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Items: 1 to 20 of 81

1.

Time dependency of molecular rates in ancient DNA data sets, a sampling artifact?

Debruyne R, Poinar HN.

Syst Biol. 2009 Jun;58(3):348-60. doi: 10.1093/sysbio/syp028. Epub 2009 Jul 1. No abstract available.

PMID:
20525589
2.

The effect of ancient DNA damage on inferences of demographic histories.

Axelsson E, Willerslev E, Gilbert MT, Nielsen R.

Mol Biol Evol. 2008 Oct;25(10):2181-7. doi: 10.1093/molbev/msn163. Epub 2008 Jul 24.

PMID:
18653730
3.

Bayesian estimation of substitution rates from ancient DNA sequences with low information content.

Ho SY, Lanfear R, Phillips MJ, Barnes I, Thomas JA, Kolokotronis SO, Shapiro B.

Syst Biol. 2011 May;60(3):366-75. doi: 10.1093/sysbio/syq099. Epub 2011 Feb 4. No abstract available.

PMID:
21296909
4.

Accommodating the effect of ancient DNA damage on inferences of demographic histories.

Rambaut A, Ho SY, Drummond AJ, Shapiro B.

Mol Biol Evol. 2009 Feb;26(2):245-8. doi: 10.1093/molbev/msn256. Epub 2008 Nov 11.

PMID:
19001634
5.

Bayesian coalescent inference of past population dynamics from molecular sequences.

Drummond AJ, Rambaut A, Shapiro B, Pybus OG.

Mol Biol Evol. 2005 May;22(5):1185-92. Epub 2005 Feb 9.

PMID:
15703244
6.

Bayesian estimation of sequence damage in ancient DNA.

Ho SY, Heupink TH, Rambaut A, Shapiro B.

Mol Biol Evol. 2007 Jun;24(6):1416-22. Epub 2007 Mar 29. Erratum in: Mol Biol Evol. 2007 Jul;24(7):1576.

PMID:
17395598
7.

Elevated substitution rates estimated from ancient DNA sequences.

Ho SY, Kolokotronis SO, Allaby RG.

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

8.

Time dependency of molecular rate estimates and systematic overestimation of recent divergence times.

Ho SY, Phillips MJ, Cooper A, Drummond AJ.

Mol Biol Evol. 2005 Jul;22(7):1561-8. Epub 2005 Apr 6.

PMID:
15814826
9.

Geological dates and molecular rates: fish DNA sheds light on time dependency.

Burridge CP, Craw D, Fletcher D, Waters JM.

Mol Biol Evol. 2008 Apr;25(4):624-33. doi: 10.1093/molbev/msm271. Epub 2008 Feb 14.

PMID:
18281273
10.

A paleogenomic perspective on evolution and gene function: new insights from ancient DNA.

Shapiro B, Hofreiter M.

Science. 2014 Jan 24;343(6169):1236573. doi: 10.1126/science.1236573. Review.

PMID:
24458647
11.

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.

12.

Elevated substitution rate estimates from ancient DNA: model violation and bias of Bayesian methods.

Navascués M, Emerson BC.

Mol Ecol. 2009 Nov;18(21):4390-7. doi: 10.1111/j.1365-294X.2009.04333.x. Epub 2009 Sep 7.

PMID:
19735451
14.

Do complex population histories drive higher estimates of substitution rate in phylogenetic reconstructions?

Ramakrishnan U, Hadly EA.

Mol Ecol. 2009 Nov;18(21):4341-3. doi: 10.1111/j.1365-294X.2009.04334.x.

PMID:
19845859
15.

Using genetic evidence to evaluate four palaeoanthropological hypotheses for the timing of Neanderthal and modern human origins.

Endicott P, Ho SY, Stringer C.

J Hum Evol. 2010 Jul;59(1):87-95. doi: 10.1016/j.jhevol.2010.04.005. Epub 2010 May 26.

PMID:
20510437
16.

Targeted retrieval and analysis of five Neandertal mtDNA genomes.

Briggs AW, Good JM, Green RE, Krause J, Maricic T, Stenzel U, Lalueza-Fox C, Rudan P, Brajkovic D, Kucan Z, Gusic I, Schmitz R, Doronichev VB, Golovanova LV, de la Rasilla M, Fortea J, Rosas A, Pääbo S.

Science. 2009 Jul 17;325(5938):318-21. doi: 10.1126/science.1174462.

17.
19.

Divergence time and evolutionary rate estimation with multilocus data.

Thorne JL, Kishino H.

Syst Biol. 2002 Oct;51(5):689-702.

PMID:
12396584
20.

Rise and fall of the Beringian steppe bison.

Shapiro B, Drummond AJ, Rambaut A, Wilson MC, Matheus PE, Sher AV, Pybus OG, Gilbert MT, Barnes I, Binladen J, Willerslev E, Hansen AJ, Baryshnikov GF, Burns JA, Davydov S, Driver JC, Froese DG, Harington CR, Keddie G, Kosintsev P, Kunz ML, Martin LD, Stephenson RO, Storer J, Tedford R, Zimov S, Cooper A.

Science. 2004 Nov 26;306(5701):1561-5.

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