunshea G, et al. 2008. Pseudogenes and DNA-based diet analyses: a cautionary tale from a relatively well sampled predator-prey system. Bull Entomol Res. 98:239-248.
    • (2008) Bull Entomol Res. , vol.98 , pp. 239-248
    • Dunshea, G.1
  • 29
    • 13244255415 scopus 로고    scopus 로고
    • MUSCLE: A multiple sequence alignment method with reduced time and space complexity
    • Edgar R. 2004. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5:113.
    • (2004) BMC Bioinformatics , vol.5 , pp. 113
    • Edgar, R.1
  • 30
    • 70349871296 scopus 로고    scopus 로고
    • Female philopatry in coastal basins and male dispersion across the North Atlantic in a highly mobile marine species, the spermwhale (Physeter macrocephalus)
    • Engelhaupt D, et al. 2009. Female philopatry in coastal basins and male dispersion across the North Atlantic in a highly mobile marine species, the spermwhale (Physeter macrocephalus). Mol Ecol. 18:4193-4205.
    • (2009) Mol Ecol. , vol.18 , pp. 4193-4205
    • Engelhaupt, D.1
  • 31
    • 30144434977 scopus 로고    scopus 로고
    • Genetic differentiation and intraspecific structure of Eastern Tropical Pacific spotted dolphins, Stenella attenuata, revealed by DNA analyses
    • Escorza-Treviño S, Archer F, Rosales M, Lang A, Dizon A. 2005. Genetic differentiation and intraspecific structure of Eastern Tropical Pacific spotted dolphins, Stenella attenuata, revealed by DNA analyses. Conserv Genet. 6:587-600.
    • (2005) Conserv Genet. , vol.6 , pp. 587-600
    • Escorza-Treviño, S.1    Archer, F.2    Rosales, M.3    Lang, A.4    Dizon, A.5
  • 32
    • 0000569073 scopus 로고
    • The retention index and homoplasy excess
    • Farris JS. 1989. The retention index and homoplasy excess. Syst Biol. 38: 406-407.
    • (1989) Syst Biol. , vol.38 , pp. 406-407
    • Farris, J.S.1
  • 34
    • 0035233646 scopus 로고    scopus 로고
    • Optimality of the genetic code with respect to protein stability and amino-Acid frequencies
    • research0049
    • Gilis D, Massar S, Cerf NJ, Rooman M. 2001. Optimality of the genetic code with respect to protein stability and amino-Acid frequencies. Genome Biol. 2:research0049.
    • (2001) Genome Biol. , vol.2
    • Gilis, D.1    Massar, S.2    Cerf, N.J.3    Rooman, M.4
  • 35
    • 45749124657 scopus 로고    scopus 로고
    • TNT, a free program for phylogenetic analysis
    • Goloboff PA, Farris JS, Nixon KC. 2008. TNT, a free program for phylogenetic analysis. Cladistics 24:774-786.
    • (2008) Cladistics , vol.24 , pp. 774-786
    • Goloboff, P.A.1    Farris, J.S.2    Nixon, K.C.3
  • 36
    • 79959467651 scopus 로고    scopus 로고
    • Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study
    • Goto H, et al. 2011. Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study. Genome Biol. 12:R59.
    • (2011) Genome Biol. , vol.12
    • Goto, H.1
  • 37
    • 84864310077 scopus 로고    scopus 로고
    • Genetic differentiation and limited gene flow among fragmented populations of New Zealand endemic Hector's and Maui's dolphins
    • Hamner R, Pichler F, Heimeier D, Constantine R, Baker C. 2012. Genetic differentiation and limited gene flow among fragmented populations of New Zealand endemic Hector's and Maui's dolphins. Conserv Genet. 13:987-1002.
    • (2012) Conserv Genet. , vol.13 , pp. 987-1002
    • Hamner, R.1    Pichler, F.2    Heimeier, D.3    Constantine, R.4    Baker, C.5
  • 38
    • 0037301283 scopus 로고    scopus 로고
    • Phylogeography and population structure of the Dall's porpoise, Phocoenoides dalli, in Japanese waters revealed by mitochondrial DNA
    • Hayano A, Amano M, Miyazaki N. 2003. Phylogeography and population structure of the Dall's porpoise, Phocoenoides dalli, in Japanese waters revealed by mitochondrial DNA. Genes Genet Syst. 78:81-91.
    • (2003) Genes Genet Syst. , vol.78 , pp. 81-91
    • Hayano, A.1    Amano, M.2    Miyazaki, N.3
  • 39
    • 77956087396 scopus 로고    scopus 로고
    • Improved characterisation of among-lineage rate variation in cetacean mitogenomes using codon-partitioned relaxed clocks
    • Ho SYW, Lanfear R. 2010. Improved characterisation of among-lineage rate variation in cetacean mitogenomes using codon-partitioned relaxed clocks. Mitochondr DNA. 21:138-146.
    • (2010) Mitochondr DNA. , vol.21 , pp. 138-146
    • Ho, S.Y.W.1    Lanfear, R.2
  • 40
    • 45449120082 scopus 로고    scopus 로고
    • The effect of inappropriate calibration: Three case studies in molecular ecology
    • Ho SYW, Saarma U, Barnett R, Haile J, Shapiro B. 2008. The effect of inappropriate calibration: three case studies in molecular ecology. PLoS One 3:e1615.
    • (2008) PLoS One , vol.3
    • Syw, H.1    Saarma, U.2    Barnett, R.3    Haile, J.4    Shapiro, B.5
  • 41
    • 0025891192 scopus 로고
    • Evolution of the cetacean mitochondrial D-loop region
    • Hoelzel AR, Hancock JM, Dover GA. 1991. Evolution of the cetacean mitochondrial D-loop region. Mol Biol Evol. 8:475-493.
    • (1991) Mol Biol Evol. , vol.8 , pp. 475-493
    • Hoelzel, A.R.1    Hancock, J.M.2    Dover, G.A.3
  • 42
    • 53149105558 scopus 로고    scopus 로고
    • Low worldwide genetic diversity in the killer whale (Orcinus orca): Implications for demographic history
    • Hoelzel AR, et al. 2002. Low worldwide genetic diversity in the killer whale (Orcinus orca): implications for demographic history. Proc Roy Soc B Biol Sci. 269:1467-1473.
    • (2002) Proc Roy Soc B Biol Sci. , vol.269 , pp. 1467-1473
    • Hoelzel, A.R.1
  • 43
    • 73349099032 scopus 로고    scopus 로고
    • Big and slow: Phylogenetic estimates of molecular evolution in baleen whales (Suborder Mysticeti)
    • Jackson JA, et al. 2009. Big and slow: phylogenetic estimates of molecular evolution in baleen whales (Suborder Mysticeti). Mol Biol Evol. 26: 2427-2440.
    • (2009) Mol Biol Evol. , vol.26 , pp. 2427-2440
    • Jackson, J.A.1
  • 45
    • 34547102483 scopus 로고    scopus 로고
    • Population genetic structure of Bryde's whales (Balaenoptera brydei) at the inter-oceanic and trans-equatorial levels
    • Kanda N, Goto M, Kato H, McPhee M, Pastene L. 2007. Population genetic structure of Bryde's whales (Balaenoptera brydei) at the inter-oceanic and trans-equatorial levels. Conserv Genet. 8:853-864.
    • (2007) Conserv Genet. , vol.8 , pp. 853-864
    • Kanda, N.1    Goto, M.2    Kato, H.3    McPhee, M.4    Pastene, L.5
  • 46
    • 84865476327 scopus 로고    scopus 로고
    • Common misconceptions in molecular ecology: Echoes of the modern synthesis
    • Karl SA, Toonen RJ, Grant WS, Bowen BW. 2012. Common misconceptions in molecular ecology: echoes of the modern synthesis. Mol Ecol. 21:4171-4189.
    • (2012) Mol Ecol. , vol.21 , pp. 4171-4189
    • Karl, S.A.1    Toonen, R.J.2    Grant, W.S.3    Bowen, B.W.4
  • 47
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
    • Kimura M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 16:111-120.
    • (1980) J Mol Evol. , vol.16 , pp. 111-120
    • Kimura, M.1
  • 48
    • 77952734936 scopus 로고    scopus 로고
    • High-throughput DNA sequencing - Concepts and limitations
    • Kircher M, Kelso J. 2010. High-throughput DNA sequencing - concepts and limitations. BioEssays 32:524-536.
    • (2010) BioEssays , vol.32 , pp. 524-536
    • Kircher, M.1    Kelso, J.2
  • 49
    • 84963036271 scopus 로고
    • Quantitative phyletics and the evolution of Anurans
    • Kluge AG, Farris JS. 1969. Quantitative phyletics and the evolution of Anurans. Syst Biol. 18:1-32.
    • (1969) Syst Biol. , vol.18 , pp. 1-32
    • Kluge, A.G.1    Farris, J.S.2
  • 50
    • 79954599493 scopus 로고    scopus 로고
    • Mitochondrial genome sequences illuminate maternal lineages of conservation concern in a rare carnivore
    • Knaus BJ, Cronn R, Liston A, Pilgrim K, Schwartz MK. 2011. Mitochondrial genome sequences illuminate maternal lineages of conservation concern in a rare carnivore. BMC Ecol. 11:10.
    • (2011) BMC Ecol. , vol.11 , pp. 10
    • Knaus, B.J.1    Cronn, R.2    Liston, A.3    Pilgrim, K.4    Schwartz, M.K.5
  • 51
    • 0031897566 scopus 로고    scopus 로고
    • The physiological basis of diving to depth: Birds and mammals
    • Kooyman GL, Ponganis PJ. 1998. The physiological basis of diving to depth: birds and mammals. Annu Rev Physiol. 60:19-32.
    • (1998) Annu Rev Physiol. , vol.60 , pp. 19-32
    • Kooyman, G.L.1    Ponganis, P.J.2
  • 52
    • 0347900646 scopus 로고    scopus 로고
    • Population structure in an inshore cetacean revealed by microsatellite and mtDNA analysis: Bottlenose dolphins (Tursiops sp.) in Shark Bay,Western Australia
    • Krützen M, Sherwin WB, Berggren P, Gales N. 2004. Population structure in an inshore cetacean revealed by microsatellite and mtDNA analysis: bottlenose dolphins (Tursiops sp.) in Shark Bay,Western Australia.Mar Mammal Sci. 20:28-47.
    • (2004) Mar Mammal Sci. , vol.20 , pp. 28-47
    • Krützen, M.1    Sherwin, W.B.2    Berggren, P.3    Gales, N.4
  • 53
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 54
    • 55549097836 scopus 로고    scopus 로고
    • Mapping short DNA sequencing reads and calling variants using mapping quality scores
    • Li H, Ruan J, Durbin R. 2008. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18: 1851-1858.
    • (2008) Genome Res. , vol.18 , pp. 1851-1858
    • Li, H.1    Ruan, J.2    Durbin, R.3
  • 55
    • 68549104404 scopus 로고    scopus 로고
    • The sequence alignment/map format and SAMtools
    • Li H, et al. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25:2078-2079.
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1
  • 56
    • 84867487186 scopus 로고    scopus 로고
    • Fidelity of captureenrichment for mtDNA genome sequencing: Influence of NUMTs
    • Li M, Schroeder R, Ko A, Stoneking M. 2012. Fidelity of captureenrichment for mtDNA genome sequencing: influence of NUMTs. Nucleic Acids Res. 40:e137.
    • (2012) Nucleic Acids Res. , vol.40
    • Li, M.1    Schroeder, R.2    Ko, A.3    Stoneking, M.4
  • 57
    • 77955562856 scopus 로고    scopus 로고
    • Detecting heteroplasmy from high-throughput sequencing of complete human mitochondrial DNA genomes
    • Li M, et al. 2010. Detecting heteroplasmy from high-throughput sequencing of complete human mitochondrial DNA genomes. Am J Hum Genet. 87:237-249.
    • (2010) Am J Hum Genet. , vol.87 , pp. 237-249
    • Li, M.1
  • 58
    • 79960617975 scopus 로고    scopus 로고
    • Analysis of global and local population stratification of finless porpoises Neophocaena phocaenoides in Chinese waters
    • Li X, et al. 2011. Analysis of global and local population stratification of finless porpoises Neophocaena phocaenoides in Chinese waters. Mar Biol. 158:1791-1804.
    • (2011) Mar Biol. , vol.158 , pp. 1791-1804
    • Li, X.1
  • 59
    • 0032494132 scopus 로고    scopus 로고
    • Global matrilineal population structure in sperm whales as indicated by mitochondrial DNA sequences
    • Lyrholm T, Gyllensten U. 1998. Global matrilineal population structure in sperm whales as indicated by mitochondrial DNA sequences. Proc Roy Soc B Biol Sci. 265:1679-1684.
    • (1998) Proc Roy Soc B Biol Sci. , vol.265 , pp. 1679-1684
    • Lyrholm, T.1    Gyllensten, U.2
  • 60
    • 0029908931 scopus 로고    scopus 로고
    • Low diversity and biased substitution patterns in the mitochondrial DNA control region of sperm whales: Implications for estimates of time since common ancestry
    • Lyrholm T, Leimar O, Gyllensten U. 1996. Low diversity and biased substitution patterns in the mitochondrial DNA control region of sperm whales: implications for estimates of time since common ancestry. Mol Biol Evol. 13:1318-1326.
    • (1996) Mol Biol Evol. , vol.13 , pp. 1318-1326
    • Lyrholm, T.1    Leimar, O.2    Gyllensten, U.3
  • 62
    • 84863509618 scopus 로고    scopus 로고
    • Population structure of island-Associated dolphins: Evidence from mitochondrial and microsatellite markers for common bottlenose dolphins (Tursiops truncatus) around the main Hawaiian Islands
    • Martien KK, et al. 2012. Population structure of island-Associated dolphins: evidence from mitochondrial and microsatellite markers for common bottlenose dolphins (Tursiops truncatus) around the main Hawaiian Islands. Mar Mammal Sci. 28:E208-E232.
    • (2012) Mar Mammal Sci. , vol.28
    • Martien, K.K.1
  • 63
    • 0027308854 scopus 로고
    • Body size, metabolic rate, generation time, and the molecular clock
    • Martin AP, Palumbi SR. 1993. Body size, metabolic rate, generation time, and the molecular clock. Proc Natl Acad Sci U S A. 90:4087-4091.
    • (1993) Proc Natl Acad Sci U S A. , vol.90 , pp. 4087-4091
    • Martin, A.P.1    Palumbi, S.R.2
  • 64
    • 79951759000 scopus 로고    scopus 로고
    • Sperm whale population structure in the eastern and central North Pacific inferred by the use of single-nucleotide polymorphisms, microsatellites and mitochondrial DNA
    • Mesnick SL, et al. 2011. Sperm whale population structure in the eastern and central North Pacific inferred by the use of single-nucleotide polymorphisms, microsatellites and mitochondrial DNA. Mol Ecol Resour. 11:278-298.
    • (2011) Mol Ecol Resour. , vol.11 , pp. 278-298
    • Mesnick, S.L.1
  • 65
    • 67349089526 scopus 로고    scopus 로고
    • Population structure of short-beaked common dolphins (Delphinus delphis) in the North Atlantic Ocean as revealed by mitochondrial and nuclear genetic markers
    • Mirimin L, et al. 2009. Population structure of short-beaked common dolphins (Delphinus delphis) in the North Atlantic Ocean as revealed by mitochondrial and nuclear genetic markers. Mar Biol. 156:821-834.
    • (2009) Mar Biol. , vol.156 , pp. 821-834
    • Mirimin, L.1
  • 66
    • 77954236362 scopus 로고    scopus 로고
    • Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species
    • Morin PA, et al. 2010. Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species. Genome Res. 20:908-916.
    • (2010) Genome Res. , vol.20 , pp. 908-916
    • Morin, P.A.1
  • 67
    • 34249083225 scopus 로고    scopus 로고
    • Comment on "population size does not influence mitochondrial genetic diversity in animals."
    • Mulligan CJ, Kitchen A, Miyamoto MM. 2006. Comment on "Population size does not influence mitochondrial genetic diversity in animals." Science 314:1390.
    • (2006) Science , vol.314 , pp. 1390
    • Mulligan, C.J.1    Kitchen, A.2    Miyamoto, M.M.3
  • 68
    • 38349192060 scopus 로고    scopus 로고
    • Strong variations of mitochondrial mutation rate across mammals - The longevity hypothesis
    • Nabholz B, Glémin S, Galtier N. 2008. Strong variations of mitochondrial mutation rate across mammals - the longevity hypothesis. Mol Biol Evol. 25:120-130.
    • (2008) Mol Biol Evol. , vol.25 , pp. 120-130
    • Nabholz, B.1    Glémin, S.2    Galtier, N.3
  • 69
    • 77956227293 scopus 로고    scopus 로고
    • Obtaining mtDNA genomes from next-generation transcriptome sequencing: A case study on the basal Passerida (Aves: Passeriformes) phylogeny
    • Nabholz B, Jarvis ED, Ellegren H. 2010. Obtaining mtDNA genomes from next-generation transcriptome sequencing: a case study on the basal Passerida (Aves: Passeriformes) phylogeny. Mol Phylogenet Evol. 57: 466-470.
    • (2010) Mol Phylogenet Evol. , vol.57 , pp. 466-470
    • Nabholz, B.1    Jarvis, E.D.2    Ellegren, H.3
  • 70
    • 24044458933 scopus 로고    scopus 로고
    • Habitat structure and the dispersal of male and female bottlenose dolphins (Tursiops truncatus)
    • Natoli A, Birkun A, Aguilar A, Lopez A, Hoelzel AR. 2005. Habitat structure and the dispersal of male and female bottlenose dolphins (Tursiops truncatus). Proc Roy Soc B Biol Sci. 272:1217-1226.
    • (2005) Proc Roy Soc B Biol Sci. , vol.272 , pp. 1217-1226
    • Natoli, A.1    Birkun, A.2    Aguilar, A.3    Lopez, A.4    Hoelzel, A.R.5
  • 71
    • 0030609728 scopus 로고    scopus 로고
    • Phylogeography, population structure and dispersal patterns of the beluga whale Delphinapterus leucas in the western Nearctic revealed by mitochondrial DNA
    • O'Corry-Crowe GM, Suydam RS, Rosenberg A, Frost KJ, Dizon AE. 1997. Phylogeography, population structure and dispersal patterns of the beluga whale Delphinapterus leucas in the western Nearctic revealed by mitochondrial DNA. Mol Ecol. 6:955-970.
    • (1997) Mol Ecol. , vol.6 , pp. 955-970
    • O'corry-Crowe, G.M.1    Suydam, R.S.2    Rosenberg, A.3    Frost, K.J.4    Dizon, A.E.5
  • 72
    • 70450245152 scopus 로고    scopus 로고
    • Worldwide mitochondrial DNA diversity and phylogeography of pilot whales (Globicephala spp.)
    • Oremus M, et al. 2009. Worldwide mitochondrial DNA diversity and phylogeography of pilot whales (Globicephala spp.). Biol J Linn Soc. 98: 729-744.
    • (2009) Biol J Linn Soc. , vol.98 , pp. 729-744
    • Oremus, M.1
  • 74
    • 0029140814 scopus 로고
    • Distribution of mtDNA haplotypes in North Atlantic humpbackwhales: The influence of behaviour on population structure
    • Palsbøll PJ, et al. 1995. Distribution ofmtDNA haplotypes in North Atlantic humpbackwhales: the influence of behaviour on population structure. Mar Ecol Prog Ser. 116:1-10.
    • (1995) Mar Ecol Prog Ser. , vol.116 , pp. 1-10
    • Palsbøll, P.J.1
  • 75
    • 33947507089 scopus 로고    scopus 로고
    • Radiation and speciation of pelagic organisms during periods of global warming: The case of the common minke whale, Balaenoptera acutorostrata
    • Pastene LA, et al. 2007. Radiation and speciation of pelagic organisms during periods of global warming: the case of the common minke whale, Balaenoptera acutorostrata. Mol Ecol. 16:1481-1495.
    • (2007) Mol Ecol. , vol.16 , pp. 1481-1495
    • Pastene, L.A.1
  • 76
  • 77
    • 0031834549 scopus 로고    scopus 로고
    • Geographic isolation of Hector's dolphin populations described by mitochondrial DNA sequences
    • Pichler FB, Dawson SM, Slooten E, Baker CS. 1998. Geographic isolation of Hector's dolphin populations described by mitochondrial DNA sequences. Conserv Biol. 12:676-682.
    • (1998) Conserv Biol. , vol.12 , pp. 676-682
    • Pichler, F.B.1    Dawson, S.M.2    Slooten, E.3    Baker, C.S.4
  • 78
    • 78049449073 scopus 로고    scopus 로고
    • Mitochondrial DNA variation and population structure of Commerson's dolphins (Cephalorhynchus commersonii) in their southernmost distribution
    • Pimper L, Baker C, Goodall R, Olavarría C, Remis M. 2010. Mitochondrial DNA variation and population structure of Commerson's dolphins (Cephalorhynchus commersonii) in their southernmost distribution. Conserv Genet. 11:2157-2168.
    • (2010) Conserv Genet. , vol.11 , pp. 2157-2168
    • Pimper, L.1    Baker, C.2    Goodall, R.3    Olavarría, C.4    Remis, M.5
  • 79
    • 77958024501 scopus 로고    scopus 로고
    • Molecular insight into the population structure of common and spotted dolphins inhabiting the pelagic waters of the Northeast Atlantic
    • Quérouil S, et al. 2010. Molecular insight into the population structure of common and spotted dolphins inhabiting the pelagic waters of the Northeast Atlantic. Mar Biol. 157:2567-2580.
    • (2010) Mar Biol. , vol.157 , pp. 2567-2580
    • Quérouil, S.1
  • 80
    • 85049365821 scopus 로고    scopus 로고
    • Last Accessed January 8, 2012)
    • Rambaut A. 2009. FigTree [Internet]. Available from: http://tree.bio.ed. ac.uk/software/figtree/ (last accessed January 8, 2012).
    • (2009) FigTree [Internet]
    • Rambaut, A.1
  • 81
    • 5344230543 scopus 로고    scopus 로고
    • last accessed January 8, 2012
    • Rambaut A, Drummond A. 2007. Tracer v1.4 [Internet]. Available from: http://beast.bio.ed.ac.uk/Tracer (last accessed January 8, 2012).
    • (2007) Tracer v1.4 [Internet]
    • Rambaut, A.1    Drummond, A.2
  • 82
    • 84860681765 scopus 로고    scopus 로고
    • Can genetic differences explain vocal dialect variation in sperm whales, Physeter macrocephalus?
    • Rendell L, Mesnick S, Dalebout M, Burtenshaw J, Whitehead H. 2012. Can genetic differences explain vocal dialect variation in sperm whales, Physeter macrocephalus? Behav Genet, 42:332-343.
    • (2012) Behav Genet , vol.42 , pp. 332-343
    • Rendell, L.1    Mesnick, S.2    Dalebout, M.3    Burtenshaw, J.4    Whitehead, H.5
  • 83
    • 0029757969 scopus 로고    scopus 로고
    • Patterns of kinship in groups of free-living sperm whales (Physeter macrocephalus) revealed by multiple molecular genetic analyses
    • Richard KR, Dillon MC, Whitehead H, Wright JM. 1996. Patterns of kinship in groups of free-living sperm whales (Physeter macrocephalus) revealed by multiple molecular genetic analyses. Proc Natl Acad Sci U S A. 93:8792-8795.
    • (1996) Proc Natl Acad Sci U S A. , vol.93 , pp. 8792-8795
    • Richard, K.R.1    Dillon, M.C.2    Whitehead, H.3    Wright, J.M.4
  • 84
    • 2442637641 scopus 로고    scopus 로고
    • NUMTs in sequenced eukaryotic genomes
    • Richly E, Leister D. 2004. NUMTs in sequenced eukaryotic genomes. Mol Biol Evol. 21:1081-1084.
    • (2004) Mol Biol Evol. , vol.21 , pp. 1081-1084
    • Richly, E.1    Leister, D.2
  • 85
    • 0035214467 scopus 로고    scopus 로고
    • Understanding patterns of genetic diversity in the oak gallwasp Biorhiza pallida: Demographic history or a Wolbachia selective sweep?
    • Rokas A, Atkinson RJ, Brown GS, West SA, Stone GN. 2001. Understanding patterns of genetic diversity in the oak gallwasp Biorhiza pallida: demographic history or a Wolbachia selective sweep? Heredity 87:294-304.
    • (2001) Heredity , vol.87 , pp. 294-304
    • Rokas, A.1    Atkinson, R.J.2    Brown, G.S.3    West, S.A.4    Stone, G.N.5
  • 86
    • 0034800521 scopus 로고    scopus 로고
    • Historical population size change of bowhead whales inferred from DNA sequence polymorphism data
    • Rooney AP, Honeycutt RL, Derr JN. 2001. Historical population size change of bowhead whales inferred from DNA sequence polymorphism data. Evolution 55:1678-1685.
    • (2001) Evolution , vol.55 , pp. 1678-1685
    • Rooney, A.P.1    Honeycutt, R.L.2    Derr, J.N.3
  • 87
    • 0033369949 scopus 로고    scopus 로고
    • Genetic structure of harbour porpoise Phocoena phocoena populations in the northwest Atlantic based on mitochondrial and nuclear markers
    • Rosel PE, France SC, Wang JY, Kocher TD. 1999. Genetic structure of harbour porpoise Phocoena phocoena populations in the northwest Atlantic based on mitochondrial and nuclear markers. Mol Ecol. 8: S41-S54.
    • (1999) Mol Ecol. , vol.8
    • Rosel, P.E.1    France, S.C.2    Wang, J.Y.3    Kocher, T.D.4
  • 88
    • 77949326296 scopus 로고    scopus 로고
    • Population structure of humpback whales from their breeding grounds in the South Atlantic and Indian Oceans
    • Rosenbaum HC, et al. 2009. Population structure of humpback whales from their breeding grounds in the South Atlantic and Indian Oceans. PLoS One 4:e7318.
    • (2009) PLoS One , vol.4
    • Rosenbaum, H.C.1
  • 90
    • 75649095276 scopus 로고    scopus 로고
    • A SNP discovery method to assess variant allele probability from next-generation resequencing data
    • Shen Y, et al. 2010. A SNP discovery method to assess variant allele probability from next-generation resequencing data. Genome Res. 20: 273-280.
    • (2010) Genome Res. , vol.20 , pp. 273-280
    • Shen, Y.1
  • 91
    • 84876526312 scopus 로고    scopus 로고
    • last accessed August 10, 2012
    • Siddall ME. 2012. ild.run [Internet]. Available from: http://tnt.insectmuseum.org/index.php/Scripts/ild.run (last accessed August 10, 2012).
    • (2012) Ild.run [Internet]
    • Siddall, M.E.1
  • 92
    • 53549085971 scopus 로고    scopus 로고
    • Rapid whole-genome mutational profiling using next-generation sequencing technologies
    • Smith DR, et al. 2008. Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Res. 18: 1638-1642.
    • (2008) Genome Res. , vol.18 , pp. 1638-1642
    • Smith, D.R.1
  • 93
    • 0031884718 scopus 로고    scopus 로고
    • Numts: A challenge for avian systematics and population biology
    • Sorenson MD, Quinn TW. 1998. Numts: a challenge for avian systematics and population biology. Auk 115:214-221.
    • (1998) Auk , vol.115 , pp. 214-221
    • Sorenson, M.D.1    Quinn, T.W.2
  • 94
    • 84868093500 scopus 로고    scopus 로고
    • Next-generation sequencing of human mitochondrial reference genomes uncovers high heteroplasmy frequency
    • Sosa MX, et al. 2012. Next-generation sequencing of human mitochondrial reference genomes uncovers high heteroplasmy frequency. PLoS Comput Biol. 8:e1002737.
    • (2012) PLoS Comput Biol. , vol.8
    • Sosa, M.X.1
  • 95
    • 84857844300 scopus 로고    scopus 로고
    • Circumpolar diversity and geographic differentiation of mtDNA in the critically endangered Antarctic Blue whale (Balaenoptera musculus intermedia)
    • Sremba AL, Hancock-Hanser B, Branch TA, LeDuc RL, Baker CS. 2012. Circumpolar diversity and geographic differentiation of mtDNA in the critically endangered Antarctic Blue whale (Balaenoptera musculus intermedia). PLoS One 7:e32579.
    • (2012) PLoS One , vol.7
    • Sremba, A.L.1    Hancock-Hanser, B.2    Branch, T.A.3    Le Duc, R.L.4    Baker, C.S.5
  • 96
    • 72949086467 scopus 로고    scopus 로고
    • Radiation of extant cetaceans driven by restructuring of the oceans
    • Steeman ME, et al. 2009. Radiation of extant cetaceans driven by restructuring of the oceans. Syst Biol. 58:573-585.
    • (2009) Syst Biol. , vol.58 , pp. 573-585
    • Steeman, M.E.1
  • 97
    • 38949091096 scopus 로고    scopus 로고
    • Strong purifying selection in transmission of mammalian mitochondrial DNA
    • Stewart JB, et al. 2008. Strong purifying selection in transmission of mammalian mitochondrial DNA. PLoS Biol. 6:e10.
    • (2008) PLoS Biol. , vol.6
    • Stewart, J.B.1
  • 98
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
    • Tamura K, et al. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 28:2731-2739.
    • (2011) Mol Biol Evol. , vol.28 , pp. 2731-2739
    • Tamura, K.1
  • 99
    • 0942267968 scopus 로고    scopus 로고
    • Unreliable mtDNA data due to nuclear insertions: A cautionary tale from analysis of humans and other great apes
    • Thalmann O, Hebler J, Poinar HN, Pääbo S, Vigilant L. 2004. Unreliable mtDNA data due to nuclear insertions: a cautionary tale from analysis of humans and other great apes. Mol Ecol. 13:321-335.
    • (2004) Mol Ecol. , vol.13 , pp. 321-335
    • Thalmann, O.1    Hebler, J.2    Poinar, H.N.3    Pääbo, S.4    Vigilant, L.5
  • 100
    • 84868551416 scopus 로고    scopus 로고
    • A novel conservation approach provides insights into the management of rare cetaceans
    • Thompson KF, et al. 2013. A novel conservation approach provides insights into the management of rare cetaceans. Biol Conserv 157: 331-340.
    • (2013) Biol Conserv , vol.157 , pp. 331-340
    • Thompson, K.F.1
  • 101
    • 0004380039 scopus 로고    scopus 로고
    • Culture and genetic evolution in whales
    • Tiedemann R, Milinkovitch MC. 1999. Culture and genetic evolution in whales. Science 284:2055.
    • (1999) Science , vol.284 , pp. 2055
    • Tiedemann, R.1    Milinkovitch, M.C.2
  • 102
    • 79952327781 scopus 로고    scopus 로고
    • Mitogenomic phylogenetic analyses of the Delphinidae with an emphasis on the Globicephalinae
    • Vilstrup J, et al. 2011. Mitogenomic phylogenetic analyses of the Delphinidae with an emphasis on the Globicephalinae. BMC Evol Biol. 11:65.
    • (2011) BMC Evol Biol. , vol.11 , pp. 65
    • Vilstrup, J.1
  • 105
    • 0032573511 scopus 로고    scopus 로고
    • Cultural selection and genetic diversity in matrilineal whales
    • Whitehead H. 1998. Cultural selection and genetic diversity in matrilineal whales. Science 282:1708-1711.
    • (1998) Science , vol.282 , pp. 1708-1711
    • Whitehead, H.1
  • 106
    • 0037175221 scopus 로고    scopus 로고
    • Estimates of the current global population size and historical trajectory for sperm whales
    • Whitehead H. 2002. Estimates of the current global population size and historical trajectory for sperm whales. Mar Ecol Prog Ser. 242: 295-304.
    • (2002) Mar Ecol Prog Ser. , vol.242 , pp. 295-304
    • Whitehead, H.1
  • 108
    • 12244312802 scopus 로고    scopus 로고
    • Genetic diversity in the matrilineal whales: Models of cultural hitchhiking and group-specific non-heritable demographic variation
    • Whitehead H. 2005. Genetic diversity in the matrilineal whales: models of cultural hitchhiking and group-specific non-heritable demographic variation. Mar Mammal Sci. 21:58-79.
    • (2005) Mar Mammal Sci. , vol.21 , pp. 58-79
    • Whitehead, H.1
  • 109
    • 0031457657 scopus 로고    scopus 로고
    • Past and distant whaling and the rapid decline of sperm whales off the Galápagos Islands
    • Whitehead H, Christal J, Dufault S. 1997. Past and distant whaling and the rapid decline of sperm whales off the Galápagos Islands. Conserv Biol. 11:1387-1396.
    • (1997) Conserv Biol. , vol.11 , pp. 1387-1396
    • Whitehead, H.1    Christal, J.2    Dufault, S.3
  • 110
    • 0031978794 scopus 로고    scopus 로고
    • Non-geographically based population structure of South Pacific sperm whales: Dialects, fluke-markings and genetics
    • Whitehead H, Dillon M, Dufault S, Weilgart L, Wright J. 1998. Non-geographically based population structure of South Pacific sperm whales: dialects, fluke-markings and genetics. J Anim Ecol. 67:253-262.
    • (1998) J Anim Ecol. , vol.67 , pp. 253-262
    • Whitehead, H.1    Dillon, M.2    Dufault, S.3    Weilgart, L.4    Wright, J.5
  • 111
    • 52649096387 scopus 로고    scopus 로고
    • Mitochondrial phylogeography and population history of finless porpoises in Sino-Japanese waters
    • Yang G, Guo LI, Bruford MW, Wei F, Zhou K. 2008. Mitochondrial phylogeography and population history of finless porpoises in Sino-Japanese waters. Bio J Linn Soc. 95:193-204.
    • (2008) Bio J Linn Soc. , vol.95 , pp. 193-204
    • Yang, G.1    Guo, L.I.2    Bruford, M.W.3    Wei, F.4    Zhou, K.5
  • 112
    • 0000387373 scopus 로고    scopus 로고
    • Nuclear integrations: Challenges for mitochondrial DNA markers
    • Zhang D-X, Hewitt GM. 1996. Nuclear integrations: challenges for mitochondrial DNA markers. Trends Ecol Evol. 11:247-251.
    • (1996) Trends Ecol Evol. , vol.11 , pp. 247-251
    • Zhang, D.-X.1    Hewitt, G.M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.