-
1
-
-
0037329391
-
Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence
-
Alfaro, M.E., Zoller, S., Lutzoni, F., 2003. Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Mol. Biol. Evol. 20, 255-266.
-
(2003)
Mol. Biol. Evol.
, vol.20
, pp. 255-266
-
-
Alfaro, M.E.1
Zoller, S.2
Lutzoni, F.3
-
2
-
-
0035358999
-
Mitochondrial pseudogenes: Evolution's misplaced witnesses
-
Bensasson, D., Zhang, D.X., Hartl, D.L., Hewitt, G.M., 2001. Mitochondrial pseudogenes: evolution's misplaced witnesses. TREE 16, 314-321.
-
(2001)
TREE
, vol.16
, pp. 314-321
-
-
Bensasson, D.1
Zhang, D.X.2
Hartl, D.L.3
Hewitt, G.M.4
-
4
-
-
0032537194
-
Gene translocation links insects and crustaceans
-
Boore, J.L., Lavrov, D.V., Brown, W.M., 1998. Gene translocation links insects and crustaceans. Nature 392, 667-668.
-
(1998)
Nature
, vol.392
, pp. 667-668
-
-
Boore, J.L.1
Lavrov, D.V.2
Brown, W.M.3
-
5
-
-
0036623259
-
Model misspecification and probabilistic tests of topology: Evidence from empirical datasets
-
Buckley, T.R., 2002. Model misspecification and probabilistic tests of topology: evidence from empirical datasets. Syst. Biol. 51, 509-523.
-
(2002)
Syst. Biol.
, vol.51
, pp. 509-523
-
-
Buckley, T.R.1
-
6
-
-
0034707202
-
Phylogenetic position of turtles among amniotes: Evidence from mitochondrial and nuclear genes
-
Cao, Y., Sorenson, M.D., Kumazawa, Y., Mindell, D.P., Hasegawa, M., 2000. Phylogenetic position of turtles among amniotes: evidence from mitochondrial and nuclear genes. Gene 259, 139-148.
-
(2000)
Gene
, vol.259
, pp. 139-148
-
-
Cao, Y.1
Sorenson, M.D.2
Kumazawa, Y.3
Mindell, D.P.4
Hasegawa, M.5
-
8
-
-
0035819804
-
Avian evolution, Gondwana biogeography and the Cretaceous-tertiary mass extinction event
-
Cracraft, J., 2001. Avian evolution, Gondwana biogeography and the Cretaceous-tertiary mass extinction event. Proc. R. Soc. Lond. B 268, 459-469.
-
(2001)
Proc. R. Soc. Lond. B
, vol.268
, pp. 459-469
-
-
Cracraft, J.1
-
9
-
-
0035172090
-
Evidence for import of a lysyl-tRNA into marsupial mitochondria
-
Dorner, M., Altmann, M., Pääbo, S., Morl, M., 2001. Evidence for import of a lysyl-tRNA into marsupial mitochondria. Mol. Biol. Cell 12, 2688-2698.
-
(2001)
Mol. Biol. Cell
, vol.12
, pp. 2688-2698
-
-
Dorner, M.1
Altmann, M.2
Pääbo, S.3
Morl, M.4
-
10
-
-
0037329108
-
Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability
-
Douady, C.J., Delsuc, F., Boucher, Y., Doolittle, W.F., Douzery, E.J.P., 2003. Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability. Mol. Biol. Evol. 20, 248-254.
-
(2003)
Mol. Biol. Evol.
, vol.20
, pp. 248-254
-
-
Douady, C.J.1
Delsuc, F.2
Boucher, Y.3
Doolittle, W.F.4
Douzery, E.J.P.5
-
11
-
-
0033062252
-
Evolutionary dynamics of a mitochondrial rearrangement "hot spot" in the Hymenoptera
-
Dowton, M., Austin, A.D., 1999. Evolutionary dynamics of a mitochondrial rearrangement "hot spot" in the Hymenoptera. Mol. Biol. Evol. 16, 298-309.
-
(1999)
Mol. Biol. Evol.
, vol.16
, pp. 298-309
-
-
Dowton, M.1
Austin, A.D.2
-
13
-
-
0037155141
-
The typically mitochondrial DNA-encoded ATP6 subunit of the F1F0-ATPase is encoded by a nuclear gene in Chlamydomonas reinhardtii
-
Funes, S., Davidson, E., Gonzalo Claros, M.G., van Lis, R., Perez-Martinez, X., Vazquez-Acevedo, M., King, M.P., Gonzalez-Halphen, D., 2002. The typically mitochondrial DNA-encoded ATP6 subunit of the F1F0-ATPase is encoded by a nuclear gene in Chlamydomonas reinhardtii. J. Biol. Chem. 277, 6051-6058.
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 6051-6058
-
-
Funes, S.1
Davidson, E.2
Gonzalo Claros, M.G.3
Van Lis, R.4
Perez-Martinez, X.5
Vazquez-Acevedo, M.6
King, M.P.7
Gonzalez-Halphen, D.8
-
14
-
-
0033548225
-
A molecular phylogeny of reptiles
-
Hedges, S.B., Poling, L.L., 1999. A molecular phylogeny of reptiles. Science 283, 998-1001.
-
(1999)
Science
, vol.283
, pp. 998-1001
-
-
Hedges, S.B.1
Poling, L.L.2
-
15
-
-
0026740213
-
A novel mitochondrial genome organization for the blue mussel, Mytilus edulis
-
Hoffmann, R.J., Boore, J.L., Brown, W.M., 1992. A novel mitochondrial genome organization for the blue mussel, Mytilus edulis. Genetics 131, 397-412.
-
(1992)
Genetics
, vol.131
, pp. 397-412
-
-
Hoffmann, R.J.1
Boore, J.L.2
Brown, W.M.3
-
16
-
-
0034849408
-
Mrbayes: Bayesian inference of phylogenetic trees
-
Huelsenbeck, J., Ronquist, F., 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754-755.
-
(2001)
Bioinformatics
, vol.17
, pp. 754-755
-
-
Huelsenbeck, J.1
Ronquist, F.2
-
17
-
-
0031757669
-
Multiple sequence alignment with Clustal X
-
Jeanmougin, F., Thompson, J.D., Gouy, M., Higgins, D.G., Gibson, T.J., 1998. Multiple sequence alignment with Clustal X. Trends Biochem. Sci. 23, 403-405.
-
(1998)
Trends Biochem. Sci.
, vol.23
, pp. 403-405
-
-
Jeanmougin, F.1
Thompson, J.D.2
Gouy, M.3
Higgins, D.G.4
Gibson, T.J.5
-
18
-
-
0024307824
-
Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea
-
Kishino, H., Hasegawa, M., 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea. J. Mol. Evol. 29, 170-179.
-
(1989)
J. Mol. Evol.
, vol.29
, pp. 170-179
-
-
Kishino, H.1
Hasegawa, M.2
-
19
-
-
0031696736
-
The complete nucleotide sequence of a snake (Dinodon semicarinatus) mitochondrial genome with two identical control regions
-
Kumazawa, Y., Ota, H., Nishida, M., Ozawa, T., 1998. The complete nucleotide sequence of a snake (Dinodon semicarinatus) mitochondrial genome with two identical control regions. Genetics 150, 313-329.
-
(1998)
Genetics
, vol.150
, pp. 313-329
-
-
Kumazawa, Y.1
Ota, H.2
Nishida, M.3
Ozawa, T.4
-
20
-
-
0032976397
-
Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees
-
Larget, B., Simon, D.L., 1999. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16, 750-759.
-
(1999)
Mol. Biol. Evol.
, vol.16
, pp. 750-759
-
-
Larget, B.1
Simon, D.L.2
-
21
-
-
0033917042
-
Phylogenies inferred from mitochondrial gene orders - A cautionary tale from the parasitic flatworms
-
Le, T.H., Blair, D., Agatsuma, T., Humair, P.P., Campbell, N.J.H., Iwagami, M., Littlewood, D.T.J., Peacock, B., Johnston, D.A., Bartley, J., Rollinson, D., Herniou, E.A., Zarlenga, D.S., McManus, D.P., 2000. Phylogenies inferred from mitochondrial gene orders - A cautionary tale from the parasitic flatworms. Mol. Biol. Evol. 17, 1123-1125.
-
(2000)
Mol. Biol. Evol.
, vol.17
, pp. 1123-1125
-
-
Le, T.H.1
Blair, D.2
Agatsuma, T.3
Humair, P.P.4
Campbell, N.J.H.5
Iwagami, M.6
Littlewood, D.T.J.7
Peacock, B.8
Johnston, D.A.9
Bartley, J.10
Rollinson, D.11
Herniou, E.A.12
Zarlenga, D.S.13
McManus, D.P.14
-
22
-
-
0034174353
-
Soft anatomy, diffuse homoplasy, and the relationships of lizards and snakes
-
Lee, M.S., 2000. Soft anatomy, diffuse homoplasy, and the relationships of lizards and snakes. Zoologica Scripta 29, 101-130.
-
(2000)
Zoologica Scripta
, vol.29
, pp. 101-130
-
-
Lee, M.S.1
-
23
-
-
0035605630
-
Molecules, morphology, and the monophyly of diapsid reptiles
-
Lee, M.S., 2001. Molecules, morphology, and the monophyly of diapsid reptiles. Contrib. Zool. 70, 1-22.
-
(2001)
Contrib. Zool.
, vol.70
, pp. 1-22
-
-
Lee, M.S.1
-
24
-
-
0031110887
-
Homology in phylogenetic analysis: Alignment of transfer RNA genes and the phylogenetic position of snakes
-
Macey, R.J., Verma, A., 1997. Homology in phylogenetic analysis: alignment of transfer RNA genes and the phylogenetic position of snakes. Mol. Phylogenet. Evol. 7, 272-279.
-
(1997)
Mol. Phylogenet. Evol.
, vol.7
, pp. 272-279
-
-
Macey, R.J.1
Verma, A.2
-
25
-
-
0032906031
-
Bayesian phylogenetic inference via Markov chain Monte Carlo methods
-
Mau, B., Newton, M., Larget, B., 1999. Bayesian phylogenetic inference via Markov chain Monte Carlo methods. Biometrics 55, 1-12.
-
(1999)
Biometrics
, vol.55
, pp. 1-12
-
-
Mau, B.1
Newton, M.2
Larget, B.3
-
26
-
-
0032169857
-
Multiple independent origins of mitochondrial gene order in birds
-
Mindell, D.P., Sorenson, M.D., Dimcheff, D.E., 1998. Multiple independent origins of mitochondrial gene order in birds. Proc. Natl. Acad. Sci. USA 95, 10693-10697.
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 10693-10697
-
-
Mindell, D.P.1
Sorenson, M.D.2
Dimcheff, D.E.3
-
27
-
-
0033084950
-
Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes
-
Mindell, D.P., Sorenson, M.D., Dimcheff, D.E., Hasegawa, M., Ast, J.C., Yuri, T., 1999. Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes. Syst. Biol. 48, 138-152.
-
(1999)
Syst. Biol.
, vol.48
, pp. 138-152
-
-
Mindell, D.P.1
Sorenson, M.D.2
Dimcheff, D.E.3
Hasegawa, M.4
Ast, J.C.5
Yuri, T.6
-
28
-
-
0026573893
-
The mitochondrial genomes of 2 nematodes, Caenorhabditis elegans and Ascaris suum
-
Okimoto, R., Macfarlane, J.L., Clary, D.O., Wolstenholme, D.R., 1992. The mitochondrial genomes of 2 nematodes, Caenorhabditis elegans and Ascaris suum. Genetics 130, 471-498.
-
(1992)
Genetics
, vol.130
, pp. 471-498
-
-
Okimoto, R.1
Macfarlane, J.L.2
Clary, D.O.3
Wolstenholme, D.R.4
-
29
-
-
0029660251
-
Turtles as diapsid reptiles
-
Rieppel, O., deBraga, M., 1996. Turtles as diapsid reptiles. Nature 384, 453-455.
-
(1996)
Nature
, vol.384
, pp. 453-455
-
-
Rieppel, O.1
Debraga, M.2
-
30
-
-
0033381933
-
The origin and early evolution of turtles
-
Rieppel, O., Reisz, R., 1999. The origin and early evolution of turtles. Annu. Rev. Ecol. Syst. 30, 1-22.
-
(1999)
Annu. Rev. Ecol. Syst.
, vol.30
, pp. 1-22
-
-
Rieppel, O.1
Reisz, R.2
-
31
-
-
0036269310
-
Novel rearrangements of arthropod mitochondrial DNA detected with long-PCR: Applications to arthropod phylogeny and evolution
-
Roehrdanz, R.L., Degrugillier, M.E., Black, W.C., 2002. Novel rearrangements of arthropod mitochondrial DNA detected with long-PCR: applications to arthropod phylogeny and evolution. Mol. Biol. Evol. 19, 841-849.
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 841-849
-
-
Roehrdanz, R.L.1
Degrugillier, M.E.2
Black, W.C.3
-
32
-
-
0030124093
-
Mitochondrial gene order adjacent to the control region in crocodile, turtle and tuatara
-
Quinn, T.W., Mindell, D.P., 1996. Mitochondrial gene order adjacent to the control region in crocodile, turtle and tuatara. Mol. Phylogenet. Evol. 5, 344-351.
-
(1996)
Mol. Phylogenet. Evol.
, vol.5
, pp. 344-351
-
-
Quinn, T.W.1
Mindell, D.P.2
-
33
-
-
0030773749
-
A nonparametric approach to estimating divergence times in the absence of rate constancy
-
Sanderson, M.J., 1997. A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol. Biol. Evol. 14, 1218-1231.
-
(1997)
Mol. Biol. Evol.
, vol.14
, pp. 1218-1231
-
-
Sanderson, M.J.1
-
34
-
-
0028348061
-
Evolution of the Wancy region in amniote mitochondrial DNA
-
Seutin, G., Lang, B.F., Mindell, D.P., Morais, R., 1994. Evolution of the WANCY region in amniote mitochondrial DNA. Mol. Biol. Evol. 11, 329-340.
-
(1994)
Mol. Biol. Evol.
, vol.11
, pp. 329-340
-
-
Seutin, G.1
Lang, B.F.2
Mindell, D.P.3
Morais, R.4
-
35
-
-
0031152764
-
Tests of turtle phylogeny: Molecular, morphological, and paleontological approaches
-
Shaffer, H.B., Meylan, P., McKnight, M.L., 1997. Tests of turtle phylogeny: molecular, morphological, and paleontological approaches. Syst. Biol. 46, 235-268.
-
(1997)
Syst. Biol.
, vol.46
, pp. 235-268
-
-
Shaffer, H.B.1
Meylan, P.2
McKnight, M.L.3
-
36
-
-
0036623258
-
An approximately unbiased test of phylogenetic tree selection
-
Shimodaira, H., 2002. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 51, 492-508.
-
(2002)
Syst. Biol.
, vol.51
, pp. 492-508
-
-
Shimodaira, H.1
-
37
-
-
0032766857
-
Multiple comparisons of log-likelihoods with applications to phylogenetic inference
-
Shimodaira, H., Hasegawa, M., 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16, 1114-1116.
-
(1999)
Mol. Biol. Evol.
, vol.16
, pp. 1114-1116
-
-
Shimodaira, H.1
Hasegawa, M.2
-
38
-
-
0036139287
-
Consel: For assessing the confidence of phylogenetic tree selection
-
Shimodaira, H., Hasegawa, M., 2001. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17, 1246-1247.
-
(2001)
Bioinformatics
, vol.17
, pp. 1246-1247
-
-
Shimodaira, H.1
Hasegawa, M.2
-
39
-
-
0033161156
-
Primers for a PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates
-
Sorenson, M.D., Ast, J.C., Dimcheff, D.E., Yuri, T., Mindell, D.P., 1999. Primers for a PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates. Mol. Phylogenet. Evol. 12, 105-114.
-
(1999)
Mol. Phylogenet. Evol.
, vol.12
, pp. 105-114
-
-
Sorenson, M.D.1
Ast, J.C.2
Dimcheff, D.E.3
Yuri, T.4
Mindell, D.P.5
-
40
-
-
41049111540
-
Inferring confidence sets of possibly misspecified gene trees
-
Strimmer, K., Rambaut, A., 2002. Inferring confidence sets of possibly misspecified gene trees. Proc. R. Soc. Lond. B 269, 137-142.
-
(2002)
Proc. R. Soc. Lond. B
, vol.269
, pp. 137-142
-
-
Strimmer, K.1
Rambaut, A.2
-
41
-
-
0037058983
-
Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics
-
Suzuki, Y., Glazko, G.V., Nei, M., 2002. Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc. Natl. Acad. Sci. USA 99, 16138-16143.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 16138-16143
-
-
Suzuki, Y.1
Glazko, G.V.2
Nei, M.3
-
42
-
-
84870782940
-
-
Sinauer, Sunderland, MA
-
Swofford, D.L., 2001. PAUP*. Sinauer, Sunderland, MA.
-
(2001)
PAUP*
-
-
Swofford, D.L.1
-
43
-
-
0036093630
-
RNAs in Trypanosoma brucei: Genomic organization, expression, and mitochondrial import
-
Tan, T.H.P., Pach, R., Crausaz, A., Ivens, A., Schneider, A., 2002. tRNAs in Trypanosoma brucei: genomic organization, expression, and mitochondrial import. Mol. Cell. Biol. 22, 3707-3716.
-
(2002)
Mol. Cell. Biol.
, vol.22
, pp. 3707-3716
-
-
Tan, T.H.P.1
Pach, R.2
Crausaz, A.3
Ivens, A.4
Schneider, A.5
-
44
-
-
0034677761
-
A fossil snake with limbs
-
Tchernov, E., Rieppel, O., Zaher, H., Polcyn, M.J., Jacobs, L.L., 2000. A fossil snake with limbs. Science 287, 2010-2012.
-
(2000)
Science
, vol.287
, pp. 2010-2012
-
-
Tchernov, E.1
Rieppel, O.2
Zaher, H.3
Polcyn, M.J.4
Jacobs, L.L.5
-
45
-
-
0021084212
-
Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes
-
Templeton, A.R., 1983. Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes. Evolution 37, 221-244.
-
(1983)
Evolution
, vol.37
, pp. 221-244
-
-
Templeton, A.R.1
-
46
-
-
0000016993
-
The eye
-
Gans, C. (Ed.), Academic Press, New York
-
Underwood, G., 1970. The eye. In: Gans, C. (Ed.), Biology of the Reptilia. Academic Press, New York, pp. 1-97.
-
(1970)
Biology of the Reptilia
, pp. 1-97
-
-
Underwood, G.1
-
47
-
-
0035752767
-
A phylogeneticfoundation for comparative mammalian genomics
-
Waddell, P.J., Kishino, H., Ota, R., 2001. A phylogeneticfoundation for comparative mammalian genomics. Genome Informat. 12, 141-154.
-
(2001)
Genome Informat.
, vol.12
, pp. 141-154
-
-
Waddell, P.J.1
Kishino, H.2
Ota, R.3
-
48
-
-
0033085003
-
Assessing the Cretaceous superordinal divergence times within birds and placental mammals using whole mitochondrial protein sequences and an extended statistical framework
-
Waddell, P.J., Cao, Y., Hasegawa, M., Mindell, D.P., 1999. Assessing the Cretaceous superordinal divergence times within birds and placental mammals using whole mitochondrial protein sequences and an extended statistical framework. Syst. Biol. 48, 119-137.
-
(1999)
Syst. Biol.
, vol.48
, pp. 119-137
-
-
Waddell, P.J.1
Cao, Y.2
Hasegawa, M.3
Mindell, D.P.4
-
49
-
-
0036431235
-
Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support
-
Wilcox, T.P., Zwickl, D.J., Heath, T.A., Hillis, D.M., 2002. Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support. Mol. Phylogenet. Evol. 25, 361-371.
-
(2002)
Mol. Phylogenet. Evol.
, vol.25
, pp. 361-371
-
-
Wilcox, T.P.1
Zwickl, D.J.2
Heath, T.A.3
Hillis, D.M.4
-
50
-
-
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
-
51
-
-
0030749810
-
Bayesian phylogenetic inference using DNA sequences: A Markov Chain Monte Carlo method
-
Yang, Z., Rannala, B., 1997. Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo method. Mol. Biol. Evol. 14, 717-724.
-
(1997)
Mol. Biol. Evol.
, vol.14
, pp. 717-724
-
-
Yang, Z.1
Rannala, B.2
-
52
-
-
0032729882
-
Complete DNA sequence of the mitochondrial genome of the ascidian Halocynthia roretxi (Chordata, Urochordata)
-
Yokobori, S., Ueda, T., Feldmaier-Fuchs, G., Pääbo, S., Ueshima, R., Kondow, A., Nishikawa, K., Watanabe, K., 1999. Complete DNA sequence of the mitochondrial genome of the ascidian Halocynthia roretxi (Chordata, Urochordata). Genetics 153, 1851-1862.
-
(1999)
Genetics
, vol.153
, pp. 1851-1862
-
-
Yokobori, S.1
Ueda, T.2
Feldmaier-Fuchs, G.3
Pääbo, S.4
Ueshima, R.5
Kondow, A.6
Nishikawa, K.7
Watanabe, K.8
-
53
-
-
0034044256
-
Mitochondrial evidence on the phylogenetic position of caecilians (Amphibia: Gymnophiona)
-
Zardoya, R., Meyer, A., 2000. Mitochondrial evidence on the phylogenetic position of caecilians (Amphibia: Gymnophiona). Genetics 155, 765-775.
-
(2000)
Genetics
, vol.155
, pp. 765-775
-
-
Zardoya, R.1
Meyer, A.2
|