-
1
-
-
0002331493
-
Molecular disease, evolution, and genic heterogeneity
-
Academic Press, M. Kasha, B. Pullman (Eds.)
-
Zuckerkandl E., Pauling L. Molecular disease, evolution, and genic heterogeneity. Horizons in Biochemistry 1962, 189-225. Academic Press. M. Kasha, B. Pullman (Eds.).
-
(1962)
Horizons in Biochemistry
, pp. 189-225
-
-
Zuckerkandl, E.1
Pauling, L.2
-
2
-
-
0014421064
-
Evolutionary rate at the molecular level
-
Kimura M. Evolutionary rate at the molecular level. Nature 1968, 217:624-626.
-
(1968)
Nature
, vol.217
, pp. 624-626
-
-
Kimura, M.1
-
3
-
-
0000941148
-
Evolutionary rate of cistrons and DNA divergence
-
Ohta T. Evolutionary rate of cistrons and DNA divergence. J. Mol. Evol. 1972, 1:150-157.
-
(1972)
J. Mol. Evol.
, vol.1
, pp. 150-157
-
-
Ohta, T.1
-
4
-
-
0014186296
-
Immunological time scale for hominid evolution
-
Sarich V.M., Wilson A.C. Immunological time scale for hominid evolution. Science 1967, 158:1200-1203.
-
(1967)
Science
, vol.158
, pp. 1200-1203
-
-
Sarich, V.M.1
Wilson, A.C.2
-
5
-
-
0020386088
-
A molecular-clock date for the origin of the animal phyla
-
Runnegar B. A molecular-clock date for the origin of the animal phyla. Lethaia 1982, 15:199-205.
-
(1982)
Lethaia
, vol.15
, pp. 199-205
-
-
Runnegar, B.1
-
6
-
-
0030023247
-
Determining divergence times of the major kingdoms of living organisms with a protein clock
-
Doolittle R.F., et al. Determining divergence times of the major kingdoms of living organisms with a protein clock. Science 1996, 271:470-477.
-
(1996)
Science
, vol.271
, pp. 470-477
-
-
Doolittle, R.F.1
-
7
-
-
20144362109
-
Molecular dating when rates vary
-
Welch J.J., Bromham L. Molecular dating when rates vary. Trends Ecol. Evol. 2005, 20:320-327.
-
(2005)
Trends Ecol. Evol.
, vol.20
, pp. 320-327
-
-
Welch, J.J.1
Bromham, L.2
-
8
-
-
22944437097
-
Molecular clocks: four decades of evolution
-
Kumar S. Molecular clocks: four decades of evolution. Nat. Rev. Genet. 2005, 6:654-662.
-
(2005)
Nat. Rev. Genet.
, vol.6
, pp. 654-662
-
-
Kumar, S.1
-
9
-
-
0037373563
-
The modern molecular clock
-
Bromham L., Penny D. The modern molecular clock. Nat. Rev. Genet. 2003, 4:216-224.
-
(2003)
Nat. Rev. Genet.
, vol.4
, pp. 216-224
-
-
Bromham, L.1
Penny, D.2
-
11
-
-
84859879901
-
The patterns and causes of variation in plant nucleotide substitution rates
-
Gaut B., et al. The patterns and causes of variation in plant nucleotide substitution rates. Annu. Rev. Ecol. Evol. Syst. 2011, 42:245-266.
-
(2011)
Annu. Rev. Ecol. Evol. Syst.
, vol.42
, pp. 245-266
-
-
Gaut, B.1
-
12
-
-
0015162882
-
The structures of cytochrome c and the rates of molecular evolution
-
Dickerson R.E. The structures of cytochrome c and the rates of molecular evolution. J. Mol. Evol. 1971, 1:26-45.
-
(1971)
J. Mol. Evol.
, vol.1
, pp. 26-45
-
-
Dickerson, R.E.1
-
13
-
-
79961055146
-
The genome as a life-history character: why rate of molecular evolution varies between mammal species
-
Bromham L. The genome as a life-history character: why rate of molecular evolution varies between mammal species. Philos. Trans. R. Soc. Lond. B 2011, 366:2503-2513.
-
(2011)
Philos. Trans. R. Soc. Lond. B
, vol.366
, pp. 2503-2513
-
-
Bromham, L.1
-
14
-
-
0023337434
-
On the overdispersed molecular clock
-
Takahata N. On the overdispersed molecular clock. Genetics 1987, 116:169-179.
-
(1987)
Genetics
, vol.116
, pp. 169-179
-
-
Takahata, N.1
-
15
-
-
0034100202
-
Understanding the overdispersed molecular clock
-
Cutler D.J. Understanding the overdispersed molecular clock. Genetics 2000, 154:1403-1417.
-
(2000)
Genetics
, vol.154
, pp. 1403-1417
-
-
Cutler, D.J.1
-
16
-
-
84870689997
-
Universal pacemaker of genome evolution
-
Snir S., et al. Universal pacemaker of genome evolution. PLOS Comput. Biol. 2012, 8:e1002785.
-
(2012)
PLOS Comput. Biol.
, vol.8
-
-
Snir, S.1
-
17
-
-
84891687862
-
Stability along with extreme variability in core genome evolution
-
Wolf Y.I., et al. Stability along with extreme variability in core genome evolution. Genome Biol. Evol. 2013, 5:1393-1402.
-
(2013)
Genome Biol. Evol.
, vol.5
, pp. 1393-1402
-
-
Wolf, Y.I.1
-
18
-
-
84902958031
-
Universal pacemaker of genome evolution in animals and fungi and variation of evolutionary rates in diverse organisms
-
Snir S., et al. Universal pacemaker of genome evolution in animals and fungi and variation of evolutionary rates in diverse organisms. Genome Biol. Evol. 2014, 6:1268-1278.
-
(2014)
Genome Biol. Evol.
, vol.6
, pp. 1268-1278
-
-
Snir, S.1
-
19
-
-
80053362389
-
Rate variation and estimation of divergence times using strict and relaxed clocks
-
Brown R.P., Yang Z. Rate variation and estimation of divergence times using strict and relaxed clocks. BMC Evol. Biol. 2011, 11:271.
-
(2011)
BMC Evol. Biol.
, vol.11
, pp. 271
-
-
Brown, R.P.1
Yang, Z.2
-
20
-
-
84857198898
-
A Dirichlet process prior for estimating lineage-specific substitution rates
-
Heath T.A., et al. A Dirichlet process prior for estimating lineage-specific substitution rates. Mol. Biol. Evol. 2012, 29:939-955.
-
(2012)
Mol. Biol. Evol.
, vol.29
, pp. 939-955
-
-
Heath, T.A.1
-
21
-
-
79955364420
-
Evaluation of Bayesian models of substitution rate evolution--parental guidance versus mutual independence
-
Linder M., et al. Evaluation of Bayesian models of substitution rate evolution--parental guidance versus mutual independence. Syst. Biol. 2011, 60:329-342.
-
(2011)
Syst. Biol.
, vol.60
, pp. 329-342
-
-
Linder, M.1
-
22
-
-
67649133122
-
An examination of phylogenetic models of substitution rate variation among lineages
-
Ho S.Y.W. An examination of phylogenetic models of substitution rate variation among lineages. Biol. Lett. 2009, 5:421-424.
-
(2009)
Biol. Lett.
, vol.5
, pp. 421-424
-
-
Ho, S.Y.W.1
-
23
-
-
37549001784
-
A general comparison of relaxed molecular clock models
-
Lepage T., et al. A general comparison of relaxed molecular clock models. Mol. Biol. Evol. 2007, 24:2669-2680.
-
(2007)
Mol. Biol. Evol.
, vol.24
, pp. 2669-2680
-
-
Lepage, T.1
-
24
-
-
17744387938
-
Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation
-
Ho S.Y.W., et al. Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation. Mol. Biol. Evol. 2005, 22:1355-1363.
-
(2005)
Mol. Biol. Evol.
, vol.22
, pp. 1355-1363
-
-
Ho, S.Y.W.1
-
25
-
-
84904666887
-
The impact of calibration and clock-model choice on molecular estimates of divergence times
-
Duchêne S., et al. The impact of calibration and clock-model choice on molecular estimates of divergence times. Mol. Phlyogenet. Evol. 2014, 78:277-289.
-
(2014)
Mol. Phlyogenet. Evol.
, vol.78
, pp. 277-289
-
-
Duchêne, S.1
-
26
-
-
84900337125
-
A synchronized global sweep of the internal genes of modern avian influenza virus
-
Worobey M., et al. A synchronized global sweep of the internal genes of modern avian influenza virus. Nature 2014, 508:254-257.
-
(2014)
Nature
, vol.508
, pp. 254-257
-
-
Worobey, M.1
-
27
-
-
77951997517
-
Performance of relaxed-clock methods in estimating evolutionary divergence times and their credibility intervals
-
Battistuzzi F.U., et al. Performance of relaxed-clock methods in estimating evolutionary divergence times and their credibility intervals. Mol. Biol. Evol. 2010, 27:1289-1300.
-
(2010)
Mol. Biol. Evol.
, vol.27
, pp. 1289-1300
-
-
Battistuzzi, F.U.1
-
28
-
-
0028064845
-
Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods
-
Yang Z. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 1994, 39:306-314.
-
(1994)
J. Mol. Evol.
, vol.39
, pp. 306-314
-
-
Yang, Z.1
-
29
-
-
84864346710
-
Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny
-
dos Reis M., et al. Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proc. R. Soc. Lond. B 2012, 279:3491-3500.
-
(2012)
Proc. R. Soc. Lond. B
, vol.279
, pp. 3491-3500
-
-
dos Reis, M.1
-
30
-
-
0036803223
-
Divergence time and evolutionary rate estimation with multilocus data
-
Thorne J.L., Kishino H. Divergence time and evolutionary rate estimation with multilocus data. Syst. Biol. 2002, 51:689-702.
-
(2002)
Syst. Biol.
, vol.51
, pp. 689-702
-
-
Thorne, J.L.1
Kishino, H.2
-
31
-
-
84902457782
-
The impact of the rate prior on Bayesian estimation of divergence times with multiple loci
-
dos Reis M., et al. The impact of the rate prior on Bayesian estimation of divergence times with multiple loci. Syst. Biol. 2014, 63:555-565.
-
(2014)
Syst. Biol.
, vol.63
, pp. 555-565
-
-
dos Reis, M.1
-
32
-
-
0037227363
-
Partitioning the variation in mammalian substitution rates
-
Smith N.G., Eyre-Walker A. Partitioning the variation in mammalian substitution rates. Mol. Biol. Evol. 2003, 20:10-17.
-
(2003)
Mol. Biol. Evol.
, vol.20
, pp. 10-17
-
-
Smith, N.G.1
Eyre-Walker, A.2
-
33
-
-
77956087396
-
Improved characterisation of among-lineage rate variation in cetacean mitogenomes using codon-partitioned relaxed clocks
-
Ho S.Y.W., Lanfear R. Improved characterisation of among-lineage rate variation in cetacean mitogenomes using codon-partitioned relaxed clocks. Mitochondrial DNA 2010, 21:138-146.
-
(2010)
Mitochondrial DNA
, vol.21
, pp. 138-146
-
-
Ho, S.Y.W.1
Lanfear, R.2
-
34
-
-
84897460299
-
ClockstaR: choosing the number of relaxed-clock models in molecular phylogenetic analysis
-
Duchêne S., et al. ClockstaR: choosing the number of relaxed-clock models in molecular phylogenetic analysis. Bioinformatics 2014, 30:1017-1019.
-
(2014)
Bioinformatics
, vol.30
, pp. 1017-1019
-
-
Duchêne, S.1
-
35
-
-
84861380450
-
Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses
-
Lanfear R., et al. Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol. Biol. Evol. 2012, 29:1695-1701.
-
(2012)
Mol. Biol. Evol.
, vol.29
, pp. 1695-1701
-
-
Lanfear, R.1
-
36
-
-
34047108602
-
The delayed rise of present-day mammals
-
Bininda-Emonds O.R.P., et al. The delayed rise of present-day mammals. Nature 2007, 446:507-512.
-
(2007)
Nature
, vol.446
, pp. 507-512
-
-
Bininda-Emonds, O.R.P.1
-
37
-
-
84869088692
-
The global diversity of birds in space and time
-
Jetz W., et al. The global diversity of birds in space and time. Nature 2012, 491:444-448.
-
(2012)
Nature
, vol.491
, pp. 444-448
-
-
Jetz, W.1
-
38
-
-
84869752137
-
Estimating divergence times in large molecular phylogenies
-
Tamura K., et al. Estimating divergence times in large molecular phylogenies. Proc. Natl. Acad. Sci. U.S.A. 2012, 109:19333-19338.
-
(2012)
Proc. Natl. Acad. Sci. U.S.A.
, vol.109
, pp. 19333-19338
-
-
Tamura, K.1
-
39
-
-
79955119965
-
A distance-based least-square method for dating speciation events
-
Xia X., Yang Q. A distance-based least-square method for dating speciation events. Mol. Phlyogenet. Evol. 2011, 59:342-353.
-
(2011)
Mol. Phlyogenet. Evol.
, vol.59
, pp. 342-353
-
-
Xia, X.1
Yang, Q.2
-
40
-
-
84870458929
-
TreePL: divergence time estimation using penalized likelihood for large phylogenies
-
Smith S.A., O'Meara B.C. treePL: divergence time estimation using penalized likelihood for large phylogenies. Bioinformatics 2012, 28:2689-2690.
-
(2012)
Bioinformatics
, vol.28
, pp. 2689-2690
-
-
Smith, S.A.1
O'Meara, B.C.2
-
41
-
-
37849053471
-
Estimating divergence times in large phylogenetic trees
-
Britton T., et al. Estimating divergence times in large phylogenetic trees. Syst. Biol. 2007, 56:741-752.
-
(2007)
Syst. Biol.
, vol.56
, pp. 741-752
-
-
Britton, T.1
-
42
-
-
79957516618
-
Evolution of modern birds revealed by mitogenomics: timing the radiation and origin of major orders
-
Pacheco M.A., et al. Evolution of modern birds revealed by mitogenomics: timing the radiation and origin of major orders. Mol. Biol. Evol. 2011, 28:1927-1942.
-
(2011)
Mol. Biol. Evol.
, vol.28
, pp. 1927-1942
-
-
Pacheco, M.A.1
-
43
-
-
84901465752
-
Persistence of the mitochondrial lineage responsible for the Irish potato famine in extant New World Phytophthora infestans
-
Martin M.D., et al. Persistence of the mitochondrial lineage responsible for the Irish potato famine in extant New World Phytophthora infestans. Mol. Biol. Evol. 2014, 31:1414-1420.
-
(2014)
Mol. Biol. Evol.
, vol.31
, pp. 1414-1420
-
-
Martin, M.D.1
-
44
-
-
40849130956
-
Divergence times in Caenorhabditis and Drosophila inferred from direct estimates of the neutral mutation rate
-
Cutter A.D. Divergence times in Caenorhabditis and Drosophila inferred from direct estimates of the neutral mutation rate. Mol. Biol. Evol. 2008, 25:778-786.
-
(2008)
Mol. Biol. Evol.
, vol.25
, pp. 778-786
-
-
Cutter, A.D.1
-
45
-
-
47749095118
-
Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees
-
Heath T.A., et al. Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees. Syst. Biol. 2008, 57:160-166.
-
(2008)
Syst. Biol.
, vol.57
, pp. 160-166
-
-
Heath, T.A.1
-
46
-
-
67449163699
-
The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference
-
Lemmon A.R., et al. The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference. Syst. Biol. 2009, 58:130-145.
-
(2009)
Syst. Biol.
, vol.58
, pp. 130-145
-
-
Lemmon, A.R.1
-
47
-
-
84906045297
-
Prospects for building large timetrees using molecular data with incomplete gene coverage among species
-
(in press)
-
Filipski A., et al. Prospects for building large timetrees using molecular data with incomplete gene coverage among species. Mol. Biol. Evol. 2014, (in press).
-
(2014)
Mol. Biol. Evol.
-
-
Filipski, A.1
-
48
-
-
71049176982
-
Genome 10K: a proposal to obtain whole-genome sequence for 10000 vertebrate species
-
Genome 10K. Community of Scientists
-
Genome 10K: a proposal to obtain whole-genome sequence for 10000 vertebrate species. J. Hered. 2009, 100:659-674. Genome 10K. Community of Scientists.
-
(2009)
J. Hered.
, vol.100
, pp. 659-674
-
-
-
49
-
-
84882791773
-
The i5K Initiative: advancing arthropod genomics for knowledge, human health, agriculture, and the environment
-
i5K Consortium
-
The i5K Initiative: advancing arthropod genomics for knowledge, human health, agriculture, and the environment. J. Hered. 2013, 104:595-600. i5K Consortium.
-
(2013)
J. Hered.
, vol.104
, pp. 595-600
-
-
-
50
-
-
77954967444
-
Bayesian estimation of divergence times from large sequence alignments
-
Guindon S. Bayesian estimation of divergence times from large sequence alignments. Mol. Biol. Evol. 2010, 27:1768-1781.
-
(2010)
Mol. Biol. Evol.
, vol.27
, pp. 1768-1781
-
-
Guindon, S.1
-
51
-
-
0031741182
-
Estimating the rate of evolution of the rate of molecular evolution
-
Thorne J.L., et al. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 1998, 15:1647-1657.
-
(1998)
Mol. Biol. Evol.
, vol.15
, pp. 1647-1657
-
-
Thorne, J.L.1
-
52
-
-
79959462209
-
Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times
-
dos Reis M., Yang Z. Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times. Mol. Biol. Evol. 2011, 28:2161-2172.
-
(2011)
Mol. Biol. Evol.
, vol.28
, pp. 2161-2172
-
-
dos Reis, M.1
Yang, Z.2
-
54
-
-
84555188616
-
BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics
-
Ayres D.L., et al. BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics. Syst. Biol. 2012, 61:170-173.
-
(2012)
Syst. Biol.
, vol.61
, pp. 170-173
-
-
Ayres, D.L.1
-
55
-
-
28944451210
-
Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds
-
Yang Z., Rannala B. Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Mol. Biol. Evol. 2006, 23:212-226.
-
(2006)
Mol. Biol. Evol.
, vol.23
, pp. 212-226
-
-
Yang, Z.1
Rannala, B.2
-
56
-
-
22844434631
-
Estimating divergence times in phylogenetic trees without a molecular clock
-
Britton T. Estimating divergence times in phylogenetic trees without a molecular clock. Syst. Biol. 2005, 54:500-507.
-
(2005)
Syst. Biol.
, vol.54
, pp. 500-507
-
-
Britton, T.1
-
57
-
-
84873505893
-
The unbearable uncertainty of Bayesian divergence time estimation
-
dos Reis M., Yang Z. The unbearable uncertainty of Bayesian divergence time estimation. J. Syst. Evol. 2013, 51:30-43.
-
(2013)
J. Syst. Evol.
, vol.51
, pp. 30-43
-
-
dos Reis, M.1
Yang, Z.2
-
58
-
-
34548556039
-
Inferring speciation times under an episodic molecular clock
-
Rannala B., Yang Z. Inferring speciation times under an episodic molecular clock. Syst. Biol. 2007, 56:453-466.
-
(2007)
Syst. Biol.
, vol.56
, pp. 453-466
-
-
Rannala, B.1
Yang, Z.2
-
59
-
-
84885927382
-
Critiquing blind dating: the dangers of over-confident date estimates in comparative genomics
-
Wheat C.W., Wahlberg N. Critiquing blind dating: the dangers of over-confident date estimates in comparative genomics. Trends Ecol. Evol. 2013, 28:636-642.
-
(2013)
Trends Ecol. Evol.
, vol.28
, pp. 636-642
-
-
Wheat, C.W.1
Wahlberg, N.2
-
60
-
-
77955657333
-
Watching the clock: studying variation in rates of molecular evolution between species
-
Lanfear R., et al. Watching the clock: studying variation in rates of molecular evolution between species. Trends Ecol. Evol. 2010, 25:495-503.
-
(2010)
Trends Ecol. Evol.
, vol.25
, pp. 495-503
-
-
Lanfear, R.1
-
61
-
-
78650493648
-
A phylogenetic model for investigating correlated evolution of substitution rates and continuous phenotypic characters
-
Lartillot N., Poujol R. A phylogenetic model for investigating correlated evolution of substitution rates and continuous phenotypic characters. Mol. Biol. Evol. 2011, 28:729-744.
-
(2011)
Mol. Biol. Evol.
, vol.28
, pp. 729-744
-
-
Lartillot, N.1
Poujol, R.2
-
62
-
-
78650476811
-
A universal molecular clock of protein folds and its power in tracing the early history of aerobic metabolism and planet oxygenation
-
Wang M., et al. A universal molecular clock of protein folds and its power in tracing the early history of aerobic metabolism and planet oxygenation. Mol. Biol. Evol. 2011, 28:567-582.
-
(2011)
Mol. Biol. Evol.
, vol.28
, pp. 567-582
-
-
Wang, M.1
-
63
-
-
84860159826
-
A total-evidence approach to dating with fossils, applied to the early radiation of the Hymenoptera
-
Ronquist F., et al. A total-evidence approach to dating with fossils, applied to the early radiation of the Hymenoptera. Syst. Biol. 2012, 61:973-999.
-
(2012)
Syst. Biol.
, vol.61
, pp. 973-999
-
-
Ronquist, F.1
-
64
-
-
79952158855
-
Dating primate divergences through an integrated analysis of palaeontological and molecular data
-
Wilkinson R.D., et al. Dating primate divergences through an integrated analysis of palaeontological and molecular data. Syst. Biol. 2011, 60:16-31.
-
(2011)
Syst. Biol.
, vol.60
, pp. 16-31
-
-
Wilkinson, R.D.1
-
65
-
-
84904626200
-
The fossilized birth-death process for coherent calibration of divergence-time estimates
-
Heath T.A., et al. The fossilized birth-death process for coherent calibration of divergence-time estimates. Proc. Natl. Acad. Sci. U.S.A. 2014, 10.1073/pnas.1319091111.
-
(2014)
Proc. Natl. Acad. Sci. U.S.A.
-
-
Heath, T.A.1
-
66
-
-
84877929456
-
Molecular dating of phylogenies by likelihood methods: a comparison of models and a new information criterion
-
Paradis E. Molecular dating of phylogenies by likelihood methods: a comparison of models and a new information criterion. Mol. Phylogenet. Evol. 2013, 67:436-444.
-
(2013)
Mol. Phylogenet. Evol.
, vol.67
, pp. 436-444
-
-
Paradis, E.1
-
67
-
-
34447333669
-
Rocks and clocks: calibrating the Tree of Life using fossils and molecules
-
Donoghue P.C., Benton M.J. Rocks and clocks: calibrating the Tree of Life using fossils and molecules. Trends Ecol. Evol. 2007, 22:424-431.
-
(2007)
Trends Ecol. Evol.
, vol.22
, pp. 424-431
-
-
Donoghue, P.C.1
Benton, M.J.2
-
68
-
-
0030773749
-
A nonparametric approach to estimating divergence times in the absence of rate constancy
-
Sanderson M.J. A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol. Biol. Evol. 1997, 14:1218-1231.
-
(1997)
Mol. Biol. Evol.
, vol.14
, pp. 1218-1231
-
-
Sanderson, M.J.1
-
69
-
-
70350103638
-
Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times
-
Ho S.Y.W., Phillips M.J. Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Syst. Biol. 2009, 58:367-380.
-
(2009)
Syst. Biol.
, vol.58
, pp. 367-380
-
-
Ho, S.Y.W.1
Phillips, M.J.2
-
70
-
-
84863116561
-
Best practices for justifying fossil calibrations
-
Parham J.F., et al. Best practices for justifying fossil calibrations. Syst. Biol. 2012, 61:346-359.
-
(2012)
Syst. Biol.
, vol.61
, pp. 346-359
-
-
Parham, J.F.1
-
71
-
-
84865256173
-
A hierarchical Bayesian model for calibrating estimates of species divergence times
-
Heath T.A. A hierarchical Bayesian model for calibrating estimates of species divergence times. Syst. Biol. 2012, 61:793-809.
-
(2012)
Syst. Biol.
, vol.61
, pp. 793-809
-
-
Heath, T.A.1
-
72
-
-
84878758292
-
A simple method for estimating informative node age priors for the fossil calibration of molecular divergence time analyses
-
Nowak M.D., et al. A simple method for estimating informative node age priors for the fossil calibration of molecular divergence time analyses. PLoS ONE 2013, 8:e66245.
-
(2013)
PLoS ONE
, vol.8
-
-
Nowak, M.D.1
-
73
-
-
60349127526
-
Phylogenetic uncertainty and molecular clock calibrations: a case study of legless lizards (Pygopodidae, Gekkota)
-
Lee M.S.Y., et al. Phylogenetic uncertainty and molecular clock calibrations: a case study of legless lizards (Pygopodidae, Gekkota). Mol. Phylogenet. Evol. 2009, 50:661-666.
-
(2009)
Mol. Phylogenet. Evol.
, vol.50
, pp. 661-666
-
-
Lee, M.S.Y.1
-
74
-
-
0042512083
-
Measurably evolving populations
-
Drummond A.J., et al. Measurably evolving populations. Trends Ecol. Evol. 2003, 18:481-488.
-
(2003)
Trends Ecol. Evol.
, vol.18
, pp. 481-488
-
-
Drummond, A.J.1
-
75
-
-
78751478795
-
A Bayesian phylogenetic method to estimate unknown sequence ages
-
Shapiro B., et al. A Bayesian phylogenetic method to estimate unknown sequence ages. Mol. Biol. Evol. 2011, 28:879-887.
-
(2011)
Mol. Biol. Evol.
, vol.28
, pp. 879-887
-
-
Shapiro, B.1
-
76
-
-
84876022648
-
Phylogenetic estimation of timescales using ancient DNA: the effects of temporal sampling scheme and uncertainty in sample ages
-
Molak M., et al. Phylogenetic estimation of timescales using ancient DNA: the effects of temporal sampling scheme and uncertainty in sample ages. Mol. Biol. Evol. 2013, 30:253-262.
-
(2013)
Mol. Biol. Evol.
, vol.30
, pp. 253-262
-
-
Molak, M.1
-
77
-
-
84864530626
-
Bayesian phylogenetics with BEAUti and the BEAST 1.7
-
Drummond A.J., et al. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 2012, 29:1969-1973.
-
(2012)
Mol. Biol. Evol.
, vol.29
, pp. 1969-1973
-
-
Drummond, A.J.1
-
78
-
-
84860109324
-
MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space
-
Ronquist F., et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 2012, 61:539-542.
-
(2012)
Syst. Biol.
, vol.61
, pp. 539-542
-
-
Ronquist, F.1
-
79
-
-
34547803197
-
PAML 4: phylogenetic analysis by maximum likelihood
-
Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 2007, 24:1586-1591.
-
(2007)
Mol. Biol. Evol.
, vol.24
, pp. 1586-1591
-
-
Yang, Z.1
-
80
-
-
69949126557
-
PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating
-
Lartillot N., et al. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 2009, 25:2286-2288.
-
(2009)
Bioinformatics
, vol.25
, pp. 2286-2288
-
-
Lartillot, N.1
-
81
-
-
84555188625
-
Calibrated tree priors for relaxed phylogenetics and divergence time estimation
-
Heled J., Drummond A.J. Calibrated tree priors for relaxed phylogenetics and divergence time estimation. Syst. Biol. 2012, 61:138-149.
-
(2012)
Syst. Biol.
, vol.61
, pp. 138-149
-
-
Heled, J.1
Drummond, A.J.2
-
82
-
-
84865291420
-
Phylogenomic resolution of paleozoic divergences in harvestmen (Arachnida, Opiliones) via analysis of next-generation transcriptome data
-
Hedin M., et al. Phylogenomic resolution of paleozoic divergences in harvestmen (Arachnida, Opiliones) via analysis of next-generation transcriptome data. PLoS ONE 2012, 7:e42888.
-
(2012)
PLoS ONE
, vol.7
-
-
Hedin, M.1
-
83
-
-
84899553363
-
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
-
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014, 30:1312-1313.
-
(2014)
Bioinformatics
, vol.30
, pp. 1312-1313
-
-
Stamatakis, A.1
-
84
-
-
84975795680
-
An integrated map of genetic variation from 1,092 human genomes
-
The 1000 Genomes Project Consortium
-
An integrated map of genetic variation from 1,092 human genomes. Nature 2012, 491:56-65. The 1000 Genomes Project Consortium.
-
(2012)
Nature
, vol.491
, pp. 56-65
-
-
-
85
-
-
84892942971
-
Reconstructing genome evolution in historic samples of the Irish potato famine pathogen
-
Martin M.D., et al. Reconstructing genome evolution in historic samples of the Irish potato famine pathogen. Nat. Commun. 2013, 4:2172.
-
(2013)
Nat. Commun.
, vol.4
, pp. 2172
-
-
Martin, M.D.1
-
86
-
-
33847302458
-
Inconsistency of phylogenetic estimates from concatenated data under coalescence
-
Kubatko L.S., Degnan J.H. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst. Biol. 2007, 56:17-24.
-
(2007)
Syst. Biol.
, vol.56
, pp. 17-24
-
-
Kubatko, L.S.1
Degnan, J.H.2
-
87
-
-
65649131928
-
Gene tree discordance, phylogenetic inference and the multispecies coalescent
-
Degnan J.H., Rosenberg N.A. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol. Evol. 2009, 24:332-340.
-
(2009)
Trends Ecol. Evol.
, vol.24
, pp. 332-340
-
-
Degnan, J.H.1
Rosenberg, N.A.2
-
88
-
-
77249086587
-
Bayesian inference of species trees from multilocus data
-
Heled J., Drummond A.J. Bayesian inference of species trees from multilocus data. Mol. Biol. Evol. 2010, 27:570-580.
-
(2010)
Mol. Biol. Evol.
, vol.27
, pp. 570-580
-
-
Heled, J.1
Drummond, A.J.2
-
89
-
-
77952703002
-
Bayesian species delimitation using multilocus sequence data
-
Yang Z., Rannala B. Bayesian species delimitation using multilocus sequence data. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:9264-9269.
-
(2010)
Proc. Natl. Acad. Sci. U.S.A.
, vol.107
, pp. 9264-9269
-
-
Yang, Z.1
Rannala, B.2
-
90
-
-
84892953320
-
Ancient hyaenas highlight the old problem of estimating evolutionary rates
-
Shapiro B., Ho S.Y.W. Ancient hyaenas highlight the old problem of estimating evolutionary rates. Mol. Ecol. 2014, 23:499-501.
-
(2014)
Mol. Ecol.
, vol.23
, pp. 499-501
-
-
Shapiro, B.1
Ho, S.Y.W.2
-
91
-
-
79960629871
-
Time-dependent rates of molecular evolution
-
Ho S.Y.W., et al. Time-dependent rates of molecular evolution. Mol. Ecol. 2011, 20:3087-3101.
-
(2011)
Mol. Ecol.
, vol.20
, pp. 3087-3101
-
-
Ho, S.Y.W.1
-
92
-
-
33947245620
-
Dates from the molecular clock: how wrong can we be?
-
Pulquério M.J., Nichols R.A. Dates from the molecular clock: how wrong can we be?. Trends Ecol. Evol. 2007, 22:180-184.
-
(2007)
Trends Ecol. Evol.
, vol.22
, pp. 180-184
-
-
Pulquério, M.J.1
Nichols, R.A.2
-
93
-
-
31444442779
-
Molecular clocks: when times are a-changin'
-
Ho S.Y.W., Larson G. Molecular clocks: when times are a-changin'. Trends Genet. 2006, 22:79-83.
-
(2006)
Trends Genet.
, vol.22
, pp. 79-83
-
-
Ho, S.Y.W.1
Larson, G.2
-
94
-
-
0030621127
-
Mass survival of birds across the Cretaceous-Tertiary boundary: molecular evidence
-
Cooper A., Penny D. Mass survival of birds across the Cretaceous-Tertiary boundary: molecular evidence. Science 1997, 275:1109-1113.
-
(1997)
Science
, vol.275
, pp. 1109-1113
-
-
Cooper, A.1
Penny, D.2
-
95
-
-
80055070300
-
Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification
-
Meredith R.W., et al. Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification. Science 2011, 334:521-524.
-
(2011)
Science
, vol.334
, pp. 521-524
-
-
Meredith, R.W.1
-
96
-
-
0000967619
-
Quantitative analysis of the timing of the origin and diversification of extant placental orders
-
Archibald J.D., Deutschman D.H. Quantitative analysis of the timing of the origin and diversification of extant placental orders. J. Mamm. Evol. 2001, 8:107-124.
-
(2001)
J. Mamm. Evol.
, vol.8
, pp. 107-124
-
-
Archibald, J.D.1
Deutschman, D.H.2
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