-
1
-
-
0031714828
-
Accelerated evolution of cytochrome b in simian primates: Adaptive evolution in concert with other mitochondrial proteins?
-
Andrews TD, Jermiin LS, Easteal S (1998). Accelerated evolution of cytochrome b in simian primates: adaptive evolution in concert with other mitochondrial proteins? J Mol Evol 47: 249-257.
-
(1998)
J Mol Evol
, vol.47
, pp. 249-257
-
-
Andrews, T.D.1
Jermiin, L.S.2
Easteal, S.3
-
2
-
-
0021003189
-
Mitochondrial DNA differentiation during the speciation process in Peromyscus
-
Avise JC, Shapira JF, Daniel SW, Aquadro CF, Lansman RA (1983). Mitochondrial DNA differentiation during the speciation process in Peromyscus. Mol Biol Evol 1: 38-56.
-
(1983)
Mol Biol Evol
, vol.1
, pp. 38-56
-
-
Avise, J.C.1
Shapira, J.F.2
Daniel, S.W.3
Aquadro, C.F.4
Lansman, R.A.5
-
3
-
-
3042842589
-
A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution
-
Bielawski JP, Yang Z (2004). A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution. J Mol Evol 59: 121-132.
-
(2004)
J Mol Evol
, vol.59
, pp. 121-132
-
-
Bielawski, J.P.1
Yang, Z.2
-
4
-
-
35548940373
-
Towards a molecular phylogeny for Peromyscus: Evidence from mitochondrial cytochrome-b sequences
-
Bradley RD, Durish ND, Rogers DS, Miller JR, Engstrom MD, Kilpatrick CW (2007). Towards a molecular phylogeny for Peromyscus: evidence from mitochondrial cytochrome-b sequences. J Mammal 88: 1146-1159.
-
(2007)
J Mammal
, vol.88
, pp. 1146-1159
-
-
Bradley, R.D.1
Durish, N.D.2
Rogers, D.S.3
Miller, J.R.4
Engstrom, M.D.5
Kilpatrick, C.W.6
-
5
-
-
0002580045
-
Systematics and evolution
-
Kirkland GL, Layne JN eds, Texas Tech University Press: Lubbock, Texas. pp
-
Carleton MD (1989). Systematics and evolution. In: Kirkland GL, Layne JN (eds). Advances in the Study of Peromyscus (Rodentia). Texas Tech University Press: Lubbock, Texas. pp 7-141.
-
(1989)
Advances in the Study of Peromyscus (Rodentia)
, pp. 7-141
-
-
Carleton, M.D.1
-
6
-
-
0021489105
-
Biochemical and physiological correlates of deer mouse alpha-chain hemoglobin polymorphisms
-
Chappell MA, Snyder LR (1984). Biochemical and physiological correlates of deer mouse alpha-chain hemoglobin polymorphisms. Proc Natl Acad Sci USA 81: 5484-5488.
-
(1984)
Proc Natl Acad Sci USA
, vol.81
, pp. 5484-5488
-
-
Chappell, M.A.1
Snyder, L.R.2
-
7
-
-
0344088685
-
Metabolic differences between three strains of Peromyscus maniculatus
-
Cook SF, Hannon JP (1954). Metabolic differences between three strains of Peromyscus maniculatus. J Mammal 35: 553-560.
-
(1954)
J Mammal
, vol.35
, pp. 553-560
-
-
Cook, S.F.1
Hannon, J.P.2
-
8
-
-
0027168787
-
Mitochondrial cytochrome-b - evolution and structure of the protein
-
Degliesposti M, Devries S, Crimi M, Ghelli A, Patarnello T, Meyer A (1993). Mitochondrial cytochrome-b - evolution and structure of the protein. Biochim Biophys Acta 1143: 243-271.
-
(1993)
Biochim Biophys Acta
, vol.1143
, pp. 243-271
-
-
Degliesposti, M.1
Devries, S.2
Crimi, M.3
Ghelli, A.4
Patarnello, T.5
Meyer, A.6
-
9
-
-
33745628747
-
Phylogeography of the deer mouse (Peromyscus maniculatus) provides a predictive framework for research on hantaviruses
-
Dragoo JW, Lackey JA, Moore KE, Lessa EP, Cook JA, Yates TL (2006). Phylogeography of the deer mouse (Peromyscus maniculatus) provides a predictive framework for research on hantaviruses. J Gen Virol 87: 1997-2003.
-
(2006)
J Gen Virol
, vol.87
, pp. 1997-2003
-
-
Dragoo, J.W.1
Lackey, J.A.2
Moore, K.E.3
Lessa, E.P.4
Cook, J.A.5
Yates, T.L.6
-
10
-
-
0842285683
-
Comparative genomics and the evolution of human mitochondrial DNA: Assessing the effects of selection
-
Elson JL, Turnbull DM, Howell N (2004). Comparative genomics and the evolution of human mitochondrial DNA: assessing the effects of selection. Am J Hum Genet 74: 229-238.
-
(2004)
Am J Hum Genet
, vol.74
, pp. 229-238
-
-
Elson, J.L.1
Turnbull, D.M.2
Howell, N.3
-
11
-
-
0019797407
-
Evolutionary trees from DNA sequences: A maximum likelihood approach
-
Felsenstein J (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17: 368-376.
-
(1981)
J Mol Evol
, vol.17
, pp. 368-376
-
-
Felsenstein, J.1
-
12
-
-
13444305420
-
Nonshivering thermogenesis capacity associated to mitochondrial DNA haplotypes and gender in the greater white-toothed shrew, Crocidura russula
-
Fontanillas P, Depraz A, Giorgi MS, Perrin N (2005). Nonshivering thermogenesis capacity associated to mitochondrial DNA haplotypes and gender in the greater white-toothed shrew, Crocidura russula. Mol Ecol 14: 661-670.
-
(2005)
Mol Ecol
, vol.14
, pp. 661-670
-
-
Fontanillas, P.1
Depraz, A.2
Giorgi, M.S.3
Perrin, N.4
-
13
-
-
0032693254
-
Mildly deleterious mutations in avian mitochondrial DNA: Evidence from neutrality tests
-
Fry AJ (1999). Mildly deleterious mutations in avian mitochondrial DNA: evidence from neutrality tests. Evolution 53: 1617-1620.
-
(1999)
Evolution
, vol.53
, pp. 1617-1620
-
-
Fry, A.J.1
-
14
-
-
0028168856
-
A codon-based model of nucleotide substitution for protein-coding DNA sequences
-
Goldman N, Yang Z (1994). A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol 5: 725-726.
-
(1994)
Mol Biol Evol
, vol.5
, pp. 725-726
-
-
Goldman, N.1
Yang, Z.2
-
15
-
-
0020486102
-
Positive selection causes purifying selection
-
Goodman M (1982). Positive selection causes purifying selection. Nature 295: 630.
-
(1982)
Nature
, vol.295
, pp. 630
-
-
Goodman, M.1
-
16
-
-
4744342460
-
Accelerated evolution of the electron transport chain in anthropoid primates
-
Grossman LI, Willdman DE, Schmidt TR, Goodman M (2004). Accelerated evolution of the electron transport chain in anthropoid primates. Trends Genet 20: 579-584.
-
(2004)
Trends Genet
, vol.20
, pp. 579-584
-
-
Grossman, L.I.1
Willdman, D.E.2
Schmidt, T.R.3
Goodman, M.4
-
18
-
-
0031729188
-
Preponderance of slightly deleterious polymorphism in mitochondrial DNA: Nonsynonymous/synonymous rate ratio is much higher within species than between species
-
Hasegawa M, Cao Y, Yang Z (1998). Preponderance of slightly deleterious polymorphism in mitochondrial DNA: nonsynonymous/synonymous rate ratio is much higher within species than between species. Mol Biol Evol 15: 1499-1505.
-
(1998)
Mol Biol Evol
, vol.15
, pp. 1499-1505
-
-
Hasegawa, M.1
Cao, Y.2
Yang, Z.3
-
19
-
-
0027142335
-
Systematic and taxonomic implications of karyotypic, electrophoretic, and mitochondrial-DNA variation in Peromyscus from the Pacific Northwest
-
Hogan KM, Hedin MC, Koh HS, Davis SK, Greenbaum AF (1993). Systematic and taxonomic implications of karyotypic, electrophoretic, and mitochondrial-DNA variation in Peromyscus from the Pacific Northwest. J Mammal 74: 819-831.
-
(1993)
J Mammal
, vol.74
, pp. 819-831
-
-
Hogan, K.M.1
Hedin, M.C.2
Koh, H.S.3
Davis, S.K.4
Greenbaum, A.F.5
-
20
-
-
4744342460
-
Accelerated evolution of the electron transport chain in anthropoid primates
-
Grossman LI, Wildman DE, Schmidt TR, Goodman M (2004). Accelerated evolution of the electron transport chain in anthropoid primates. Trends Genet 20: 579-584.
-
(2004)
Trends Genet
, vol.20
, pp. 579-584
-
-
Grossman, L.I.1
Wildman, D.E.2
Schmidt, T.R.3
Goodman, M.4
-
21
-
-
13444259388
-
TREEFINDER: A powerful graphical analysis environment for molecular phylogenetics
-
Jobb G, von Haeseler A, Strimmer K (2004). TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol Biol 4: 18.
-
(2004)
BMC Evol Biol
, vol.4
, pp. 18
-
-
Jobb, G.1
von Haeseler, A.2
Strimmer, K.3
-
22
-
-
33244457956
-
The role of selection in the evolution of human mitochondrial genomes
-
Kivisild T, Shen P, Wall DP, Do B, Sung R, Davis K et al. (2006). The role of selection in the evolution of human mitochondrial genomes. Genetics 172: 373-387.
-
(2006)
Genetics
, vol.172
, pp. 373-387
-
-
Kivisild, T.1
Shen, P.2
Wall, D.P.3
Do, B.4
Sung, R.5
Davis, K.6
-
23
-
-
3242810318
-
MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment
-
Kumar S, Tamura K, Nei M (2004). MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5: 150-163.
-
(2004)
Brief Bioinform
, vol.5
, pp. 150-163
-
-
Kumar, S.1
Tamura, K.2
Nei, M.3
-
24
-
-
0021058867
-
Extensive genetic variation in mitochondrial DNA's among geographic populations of the deer mouse, Peromyscus maniculatus
-
Lansman RA, Avise JC, Aquadro CF (1983). Extensive genetic variation in mitochondrial DNA's among geographic populations of the deer mouse, Peromyscus maniculatus. Evolution 37: 1-16.
-
(1983)
Evolution
, vol.37
, pp. 1-16
-
-
Lansman, R.A.1
Avise, J.C.2
Aquadro, C.F.3
-
25
-
-
2442581218
-
The importance of proper model assumption in Bayesian phylogenetics
-
Lemmon AR, Moriarty EC (2004). The importance of proper model assumption in Bayesian phylogenetics. Syst Biol 53: 265-277.
-
(2004)
Syst Biol
, vol.53
, pp. 265-277
-
-
Lemmon, A.R.1
Moriarty, E.C.2
-
26
-
-
0001621774
-
Adaptive physiology
-
Kirkland GL, Layne JN eds, Texas Tech University Press: Lubbock, Texas. pp
-
MacMillen RE, Garland TJ (1989). Adaptive physiology. In: Kirkland GL, Layne JN (eds). Advances in the Study of Peromyscus (Rodentia). Texas Tech University Press: Lubbock, Texas. pp 143-168.
-
(1989)
Advances in the Study of Peromyscus (Rodentia)
, pp. 143-168
-
-
MacMillen, R.E.1
Garland, T.J.2
-
27
-
-
0010956475
-
Interactive analysis of phylogeny and character evolution using the computer program MacClade
-
Maddison WP, Maddison DR (1989). Interactive analysis of phylogeny and character evolution using the computer program MacClade. Folia Primatol (Basel) 53: 190-202.
-
(1989)
Folia Primatol (Basel)
, vol.53
, pp. 190-202
-
-
Maddison, W.P.1
Maddison, D.R.2
-
28
-
-
14544300682
-
Physicochemical evolution and molecular adaptation of the cetacean and artiodactyl cytochrome b proteins
-
McClellan DA, Palfreyman EJ, Smith MJ, Moss JL, Christensen RG, Sailsbery JK (2005). Physicochemical evolution and molecular adaptation of the cetacean and artiodactyl cytochrome b proteins. Mol Biol Evol 22: 437-455.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 437-455
-
-
McClellan, D.A.1
Palfreyman, E.J.2
Smith, M.J.3
Moss, J.L.4
Christensen, R.G.5
Sailsbery, J.K.6
-
29
-
-
0026428610
-
Adaptive protein evolution at the Adh locus in Drosophila
-
McDonald JH, Kreitman M (1991). Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654.
-
(1991)
Nature
, vol.351
, pp. 652-654
-
-
McDonald, J.H.1
Kreitman, M.2
-
30
-
-
0037422550
-
Natural selection shaped regional mtDNA variation in humans
-
Mishmar D, Ruiz-Pesini E, Golik P, Macaulay V, Clark AG, Hosseini S et al. (2003). Natural selection shaped regional mtDNA variation in humans. Proc Natl Acad Sci USA 100: 171-176.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 171-176
-
-
Mishmar, D.1
Ruiz-Pesini, E.2
Golik, P.3
Macaulay, V.4
Clark, A.G.5
Hosseini, S.6
-
31
-
-
0041571792
-
Phylogenetic network and physicochemical properties of nonsynonymous mutations in the protein-coding genes of human mitochondrial DNA
-
Moilanen JS, Majamaa K (2003). Phylogenetic network and physicochemical properties of nonsynonymous mutations in the protein-coding genes of human mitochondrial DNA. Mol Biol Evol 20: 1195-1210.
-
(2003)
Mol Biol Evol
, vol.20
, pp. 1195-1210
-
-
Moilanen, J.S.1
Majamaa, K.2
-
32
-
-
7344225509
-
Deleterious mutations in animal mitochondrial DNA
-
Nachman MW (1998). Deleterious mutations in animal mitochondrial DNA. Genetica 102-103: 61-69.
-
(1998)
Genetica
, vol.102-103
, pp. 61-69
-
-
Nachman, M.W.1
-
33
-
-
0030011347
-
Nonneutral mitochondrial DNA variation in humans and chimpanzees
-
Nachman MW, Brown WM, Stoneking M, Aquadro CF (1996). Nonneutral mitochondrial DNA variation in humans and chimpanzees. Genetics 142: 953-963.
-
(1996)
Genetics
, vol.142
, pp. 953-963
-
-
Nachman, M.W.1
Brown, W.M.2
Stoneking, M.3
Aquadro, C.F.4
-
34
-
-
0031972161
-
Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
-
Nielsen R, Yang Z (1998). Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148: 929-936.
-
(1998)
Genetics
, vol.148
, pp. 929-936
-
-
Nielsen, R.1
Yang, Z.2
-
35
-
-
0031773680
-
Modeltest: Testing the model of DNA substitution
-
Posada D, Crandall KA (1998). Modeltest: testing the model of DNA substitution. Bioinformatics 14: 817-818.
-
(1998)
Bioinformatics
, vol.14
, pp. 817-818
-
-
Posada, D.1
Crandall, K.A.2
-
36
-
-
0030000951
-
Excess amino acid polymorphism in mitochondrial DNA: Contrasts among genes from Drosophila, mice, and humans
-
Rand DM, Kann LM (1996). Excess amino acid polymorphism in mitochondrial DNA: contrasts among genes from Drosophila, mice, and humans. Mol Biol Evol 13: 735-748.
-
(1996)
Mol Biol Evol
, vol.13
, pp. 735-748
-
-
Rand, D.M.1
Kann, L.M.2
-
37
-
-
7344244917
-
Mutation and selection at silent and replacement sites in the evolution of animal mitochondrial DNA
-
Rand DM, Kann LM (1998). Mutation and selection at silent and replacement sites in the evolution of animal mitochondrial DNA. Genetica 102-103: 393-407.
-
(1998)
Genetica
, vol.102-103
, pp. 393-407
-
-
Rand, D.M.1
Kann, L.M.2
-
38
-
-
0030854715
-
Cellular energy utilization and molecular origin of standard metabolic rate in mammals
-
Rolfe DF, Brown GC (1997). Cellular energy utilization and molecular origin of standard metabolic rate in mammals. Physiol Rev 77: 731-758.
-
(1997)
Physiol Rev
, vol.77
, pp. 731-758
-
-
Rolfe, D.F.1
Brown, G.C.2
-
39
-
-
0041386108
-
MrBayes 3: Bayesian phylogenetic inference under mixed models
-
Ronquist F, Huelsenbeck JP (2003). MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
-
(2003)
Bioinformatics
, vol.19
, pp. 1572-1574
-
-
Ronquist, F.1
Huelsenbeck, J.P.2
-
40
-
-
0347513220
-
DnaSP, DNA polymorphism analyses by the coalescent and other methods
-
Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R (2003). DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19: 2496-2497.
-
(2003)
Bioinformatics
, vol.19
, pp. 2496-2497
-
-
Rozas, J.1
Sanchez-DelBarrio, J.C.2
Messeguer, X.3
Rozas, R.4
-
41
-
-
0347356538
-
Effects of purifying and adaptive selection on regional variation in human mtDNA
-
Ruiz-Pesini E, Mishmar D, Brandon M, Procaccio V, Wallace DC (2004). Effects of purifying and adaptive selection on regional variation in human mtDNA. Science 303: 223-226.
-
(2004)
Science
, vol.303
, pp. 223-226
-
-
Ruiz-Pesini, E.1
Mishmar, D.2
Brandon, M.3
Procaccio, V.4
Wallace, D.C.5
-
42
-
-
33847668843
-
Hemoglobin function and physiological adaptation to hypoxia in high-altitude mammals
-
Storz JF 2007. Hemoglobin function and physiological adaptation to hypoxia in high-altitude mammals. J Mammal 88: 24-31.
-
(2007)
J Mammal
, vol.88
, pp. 24-31
-
-
Storz, J.F.1
-
43
-
-
56049122929
-
Effects of spatially varying selection on nucleotide diversity and linkage disequilibrium: Insights from deer mouse globin genes
-
Storz JF, Kelly JK 2008. Effects of spatially varying selection on nucleotide diversity and linkage disequilibrium: Insights from deer mouse globin genes. Genetics 180: 367-379.
-
(2008)
Genetics
, vol.180
, pp. 367-379
-
-
Storz, J.F.1
Kelly, J.K.2
-
44
-
-
34047218882
-
-
Storz JF, Sabatino SJ, Hoffmann FG, Gering EJ, Moriyama H, Ferrand N et al. 2007. The molecular basis of high-altitude adaptation in deer mice. PLoS Genet 3: e45, 0448-0459.
-
Storz JF, Sabatino SJ, Hoffmann FG, Gering EJ, Moriyama H, Ferrand N et al. 2007. The molecular basis of high-altitude adaptation in deer mice. PLoS Genet 3: e45, 0448-0459.
-
-
-
-
45
-
-
33846799015
-
The role of climate in human mitochondrial DNA evolution: A reappraisal
-
Sun C, Kong Q, Zhang Y (2007). The role of climate in human mitochondrial DNA evolution: a reappraisal. Genomics 89: 338-342.
-
(2007)
Genomics
, vol.89
, pp. 338-342
-
-
Sun, C.1
Kong, Q.2
Zhang, Y.3
-
46
-
-
0030683599
-
PAML: A program package for phylogenetic analysis by maximum likelihood
-
Yang Z (1997). PAML: a program package for phylogenetic analysis by maximum likelihood. CABIOS 13: 555-556.
-
(1997)
CABIOS
, vol.13
, pp. 555-556
-
-
Yang, Z.1
-
47
-
-
0033979433
-
Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models
-
Yang Z, Nielsen R (2000). Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol 17: 32-43.
-
(2000)
Mol Biol Evol
, vol.17
, pp. 32-43
-
-
Yang, Z.1
Nielsen, R.2
-
48
-
-
0036270185
-
Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages
-
Yang Z, Nielsen R (2002). Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol 19: 908-917.
-
(2002)
Mol Biol Evol
, vol.19
, pp. 908-917
-
-
Yang, Z.1
Nielsen, R.2
-
49
-
-
27844439855
-
Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level
-
Zhang J, Nielsen R, Yang Z (2005). Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol 22: 2472-2479.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 2472-2479
-
-
Zhang, J.1
Nielsen, R.2
Yang, Z.3
|