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The Effect of Fossil Sampling on the Estimation of Divergence Times With The Fossilised Birth Death Process.

O'Reilly JE, Donoghue PCJ.

Syst Biol. 2019 May 25. pii: syz037. doi: 10.1093/sysbio/syz037. [Epub ahead of print]


The dermal skeleton of the jawless vertebrate Tremataspis mammillata (Osteostraci, stem-Gnathostomata).

O'Shea J, Keating JN, Donoghue PCJ.

J Morphol. 2019 Jul;280(7):999-1025. doi: 10.1002/jmor.20997. Epub 2019 May 8.


Anatomy of the Ediacaran rangeomorph Charnia masoni.

Dunn FS, Wilby PR, Kenchington CG, Grazhdankin DV, Donoghue PCJ, Liu AG.

Pap Palaeontol. 2019 Feb;5(1):157-176. doi: 10.1002/spp2.1234. Epub 2018 Sep 11.


Nuclear protein phylogenies support the monophyly of the three bryophyte groups (Bryophyta Schimp.).

de Sousa F, Foster PG, Donoghue PCJ, Schneider H, Cox CJ.

New Phytol. 2019 Apr;222(1):565-575. doi: 10.1111/nph.15587. Epub 2018 Dec 7.


Unicellular Origin of the Animal MicroRNA Machinery.

Bråte J, Neumann RS, Fromm B, Haraldsen AAB, Tarver JE, Suga H, Donoghue PCJ, Peterson KJ, Ruiz-Trillo I, Grini PE, Shalchian-Tabrizi K.

Curr Biol. 2018 Oct 22;28(20):3288-3295.e5. doi: 10.1016/j.cub.2018.08.018. Epub 2018 Oct 11.


Reply to Hedges et al.: Accurate timetrees do indeed require accurate calibrations.

Morris JL, Puttick MN, Clark JW, Edwards D, Kenrick P, Pressel S, Wellman CH, Yang Z, Schneider H, Donoghue PCJ.

Proc Natl Acad Sci U S A. 2018 Oct 9;115(41):E9512-E9513. doi: 10.1073/pnas.1812816115. Epub 2018 Sep 28. No abstract available.


Evolution of metazoan morphological disparity.

Deline B, Greenwood JM, Clark JW, Puttick MN, Peterson KJ, Donoghue PCJ.

Proc Natl Acad Sci U S A. 2018 Sep 18;115(38):E8909-E8918. doi: 10.1073/pnas.1810575115. Epub 2018 Sep 4.


Integrated genomic and fossil evidence illuminates life's early evolution and eukaryote origin.

Betts HC, Puttick MN, Clark JW, Williams TA, Donoghue PCJ, Pisani D.

Nat Ecol Evol. 2018 Oct;2(10):1556-1562. doi: 10.1038/s41559-018-0644-x. Epub 2018 Aug 20.


Whole-Genome Duplication and Plant Macroevolution.

Clark JW, Donoghue PCJ.

Trends Plant Sci. 2018 Oct;23(10):933-945. doi: 10.1016/j.tplants.2018.07.006. Epub 2018 Aug 16. Review.


The nature of aspidin and the evolutionary origin of bone.

Keating JN, Marquart CL, Marone F, Donoghue PCJ.

Nat Ecol Evol. 2018 Sep;2(9):1501-1506. doi: 10.1038/s41559-018-0624-1. Epub 2018 Jul 31.


Well-Annotated microRNAomes Do Not Evidence Pervasive miRNA Loss.

Tarver JE, Taylor RS, Puttick MN, Lloyd GT, Pett W, Fromm B, Schirrmeister BE, Pisani D, Peterson KJ, Donoghue PCJ.

Genome Biol Evol. 2018 Jun 1;10(6):1457-1470. doi: 10.1093/gbe/evy096.


The timescale of early land plant evolution.

Morris JL, Puttick MN, Clark JW, Edwards D, Kenrick P, Pressel S, Wellman CH, Yang Z, Schneider H, Donoghue PCJ.

Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):E2274-E2283. doi: 10.1073/pnas.1719588115. Epub 2018 Feb 20.


The Interrelationships of Land Plants and the Nature of the Ancestral Embryophyte.

Puttick MN, Morris JL, Williams TA, Cox CJ, Edwards D, Kenrick P, Pressel S, Wellman CH, Schneider H, Pisani D, Donoghue PCJ.

Curr Biol. 2018 Mar 5;28(5):733-745.e2. doi: 10.1016/j.cub.2018.01.063. Epub 2018 Feb 15.


Constraining uncertainty in the timescale of angiosperm evolution and the veracity of a Cretaceous Terrestrial Revolution.

Barba-Montoya J, Dos Reis M, Schneider H, Donoghue PCJ, Yang Z.

New Phytol. 2018 Apr;218(2):819-834. doi: 10.1111/nph.15011. Epub 2018 Feb 5.


Probabilistic methods surpass parsimony when assessing clade support in phylogenetic analyses of discrete morphological data.

O'Reilly JE, Puttick MN, Pisani D, Donoghue PCJ.

Palaeontology. 2018 Jan;61(1):105-118. doi: 10.1111/pala.12330. Epub 2017 Oct 31.


The early Cambrian fossil embryo Pseudooides is a direct-developing cnidarian, not an early ecdysozoan.

Duan B, Dong XP, Porras L, Vargas K, Cunningham JA, Donoghue PCJ.

Proc Biol Sci. 2017 Dec 20;284(1869). pii: 20172188. doi: 10.1098/rspb.2017.2188.


Ediacaran developmental biology.

Dunn FS, Liu AG, Donoghue PCJ.

Biol Rev Camb Philos Soc. 2018 May;93(2):914-932. doi: 10.1111/brv.12379. Epub 2017 Nov 3.


Parsimony and maximum-likelihood phylogenetic analyses of morphology do not generally integrate uncertainty in inferring evolutionary history: a response to Brown et al.

Puttick MN, O'Reilly JE, Oakley D, Tanner AR, Fleming JF, Clark J, Holloway L, Lozano-Fernandez J, Parry LA, Tarver JE, Pisani D, Donoghue PCJ.

Proc Biol Sci. 2017 Oct 11;284(1864). pii: 20171636. doi: 10.1098/rspb.2017.1636. No abstract available.


Constraining the timing of whole genome duplication in plant evolutionary history.

Clark JW, Donoghue PCJ.

Proc Biol Sci. 2017 Jul 12;284(1858). pii: 20170912. doi: 10.1098/rspb.2017.0912.


Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution.

Warnock RCM, Yang Z, Donoghue PCJ.

Proc Biol Sci. 2017 Jun 28;284(1857). pii: 20170227. doi: 10.1098/rspb.2017.0227.


RelTime Rates Collapse to a Strict Clock When Estimating the Timeline of Animal Diversification.

Lozano-Fernandez J, Dos Reis M, Donoghue PCJ, Pisani D.

Genome Biol Evol. 2017 May 1;9(5):1320-1328. doi: 10.1093/gbe/evx079.


Open data and digital morphology.

Davies TG, Rahman IA, Lautenschlager S, Cunningham JA, Asher RJ, Barrett PM, Bates KT, Bengtson S, Benson RB, Boyer DM, Braga J, Bright JA, Claessens LP, Cox PG, Dong XP, Evans AR, Falkingham PL, Friedman M, Garwood RJ, Goswami A, Hutchinson JR, Jeffery NS, Johanson Z, Lebrun R, Martínez-Pérez C, Marugán-Lobón J, O'Higgins PM, Metscher B, Orliac M, Rowe TB, Rücklin M, Sánchez-Villagra MR, Shubin NH, Smith SY, Starck JM, Stringer C, Summers AP, Sutton MD, Walsh SA, Weisbecker V, Witmer LM, Wroe S, Yin Z, Rayfield EJ, Donoghue PC.

Proc Biol Sci. 2017 Apr 12;284(1852). pii: 20170194. doi: 10.1098/rspb.2017.0194. Epub 2017 Apr 12. Review.


Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data.

Puttick MN, O'Reilly JE, Tanner AR, Fleming JF, Clark J, Holloway L, Lozano-Fernandez J, Parry LA, Tarver JE, Pisani D, Donoghue PC.

Proc Biol Sci. 2017 Jan 11;284(1846). pii: 20162290. doi: 10.1098/rspb.2016.2290.


MicroRNA annotation of plant genomes - Do it right or not at all.

Taylor RS, Tarver JE, Foroozani A, Donoghue PC.

Bioessays. 2017 Feb;39(2). doi: 10.1002/bies.201600113. Epub 2017 Jan 5. Review.


The origin of animals: Can molecular clocks and the fossil record be reconciled?

Cunningham JA, Liu AG, Bengtson S, Donoghue PC.

Bioessays. 2017 Jan;39(1):1-12. doi: 10.1002/bies.201600120. Epub 2016 Dec 5. Review.


A multicellular organism with embedded cell clusters from the Ediacaran Weng'an biota (Doushantuo Formation, South China).

Cunningham JA, Vargas K, Marone F, Bengtson S, Donoghue PC.

Evol Dev. 2016 Dec;18(5-6):308-316. doi: 10.1111/ede.12210.


Reply to 'placoderms and the evolutionary origin of teeth': Burrow et al. (2016).

Rücklin M, Donoghue PC.

Biol Lett. 2016 Sep;12(9). pii: 20160526. No abstract available.


Pigmented anatomy in Carboniferous cyclostomes and the evolution of the vertebrate eye.

Gabbott SE, Donoghue PC, Sansom RS, Vinther J, Dolocan A, Purnell MA.

Proc Biol Sci. 2016 Aug 17;283(1836). pii: 20161151. doi: 10.1098/rspb.2016.1151.


Evolution of the Calcium-Based Intracellular Signaling System.

Marchadier E, Oates ME, Fang H, Donoghue PC, Hetherington AM, Gough J.

Genome Biol Evol. 2016 Jul 14;8(7):2118-32. doi: 10.1093/gbe/evw139.


Tectonic blocks and molecular clocks.

De Baets K, Antonelli A, Donoghue PC.

Philos Trans R Soc Lond B Biol Sci. 2016 Jul 19;371(1699). pii: 20160098. doi: 10.1098/rstb.2016.0098. Review.


The evolution of methods for establishing evolutionary timescales.

Donoghue PC, Yang Z.

Philos Trans R Soc Lond B Biol Sci. 2016 Jul 19;371(1699). pii: 20160020. doi: 10.1098/rstb.2016.0020. Review.


Dating species divergences using rocks and clocks.

Yang Z, Donoghue PC.

Philos Trans R Soc Lond B Biol Sci. 2016 Jul 19;371(1699). pii: 20150126. doi: 10.1098/rstb.2015.0126. No abstract available.


Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data.

O'Reilly JE, Puttick MN, Parry L, Tanner AR, Tarver JE, Fleming J, Pisani D, Donoghue PC.

Biol Lett. 2016 Apr;12(4). pii: 20160081. doi: 10.1098/rsbl.2016.0081.


Tips and nodes are complementary not competing approaches to the calibration of molecular clocks.

O'Reilly JE, Donoghue PC.

Biol Lett. 2016 Apr;12(4). pii: 20150975. doi: 10.1098/rsbl.2015.0975.


Histology and affinity of anaspids, and the early evolution of the vertebrate dermal skeleton.

Keating JN, Donoghue PC.

Proc Biol Sci. 2016 Mar 16;283(1826):20152917. doi: 10.1098/rspb.2015.2917.


Cyanobacteria and the Great Oxidation Event: evidence from genes and fossils.

Schirrmeister BE, Gugger M, Donoghue PC.

Palaeontology. 2015 Sep;58(5):769-785. Epub 2015 Jun 23.


The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference.

Tarver JE, Dos Reis M, Mirarab S, Moran RJ, Parker S, O'Reilly JE, King BL, O'Connell MJ, Asher RJ, Warnow T, Peterson KJ, Donoghue PC, Pisani D.

Genome Biol Evol. 2016 Jan 5;8(2):330-44. doi: 10.1093/gbe/evv261.


Bayesian molecular clock dating of species divergences in the genomics era.

dos Reis M, Donoghue PC, Yang Z.

Nat Rev Genet. 2016 Feb;17(2):71-80. doi: 10.1038/nrg.2015.8. Epub 2015 Dec 21. Review.


Size is not everything: rates of genome size evolution, not C-value, correlate with speciation in angiosperms.

Puttick MN, Clark J, Donoghue PC.

Proc Biol Sci. 2015 Dec 7;282(1820):20152289. doi: 10.1098/rspb.2015.2289.


Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales.

dos Reis M, Thawornwattana Y, Angelis K, Telford MJ, Donoghue PC, Yang Z.

Curr Biol. 2015 Nov 16;25(22):2939-50. Epub 2015 Oct 22.


Constraining the Deep Origin of Parasitic Flatworms and Host-Interactions with Fossil Evidence.

De Baets K, Dentzien-Dias P, Upeniece I, Verneau O, Donoghue PC.

Adv Parasitol. 2015;90:93-135. doi: 10.1016/bs.apar.2015.06.002. Epub 2015 Jul 17. Review.


Dating Tips for Divergence-Time Estimation.

O'Reilly JE, Dos Reis M, Donoghue PCJ.

Trends Genet. 2015 Nov;31(11):637-650. doi: 10.1016/j.tig.2015.08.001. Epub 2015 Oct 1. Review.



Rücklin M, Donoghue PC, Cunningham JA, Marone F, Stampanoni M.

J Paleontol. 2014 Jul 1;88(4):676-683.


Critical appraisal of tubular putative eumetazoans from the Ediacaran Weng'an Doushantuo biota.

Cunningham JA, Vargas K, Pengju L, Belivanova V, Marone F, Martínez-Pérez C, Guizar-Sicairos M, Holler M, Bengtson S, Donoghue PC.

Proc Biol Sci. 2015 Aug 7;282(1812):20151169. doi: 10.1098/rspb.2015.1169.


Romundina and the evolutionary origin of teeth.

Rücklin M, Donoghue PC.

Biol Lett. 2015 Jun;11(6):20150326. doi: 10.1098/rsbl.2015.0326.


Experimental taphonomy of Artemia reveals the role of endogenous microbes in mediating decay and fossilization.

Butler AD, Cunningham JA, Budd GE, Donoghue PC.

Proc Biol Sci. 2015 Jun 7;282(1808):20150476. doi: 10.1098/rspb.2015.0476.


The Fossil Calibration Database-A New Resource for Divergence Dating.

Ksepka DT, Parham JF, Allman JF, Benton MJ, Carrano MT, Cranston KA, Donoghue PC, Head JJ, Hermsen EJ, Irmis RB, Joyce WG, Kohli M, Lamm KD, Leehr D, Patané JL, Polly PD, Phillips MJ, Smith NA, Smith ND, Van Tuinen M, Ware JL, Warnock RC.

Syst Biol. 2015 Sep;64(5):853-9. doi: 10.1093/sysbio/syv025. Epub 2015 Apr 27.


Histology of the heterostracan dermal skeleton: Insight into the origin of the vertebrate mineralised skeleton.

Keating JN, Marquart CL, Donoghue PC.

J Morphol. 2015 Jun;276(6):657-80. doi: 10.1002/jmor.20370. Epub 2015 Mar 30.


Discriminating signal from noise in the fossil record of early vertebrates reveals cryptic evolutionary history.

Sansom RS, Randle E, Donoghue PC.

Proc Biol Sci. 2015 Feb 7;282(1800):20142245. doi: 10.1098/rspb.2014.2245.

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