-
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., S. Zoller, and F. Lutzoni. 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
-
-
1342309210
-
Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference
-
Altekar, G., S. Dwarkadas, J. P. Huelsenbeck, and F. Ronquist. 2004. Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics 20:407-415.
-
(2004)
Bioinformatics
, vol.20
, pp. 407-415
-
-
Altekar, G.1
Dwarkadas, S.2
Huelsenbeck, J.P.3
Ronquist, F.4
-
3
-
-
0019423856
-
Sequence and organization of the human mitochondrial genome
-
Anderson, S., A. T. Bankier, B. G. Barrell, M. H. L. de Bruijn, A. R. Coulson, J. Drouin, I. C. Eperon, D. P. Nierlich, B. A. Roe, F. Sanger, P. H. Schreier, A. J. H. Smith, R. Staden, and I. G. Young. 1981. Sequence and organization of the human mitochondrial genome. Nature 290: 457-465.
-
(1981)
Nature
, vol.290
, pp. 457-465
-
-
Anderson, S.1
Bankier, A.T.2
Barrell, B.G.3
De Bruijn, M.H.L.4
Coulson, A.R.5
Drouin, J.6
Eperon, I.C.7
Nierlich, D.P.8
Roe, B.A.9
Sanger, F.10
Schreier, P.H.11
Smith, A.J.H.12
Staden, R.13
Young, I.G.14
-
4
-
-
0002365848
-
Fishbiogeography and molecular clocks: Perspectives from the Panamanian Isthmus
-
(T. D. Kocher, and C. A. Stepien, eds.). Academic Press, San Diego, California
-
Bermingham, E., S. S. McCafferty, and A. P. Martin. 1997. Fishbiogeography and molecular clocks: Perspectives from the Panamanian Isthmus. Pages 113-128 in Molecular systematics of fishes (T. D. Kocher, and C. A. Stepien, eds.). Academic Press, San Diego, California.
-
(1997)
Molecular Systematics of Fishes
, pp. 113-128
-
-
Bermingham, E.1
McCafferty, S.S.2
Martin, A.P.3
-
5
-
-
43949160320
-
Branch support and tree stability
-
Bremer, K. 1994. Branch support and tree stability. Cladistics 10:295-304.
-
(1994)
Cladistics
, vol.10
, pp. 295-304
-
-
Bremer, K.1
-
6
-
-
0036623259
-
Model misspecification and probabilistic tests of topology: Evidence from empirical data sets
-
Buckley T. R. 2002. Model misspecification and probabilistic tests of topology: Evidence from empirical data sets. Syst. Biol. 51:509-523.
-
(2002)
Syst. Biol.
, vol.51
, pp. 509-523
-
-
Buckley, T.R.1
-
7
-
-
0035143485
-
Evaluating hypotheses on the origin and evolution of the New Zealand alpine cicadas (Maoricicada) using multiple-comparison tests of tree topology
-
Buckley, T. R., C. Simon, S. Shimodaira, and G. K. Chambers. 2001. Evaluating hypotheses on the origin and evolution of the New Zealand alpine cicadas (Maoricicada) using multiple-comparison tests of tree topology. Mol. Biol. Evol. 18:223-234.
-
(2001)
Mol. Biol. Evol.
, vol.18
, pp. 223-234
-
-
Buckley, T.R.1
Simon, C.2
Shimodaira, S.3
Chambers, G.K.4
-
8
-
-
11844257707
-
Phylogenetic evidence for a major reversal of life-history evolution in plethodontid salamanders
-
Chippindale, P. T., R. M. Bonnet, A. S. Baldwin, and J. J. Wiens. 2004. Phylogenetic evidence for a major reversal of life-history evolution in plethodontid salamanders. Evolution 58:2809-2822.
-
(2004)
Evolution
, vol.58
, pp. 2809-2822
-
-
Chippindale, P.T.1
Bonnet, R.M.2
Baldwin, A.S.3
Wiens, J.J.4
-
9
-
-
0024927549
-
Phylogenies and the analysis of evolutionary sequences, with examples from seed plants
-
Donoghue, M. J. 1989. Phylogenies and the analysis of evolutionary sequences, with examples from seed plants. Evolution 43:1137-1156.
-
(1989)
Evolution
, vol.43
, pp. 1137-1156
-
-
Donoghue, M.J.1
-
10
-
-
0001610065
-
The suitability of molecular and morphological evidence in reconstructing plant phylogeny
-
(P. S. Soltis, D. E. Soltis, and J. J, Doyle, eds.). Chapman and Hall, New York
-
Donoghue, M. J., and M. J. Sanderson. 1992. The suitability of molecular and morphological evidence in reconstructing plant phylogeny. Pages 340-368 in Molecular systematics of plants (P. S. Soltis, D. E. Soltis, and J. J, Doyle, eds.). Chapman and Hall, New York.
-
(1992)
Molecular Systematics of Plants
, pp. 340-368
-
-
Donoghue, M.J.1
Sanderson, M.J.2
-
12
-
-
84959798530
-
Cases in which parsimony or compatibility methods will be positively misleading
-
Felsenstein, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27:401-410.
-
(1978)
Syst. Zool.
, vol.27
, pp. 401-410
-
-
Felsenstein, J.1
-
13
-
-
0001641598
-
Confidence limits on phylogenies with a molecular clock
-
Felsenstein, J. 1985. Confidence limits on phylogenies with a molecular clock. Syst. Zool. 34:152-161.
-
(1985)
Syst. Zool.
, vol.34
, pp. 152-161
-
-
Felsenstein, J.1
-
14
-
-
0035527390
-
Phylogeny of Saxifragales (Angiosperms, Eudicots): Analysis of a rapid, ancient radiation
-
Fishbein, M., C. Hibsch-Jetter, D. E. Soltis, and L. Hufford. 2001. Phylogeny of Saxifragales (Angiosperms, Eudicots): Analysis of a rapid, ancient radiation. Syst. Biol. 50:817-847.
-
(2001)
Syst. Biol.
, vol.50
, pp. 817-847
-
-
Fishbein, M.1
Hibsch-Jetter, C.2
Soltis, D.E.3
Hufford, L.4
-
15
-
-
0035967144
-
Late Jurassic salamanders from northern China
-
Gao, K. Q., and N. H. Shubin. 2001. Late Jurassic salamanders from northern China. Nature 410:574-577.
-
(2001)
Nature
, vol.410
, pp. 574-577
-
-
Gao, K.Q.1
Shubin, N.H.2
-
16
-
-
0037468807
-
Earliest known crown-group salamanders
-
Gao, K. Q., and N. H. Shubin. 2003. Earliest known crown-group salamanders. Nature 422:424-428.
-
(2003)
Nature
, vol.422
, pp. 424-428
-
-
Gao, K.Q.1
Shubin, N.H.2
-
17
-
-
0034351387
-
Likelihood-based tests of topologies in phylogenetics
-
Goldman, N., J. P. Anderson, and A. G. Rodrigo. 2000. Likelihood-based tests of topologies in phylogenetics. Syst. Biol. 49:652-670.
-
(2000)
Syst. Biol.
, vol.49
, pp. 652-670
-
-
Goldman, N.1
Anderson, J.P.2
Rodrigo, A.G.3
-
18
-
-
0034079389
-
Statistical tests of gamma-distributed rate heterogeneity in models of sequence evolution in phylogenetics
-
Goldman, N., and S. Whelan. 2000. Statistical tests of gamma-distributed rate heterogeneity in models of sequence evolution in phylogenetics. Mol. Biol. Evol. 17:975-978.
-
(2000)
Mol. Biol. Evol.
, vol.17
, pp. 975-978
-
-
Goldman, N.1
Whelan, S.2
-
19
-
-
22444455331
-
Considerations for reconstructing metazoan history: Signal, resolution, and hypothesis testing
-
Halanych, K. M. 1998. Considerations for reconstructing metazoan history: Signal, resolution, and hypothesis testing. Am. Zool. 38:929-941.
-
(1998)
Am. Zool.
, vol.38
, pp. 929-941
-
-
Halanych, K.M.1
-
20
-
-
0033087736
-
Cytochrome b phylogeny of North American hares and jackrabbits (Lepus, Lagomorpha) and the effects of saturation in outgroup taxa
-
Halanych, K. M., J. R. Demboski, J. R., B. J. van Vuuren, D. R. Klein, and J. A. Cook. 1999. Cytochrome b phylogeny of North American hares and jackrabbits (Lepus, Lagomorpha) and the effects of saturation in outgroup taxa. Mol. Phylogenet. Evol. 11:213-221.
-
(1999)
Mol. Phylogenet. Evol.
, vol.11
, pp. 213-221
-
-
Halanych, K.M.1
Demboski, J.R.2
Van Vuuren, B.J.3
Klein, D.R.4
Cook, J.A.5
-
21
-
-
0022376704
-
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
-
Hasegawa, M., H. Kishino, and T. Yano. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 21:160-174.
-
(1985)
J. Mol. Evol.
, vol.21
, pp. 160-174
-
-
Hasegawa, M.1
Kishino, H.2
Yano, T.3
-
22
-
-
0029132262
-
Phylogenetic relationships of amphibian families inferred from DNA sequences of mitochondrial 12S and 16S ribosomal RNA genes
-
Hay, J. M., I. Ruvinsky, S. B. Hedges, and L. R. Maxson. 1995. Phylogenetic relationships of amphibian families inferred from DNA sequences of mitochondrial 12S and 16S ribosomal RNA genes. Mol. Biol. Evol. 12:928-937.
-
(1995)
Mol. Biol. Evol.
, vol.12
, pp. 928-937
-
-
Hay, J.M.1
Ruvinsky, I.2
Hedges, S.B.3
Maxson, L.R.4
-
23
-
-
0029834661
-
Inferring complex phylogenies
-
Hillis, D. M. 1996. Inferring complex phylogenies. Nature 383:130-131.
-
(1996)
Nature
, vol.383
, pp. 130-131
-
-
Hillis, D.M.1
-
24
-
-
0028362880
-
Application and accuracy of molecular phylogenies
-
Hillis, D. M., J. P. Huelsenbeck, and C. W. Cunningham. 1994. Application and accuracy of molecular phylogenies. Science 264: 671-677.
-
(1994)
Science
, vol.264
, pp. 671-677
-
-
Hillis, D.M.1
Huelsenbeck, J.P.2
Cunningham, C.W.3
-
25
-
-
0032832492
-
The evolution of diapause in the killifish family Rivulidae (Atherinomorpha, Cyprinodontiformes): A molecular phylogenetic and biogeographic perspective
-
Hrbek, T, and A. Larson. 1999. The evolution of diapause in the killifish family Rivulidae (Atherinomorpha, Cyprinodontiformes): A molecular phylogenetic and biogeographic perspective. Evolution 53:1200-1216.
-
(1999)
Evolution
, vol.53
, pp. 1200-1216
-
-
Hrbek, T.1
Larson, A.2
-
26
-
-
11944268967
-
Performance of phylogenetic methods in simulation
-
Huelsenbeck, J. P. 1995. Performance of phylogenetic methods in simulation. Syst. Biol. 44:17-48.
-
(1995)
Syst. Biol.
, vol.44
, pp. 17-48
-
-
Huelsenbeck, J.P.1
-
27
-
-
0031084114
-
Is the Felsenstein zone a fly trap?
-
Huelsenbeck, J. P. 1997. Is the Felsenstein zone a fly trap? Syst. Biol. 46:69-74.
-
(1997)
Syst. Biol.
, vol.46
, pp. 69-74
-
-
Huelsenbeck, J.P.1
-
28
-
-
0032148641
-
Systematic bias in phylogenetic analysis: Is the Strepsiptera problem solved?
-
Huelsenbeck, J. P. 1998. Systematic bias in phylogenetic analysis: Is the Strepsiptera problem solved? Syst. Biol. 47:519-537.
-
(1998)
Syst. Biol.
, vol.47
, pp. 519-537
-
-
Huelsenbeck, J.P.1
-
29
-
-
0034849408
-
MRBAYES: Bayesian inference of phylogenetic trees
-
Huelsenbeck, J. P., and F. Ronquist. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755.
-
(2001)
Bioinformatics
, vol.17
, pp. 754-755
-
-
Huelsenbeck, J.P.1
Ronquist, F.2
-
30
-
-
0035861456
-
Bayesian inference of phylogeny and its impact on evolutionary biology
-
Huelsenbeck, J. P., F. Ronquist, R. Nielsen, and J. P. Bollback. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294:2310-2314.
-
(2001)
Science
, vol.294
, pp. 2310-2314
-
-
Huelsenbeck, J.P.1
Ronquist, F.2
Nielsen, R.3
Bollback, J.P.4
-
31
-
-
0033457132
-
Phylogenetic relationships and tempo of early diversification in Anolis lizards
-
Jackman, T. R., A. Larson, K. de Queiroz, and J. B. Losos. 1999. Phylogenetic relationships and tempo of early diversification in Anolis lizards. Syst. Biol. 48:254-285.
-
(1999)
Syst. Biol.
, vol.48
, pp. 254-285
-
-
Jackman, T.R.1
Larson, A.2
De Queiroz, K.3
Losos, J.B.4
-
32
-
-
0033823253
-
Tests of Pleistocene speciation in montane grasshoppers (genus Melanopus) from the sky islands of western North America
-
Knowles, L. L. 2000. Tests of Pleistocene speciation in montane grasshoppers (genus Melanopus) from the sky islands of western North America. Evolution 54:1337-1348.
-
(2000)
Evolution
, vol.54
, pp. 1337-1348
-
-
Knowles, L.L.1
-
33
-
-
0027482104
-
Sequence evolution of mitochondrial transfer RNA genes and deep-branch animal phylogenetics
-
Kumazawa, Y., and M. Nishida. 1993. Sequence evolution of mitochondrial transfer RNA genes and deep-branch animal phylogenetics. J. Mol. Evol. 37:380-398.
-
(1993)
J. Mol. Evol.
, vol.37
, pp. 380-398
-
-
Kumazawa, Y.1
Nishida, M.2
-
34
-
-
0032976397
-
Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees
-
Larget, B., and D. L. Simon. 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
-
35
-
-
0000831631
-
A molecular perspective on the evolutionary relationships of the salamander families
-
Larson, A. 1991. A molecular perspective on the evolutionary relationships of the salamander families. Evol. Biol. 25:211-277.
-
(1991)
Evol. Biol.
, vol.25
, pp. 211-277
-
-
Larson, A.1
-
36
-
-
0000543596
-
The comparison of morphological and molecular data in phylogenetic systematics
-
(R. DeSalle, and B. Schierwater, eds.). Birkhäuser Verlag, Basel, Switzerland
-
Larson, A. 1998. The comparison of morphological and molecular data in phylogenetic systematics. Pages 275-296 in Molecular ecology and evolution: Approaches and applications (R. DeSalle, and B. Schierwater, eds.). Birkhäuser Verlag, Basel, Switzerland.
-
(1998)
Molecular Ecology and Evolution: Approaches and Applications
, pp. 275-296
-
-
Larson, A.1
-
37
-
-
0000909790
-
Phylogenetic relationships of the salamander families: An analysis of congruence among morphological and molecular characters
-
Larson, A., and W. W. Dimmick. 1993. Phylogenetic relationships of the salamander families: An analysis of congruence among morphological and molecular characters. Herpetol. Monogr. 7:77-93.
-
(1993)
Herpetol. Monogr.
, vol.7
, pp. 77-93
-
-
Larson, A.1
Dimmick, W.W.2
-
38
-
-
0141664844
-
Phylogenetic systematics of salamanders (Amphibia: Urodela), a review
-
D. M. Sever (ed.). Science Publishers, Inc., Enfield, New Hampshire
-
Larson, A., D. W. Weisrock and K. H. Kozak. 2003. Phylogenetic systematics of salamanders (Amphibia: Urodela), a review. Pages 31-108 in Reproductive biology and phylogeny of Urodela (Amphibia) (D. M. Sever (ed.). Science Publishers, Inc., Enfield, New Hampshire.
-
(2003)
Reproductive Biology and Phylogeny of Urodela (Amphibia)
, pp. 31-108
-
-
Larson, A.1
Weisrock, D.W.2
Kozak, K.H.3
-
39
-
-
2442581218
-
The importance of proper model assumption in Bayesian phylogenetics
-
Lemmon, A. R. and E. C. Moriarty. 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
-
40
-
-
0035527396
-
A likelihood approach to estimating phylogeny from discrete morphological character data
-
Lewis, P. O. 2001. A likelihood approach to estimating phylogeny from discrete morphological character data. Syst. Biol. 50:913-925.
-
(2001)
Syst. Biol.
, vol.50
, pp. 913-925
-
-
Lewis, P.O.1
-
41
-
-
0031012089
-
Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome
-
Macey, J. R., A. Larson, N. B. Ananjeva, Z. L. Fang, and T. J. Papenfuss. 1997a. Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome. Mol. Biol. Evol. 14:91-104.
-
(1997)
Mol. Biol. Evol.
, vol.14
, pp. 91-104
-
-
Macey, J.R.1
Larson, A.2
Ananjeva, N.B.3
Fang, Z.L.4
Papenfuss, T.J.5
-
42
-
-
0031031728
-
Replication slippage may cause parallel evolution in the secondary structures of mitochondrial transfer RNAs
-
Macey, J. R., A. Larson, N. B. Ananjeva, and T. J. Papenfuss. 1997b. Replication slippage may cause parallel evolution in the secondary structures of mitochondrial transfer RNAs. Mol. Biol. Evol. 14:30-39.
-
(1997)
Mol. Biol. Evol.
, vol.14
, pp. 30-39
-
-
Macey, J.R.1
Larson, A.2
Ananjeva, N.B.3
Papenfuss, T.J.4
-
43
-
-
0032132881
-
Phylogenetic relationships among agamid lizards of the Laudakia caucasia species group: Testing hypotheses of biogeographic fragmentation and an area cladogram for the Iranian Plateau
-
Macey, J. R., J. A. Schulte, N. B. Ananjeva, A. Larson, N. Rastegar-Pouyani, S. M. Shammakov, and T. J. Papenfuss. 1998a. Phylogenetic relationships among agamid lizards of the Laudakia caucasia species group: Testing hypotheses of biogeographic fragmentation and an area cladogram for the Iranian Plateau. Mol. Phylogenet. Evol. 10:118-131.
-
(1998)
Mol. Phylogenet. Evol.
, vol.10
, pp. 118-131
-
-
Macey, J.R.1
Schulte, J.A.2
Ananjeva, N.B.3
Larson, A.4
Rastegar-Pouyani, N.5
Shammakov, S.M.6
Papenfuss, T.J.7
-
44
-
-
0034350424
-
Evaluating trans-Tethys migration: An example using acrodont lizard phylogenetics
-
Macey, J. R., J. A. Schulte, A. Larson, N. B. Ananjeva, Y. Z. Wang, R. Pethiyagoda, N. Rastegar-Pouyani, and T. J. Papenfuss. 2000. Evaluating trans-Tethys migration: An example using acrodont lizard phylogenetics. Syst. Biol. 49:233-256.
-
(2000)
Syst. Biol.
, vol.49
, pp. 233-256
-
-
Macey, J.R.1
Schulte, J.A.2
Larson, A.3
Ananjeva, N.B.4
Wang, Y.Z.5
Pethiyagoda, R.6
Rastegar-Pouyani, N.7
Papenfuss, T.J.8
-
45
-
-
0031992652
-
Phylogenetic relationships of toads in the Bufo bufo species group from the eastern escarpment of the Tibetan Plateau: A case of vicariance and dispersal
-
Macey, J. R., J. A. Schulte, A. Larson, Z. L. Fang, Y. Z. Wang, B. S. Tuniyev, and T. J. Papenfuss. 1998b. Phylogenetic relationships of toads in the Bufo bufo species group from the eastern escarpment of the Tibetan Plateau: A case of vicariance and dispersal. Mol. Phylogenet. Evol. 9:80-87.
-
(1998)
Mol. Phylogenet. Evol.
, vol.9
, pp. 80-87
-
-
Macey, J.R.1
Schulte, J.A.2
Larson, A.3
Fang, Z.L.4
Wang, Y.Z.5
Tuniyev, B.S.6
Papenfuss, T.J.7
-
46
-
-
0033176443
-
Molecular phylogenetics, tRNA evolution, and historical biogeography in anguid lizards and related taxonomic families
-
Macey, J. R., J. A. Schulte, A. Larson, B. S. Tuniyev, N. Orlov, and T. J. Papenfuss. 1999. Molecular phylogenetics, tRNA evolution, and historical biogeography in anguid lizards and related taxonomic families. Mol. Phylogenet. Evol. 12:250-272.
-
(1999)
Mol. Phylogenet. Evol.
, vol.12
, pp. 250-272
-
-
Macey, J.R.1
Schulte, J.A.2
Larson, A.3
Tuniyev, B.S.4
Orlov, N.5
Papenfuss, T.J.6
-
47
-
-
0034771902
-
Molecular phylogenetics of western North American frogs of the Rana boylii species group
-
Macey, J. R., J. L. Strasburg, J. A. Brisson, V. T. Vredenburg, M. Jennings, and A. Larson. 2001. Molecular phylogenetics of western North American frogs of the Rana boylii species group. Mol. Phylogenet. Evol. 19:131-143.
-
(2001)
Mol. Phylogenet. Evol.
, vol.19
, pp. 131-143
-
-
Macey, J.R.1
Strasburg, J.L.2
Brisson, J.A.3
Vredenburg, V.T.4
Jennings, M.5
Larson, A.6
-
48
-
-
0024940670
-
Reconstructing character evolution on polytomous cladograms
-
Maddison, W. P. 1989. Reconstructing character evolution on polytomous cladograms. Cladistics 5:365-377.
-
(1989)
Cladistics
, vol.5
, pp. 365-377
-
-
Maddison, W.P.1
-
49
-
-
0003766436
-
-
Sinauer Associates, Sunderland, Massachusetts
-
Maddison, W. P., and D. R. Maddison. 2000. MacClade4: Analysis of phylogeny and character evolution, version 4.0. Sinauer Associates, Sunderland, Massachusetts.
-
(2000)
MacClade4: Analysis of Phylogeny and Character Evolution, Version 4.0
-
-
Maddison, W.P.1
Maddison, D.R.2
-
50
-
-
0035152263
-
Phylogenetic signal and its decay in mitochondrial SSU and LSU rRNA gene fragments of Anisoptera
-
Misof, B., A. M. Rickert, T. R. Buckley, G. Fleck, and K. P. Sauer. 2001. Phylogenetic signal and its decay in mitochondrial SSU and LSU rRNA gene fragments of Anisoptera. Mol. Biol. Evol. 18:27-37.
-
(2001)
Mol. Biol. Evol.
, vol.18
, pp. 27-37
-
-
Misof, B.1
Rickert, A.M.2
Buckley, T.R.3
Fleck, G.4
Sauer, K.P.5
-
51
-
-
1642341403
-
Bayesian phylogenetic analysis of combined data
-
Nylander, J. A. A., F. Ronquist, J. P. Huelsenbeck, and J. L. Nieves-Aldrey. 2004. Bayesian phylogenetic analysis of combined data. Syst. Biol. 53:47-67.
-
(2004)
Syst. Biol.
, vol.53
, pp. 47-67
-
-
Nylander, J.A.A.1
Ronquist, F.2
Huelsenbeck, J.P.3
Nieves-Aldrey, J.L.4
-
52
-
-
0028578194
-
Can the Cambrian explosion be inferred through molecular phylogeny?
-
Cambridge
-
Philippe, H., A. Chenuil, and A. Adoutte. 1994. Can the Cambrian explosion be inferred through molecular phylogeny? Development (Cambridge) Supplement:15-25.
-
(1994)
Development
, Issue.SUPPL.
, pp. 15-25
-
-
Philippe, H.1
Chenuil, A.2
Adoutte, A.3
-
53
-
-
0038487279
-
Evaluation of the strategy of long-branch subdivision to improve accuracy of phylogenetic methods
-
Poe, S. 2003. Evaluation of the strategy of long-branch subdivision to improve accuracy of phylogenetic methods. Syst. Biol. 52:423-428.
-
(2003)
Syst. Biol.
, vol.52
, pp. 423-428
-
-
Poe, S.1
-
54
-
-
1642401431
-
Birds in a bush: Five genes indicate explosive evolution of avian orders
-
Poe, S., and A. L. Chubb. 2004. Birds in a bush: Five genes indicate explosive evolution of avian orders. Syst. Biol. 58:404-415.
-
(2004)
Syst. Biol.
, vol.58
, pp. 404-415
-
-
Poe, S.1
Chubb, A.L.2
-
55
-
-
0033602474
-
Taxon sampling revisited
-
Poe, S., and D. L. Swofford. 1999. Taxon sampling revisited. Nature 398:299-300.
-
(1999)
Nature
, vol.398
, pp. 299-300
-
-
Poe, S.1
Swofford, D.L.2
-
56
-
-
0031773680
-
Model Test: Testing the model of DNA substitution
-
Posada, D., and K. A. Crandall. 1998. Model Test: Testing the model of DNA substitution. Bioinformatics 14:817-818.
-
(1998)
Bioinformatics
, vol.14
, pp. 817-818
-
-
Posada, D.1
Crandall, K.A.2
-
57
-
-
0030928378
-
Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
-
Rambaut, A., and N. C. Grassly. 1997. Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13:235-238.
-
(1997)
Comput. Appl. Biosci.
, vol.13
, pp. 235-238
-
-
Rambaut, A.1
Grassly, N.C.2
-
59
-
-
0019885846
-
Nucleotide sequence of Xenopus laevis 18S ribosomal RNA inferred from the gene sequence
-
Salim, M., and B. E. H. Maden. 1981. Nucleotide sequence of Xenopus laevis 18S ribosomal RNA inferred from the gene sequence. Nature 291:205-208.
-
(1981)
Nature
, vol.291
, pp. 205-208
-
-
Salim, M.1
Maden, B.E.H.2
-
61
-
-
0026279545
-
Comparative anatomy and phylogeny of the cloacae of salamanders (Amphibia, Caudata). 1. Evolution at the family level
-
Sever, D. M. 1991a. Comparative anatomy and phylogeny of the cloacae of salamanders (Amphibia, Caudata). 1. Evolution at the family level. Herpetologica 47:165-193.
-
(1991)
Herpetologica
, vol.47
, pp. 165-193
-
-
Sever, D.M.1
-
62
-
-
84993907771
-
Comparative anatomy and phylogeny of the cloacae of salamanders (Amphibia, Caudata). 2. Cryptobranchidae, Hynobiidae, and Sirenidae
-
Sever, D. M. 1991b. Comparative anatomy and phylogeny of the cloacae of salamanders (Amphibia, Caudata). 2. Cryptobranchidae, Hynobiidae, and Sirenidae. J. Morphol. 207:283-301.
-
(1991)
J. Morphol.
, vol.207
, pp. 283-301
-
-
Sever, D.M.1
-
63
-
-
0000374135
-
Observations on regionalization of secretory activity in the spermathecae of salamanders and comments on phylogeny of sperm storage in female amphibians
-
Sever, D. M. 1994. Observations on regionalization of secretory activity in the spermathecae of salamanders and comments on phylogeny of sperm storage in female amphibians. Herpetologica 50:383-397.
-
(1994)
Herpetologica
, vol.50
, pp. 383-397
-
-
Sever, D.M.1
-
64
-
-
3643075026
-
Comparative biology of sperm storage in female salamanders
-
Sever, D.M., and R. Brizzi. 1998. Comparative biology of sperm storage in female salamanders. J. Exp. Zool. 282:460-476.
-
(1998)
J. Exp. Zool.
, vol.282
, pp. 460-476
-
-
Sever, D.M.1
Brizzi, R.2
-
65
-
-
0011209185
-
Reproduction of the salamander Siren intermedia Le Conte with special reference to oviducal anatomy and mode of fertilization
-
Sever, D. M., L. C. Rania, and J. D. Krenz. 1996. Reproduction of the salamander Siren intermedia Le Conte with special reference to oviducal anatomy and mode of fertilization. J. Morphol. 227:335-348.
-
(1996)
J. Morphol.
, vol.227
, pp. 335-348
-
-
Sever, D.M.1
Rania, L.C.2
Krenz, J.D.3
-
66
-
-
0032766857
-
Multiple comparisons of log-likelihoods with applications to phylogenetic inference
-
Shimodaira, H., and M. Hasegawa. 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
-
70
-
-
0002618746
-
Are guinea pigs rodents? The utility of models in molecular phylogenetics
-
Sullivan, J., and D. L. Swofford. 1997. Are guinea pigs rodents? The utility of models in molecular phylogenetics. J. Mammal. Evol. 4:77-86.
-
(1997)
J. Mammal. Evol.
, vol.4
, pp. 77-86
-
-
Sullivan, J.1
Swofford, D.L.2
-
71
-
-
0037058983
-
Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics
-
USA
-
Suzuki, Y., G. V. Glazko, and M. Nei. 2002. Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc. Natl. Acad. Sci. USA 99:16138-16143.
-
(2002)
Proc. Natl. Acad. Sci.
, vol.99
, pp. 16138-16143
-
-
Suzuki, Y.1
Glazko, G.V.2
Nei, M.3
-
73
-
-
31344481026
-
Optimality criteria II: Methods based on models of evolutionary change
-
(D. M. Hillis, C. Moritz, and B. K. Mable, eds.). Sinauer Associates, Sunderland, Massachusetts
-
Swofford, D. L., G. J. Olsen, P. J. Waddell, and D. M. Hillis. 1996. Optimality criteria II: Methods based on models of evolutionary change. Pages 426-503 in Molecular systematics (D. M. Hillis, C. Moritz, and B. K. Mable, eds.). Sinauer Associates, Sunderland, Massachusetts.
-
(1996)
Molecular Systematics
, pp. 426-503
-
-
Swofford, D.L.1
Olsen, G.J.2
Waddell, P.J.3
Hillis, D.M.4
-
74
-
-
0035527406
-
Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods
-
Swofford, D. L., P. J. Waddell, J. P. Huelsenbeck, P. G. Foster, P. O. Lewis, and J. S. Rogers. 2001. Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Syst. Biol. 50:525-539.
-
(2001)
Syst. Biol.
, vol.50
, pp. 525-539
-
-
Swofford, D.L.1
Waddell, P.J.2
Huelsenbeck, J.P.3
Foster, P.G.4
Lewis, P.O.5
Rogers, J.S.6
-
75
-
-
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
-
76
-
-
0029494866
-
A molecular phylogenetic perspective on the evolutionary radiation of the salamander family Salamandridae
-
Titus, T. A., and A. Larson. 1995. A molecular phylogenetic perspective on the evolutionary radiation of the salamander family Salamandridae. Syst. Biol. 44:125-151.
-
(1995)
Syst. Biol.
, vol.44
, pp. 125-151
-
-
Titus, T.A.1
Larson, A.2
-
77
-
-
0346901954
-
Monophyly of the family Proteidae (Amphibia: Caudata) tested by phylogenetic analysis of mitochondrial 12S rDNA sequences
-
Trontelj, P., and S. Goricki. 2003. Monophyly of the family Proteidae (Amphibia: Caudata) tested by phylogenetic analysis of mitochondrial 12S rDNA sequences. Nat. Croat. 12:113-120.
-
(2003)
Nat. Croat.
, vol.12
, pp. 113-120
-
-
Trontelj, P.1
Goricki, S.2
-
78
-
-
0000513819
-
Patterns of cranial diversity among the Lissamphibia
-
(J. Hanken, and B. K. Hall, eds.). University of Chicago Press, Chicago, Illinois
-
Trueb, L. 1993. Patterns of cranial diversity among the Lissamphibia. Pages 255-343 in The skull (J. Hanken, and B. K. Hall, eds.). University of Chicago Press, Chicago, Illinois.
-
(1993)
The Skull
, pp. 255-343
-
-
Trueb, L.1
-
79
-
-
0035752767
-
A phylogenetic foundation for comparative mammalian genomics
-
Waddell, P. J., H. Kishino, and H. Ota. 2001. A phylogenetic foundation for comparative mammalian genomics. Genome Informatics 12:141-154.
-
(2001)
Genome Informatics
, vol.12
, pp. 141-154
-
-
Waddell, P.J.1
Kishino, H.2
Ota, H.3
-
80
-
-
0032805794
-
Polytomies and the power of phylogenetic inference
-
Walsh, H. E., M. G. Kidd, T. Moum, and V. L. Friesen. 1999. Polytomies and the power of phylogenetic inference. Evolution 53:932-937.
-
(1999)
Evolution
, vol.53
, pp. 932-937
-
-
Walsh, H.E.1
Kidd, M.G.2
Moum, T.3
Friesen, V.L.4
-
81
-
-
0035731549
-
Molecular phylogenetics and historical biogeography among salamandrids of the "true" salamander clade: Rapid branching of numerous highly divergent lineages in Mertensiella luschani associated with the rise of Anatolia
-
Weisrock, D. W., J. R. Macey, I. H. Ugurtas, A. Larson, and T. J. Papenfuss. 2001. Molecular phylogenetics and historical biogeography among salamandrids of the "true" salamander clade: Rapid branching of numerous highly divergent lineages in Mertensiella luschani associated with the rise of Anatolia. Mol. Phylogenet. Evol. 18:434-448.
-
(2001)
Mol. Phylogenet. Evol.
, vol.18
, pp. 434-448
-
-
Weisrock, D.W.1
Macey, J.R.2
Ugurtas, I.H.3
Larson, A.4
Papenfuss, T.J.5
-
82
-
-
0042905752
-
Missing data, incomplete taxa, and phylogenetic accuracy
-
Wiens, J. J. 2003. Missing data, incomplete taxa, and phylogenetic accuracy. Syst. Biol. 52:528-538.
-
(2003)
Syst. Biol.
, vol.52
, pp. 528-538
-
-
Wiens, J.J.1
-
83
-
-
15944413439
-
Ontogeny discombobulates phylogeny: Paedomorphosis and higher-level salamander relationships
-
Wiens, J. J., R. M. Bonett, and P. T. Chippindale. 2005. Ontogeny discombobulates phylogeny: Paedomorphosis and higher-level salamander relationships. Syst. Biol. 54:91-110.
-
(2005)
Syst. Biol.
, vol.54
, pp. 91-110
-
-
Wiens, J.J.1
Bonett, R.M.2
Chippindale, P.T.3
-
84
-
-
0036431235
-
Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support
-
Wilcox, T. P., D. J. Zwickl, T. A. Heath, and D. M. Hillis. 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
-
85
-
-
0028064845
-
Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
-
Yang, Z. H. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. J. Mol. Evol. 39:306-314.
-
(1994)
J. Mol. Evol.
, vol.39
, pp. 306-314
-
-
Yang, Z.H.1
-
86
-
-
0030749810
-
Bayesian phylogenetic inference using DNA sequences: A Markov Chain Monte Carlo method
-
Yang, Z. H., and B. Rannala. 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.H.1
Rannala, B.2
|