-
1
-
-
84859206090
-
Many neglected tropical diseases may have originated in the Paleolithic or before: New insights from genetics
-
Trueba G, Dunthorn M (2012) Many neglected tropical diseases may have originated in the Paleolithic or before: New insights from genetics. PLoS Negl Trop Dis 6(3):e1393.
-
(2012)
PLoS Negl Trop Dis
, vol.6
, Issue.3
-
-
Trueba, G.1
Dunthorn, M.2
-
2
-
-
79960130696
-
TimeTree2: Species divergence times on the iPhone
-
Kumar S, Hedges SB (2011) TimeTree2: Species divergence times on the iPhone. Bioinformatics 27(14):2023-2024.
-
(2011)
Bioinformatics
, vol.27
, Issue.14
, pp. 2023-2024
-
-
Kumar, S.1
Hedges, S.B.2
-
3
-
-
82255195530
-
The Cambrian conundrum: Early divergence and later ecological success in the early history of animals
-
Erwin DH, et al. (2011) The Cambrian conundrum: Early divergence and later ecological success in the early history of animals. Science 334(6059):1091-1097.
-
(2011)
Science
, vol.334
, Issue.6059
, pp. 1091-1097
-
-
Erwin, D.H.1
-
4
-
-
80055070300
-
Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification
-
Meredith RW, et al. (2011) Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification. Science 334(6055):521-524.
-
(2011)
Science
, vol.334
, Issue.6055
, pp. 521-524
-
-
Meredith, R.W.1
-
5
-
-
70349298549
-
-
eds Hedges SB, Kumar S (Oxford Univ Press, New York)
-
Hedges SB, Kumar S (2009) The Timetree of Life, eds Hedges SB, Kumar S (Oxford Univ Press, New York).
-
(2009)
The Timetree of Life
-
-
Hedges, S.B.1
Kumar, S.2
-
6
-
-
80052179542
-
Fast and slow implementations of relaxed-clock methods show similar patterns of accuracy in estimating divergence times
-
Battistuzzi FU, Billing-Ross P, Paliwal A, Kumar S (2011) Fast and slow implementations of relaxed-clock methods show similar patterns of accuracy in estimating divergence times. Mol Biol Evol 28(9):2439-2442.
-
(2011)
Mol Biol Evol
, vol.28
, Issue.9
, pp. 2439-2442
-
-
Battistuzzi, F.U.1
Billing-Ross, P.2
Paliwal, A.3
Kumar, S.4
-
7
-
-
79959462209
-
Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times
-
dos Reis M, Yang Z (2011) Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times. Mol Biol Evol 28(7):2161-2172.
-
(2011)
Mol Biol Evol
, vol.28
, Issue.7
, pp. 2161-2172
-
-
Dos Reis, M.1
Yang, Z.2
-
8
-
-
0031741182
-
Estimating the rate of evolution of the rate of molecular evolution
-
Thorne JL, Kishino H, Painter IS (1998) Estimating the rate of evolution of the rate of molecular evolution. Mol Biol Evol 15(12):1647-1657.
-
(1998)
Mol Biol Evol
, vol.15
, Issue.12
, pp. 1647-1657
-
-
Thorne, J.L.1
Kishino, H.2
Painter, I.S.3
-
9
-
-
0036803223
-
Divergence time and evolutionary rate estimation with multilocus data
-
Thorne JL, Kishino H (2002) Divergence time and evolutionary rate estimation with multilocus data. Syst Biol 51(5):689-702.
-
(2002)
Syst Biol
, vol.51
, Issue.5
, pp. 689-702
-
-
Thorne, J.L.1
Kishino, H.2
-
11
-
-
38649110663
-
BEAST: Bayesian evolutionary analysis by sampling trees
-
Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214.
-
(2007)
BMC Evol Biol
, vol.7
, pp. 214
-
-
Drummond, A.J.1
Rambaut, A.2
-
12
-
-
34547803197
-
PAML 4: Phylogenetic analysis by maximum likelihood
-
Yang ZH (2007) PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol 24(8):1586-1591.
-
(2007)
Mol Biol Evol
, vol.24
, Issue.8
, pp. 1586-1591
-
-
Yang, Z.H.1
-
13
-
-
37549001784
-
A general comparison of relaxed molecular clock models
-
Lepage T, Bryant D, Philippe H, Lartillot N (2007) A general comparison of relaxed molecular clock models. Mol Biol Evol 24(12):2669-2680.
-
(2007)
Mol Biol Evol
, vol.24
, Issue.12
, pp. 2669-2680
-
-
Lepage, T.1
Bryant, D.2
Philippe, H.3
Lartillot, N.4
-
14
-
-
67649133122
-
An examination of phylogenetic models of substitution rate variation among lineages
-
Ho SYW (2009) An examination of phylogenetic models of substitution rate variation among lineages. Biol Lett 5(3):421-424.
-
(2009)
Biol Lett
, vol.5
, Issue.3
, pp. 421-424
-
-
Ho, S.Y.W.1
-
15
-
-
77951997517
-
Performance of relaxed-clock methods in estimating evolutionary divergence times and their credibility intervals
-
Battistuzzi FU, Filipski A, Hedges SB, Kumar S (2010) Performance of relaxed-clock methods in estimating evolutionary divergence times and their credibility intervals. Mol Biol Evol 27(6):1289-1300.
-
(2010)
Mol Biol Evol
, vol.27
, Issue.6
, pp. 1289-1300
-
-
Battistuzzi, F.U.1
Filipski, A.2
Hedges, S.B.3
Kumar, S.4
-
16
-
-
79960629871
-
Time-dependent rates of molecular evolution
-
Ho SYW, et al. (2011) Time-dependent rates of molecular evolution. Mol Ecol 20(15):3087-3101.
-
(2011)
Mol Ecol
, vol.20
, Issue.15
, pp. 3087-3101
-
-
Ho, S.Y.W.1
-
17
-
-
1942422549
-
Precision of molecular time estimates
-
Hedges SB, Kumar S (2004) Precision of molecular time estimates. Trends Genet 20(5):242-247.
-
(2004)
Trends Genet
, vol.20
, Issue.5
, pp. 242-247
-
-
Hedges, S.B.1
Kumar, S.2
-
18
-
-
70350116756
-
Calibrating and constraining molecular clocks
-
eds Hedges SB, Kumar S (Oxford Univ Press, New York)
-
Benton MJ, Donoghue PCJ, Asher RJ (2009) Calibrating and constraining molecular clocks. The Timetree of Life, eds Hedges SB, Kumar S (Oxford Univ Press, New York), pp 35-86.
-
(2009)
The Timetree of Life
, pp. 35-86
-
-
Benton, M.J.1
Donoghue, P.C.J.2
Asher, R.J.3
-
19
-
-
84863116561
-
Best practices for justifying fossil calibrations
-
Parham JF, et al. (2012) Best practices for justifying fossil calibrations. Syst Biol 61(2):346-359.
-
(2012)
Syst Biol
, vol.61
, Issue.2
, pp. 346-359
-
-
Parham, J.F.1
-
20
-
-
33747798028
-
The origin and diversification of eukaryotes: Problems with molecular phylogenetics and molecular clock estimation
-
Roger AJ, Hug LA (2006) The origin and diversification of eukaryotes: Problems with molecular phylogenetics and molecular clock estimation. Philos Trans R Soc Lond B Biol Sci 361(1470):1039-1054.
-
(2006)
Philos Trans R Soc Lond B Biol Sci
, vol.361
, Issue.1470
, pp. 1039-1054
-
-
Roger, A.J.1
Hug, L.A.2
-
21
-
-
34547762740
-
The impact of fossils and taxon sampling on ancient molecular dating analyses
-
Hug LA, Roger AJ (2007) The impact of fossils and taxon sampling on ancient molecular dating analyses. Mol Biol Evol 24(8):1889-1897.
-
(2007)
Mol Biol Evol
, vol.24
, Issue.8
, pp. 1889-1897
-
-
Hug, L.A.1
Roger, A.J.2
-
22
-
-
8144221423
-
Assessing the quality of molecular divergence time estimates by fossil calibrations and fossil-based model selection
-
Near TJ, Sanderson MJ (2004) Assessing the quality of molecular divergence time estimates by fossil calibrations and fossil-based model selection. Philos Trans R Soc Lond B Biol Sci 359(1450):1477-1483.
-
(2004)
Philos Trans R Soc Lond B Biol Sci
, vol.359
, Issue.1450
, pp. 1477-1483
-
-
Near, T.J.1
Sanderson, M.J.2
-
23
-
-
13944259078
-
Assessing concordance of fossil calibration points in molecular clock studies: An example using turtles
-
Near TJ, Meylan PA, Shaffer HB (2005) Assessing concordance of fossil calibration points in molecular clock studies: An example using turtles. Am Nat 165(2):137-146.
-
(2005)
Am Nat
, vol.165
, Issue.2
, pp. 137-146
-
-
Near, T.J.1
Meylan, P.A.2
Shaffer, H.B.3
-
24
-
-
70350103638
-
Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times
-
Ho SYW, Phillips MJ (2009) Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Syst Biol 58(3):367-380.
-
(2009)
Syst Biol
, vol.58
, Issue.3
, pp. 367-380
-
-
Ho, S.Y.W.1
Phillips, M.J.2
-
25
-
-
72049121650
-
The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times
-
Inoue J, Donoghue PCJ, Yang Z (2010) The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times. Syst Biol 59(1):74-89.
-
(2010)
Syst Biol
, vol.59
, Issue.1
, pp. 74-89
-
-
Inoue, J.1
Donoghue, P.C.J.2
Yang, Z.3
-
27
-
-
79959483593
-
Integrating fossil preservation biases in the selection of calibrations for molecular divergence time estimation
-
Dornburg A, Beaulieu JM, Oliver JC, Near TJ (2011) Integrating fossil preservation biases in the selection of calibrations for molecular divergence time estimation. Syst Biol 60(4):519-527.
-
(2011)
Syst Biol
, vol.60
, Issue.4
, pp. 519-527
-
-
Dornburg, A.1
Beaulieu, J.M.2
Oliver, J.C.3
Near, T.J.4
-
28
-
-
0004128472
-
-
Cambridge Univ Press, Cambridge, UK
-
Edwards AWF (1972) Likelihood (Cambridge Univ Press, Cambridge, UK).
-
(1972)
Likelihood
-
-
Edwards, A.W.F.1
-
29
-
-
0028088997
-
Weak male-driven molecular evolution in rodents
-
Chang BH, Shimmin LC, Shyue SK, Hewett-Emmett D, Li WH (1994) Weak male-driven molecular evolution in rodents. Proc Natl Acad Sci USA 91(2):827-831.
-
(1994)
Proc Natl Acad Sci USA
, vol.91
, Issue.2
, pp. 827-831
-
-
Chang, B.H.1
Shimmin, L.C.2
Shyue, S.K.3
Hewett-Emmett, D.4
Li, W.H.5
-
30
-
-
0028151465
-
Contrasting rates of nucleotide substitution in the X-linked and Y-linked zinc finger genes
-
Shimmin LC, Chang BH, Li WH (1994) Contrasting rates of nucleotide substitution in the X-linked and Y-linked zinc finger genes. J Mol Evol 39(6):569-578.
-
(1994)
J Mol Evol
, vol.39
, Issue.6
, pp. 569-578
-
-
Shimmin, L.C.1
Chang, B.H.2
Li, W.H.3
-
31
-
-
0037572240
-
Differential rates of evolution for the ZFY-related zinc finger genes, Zfy, Zfx, and Zfa in the mouse genus Mus
-
Tucker PK, Adkins RM, Rest JS (2003) Differential rates of evolution for the ZFY-related zinc finger genes, Zfy, Zfx, and Zfa in the mouse genus Mus. Mol Biol Evol 20 (6):999-1005.
-
(2003)
Mol Biol Evol
, vol.20
, Issue.6
, pp. 999-1005
-
-
Tucker, P.K.1
Adkins, R.M.2
Rest, J.S.3
-
32
-
-
38349150505
-
Fast genes and slow clades: Comparative rates of molecular evolution in mammals
-
Bininda-Emonds ORP (2007) Fast genes and slow clades: Comparative rates of molecular evolution in mammals. Evol Bioinform Online 3:59-85.
-
(2007)
Evol Bioinform Online
, vol.3
, pp. 59-85
-
-
Bininda-Emonds, O.R.P.1
-
33
-
-
0036135468
-
Estimating absolute rates of molecular evolution and divergence times: A penalized likelihood approach
-
Sanderson MJ (2002) Estimating absolute rates of molecular evolution and divergence times: A penalized likelihood approach. Mol Biol Evol 19(1):101-109.
-
(2002)
Mol Biol Evol
, vol.19
, Issue.1
, pp. 101-109
-
-
Sanderson, M.J.1
-
34
-
-
0032580152
-
A molecular timescale for vertebrate evolution
-
Kumar S, Hedges SB (1998) A molecular timescale for vertebrate evolution. Nature 392(6679):917-920.
-
(1998)
Nature
, vol.392
, Issue.6679
, pp. 917-920
-
-
Kumar, S.1
Hedges, S.B.2
-
35
-
-
0037227485
-
The temporal distribution of gene duplication events in a set of highly conserved human gene families
-
Friedman R, Hughes AL (2003) The temporal distribution of gene duplication events in a set of highly conserved human gene families. Mol Biol Evol 20(1):154-161.
-
(2003)
Mol Biol Evol
, vol.20
, Issue.1
, pp. 154-161
-
-
Friedman, R.1
Hughes, A.L.2
-
36
-
-
23744452485
-
Estimating the tempo and mode of gene family evolution from comparative genomic data
-
Hahn MW, De Bie T, Stajich JE, Nguyen C, Cristianini N (2005) Estimating the tempo and mode of gene family evolution from comparative genomic data. Genome Res 15 (8):1153-1160.
-
(2005)
Genome Res
, vol.15
, Issue.8
, pp. 1153-1160
-
-
Hahn, M.W.1
De Bie, T.2
Stajich, J.E.3
Nguyen, C.4
Cristianini, N.5
-
37
-
-
56549119570
-
Turning a hobby into a job: How duplicated genes find new functions
-
Conant GC, Wolfe KH (2008) Turning a hobby into a job: How duplicated genes find new functions. Nat Rev Genet 9(12):938-950.
-
(2008)
Nat Rev Genet
, vol.9
, Issue.12
, pp. 938-950
-
-
Conant, G.C.1
Wolfe, K.H.2
-
38
-
-
0037387372
-
Heterogeneity of nucleotide frequencies among evolutionary lineages and phylogenetic inference
-
Rosenberg MS, Kumar S (2003) Heterogeneity of nucleotide frequencies among evolutionary lineages and phylogenetic inference. Mol Biol Evol 20(4):610-621.
-
(2003)
Mol Biol Evol
, vol.20
, Issue.4
, pp. 610-621
-
-
Rosenberg, M.S.1
Kumar, S.2
-
39
-
-
0035103260
-
Performance of a divergence time estimation method under a probabilistic model of rate evolution
-
Kishino H, Thorne JL, Bruno WJ (2001) Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol Biol Evol 18(3):352-361.
-
(2001)
Mol Biol Evol
, vol.18
, Issue.3
, pp. 352-361
-
-
Kishino, H.1
Thorne, J.L.2
Bruno, W.J.3
-
40
-
-
0030928378
-
Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
-
Rambaut A, Grassly NC (1997) Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput Appl Biosci 13(3):235-238.
-
(1997)
Comput Appl Biosci
, vol.13
, Issue.3
, pp. 235-238
-
-
Rambaut, A.1
Grassly, N.C.2
-
41
-
-
0022376704
-
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
-
Hasegawa M, Kishino H, Yano TA (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22(2):160-174.
-
(1985)
J Mol Evol
, vol.22
, Issue.2
, pp. 160-174
-
-
Hasegawa, M.1
Kishino, H.2
Yano, T.A.3
-
42
-
-
72649094717
-
Discovering the timetree of life
-
Oxford Univ Press, New York
-
Hedges SB, Kumar S (2009) Discovering the timetree of life. The Timetree of Life (Oxford Univ Press, New York), pp 3-18.
-
(2009)
The Timetree of Life
, pp. 3-18
-
-
Hedges, S.B.1
Kumar, S.2
-
43
-
-
79957613599
-
MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
-
Tamura K, et al. (2011) MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10):2731-2739.
-
(2011)
Mol Biol Evol
, vol.28
, Issue.10
, pp. 2731-2739
-
-
Tamura, K.1
|