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Items: 1 to 20 of 104

1.

A Bayesian phylogenetic method to estimate unknown sequence ages.

Shapiro B, Ho SY, Drummond AJ, Suchard MA, Pybus OG, Rambaut A.

Mol Biol Evol. 2011 Feb;28(2):879-87. doi: 10.1093/molbev/msq262. Epub 2010 Oct 1.

2.

Phylogenetic estimation of timescales using ancient DNA: the effects of temporal sampling scheme and uncertainty in sample ages.

Molak M, Lorenzen ED, Shapiro B, Ho SY.

Mol Biol Evol. 2013 Feb;30(2):253-62. doi: 10.1093/molbev/mss232. Epub 2012 Oct 3.

PMID:
23024187
3.

Empirical calibrated radiocarbon sampler: a tool for incorporating radiocarbon-date and calibration error into Bayesian phylogenetic analyses of ancient DNA.

Molak M, Suchard MA, Ho SY, Beilman DW, Shapiro B.

Mol Ecol Resour. 2015 Jan;15(1):81-6. doi: 10.1111/1755-0998.12295. Epub 2014 Jul 4.

4.

Phylogeny and temporal diversification of darters (Percidae: Etheostomatinae).

Near TJ, Bossu CM, Bradburd GS, Carlson RL, Harrington RC, Hollingsworth PR Jr, Keck BP, Etnier DA.

Syst Biol. 2011 Oct;60(5):565-95. doi: 10.1093/sysbio/syr052. Epub 2011 Jul 20.

PMID:
21775340
5.

Elevated substitution rates estimated from ancient DNA sequences.

Ho SY, Kolokotronis SO, Allaby RG.

Biol Lett. 2007 Dec 22;3(6):702-5.

6.

Characterization of the uncertainty of divergence time estimation under relaxed molecular clock models using multiple loci.

Zhu T, Dos Reis M, Yang Z.

Syst Biol. 2015 Mar;64(2):267-80. doi: 10.1093/sysbio/syu109. Epub 2014 Dec 11.

7.

Integration of Bayesian molecular clock methods and fossil-based soft bounds reveals early Cenozoic origin of African lacertid lizards.

Hipsley CA, Himmelmann L, Metzler D, Müller J.

BMC Evol Biol. 2009 Jul 1;9:151. doi: 10.1186/1471-2148-9-151.

9.

Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages.

Brown JW, Rest JS, García-Moreno J, Sorenson MD, Mindell DP.

BMC Biol. 2008 Jan 28;6:6. doi: 10.1186/1741-7007-6-6.

10.

Novel non-parametric models to estimate evolutionary rates and divergence times from heterochronous sequence data.

Fourment M, Holmes EC.

BMC Evol Biol. 2014 Jul 24;14:163. doi: 10.1186/s12862-014-0163-6.

11.

The impact of calibration and clock-model choice on molecular estimates of divergence times.

Duchêne S, Lanfear R, Ho SY.

Mol Phylogenet Evol. 2014 Sep;78:277-89. doi: 10.1016/j.ympev.2014.05.032. Epub 2014 Jun 6.

PMID:
24910154
12.

Bayesian random local clocks, or one rate to rule them all.

Drummond AJ, Suchard MA.

BMC Biol. 2010 Aug 31;8:114. doi: 10.1186/1741-7007-8-114.

13.

Phylogenetic relationships and timing of diversification in gonorynchiform fishes inferred using nuclear gene DNA sequences (Teleostei: Ostariophysi).

Near TJ, Dornburg A, Friedman M.

Mol Phylogenet Evol. 2014 Nov;80:297-307. doi: 10.1016/j.ympev.2014.07.013. Epub 2014 Aug 1.

PMID:
25087656
14.

Using multiple relaxed-clock models to estimate evolutionary timescales from DNA sequence data.

Duchêne S, Ho SY.

Mol Phylogenet Evol. 2014 Aug;77:65-70. doi: 10.1016/j.ympev.2014.04.010. Epub 2014 Apr 18.

PMID:
24747129
15.

Evaluating fossil calibrations for dating phylogenies in light of rates of molecular evolution: a comparison of three approaches.

Lukoschek V, Scott Keogh J, Avise JC.

Syst Biol. 2012 Jan;61(1):22-43. doi: 10.1093/sysbio/syr075. Epub 2011 Aug 13.

PMID:
21840843
16.

Bayesian coestimation of phylogeny and sequence alignment.

Lunter G, Miklós I, Drummond A, Jensen JL, Hein J.

BMC Bioinformatics. 2005 Apr 1;6:83.

17.

A dirichlet process prior for estimating lineage-specific substitution rates.

Heath TA, Holder MT, Huelsenbeck JP.

Mol Biol Evol. 2012 Mar;29(3):939-55. doi: 10.1093/molbev/msr255. Epub 2011 Nov 2.

18.

Inferring speciation times under an episodic molecular clock.

Rannala B, Yang Z.

Syst Biol. 2007 Jun;56(3):453-66.

PMID:
17558967
19.

An evaluation of phylogenetic methods for reconstructing transmitted HIV variants using longitudinal clonal HIV sequence data.

McCloskey RM, Liang RH, Harrigan PR, Brumme ZL, Poon AF.

J Virol. 2014 Jun;88(11):6181-94. doi: 10.1128/JVI.00483-14. Epub 2014 Mar 19.

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