-
1
-
-
17444424295
-
Serial SimCoal: A population genetics model for data from multiple populations and points in time
-
Anderson CN, Ramakrishnan U, Chan Y.L., Hadly EA. 2005. Serial SimCoal: a population genetics model for data from multiple populations and points in time. Bioinformatics 21: 1733-1734.
-
(2005)
Bioinformatics
, vol.21
, pp. 1733-1734
-
-
Anderson, C.N.1
Ramakrishnan, U.2
Chan, Y.L.3
Hadly, E.A.4
-
2
-
-
0036909632
-
Estimating divergence times from molecular data on phylogenetic and population genetic timescales
-
Arbogast BS, Edwards SV, Wakeley J, Beerli P., Slowinski JB. 2002. Estimating divergence times from molecular data on phylogenetic and population genetic timescales. Annu Rev Ecol Syst 33: 707-740.
-
(2002)
Annu Rev Ecol Syst
, vol.33
, pp. 707-740
-
-
Arbogast, B.S.1
Edwards, S.V.2
Wakeley, J.3
Beerli, P.4
Slowinski, J.B.5
-
3
-
-
63849272881
-
Phylogeography of lions (Panthera leo ssp.) reveals three distinct taxa and a late pleistocene reduction in genetic diversity
-
(17 co-authors)
-
Barnett R, Shapiro B, Barnes I., et al. (17 co-authors). 2009. Phylogeography of lions (Panthera leo ssp.) reveals three distinct taxa and a late Pleistocene reduction in genetic diversity. Mol Ecol. 18: 1668-1677.
-
(2009)
Mol Ecol.
, vol.18
, pp. 1668-1677
-
-
Barnett, R.1
Shapiro, B.2
Barnes, I.3
-
4
-
-
0034895188
-
Environmental influences on dietary carbon and C-14 ages in modern rats and other species
-
Beavan-Athfield N.R., McFadgen BG, Sparks RJ. 2001. Environmental influences on dietary carbon and C-14 ages in modern rats and other species. Radiocarbon 43: 7-14.
-
(2001)
Radiocarbon
, vol.43
, pp. 7-14
-
-
Beavan-Athfield, N.R.1
McFadgen, B.G.2
Sparks, R.J.3
-
6
-
-
0029434296
-
Radiocarbon calibration and analysis of stratigraphy: The OxCal program
-
Bronk Ramsey C 1995. Radiocarbon calibration and analysis of stratigraphy: the OxCal program. Radiocarbon 37: 425-430.
-
(1995)
Radiocarbon
, vol.37
, pp. 425-430
-
-
Bronk Ramsey, C.1
-
7
-
-
80053362389
-
Rate variation and estimation of divergence times using stria and relaxed clocks
-
Brown RP, Yang Z. 2011. Rate variation and estimation of divergence times using stria and relaxed clocks. BMC Evol Biol. 11: 271.
-
(2011)
BMC Evol Biol.
, vol.11
, pp. 271
-
-
Brown, R.P.1
Yang, Z.2
-
8
-
-
77950437916
-
Ancient DNA analyses exclude humans as the driving force behind late pleistocene musk ox (Ovibos moschatus) population dynamics
-
(20 co-authors)
-
Campos PF, Willerslev E, Sher A., et al. (20 co-authors). 2010. Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics. Proc Natl Acad Sci USA 107: 5675-5680.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 5675-5680
-
-
Campos, P.F.1
Willerslev, E.2
Sher, A.3
-
9
-
-
33646483919
-
Bayesian estimation of the timing and severity of a population bottleneck from ancient DNA
-
Chan YL, Anderson CN, Hadly EA. 2006. Bayesian estimation of the timing and severity of a population bottleneck from ancient DNA. PLoS Genet 2: e59.
-
(2006)
PLoS Genet
, vol.2
-
-
Chan, Y.L.1
Anderson, C.N.2
Hadly, E.A.3
-
10
-
-
34249850055
-
Ancient DNA reveals lack of postglacial habitat tracking in the arctic fox
-
Dalén L., Nyström V, Valdiosera C Germonpré M, Sablin M, Turner E, Angerbjörn A, Arsuaga JL, Götherström A. 2007. Ancient DNA reveals lack of postglacial habitat tracking in the arctic fox. Proc Natl Acad Sci USA 104: 6726-6729.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 6726-6729
-
-
Dalén, L.1
Nyström, V.2
Valdiosera, C.3
Germonpré, M.4
Sablin, M.5
Turner, E.6
Angerbjörn, A.7
Arsuaga, J.L.8
Götherström, A.9
-
12
-
-
84859783215
-
A molecular approach to neanderthal extinction
-
Dodge DR. 2012. A molecular approach to Neanderthal extinction. Quatern Int 259: 22-32.
-
(2012)
Quatern Int
, vol.259
, pp. 22-32
-
-
Dodge, D.R.1
-
14
-
-
0036021407
-
Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data
-
Drummond AJ, Nicholls GK, Rodrigo A.G., Solomon W. 2002. Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 161: 1307-1320.
-
(2002)
Genetics
, vol.161
, pp. 1307-1320
-
-
Drummond, A.J.1
Nicholls, G.K.2
Rodrigo, A.G.3
Solomon, W.4
-
15
-
-
79955933731
-
Genealogies from time-stamped sequence data
-
Buck CE, Maillard AR, editors London: Springer-Verlag
-
Drummond AJ, Nicholls GK, Rodrigo A.G., Solomon W. 2004. Genealogies from time-stamped sequence data. In: Buck CE, Maillard AR, editors. Tools for constructing chronologies: crossing disciplinary boundaries. London: Springer-Verlag p. 149-171.
-
(2004)
Tools for Constructing Chronologies: Crossing Disciplinary Boundaries
, pp. 149-171
-
-
Drummond, A.J.1
Nicholls, G.K.2
Rodrigo, A.G.3
Solomon, W.4
-
16
-
-
0042512083
-
Measurably evolving populations
-
Drummond AJ, Pybus OG, Rambaut A, Forsberg R., Rodrigo AG. 2003. Measurably evolving populations. Trends Ecol Evol. 18: 481-488.
-
(2003)
Trends Ecol Evol.
, vol.18
, pp. 481-488
-
-
Drummond, A.J.1
Pybus, O.G.2
Rambaut, A.3
Forsberg, R.4
Rodrigo, A.G.5
-
17
-
-
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
-
18
-
-
0034496840
-
Perspective gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies
-
Edwards SV, Beerli P. 2000. Perspective gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution 54: 1839-1854.
-
(2000)
Evolution
, vol.54
, pp. 1839-1854
-
-
Edwards, S.V.1
Beerli, P.2
-
19
-
-
0034491799
-
SIMCOAL a general coales-cent program for the simulation of molecular data in interconnected populations with arbitrary demography
-
Excoffier L, Novembre J, Schneider S. 2000. SIMCOAL a general coales-cent program for the simulation of molecular data in interconnected populations with arbitrary demography. J Hered. 91: 506-509.
-
(2000)
J Hered.
, vol.91
, pp. 506-509
-
-
Excoffier, L.1
Novembre, J.2
Schneider, S.3
-
20
-
-
77954440480
-
Using time-structured data to estimate evolutionary rates of double-stranded DNA viruses
-
Firth C Kitchen A, Shapiro B, Suchard MA Holmes EC Rambaut A. 2010. Using time-structured data to estimate evolutionary rates of double-stranded DNA viruses. Mol Biol Evol. 27: 2038-2051.
-
(2010)
Mol Biol Evol.
, vol.27
, pp. 2038-2051
-
-
Firth, C.1
Kitchen, A.2
Shapiro, B.3
Suchard, M.A.4
Holmes, E.C.5
Rambaut, A.6
-
21
-
-
34047240363
-
Ancient DNA chronology within sediment deposits: Are paleobiological reconstructions possible and is DNA leaching a factor?
-
Haile J, Holdaway R, Oliver K., Bunce M, Gilbert MTP, Nielsen R, Munch K., Ho SYW, Shapiro B, Willerslev E 2007. Ancient DNA chronology within sediment deposits: are paleobiological reconstructions possible and is DNA leaching a factor? Mol Biol Evol. 24: 382-989.
-
(2007)
Mol Biol Evol.
, vol.24
, pp. 382-989
-
-
Haile, J.1
Holdaway, R.2
Oliver, K.3
Bunce, M.4
Gilbert, M.T.P.5
Nielsen, R.6
Munch, K.7
Ho, S.Y.W.8
Shapiro, B.9
Willerslev, E.10
-
22
-
-
39649093865
-
Rapid molecular evolution in a living fossil
-
Hay JM, Subramanian S, Millar C.D., Mohandesan E., Lambert DM. 2008. Rapid molecular evolution in a living fossil. Trends Genet 24: 106-109.
-
(2008)
Trends Genet
, vol.24
, pp. 106-109
-
-
Hay, J.M.1
Subramanian, S.2
Millar, C.D.3
Mohandesan, E.4
Lambert, D.M.5
-
23
-
-
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: 421-424.
-
(2009)
Biol Lett
, vol.5
, pp. 421-424
-
-
Ho, S.Y.W.1
-
24
-
-
38449100326
-
Elevated substitution rates estimated from ancient DNA sequences
-
Ho SYW, Kolokotronis SO, Allaby RG. 2007. Elevated substitution rates estimated from ancient DNA sequences. Biol Lett 3: 702-705.
-
(2007)
Biol Lett
, vol.3
, pp. 702-705
-
-
Ho, S.Y.W.1
Kolokotronis, S.O.2
Allaby, R.G.3
-
25
-
-
79960629871
-
Time-dependent rates of molecular evolution
-
Ho SYW, Lanfear R, Bromham L., Phillips MJ, Soubrier J, Rodrigo AG, Cooper A. 2011. Time-dependent rates of molecular evolution. Mol Ecol. 20: 3087-3101.
-
(2011)
Mol Ecol.
, vol.20
, pp. 3087-3101
-
-
Ho, S.Y.W.1
Lanfear, R.2
Bromham, L.3
Phillips, M.J.4
Soubrier, J.5
Rodrigo, A.G.6
Cooper, A.7
-
26
-
-
79955457408
-
Bayesian estimation of substitution rates from ancient DNA sequences with low information content
-
Ho SYW, Lanfear R, Phillips M.J., Barnes I., Thomas JA, Kolokotronis SO, Shapiro B. 2011. Bayesian estimation of substitution rates from ancient DNA sequences with low information content. Syst Biol. 60: 366-375.
-
(2011)
Syst Biol.
, vol.60
, pp. 366-375
-
-
Ho, S.Y.W.1
Lanfear, R.2
Phillips, M.J.3
Barnes, I.4
Thomas, J.A.5
Kolokotronis, S.O.6
Shapiro, B.7
-
27
-
-
31444442779
-
Molecular clocks: When times are a-changin
-
Ho SYW, Larson G. 2006. Molecular clocks: when times are a-changin'. Trends Genet 22: 79-83.
-
(2006)
Trends Genet
, vol.22
, pp. 79-83
-
-
Ho, S.Y.W.1
Larson, G.2
-
28
-
-
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: 367-380.
-
(2009)
Syst Biol.
, vol.58
, pp. 367-380
-
-
Ho, S.Y.W.1
Phillips, M.J.2
-
29
-
-
45449120082
-
The effect of inappropriate calibration: Three case studies in molecular ecology
-
Ho SYW, Saarma U, Barnett R., Haile J, Shapiro B. 2008. The effect of inappropriate calibration: three case studies in molecular ecology. PLoS One 3:e1615.
-
(2008)
PLoS One
, vol.3
-
-
Ho, S.Y.W.1
Saarma, U.2
Barnett, R.3
Haile, J.4
Shapiro, B.5
-
30
-
-
33645816587
-
Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified
-
Keane TM, Creevey CJ, Pentony M.M., Naughton TJ, McLnerney JO. 2006. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol Biol. 6: 29.
-
(2006)
BMC Evol Biol.
, vol.6
, pp. 29
-
-
Keane, T.M.1
Creevey, C.J.2
Pentony, M.M.3
Naughton, T.J.4
McLnerney, J.O.5
-
31
-
-
65549148462
-
Sudden expansion of a single brown bear maternal lineage across northern continental eurasia after the last ice age: A general demographic model for mammals?
-
(24 co-authors)
-
Korsten M, Ho SYW, Davison J, et al. (24 co-authors). 2009. Sudden expansion of a single brown bear maternal lineage across northern continental Eurasia after the last ice age: a general demographic model for mammals? Mol Ecol. 18: 1963-1979.
-
(2009)
Mol Ecol.
, vol.18
, pp. 1963-1979
-
-
Korsten, M.1
Ho, S.Y.W.2
Davison, J.3
-
32
-
-
60349127526
-
Phylogenetic uncertainty and molecular clock calibrations: A case study of legless lizards (Pygopodidae, gekkota)
-
Lee MSY, Oliver PM, Hutchinson MN. 2009. Phylogenetic uncertainty and molecular clock calibrations: a case study of legless lizards (Pygopodidae, Gekkota). Mol Phylogenet Evol. 50: 661-666.
-
(2009)
Mol Phylogenet Evol.
, vol.50
, pp. 661-666
-
-
Lee, M.S.Y.1
Oliver, P.M.2
Hutchinson, M.N.3
-
33
-
-
77950400446
-
Complete mitochondrial genome of a pleistocene jawbone unveils the origin of polar bear
-
(14 co-authors)
-
Lindqvist C, Schuster SC Sun Y, et al. (14 co-authors). 2010. Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear. Proc Natl Acad Sci USA. 107: 5053-5057.
-
(2010)
Proc Natl Acad Sci USA.
, vol.107
, pp. 5053-5057
-
-
Lindqvist, C.1
Schuster, S.C.2
Sun, Y.3
-
34
-
-
81555200041
-
Species-specific responses of late quaternary megafauna to climate and humans
-
(55 co-authors)
-
Lorenzen ED, Nogues-Bravo D, Orlando L., et al. (55 co-authors). 2011. Species-specific responses of Late Quaternary megafauna to climate and humans. Nature 479: 359-364.
-
(2011)
Nature
, vol.479
, pp. 359-364
-
-
Lorenzen, E.D.1
Nogues-Bravo, D.2
Orlando, L.3
-
35
-
-
77955290199
-
Performance of criteria for selecting evolutionary models in phylo-genetics: A comprehensive study based on simulated datasets
-
Luo A, Qiao H, Zhang Y., Shi W, Ho SYW, Xu W, Zhang A., Zhu C 2010. Performance of criteria for selecting evolutionary models in phylo-genetics: a comprehensive study based on simulated datasets. BMC Evol Biol. 10: 242.
-
(2010)
BMC Evol Biol.
, vol.10
, pp. 242
-
-
Luo, A.1
Qiao, H.2
Zhang, Y.3
Shi, W.4
Ho, S.Y.W.5
Xu, W.6
Zhang, A.7
Zhu, C.8
-
36
-
-
0036854283
-
Fossil calibration of molecular clocks and the divergence times of geminate species pairs separated by the isthmus of panama
-
Marko PB. 2002. Fossil calibration of molecular clocks and the divergence times of geminate species pairs separated by the Isthmus of Panama. Mol Biol Evol. 19: 2005-2021.
-
(2002)
Mol Biol Evol.
, vol.19
, pp. 2005-2021
-
-
Marko, P.B.1
-
37
-
-
33644545086
-
A new radiocarbon revolution and the dispersal of modem humans in eurasia
-
Mellars P. 2006. A new radiocarbon revolution and the dispersal of modem humans in Eurasia. Nature 439: 331-935.
-
(2006)
Nature
, vol.439
, pp. 331-935
-
-
Mellars, P.1
-
39
-
-
62849103887
-
Using phylochronology to reveal cryptic population histories: Review and synthesis of 29 ancient DNA studies
-
Ramakrishnan U, Hadly EA. 2009. Using phylochronology to reveal cryptic population histories: review and synthesis of 29 ancient DNA studies. Mol Ecol. 18: 1310-1330.
-
(2009)
Mol Ecol.
, vol.18
, pp. 1310-1330
-
-
Ramakrishnan, U.1
Hadly, E.A.2
-
40
-
-
0034044313
-
Estimating the rate of molecular evolution: Incorporating non-contemporaneous sequences into maximum likelihood phytogenies
-
Rambaut A. 2000. Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phytogenies. Bioinformatics 16: 395-399.
-
(2000)
Bioinformatics
, vol.16
, pp. 395-399
-
-
Rambaut, A.1
-
41
-
-
77955300661
-
-
last accessed May 2, 2011
-
Rambaut A, Drummond AJ. 2007. Tracer v1.5. Available from: http://beast.bio.edac.uk/Tracer, last accessed May 2, 2011.
-
(2007)
Tracer V1.5
-
-
Rambaut, A.1
Drummond, A.J.2
-
42
-
-
57749178865
-
Hantavirus evolution in relation to its rodent and insectivore hosts: No evidence for codivergence
-
Ramsden C, Holmes EC, Charleston MA. 2009. Hantavirus evolution in relation to its rodent and insectivore hosts: no evidence for codivergence. Mol Biol Evol. 26: 143-153.
-
(2009)
Mol Biol Evol.
, vol.26
, pp. 143-153
-
-
Ramsden, C.1
Holmes, E.C.2
Charleston, M.A.3
-
43
-
-
0037314098
-
R8s: Inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock
-
Sanderson MJ. 2003. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 19: 301-302.
-
(2003)
Bioinformatics
, vol.19
, pp. 301-302
-
-
Sanderson, M.J.1
-
44
-
-
9444220256
-
Rise and fall of the beringian steppe bison
-
(27 co-authors)
-
Shapiro B, Drummond AJ, Rambaut A, et al. (27 co-authors). 2004. Rise and fall of the Beringian steppe bison. Science 306: 1561-1565.
-
(2004)
Science
, vol.306
, pp. 1561-1565
-
-
Shapiro, B.1
Drummond, A.J.2
Rambaut, A.3
-
45
-
-
78751478795
-
A Bayesian phylogenetic method to estimate unknown sequence ages
-
Shapiro B, Ho SYW, Drummond AJ, Suchard M.A., Pybus OC, Rambaut A. 2011. A Bayesian phylogenetic method to estimate unknown sequence ages. Mol Biol Evol. 28: 579-887.
-
(2011)
Mol Biol Evol.
, vol.28
, pp. 579-887
-
-
Shapiro, B.1
Ho, S.Y.W.2
Drummond, A.J.3
Suchard, M.A.4
Pybus, O.C.5
Rambaut, A.6
-
47
-
-
0034983646
-
Bayesian selection of continuous-time Markov chain evolutionary models
-
Suchard MA, Weiss RE, Sinsheimer JS. 2001. Bayesian selection of continuous-time Markov chain evolutionary models. Mol Biol Evol. 18: 1001-1013.
-
(2001)
Mol Biol Evol.
, vol.18
, pp. 1001-1013
-
-
Suchard, M.A.1
Weiss, R.E.2
Sinsheimer, J.S.3
-
48
-
-
41549095952
-
A 60,000-year Greenland stratigraphie ice core chronology
-
(14 co-authors)
-
Svensson A, Andersen KK, Bigler M, et al. (14 co-authors). 2008. A 60,000-year Greenland stratigraphie ice core chronology. Clim Past 4: 47-57.
-
(2008)
Clim Past
, vol.4
, pp. 47-57
-
-
Svensson, A.1
Andersen, K.K.2
Bigler, M.3
-
50
-
-
2642526307
-
Prehistorie sado island populations of sus. Scrofa distinguished from contemporary Japanese wild boar by ancient mitochondrial DNA
-
Waranobe T, Ishiguro N, Nakano M., Matsui A, Hongo H, Yamazaki K., Takahashi O. 2004. Prehistorie Sado Island populations of Sus. scrofa distinguished from contemporary Japanese wild boar by ancient mitochondrial DNA. Zool Sci. 21: 219-228.
-
(2004)
Zool Sci.
, vol.21
, pp. 219-228
-
-
Waranobe, T.1
Ishiguro, N.2
Nakano, M.3
Matsui, A.4
Hongo, H.5
Yamazaki, K.6
Takahashi, O.7
-
51
-
-
0035046017
-
Ancient mitochondrial DNA reveals the origin of sus. Scrofa from rebun island, Japan
-
Waranobe T, Ishiguro N, Okumura N., Nakano M, Matsui A, Hongo H., Ushiro H. 2001. Ancient mitochondrial DNA reveals the origin of Sus. scrofa from Rebun Island, Japan. J Mol Evol. 52: 281-289.
-
(2001)
J Mol Evol.
, vol.52
, pp. 281-289
-
-
Waranobe, T.1
Ishiguro, N.2
Okumura, N.3
Nakano, M.4
Matsui, A.5
Hongo, H.6
Ushiro, H.7
-
52
-
-
77956210916
-
The re-emergence of H1N1 influenza virus in 1977: A cautionary tale for estimating divergence times using biologically unrealistic sampling dates
-
Wertheim JO. 2010. The re-emergence of H1N1 influenza virus in 1977:a cautionary tale for estimating divergence times using biologically unrealistic sampling dates. PLoS One 5:e11184.
-
(2010)
PLoS One
, vol.5
-
-
Wertheim, J.O.1
-
53
-
-
34547803197
-
PAML 4: Phylogenetic analysis by maximum likelihood
-
Yang ZH. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24: 1586-1591.
-
(2007)
Mol Biol Evol.
, vol.24
, pp. 1586-1591
-
-
Yang, Z.H.1
|