Improving Bayesian methods for estimating divergence times integrating genomic and trait data

Research output

Research output per year 2016 2016 2017 2018 2019 2021 2024

• 31 Article (Academic Journal)
• 4 Comment/debate (Academic Journal)
• 3 Review article (Academic Journal)

Research output per year

Research output per year

Search results

• 2024

  Ediacaran origin and Ediacaran-Cambrian diversification of Metazoa

  Carlisle, E. M., Yin, Z., Pisani, D. & Donoghue, P. C. J., 30 Sept 2024, (Accepted/In press) In: Science Advances.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  • Ediacaran 100%
  • Fossil Record 22%
  • Phylogenetics 11%
• 2022

  A species-level timeline of mammal evolution integrating phylogenomic data

  Alvarez-Carretero, S., Tamuri, A. U., Battini, M., Nascimento, F. F., Carlisle, E. M., Asher, R. J., Yang, Z., Donoghue, P. C. J. & dos Reis, M., 10 Feb 2022, In: Nature. 602, 7896, p. 263-267 13 p.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • State of the Art 100%
  • Late Cretaceous 100%
  • Eocene 100%
  • Paleocene 100%
  • Phylogenomics 100%
  82 Citations (Scopus)

  374 Downloads (Pure)
• 2021

  Diversification dynamics of total-, stem-, and crown-groups are compatible with molecular clock estimates of divergence times

  Beavan, A. J. S., Pisani, D. & Donoghue , P. C. J., 11 Jun 2021, In: Science Advances. 7, 24, 8 p., eabf2257.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Dynamics 100%
  • Molecular Clock 100%
  • Species Differentiation 100%
  • Evolution 100%
  • Cladistics 100%
  8 Citations (Scopus)

  143 Downloads (Pure)

• Experimental taphonomy of organelles and the fossil record of early eukaryote evolution

  Carlisle, E. M., Jobbins, M., Pankhania, V., Cunningham, J. A. & Donoghue , P. C. J., 27 Jan 2021, In: Science Advances. 7, 5, 8 p., eabe9487.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Organelle 100%
  • Taphonomy 100%
  • Fossil Record 100%
  • Chloroplast 75%
  • Pyrenoid 50%
  21 Citations (Scopus)

  87 Downloads (Pure)

• Fossil data support a pre-Cretaceous origin of flowering plants

  Silvestro, D., Bacon, C., Ding, W., Zhang, Q., Donoghue , P. C. J., Alexandre, A. & Xing, Y., 28 Jan 2021, In: Nature Ecology and Evolution. 5, 4, p. 449-457 9 p.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Angiosperm 100%
  • Molecular Clock 33%
  • Lineages 16%
  52 Citations (Scopus)

  674 Downloads (Pure)

• Fossilization processes have little impact on tip-calibrated divergence time analyses

  O'Reilly, J. E. & Donoghue , P. C. J., Sept 2021, In: Palaeontology. 64, 5, p. 687-697 11 p.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Resulting Process 100%
  • Evidence Total 100%
  • Anatomical Information 100%
  • Successive Stage 100%
  • Statistical Distribution 100%
  2 Citations (Scopus)

  62 Downloads (Pure)

• The evolutionary emergence of land plants

  Donoghue, P. C. J., Harrison, C. J., Paps Montserrat, J. & Schneider, H., 11 Oct 2021, In: Current Biology. 31, 19, p. R1281-R1298 18 p.

  Research output: Contribution to journal › Review article (Academic Journal) › peer-review

  Open Access

  File

  • Vascular Plant 100%
  • Evolution 100%
  • Bryophyte 100%
  • Embryophyta 66%
  • Moss 66%
  77 Citations (Scopus)

  367 Downloads (Pure)
• 2020

  Disparities in the analysis of morphological disparity

  Guillerme, T., Natalie, C., Brusatte, S., Davis, K., Jackson, A., Gerber, S., Goswami, A., Healy, K., Hopkins, M., Jones, M., Lloyd, G., O'Reilly, J. E., Pate, A., Puttick, M. N., Rayfield, E. J., Saupe, E., Sherratt, E., Slater, G., Weisbecker, V. & Thomas, G. & 1 others, Donoghue, P. C. J., 29 Jul 2020, In: Biology Letters. 16, 7, 8 p.

  Research output: Contribution to journal › Review article (Academic Journal) › peer-review

  Open Access

  File

  • Selection Method 100%
  61 Citations (Scopus)

  77 Downloads (Pure)

• Integrated phylogenomic and fossil evidence of stick and leaf insects (Phasmatodea) reveal a Permian-Triassic co-origination with insectivores

  Tihelka, E., Cai, C., Giacomelli, M., Pisani, D. & Donoghue , P. C. J., 11 Nov 2020, In: Royal Society Open Science. 7, 11, 12 p., 201689.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Cladistics 100%
  • Sisters 50%
  • Molecular Clock 50%
  • Transcriptomics 50%
  • Plant Tissue 50%
  28 Citations (Scopus)

  67 Downloads (Pure)

• Performance of a priori and a posteriori calibration strategies in divergence time estimation

  Beavan, A. J. S., Donoghue, P. C. J., Beaumont, M. A. & Pisani, D., 22 May 2020, In: Genome Biology and Evolution. 12, 7, p. 1087-1098 12 p., evaa105.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Posteriori 100%
  • Time Estimation 100%
  • Molecular Clock 100%
  • Time Perception 100%
  • Bayesian Analysis 100%
  7 Citations (Scopus)

  67 Downloads (Pure)
• 2019

  Evolution: The Flowering of Land Plant Evolution

  Donoghue, P., 5 Aug 2019, In: Current Biology. 29, 15, p. R753-R756 4 p.

  Research output: Contribution to journal › Comment/debate (Academic Journal)

  Open Access

  File

  • Angiosperm 100%
  • Plant Evolution 100%
  • Anthesis 100%
  • Evolution 50%
  11 Citations (Scopus)

  67 Downloads (Pure)

• Origin of horsetails and the role of whole-genome duplication in plant macroevolution

  Clark, J. W., Puttick, M. N. & Donoghue, P. C. J., 6 Nov 2019, In: Proceedings of the Royal Society B: Biological Sciences. 286, 1914, 10 p.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Equisetum 100%
  • Equisetopsida 100%
  • Lineages 50%
  • Angiosperm 37%
  • Transcriptome 12%
  22 Citations (Scopus)

  154 Downloads (Pure)

• Probabilistic methods outperform parsimony in the phylogenetic analysis of data simulated without a probabilistic model

  Puttick, M. N., O'Reilly, J. E., Pisani, D. & Donoghue, P. C. J., Jan 2019, In: Palaeontology. 62, 1, p. 1-17 17 p.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Phylogenetic Analysis 100%
  • Data Analysis 100%
  • maximum-likelihood 100%
  • Probabilistic Method 100%
  • Branches 100%
  43 Citations (Scopus)

  291 Downloads (Pure)

• The apparatus composition and architecture of Erismodus quadridactylus and the implications for element homology in prioniodinin conodonts

  Dhanda, R., Murdock, D. J. E., Repetski, J. E., Donoghue, P. C. J. & Smith, M. P., 1 Nov 2019, In: Papers in Palaeontology. 5, 4, p. 657-677 21 p.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Conodont 100%
  • United States of America 25%
  • Paleozoic 25%
  • Late Ordovician 25%
  • North Dakota 25%
  3 Citations (Scopus)

  186 Downloads (Pure)

• The effect of fossil sampling on the estimation of divergence times with the fossilised birth death process

  O'Reilly, J. & Donoghue, P., 17 May 2019, (Accepted/In press) In: Systematic Biology. syz037.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • divergence 100%
  24 Citations (Scopus)

  301 Downloads (Pure)

• The impact of fossil stratigraphic ranges on tip-calibration, and the accuracy and precision of divergence time estimates

  Püschel, H., O'Reilly, J., Pisani, D. & Donoghue, P., 21 Aug 2019, In: Palaeontology. 17 p.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Morphology 100%
  • Fossil 100%
  • Confidence Interval 50%
  22 Citations (Scopus)

  131 Downloads (Pure)
• 2018

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

  Barba-Montoya, J., dos Reis, M., Harald, S., Donoghue, P. & Yang, Z., 5 Feb 2018, (E-pub ahead of print) In: New Phytologist. 16 p.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Angiosperm 100%
  • Pollinator 22%
  • Molecular Clock 22%
  134 Citations (Scopus)

  340 Downloads (Pure)

• Empirical realism of simulated data is more important than the model used to generate it: a reply to Goloboff et al.

  O'Reilly, J. E., Puttick, M. N., Pisani, D. & Donoghue, P. C. J., 1 Jul 2018, In: Palaeontology. 61, 4, p. 631-635 5 p.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Realism 100%
  • Simulated Data 100%
  25 Citations (Scopus)

  403 Downloads (Pure)

• Integrated genomic and fossil evidence illuminates life’s early evolution and eukaryote origin

  Betts, H. C., Puttick, M. N., Clark, J. W., Williams, T. A., Donoghue, P. C. J. & Pisani, D., Oct 2018, In: Nature Ecology and Evolution. 2, 10, p. 1556-1562 7 p.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Mitochondrion 100%
  • Eukaryote 100%
  • Genomics 100%
  • Lineages 100%
  • Photosystem 50%
  253 Citations (Scopus)

  558 Downloads (Pure)

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

  Morris, J. L., Puttick, M., Clark, J., Edwards, D., Kenrick, P., Pressel, S., Wellman, C. H., Yang, Z., Schneider, H. & Donoghue, P., 9 Oct 2018, In: Proceedings of the National Academy of Sciences of the United States of America. 115, 41, p. E9512-9513 2 p.

  Research output: Contribution to journal › Comment/debate (Academic Journal) › peer-review

  Open Access

  File
  11 Citations (Scopus)

  284 Downloads (Pure)

• The Efficacy of Consensus Tree Methods for Summarizing Phylogenetic Relationships from a Posterior Sample of Trees Estimated from Morphological Data

  O'Reilly, J. & Donoghue, P., 1 Mar 2018, In: Systematic Biology. 67, 2, p. 354-362 9 p., syz086.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Cladistics 100%
  • Branches 18%
  39 Citations (Scopus)

  233 Downloads (Pure)

• The nature of aspidin and the evolutionary origin of bone

  Keating, J., Marone, F., Donoghue, P. & Marquart, C. L., 1 Sept 2018, In: Nature Ecology and Evolution. 2, 9, p. 1501-1506 6 p.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Evolution 100%
  • Dentin 100%
  • X Ray 100%
  • Cyclostome 100%
  • Skeleton 33%
  27 Citations (Scopus)

  325 Downloads (Pure)

• The timescale of early land plant evolution

  Morris, J. L., Puttick, M. N., Clark, J. W., Edwards, D., Kenrick, P., Pressel, S., Wellman, C. H., Yang, Z., Schneider, H. & Donoghue, P. C. J., 6 Mar 2018, In: Proceedings of the National Academy of Sciences of the United States of America. 115, 10, p. E2274-E2283 10 p.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Fossil Record 100%
  • Vascular Plant 100%
  • Molecular Clock 100%
  • Embryophyta 66%
  • Viridiplantae 66%
  591 Citations (Scopus)

  746 Downloads (Pure)

• Whole-Genome Duplication and Plant Macroevolution

  Clark, J. W. & Donoghue, P. C. J., 1 Oct 2018, In: Trends in Plant Science. 23, 10, p. 933-945 13 p.

  Research output: Contribution to journal › Review article (Academic Journal) › peer-review

  Open Access

  File

  • Lineages 100%
  • Molecular Clock 100%
  • Evolution 100%
  • Plant Evolution 100%
  210 Citations (Scopus)

  970 Downloads (Pure)
• 2017

  Constraining the timing of whole genome duplication in plant evolutionary history

  Clark, J. W. & Donoghue, P. C. J., 12 Jul 2017, In: Proceedings of the Royal Society B: Biological Sciences. 284, 1858, 20170912.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Angiosperm 100%
  • Evolution 100%
  • Seed Plant 100%
  • Multigene Family 50%
  • Molecular Clock 50%
  49 Citations (Scopus)

  328 Downloads (Pure)

• Ediacaran developmental biology

  Dunn, F., Liu, A. & Donoghue, P., 3 Nov 2017, (E-pub ahead of print) In: Biological Reviews. 19 p.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Taxon 100%
  • Animal 100%
  • Biological Sciences 100%
  • Developmental Biology 100%
  • Ediacaran 100%
  83 Citations (Scopus)

  490 Downloads (Pure)

• Parsimony and Maximum Likelihood phylogenetic analyses of morphology do not generally integrate uncertainty in inferring evolutionary history: A response to Brown et al.

  Puttick, M. N., O’Reilly, J. E., Oakley, D., Tanner, A. R., Fleming, J. F., Clark, J., Holloway, L., Lozano-Fernandez, J., Parry, L. A., Tarver, J. E., Pisani, D. & Donoghue, P. C. J., 11 Oct 2017, In: Proceedings of the Royal Society B: Biological Sciences. 284, 1864, 3 p., 20171636.

  Research output: Contribution to journal › Comment/debate (Academic Journal) › peer-review

  Open Access

  File

  • Cladistics 100%
  • Evolution 100%
  24 Citations (Scopus)

  317 Downloads (Pure)

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

  O'Reilly, J., Puttick, M., Pisani, D. & Donoghue, P., 31 Oct 2017, (E-pub ahead of print) In: Palaeontology. 14 p.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Cladistics 100%
  • Fossil 22%
  • Branches 11%
  • Probabilistic Models 11%
  • Evolution 11%
  63 Citations (Scopus)

  437 Downloads (Pure)

• RelTime rates collapse to a strict clock when estimating the timeline of animal diversification

  Lozano-Fernandez, J., dos Reis, M., Donoghue, P. & Pisani, D., 1 May 2017, In: Genome Biology and Evolution. 9, 5, p. 1320-1328 9 p., evx079.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Molecular Clock 100%
  • Animal 100%
  • Ediacaran 100%
  • Branches 50%
  • Cladistics 50%
  26 Citations (Scopus)

  394 Downloads (Pure)

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

  Warnock, R. C. M., Yang, Z. & Donoghue, P. C. J., 28 Jun 2017, In: Proceedings of the Royal Society B: Biological Sciences. 284, 1857, 10 p., 20170227.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Nonuniform 100%
  • Bayesian 100%
  • Timescale 100%
  • Time Estimation 100%
  • Statistical Approach 100%
  35 Citations (Scopus)

  314 Downloads (Pure)

• Uncertain-tree: Discriminating among competing approaches to the phylogenetic analysis of phenotype data

  Puttick, M., O'Reilly, J., Tanner, A., Fleming, J., Clark, J., Holloway, L., Lozano-Fernandez, J., Parry, L., Tarver, J., Pisani, D. & Donoghue, P., 11 Jan 2017, In: Proceedings of the Royal Society B: Biological Sciences. 284, 1846, 9 p., 20162290.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Cladistics 100%
  • Bayesian 100%
  • Phylogenetics 100%
  • Life History 25%
  104 Citations (Scopus)

  322 Downloads (Pure)
• 2016

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

  O'Reilly, J., Puttick, M. N., Parry, L. A., Tanner, A., Tarver, J. E., Fleming, J., Pisani, D. & Donoghue, P. C. J., Apr 2016, In: Biology Letters. 12, 4, 5 p., 20160081.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Morphology 100%
  • Cladistics 100%
  • Parsimony 100%
  • Bayesian 100%
  • Phylogenetics 100%
  161 Citations (Scopus)

  359 Downloads (Pure)

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

  dos Reis, M., Donoghue, P. C. J. & Yang, Z., Feb 2016, In: Nature Reviews Genetics. 17, 2, p. 71-80 10 p.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Molecular Clock 100%
  • Genomics 100%
  • Genetics 33%
  • Species Differentiation 33%
  • Evolution 33%
  203 Citations (Scopus)

  741 Downloads (Pure)

• Dating species divergences using rocks and clocks

  Yang, Z. & Donoghue, P. C. J., 19 Jul 2016, In: Philosophical Transactions B: Biological Sciences. 371, 1699, 4 p., 20150126.

  Research output: Contribution to journal › Comment/debate (Academic Journal)

  Open Access

  File

  • Rock 100%
  8 Citations (Scopus)

  299 Downloads (Pure)

• Developmental biology of the Early Cambrian cnidarian Olivooides

  Dong, X. P., Vargas, K., Cunningham, J. A., Zhang, H., Liu, T., Chen, F., Liu, J., Bengtson, S. & Donoghue, P. C. J., May 2016, In: Palaeontology. 59, 3, p. 387-407 21 p.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Biological Sciences 100%
  • Cnidaria 100%
  • Gut 100%
  • Phylogeny 100%
  • Cladistics 66%
  33 Citations (Scopus)

  500 Downloads (Pure)

• Tectonic blocks and molecular clocks

  De Baets, K., Antonelli, A. & Donoghue, P., 19 Jul 2016, In: Philosophical Transactions B: Biological Sciences. 371, 1699, 12 p., 20160098.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Tectonics 100%
  • Biogeography 100%
  • Phylogenetics 50%
  • New Zealand 50%
  • Atlantic Ocean 50%
  38 Citations (Scopus)

  334 Downloads (Pure)

• The evolution of methods for establishing evolutionary timescales

  Donoghue, P. C. J. & Yang, Z., 31 Jul 2016, In: Philosophical Transactions B: Biological Sciences. 371, 1699, 11 p., 20160020.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Lineages 100%
  • Evolution 100%
  • Fossil 100%
  • probability density ρ 100%
  • Timescale 100%
  78 Citations (Scopus)

  388 Downloads (Pure)

• Tips and nodes are complimentary not competing approaches to the calibration of molecular clocks

  O'Reilly, J. & Donoghue, P., 19 Apr 2016, In: Biology Letters. 12, 4, 9 p., 20150975.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Cladistics 100%
  • Molecular Clock 100%
  • Evolution 100%
  • Fossil 50%
  35 Citations (Scopus)

  424 Downloads (Pure)