-
1
-
-
0033561361
-
Animal mitochondrial genomes
-
Boore JL, (1999) Animal mitochondrial genomes. Nucleic Acids Res 27: 1767-1780.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 1767-1780
-
-
Boore, J.L.1
-
2
-
-
27744526687
-
Origin, evolution and genetic effects of nuclear insertions of organelle DNA
-
Leister D, (2005) Origin, evolution and genetic effects of nuclear insertions of organelle DNA. Trends Genet 21: 655-663.
-
(2005)
Trends Genet
, vol.21
, pp. 655-663
-
-
Leister, D.1
-
3
-
-
0035358999
-
Mitochondrial pseudogenes: evolution's misplaced witnesses
-
Bensasson D, Zhang D, Hartl DL, Hewitt GM, (2001a) Mitochondrial pseudogenes: evolution's misplaced witnesses. Trends Ecol Evol 16: 314-321.
-
(2001)
Trends Ecol Evol
, vol.16
, pp. 314-321
-
-
Bensasson, D.1
Zhang, D.2
Hartl, D.L.3
Hewitt, G.M.4
-
4
-
-
77649210966
-
Molecular poltergeists: mitochondrial DNA copies (numts) in sequenced nuclear genomes
-
Hazkani-Covo E, Zeller RM, Martin W, (2010) Molecular poltergeists: mitochondrial DNA copies (numts) in sequenced nuclear genomes. PLoS Genet 6: e1000834.
-
(2010)
PLoS Genet
, vol.6
-
-
Hazkani-Covo, E.1
Zeller, R.M.2
Martin, W.3
-
5
-
-
0028363062
-
Numt, a recent transfer and tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat
-
Lopez JV, Yuhki N, Masuda R, Modi W, O'Brien SJ, (1994) Numt, a recent transfer and tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat. J Mol Evol 39: 174-190.
-
(1994)
J Mol Evol
, vol.39
, pp. 174-190
-
-
Lopez, J.V.1
Yuhki, N.2
Masuda, R.3
Modi, W.4
O'Brien, S.J.5
-
6
-
-
0037309706
-
Evolutionary dynamics of large numts in the human genome: rarity of independent insertions and abundance of post-insertion duplications
-
Hazkani-Covo E, Sorek R, Graur D, (2003) Evolutionary dynamics of large numts in the human genome: rarity of independent insertions and abundance of post-insertion duplications. J Mol Evol 56: 169-174.
-
(2003)
J Mol Evol
, vol.56
, pp. 169-174
-
-
Hazkani-Covo, E.1
Sorek, R.2
Graur, D.3
-
7
-
-
36549008558
-
Nuclear insertions of organellar DNA can create novel patches of functional exon sequences
-
Noutsos C, Kleine T, Armbruster U, DalCorso G, Leister D, (2007) Nuclear insertions of organellar DNA can create novel patches of functional exon sequences. Trends Genet 23: 597-601.
-
(2007)
Trends Genet
, vol.23
, pp. 597-601
-
-
Noutsos, C.1
Kleine, T.2
Armbruster, U.3
DalCorso, G.4
Leister, D.5
-
8
-
-
0043197403
-
Rates of DNA duplication and mitochondrial DNA insertion in the human genome
-
Bensasson D, Feldman MW, Petrov DA, (2003) Rates of DNA duplication and mitochondrial DNA insertion in the human genome. J Mol Evol 57: 343-354.
-
(2003)
J Mol Evol
, vol.57
, pp. 343-354
-
-
Bensasson, D.1
Feldman, M.W.2
Petrov, D.A.3
-
9
-
-
33845907665
-
A comparative analysis of numt evolution in human and chimpanzee
-
Hazkani-Covo E, Graur D, (2007) A comparative analysis of numt evolution in human and chimpanzee. Mol Biol Evol 24: 13-18.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 13-18
-
-
Hazkani-Covo, E.1
Graur, D.2
-
10
-
-
0034882969
-
The Human Genome Project reveals a continuous transfer of large mitochondrial fragments to the nucleus
-
Mourier T, Hansen AJ, Willerslev E, Arctander P, (2001) The Human Genome Project reveals a continuous transfer of large mitochondrial fragments to the nucleus. Mol Biol Evol 18: 1833-1837.
-
(2001)
Mol Biol Evol
, vol.18
, pp. 1833-1837
-
-
Mourier, T.1
Hansen, A.J.2
Willerslev, E.3
Arctander, P.4
-
11
-
-
70449379045
-
Genome sequence, comparative analysis, and population genetics of the domestic horse
-
Wade CM, Giulotto E, Sigurdsson S, Zoli M, Gnerre S, et al. (2009) Genome sequence, comparative analysis, and population genetics of the domestic horse. Science 326: 865-867.
-
(2009)
Science
, vol.326
, pp. 865-867
-
-
Wade, C.M.1
Giulotto, E.2
Sigurdsson, S.3
Zoli, M.4
Gnerre, S.5
-
12
-
-
78449284241
-
Mitochondrial DNA insertions in the nuclear horse genome
-
Nergadze SG, Lupotto M, Pellanda P, Santagostino M, Vitelli V, et al. (2010) Mitochondrial DNA insertions in the nuclear horse genome. Anim Genet 41 (Suppl 2): 176-185.
-
(2010)
Anim Genet
, vol.41
, Issue.SUPPL. 2
, pp. 176-185
-
-
Nergadze, S.G.1
Lupotto, M.2
Pellanda, P.3
Santagostino, M.4
Vitelli, V.5
-
13
-
-
0035222174
-
Nucleotide substitutions and the evolution of duplicate genes
-
Conery JS, Lynch M, (2001) Nucleotide substitutions and the evolution of duplicate genes. Pac Symp Biocomput pp. 167-178.
-
(2001)
Pac Symp Biocomput
, pp. 167-178
-
-
Conery, J.S.1
Lynch, M.2
-
14
-
-
0034634395
-
The evolutionary fate and consequences of duplicate genes
-
Lynch M, Conery JS, (2000) The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155.
-
(2000)
Science
, vol.290
, pp. 1151-1155
-
-
Lynch, M.1
Conery, J.S.2
-
15
-
-
0031891484
-
High rate of DNA loss in the Drosophila melanogaster and Drosophila virilis species groups
-
Petrov DA, Hartl DL, (1998) High rate of DNA loss in the Drosophila melanogaster and Drosophila virilis species groups. Mol Biol Evol 15: 293-302.
-
(1998)
Mol Biol Evol
, vol.15
, pp. 293-302
-
-
Petrov, D.A.1
Hartl, D.L.2
-
16
-
-
0024591558
-
On the rate of DNA sequence evolution in Drosophila
-
Sharp PM, Li WH, (1989) On the rate of DNA sequence evolution in Drosophila. J Mol Evol 28: 398-402.
-
(1989)
J Mol Evol
, vol.28
, pp. 398-402
-
-
Sharp, P.M.1
Li, W.H.2
-
17
-
-
0019726330
-
Pseudogenes as a paradigm of neutral evolution
-
Li WH, Gojobori T, Nei M, (1981) Pseudogenes as a paradigm of neutral evolution. Nature 292: 237-239.
-
(1981)
Nature
, vol.292
, pp. 237-239
-
-
Li, W.H.1
Gojobori, T.2
Nei, M.3
-
18
-
-
0345306317
-
Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes
-
Zhang Z, Gerstein M, (2003) Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes. Nucleic Acids Res 31: 5338-5348.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 5338-5348
-
-
Zhang, Z.1
Gerstein, M.2
-
20
-
-
47149117454
-
Evolution of genes and genomes on the Drosophila phylogeny
-
Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, et al. (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-218.
-
(2007)
Nature
, vol.450
, pp. 203-218
-
-
Clark, A.G.1
Eisen, M.B.2
Smith, D.R.3
Bergman, C.M.4
Oliver, B.5
-
21
-
-
2442637641
-
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
-
22
-
-
34548127994
-
Exceptionally high density of NUMTs in the honeybee genome
-
Pamilo P, Viljakainen L, Vihavainen A, (2007) Exceptionally high density of NUMTs in the honeybee genome. Mol Biol Evol 24: 1340-1346.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 1340-1346
-
-
Pamilo, P.1
Viljakainen, L.2
Vihavainen, A.3
-
23
-
-
0036021703
-
DNA loss and evolution of genome size in Drosophila
-
Petrov DA, (2002) DNA loss and evolution of genome size in Drosophila. Genetica 115: 81-91.
-
(2002)
Genetica
, vol.115
, pp. 81-91
-
-
Petrov, D.A.1
-
24
-
-
1842452864
-
Rapid sequence turnover at an intergenic locus in Drosophila
-
Singh ND, Petrov DA, (2004) Rapid sequence turnover at an intergenic locus in Drosophila. Mol Biol Evol 21: 670-680.
-
(2004)
Mol Biol Evol
, vol.21
, pp. 670-680
-
-
Singh, N.D.1
Petrov, D.A.2
-
25
-
-
50249101192
-
Potential gene flow in natural populations of the Drosophila ananassae species cluster inferred from a nuclear mitochondrial pseudogene
-
Sawamura K, Koganebuchi K, Sato H, Kamiya K, Matsuda M, et al. (2008) Potential gene flow in natural populations of the Drosophila ananassae species cluster inferred from a nuclear mitochondrial pseudogene. Mol Phylogenet Evol 48: 1087-1093.
-
(2008)
Mol Phylogenet Evol
, vol.48
, pp. 1087-1093
-
-
Sawamura, K.1
Koganebuchi, K.2
Sato, H.3
Kamiya, K.4
Matsuda, M.5
-
26
-
-
34547657301
-
Analysis of nuclear copies of mitochondrial sequences in honeybee (Apis mellifera) genome
-
Behura SK, (2007) Analysis of nuclear copies of mitochondrial sequences in honeybee (Apis mellifera) genome. Mol Biol Evol 24: 1492-1505.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 1492-1505
-
-
Behura, S.K.1
-
27
-
-
70649104995
-
-
Accessed 2006 Sep 21
-
Gish W, (1996-2004) WUBlast 2.0MP. http://blast.wustl.edu. Accessed 2006 Sep 21.
-
(1996)
WUBlast 2.0MP
-
-
Gish, W.1
-
28
-
-
67650340725
-
Comparative genomics of Drosophila mtDNA: Novel features of conservation and change across functional domains and lineages
-
Montooth KL, Abt DN, Hofmann JW, Rand DM, (2009) Comparative genomics of Drosophila mtDNA: Novel features of conservation and change across functional domains and lineages. J Mol Evol 69: 94-114.
-
(2009)
J Mol Evol
, vol.69
, pp. 94-114
-
-
Montooth, K.L.1
Abt, D.N.2
Hofmann, J.W.3
Rand, D.M.4
-
29
-
-
0029901640
-
Analysis of compositionally biased regions in sequence databases
-
Wootton JC, Federhen S, (1996) Analysis of compositionally biased regions in sequence databases. Methods Enzymol 266: 554-571.
-
(1996)
Methods Enzymol
, vol.266
, pp. 554-571
-
-
Wootton, J.C.1
Federhen, S.2
-
30
-
-
0028269905
-
Sequence, organization, and evolution of the A+T region of Drosophila melanogaster mitochondrial DNA
-
Lewis DL, Farr CL, Farquhar AL, Kaguni LS, (1994) Sequence, organization, and evolution of the A+T region of Drosophila melanogaster mitochondrial DNA. Mol Biol Evol 11: 523-538.
-
(1994)
Mol Biol Evol
, vol.11
, pp. 523-538
-
-
Lewis, D.L.1
Farr, C.L.2
Farquhar, A.L.3
Kaguni, L.S.4
-
32
-
-
23844525077
-
Repbase Update, a database of eukaryotic repetitive elements
-
Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, et al. (2005) Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110: 462-467.
-
(2005)
Cytogenet Genome Res
, vol.110
, pp. 462-467
-
-
Jurka, J.1
Kapitonov, V.V.2
Pavlicek, A.3
Klonowski, P.4
Kohany, O.5
-
33
-
-
45949107473
-
Recent developments in the MAFFT multiple sequence alignment program
-
Katoh K, Toh H, (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 9: 286-298.
-
(2008)
Brief Bioinform
, vol.9
, pp. 286-298
-
-
Katoh, K.1
Toh, H.2
-
34
-
-
0003437302
-
PHYLIP (Phylogeny Inference Package) version 3.6
-
Department of Genome Sciences, University of Washington, Seattle
-
Felsenstein J, (2005) PHYLIP (Phylogeny Inference Package) version 3.6. Department of Genome Sciences, University of Washington, Seattle.
-
(2005)
-
-
Felsenstein, J.1
-
35
-
-
0036245495
-
Segmental duplications and the evolution of the primate genome
-
Samonte RV, Eichler EE, (2002) Segmental duplications and the evolution of the primate genome. Nat Rev Genet 3: 65-72.
-
(2002)
Nat Rev Genet
, vol.3
, pp. 65-72
-
-
Samonte, R.V.1
Eichler, E.E.2
-
36
-
-
0030854739
-
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence
-
Lowe TM, Eddy SR, (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955-964.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 955-964
-
-
Lowe, T.M.1
Eddy, S.R.2
-
37
-
-
0030845166
-
Synonymous substitution rates in Drosophila: mitochondrial versus nuclear genes
-
Moriyama EN, Powell JR, (1997) Synonymous substitution rates in Drosophila: mitochondrial versus nuclear genes. J Mol Evol 45: 378-391.
-
(1997)
J Mol Evol
, vol.45
, pp. 378-391
-
-
Moriyama, E.N.1
Powell, J.R.2
-
38
-
-
0035732912
-
Recombination among multiple mitochondrial pseudogenes from a Passerine genus
-
Klitgaard Nielsen K, Arctander P, (2001) Recombination among multiple mitochondrial pseudogenes from a Passerine genus. Mol Phylogenet Evol 18: 362-369.
-
(2001)
Mol Phylogenet Evol
, vol.18
, pp. 362-369
-
-
Klitgaard Nielsen, K.1
Arctander, P.2
-
39
-
-
0035140685
-
Genomic gigantism: DNA loss is slow in mountain grasshoppers
-
Bensasson D, Petrov DA, Zhang DX, Hartl DL, Hewitt GM, (2001b) Genomic gigantism: DNA loss is slow in mountain grasshoppers. Mol Biol Evol 18: 246-253.
-
(2001)
Mol Biol Evol
, vol.18
, pp. 246-253
-
-
Bensasson, D.1
Petrov, D.A.2
Zhang, D.X.3
Hartl, D.L.4
Hewitt, G.M.5
-
40
-
-
19344368527
-
Continued colonization of the human genome by mitochondrial DNA
-
Ricchetti M, Tekaia F, Dujon B, (2004) Continued colonization of the human genome by mitochondrial DNA. PLoS Biol 2: E273.
-
(2004)
PLoS Biol
, vol.2
-
-
Ricchetti, M.1
Tekaia, F.2
Dujon, B.3
-
41
-
-
33646071891
-
LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease: mutation detection bias and multiple mechanisms of target gene disruption
-
Chen JM, Ferec C, Cooper DN, (2006) LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease: mutation detection bias and multiple mechanisms of target gene disruption. J Biomed Biotechnol 2006: 56182.
-
(2006)
J Biomed Biotechnol
, vol.2006
, pp. 56182
-
-
Chen, J.M.1
Ferec, C.2
Cooper, D.N.3
-
42
-
-
1042299965
-
Mitochondrial DNA-like sequences in the nucleus (NUMTs): insights into our African origins and the mechanism of foreign DNA integration
-
Mishmar D, Ruiz-Pesini E, Brandon M, Wallace DC, (2004) Mitochondrial DNA-like sequences in the nucleus (NUMTs): insights into our African origins and the mechanism of foreign DNA integration. Hum Mutat 23: 125-133.
-
(2004)
Hum Mutat
, vol.23
, pp. 125-133
-
-
Mishmar, D.1
Ruiz-Pesini, E.2
Brandon, M.3
Wallace, D.C.4
-
43
-
-
58949104692
-
Instability of plastid DNA in the nuclear genome
-
Sheppard AE, Timmis JN, (2009) Instability of plastid DNA in the nuclear genome. PLoS Genet 5: e1000323.
-
(2009)
PLoS Genet
, vol.5
-
-
Sheppard, A.E.1
Timmis, J.N.2
-
44
-
-
0003421005
-
-
Sunderland, MA, Sinauer Associates
-
Li W-H, (1997) Molecular Evolution Sunderland, MA Sinauer Associates.
-
(1997)
Molecular Evolution
-
-
Li, W.-H.1
-
45
-
-
0029856377
-
High intrinsic rate of DNA loss in Drosophila
-
Petrov DA, Lozovskaya ER, Hartl DL, (1996) High intrinsic rate of DNA loss in Drosophila. Nature 384: 346-349.
-
(1996)
Nature
, vol.384
, pp. 346-349
-
-
Petrov, D.A.1
Lozovskaya, E.R.2
Hartl, D.L.3
-
46
-
-
36048950933
-
Gene family evolution across 12 Drosophila genomes
-
Hahn MW, Han MV, Han SG, (2007) Gene family evolution across 12 Drosophila genomes. PLoS Genet 3: e197.
-
(2007)
PLoS Genet
, vol.3
-
-
Hahn, M.W.1
Han, M.V.2
Han, S.G.3
-
47
-
-
33751381461
-
TimeTree: a public knowledge-base of divergence times among organisms
-
Hedges SB, Dudley J, Kumar S, (2006) TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics 22: 2971-2972.
-
(2006)
Bioinformatics
, vol.22
, pp. 2971-2972
-
-
Hedges, S.B.1
Dudley, J.2
Kumar, S.3
-
48
-
-
55449118548
-
ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun
-
Li R, Ye J, Li S, Wang J, Han Y, et al. (2005) ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun. PLoS Comput Biol 1: e43.
-
(2005)
PLoS Comput Biol
, vol.1
-
-
Li, R.1
Ye, J.2
Li, S.3
Wang, J.4
Han, Y.5
|