Joe O'Reilly

epidemiology - statistical inference - phylogenetics - data science



Research Overview

I am a statistical epidemiologist currently employed as a postdoctoral biostatistician/epidemiologist based in Professor Helen Colhoun’s research group in IGC at The University of Edinburgh. My research primarily focuses on the epidemiology of type 1 diabetes and its associated complications. To achieve this I use the national register of people with type 1 diabetes in Scotland to perform analyses employing a range of statistical methods including Bayesian hierarchical regression, prediction modelling, and survival analysis.

I also have a PhD in Bayesian phylogenetic methods which I obtained in The University of Bristol Palaeobiology Research Group under the supervision of Professor Phil Donoghue. My phylogenetic research interests include the relative efficacy of Bayesian, frequentist and non-parametric topology estimation frameworks; the construction of prior probability distributions for divergence time estimation analyses; and empirical applications of cutting edge phylogenetic methods to provide insight into the mechanism of evolutionary processes.

Peer Reviewed Publications

A complete list of all of my peer-reviewed publications is available on my Google Scholar profile page.


O’Reilly, J.E., Donoghue, P.C., 2021. Fossilization processes have little impact on tip-calibrated divergence time analyses. Palaeontology.

Höhn, A., Jeyam, A., Caparrotta, T.M., McGurnaghan, S.J., O’Reilly, J.E., Blackbourn, L.A., McCrimmon, R.J., Leese, G.P., McKnight, J.A., Kennon, B., others, 2021. The association of polypharmacy and high-risk drug classes with adverse health outcomes in the Scottish population with type 1 diabetes. Diabetologia 64, 1309–1319.

O’Reilly, J.E., Jeyam, A., Caparrotta, T.M., Mellor, J., Hohn, A., McKeigue, P.M., McGurnaghan, S.J., Blackbourn, L.A., McCrimmon, R., Wild, S.H., others, 2021. Rising Rates and Widening Socioeconomic Disparities in Diabetic Ketoacidosis in Type 1 Diabetes in Scotland: A Nationwide Retrospective Cohort Observational Study. Diabetes Care.

Smith, T.J., Puttick, M.N., O’Reilly, J.E., Pisani, D., Donoghue, P.C., 2021. Phylogenetic sampling affects evolutionary patterns of morphological disparity. Palaeontology.

Jeyam, A., Gibb, F.W., McKnight, J.A., Kennon, B., O’Reilly, J.E., Caparrotta, T.M., Höhn, A., McGurnaghan, S.J., Blackbourn, L.A., Hatam, S., others, 2021. Marked improvements in glycaemic outcomes following insulin pump therapy initiation in people with type 1 diabetes: a nationwide observational study in Scotland. Diabetologia 64, 1320–1331.

Püschel, H.P., Bertrand, O.C., O’Reilly, J.E., Bobe, R., Püschel, T.A., 2021. Divergence-time estimates for hominins provide insight into encephalization and body mass trends in human evolution. Nat. Ecol. Evol. 5, 808–819.

McGurnaghan, S.J., Weir, A., Bishop, J., Kennedy, S., Blackbourn, L.A., McAllister, D.A., Hutchinson, S., Caparrotta, T.M., Mellor, J., Jeyam, A., others, 2021. Risks of and risk factors for COVID-19 disease in people with diabetes: a cohort study of the total population of Scotland. Lancet Diabetes Endocrinol. 9, 82–93.

Murphy, J.L., Puttick, M.N., O’Reilly, J.E., Pisani, D., Donoghue, P.C., 2021. Empirical distributions of homoplasy in morphological data. Palaeontology 64, 505–518.


O’Reilly, J.E., Blackbourn, L.A., Caparrotta, T.M., Jeyam, A., Kennon, B., Leese, G.P., Lindsay, R.S., McCrimmon, R.J., McGurnaghan, S.J., McKeigue, P.M., others, 2020. Time trends in deaths before age 50 years in people with type 1 diabetes: a nationwide analysis from Scotland 2004–2017. Diabetologia 63, 1626–1636.

O’Reilly, J.E., Donoghue, P.C., 2020. The effect of fossil sampling on the estimation of divergence times with the fossilized birth–death process. Syst. Biol. 69, 124–138.

Püschel, H.P., O’Reilly, J.E., Pisani, D., Donoghue, P.C., 2020. The impact of fossil stratigraphic ranges on tip-calibration, and the accuracy and precision of divergence time estimates. Palaeontology 63, 67–83.


Puttick, M.N., O’Reilly, J.E., Pisani, D., Donoghue, P.C., 2019. Probabilistic methods outperform parsimony in the phylogenetic analysis of data simulated without a probabilistic model. Palaeontology 62, 1–17.

Barido-Sottani, J., Pett, W., O’Reilly, J.E., Warnock, R.C., 2019. FossilSim: An r package for simulating fossil occurrence data under mechanistic models of preservation and recovery. Methods Ecol. Evol. 10, 835–840.


O’Reilly, J.E., Puttick, M.N., Pisani, D., Donoghue, P.C., 2018a. Probabilistic methods surpass parsimony when assessing clade support in phylogenetic analyses of discrete morphological data. Palaeontology 61, 105–118.

O’Reilly, J.E., Puttick, M.N., Pisani, D., Donoghue, P.C., 2018b. Empirical realism of simulated data is more important than the model used to generate it: a reply to Goloboff et al. Palaeontology 61, 631–635.

O’Reilly, J.E., Donoghue, P.C., 2018. The efficacy of consensus tree methods for summarizing phylogenetic relationships from a posterior sample of trees estimated from morphological data. Syst. Biol. 67, 354–362.


Puttick, M., O’Reilly, J., Oakley, D., Tanner, A., Fleming, J., Clark, J.,... Donoghue, PCJ, 2017. Parsimony and Maximum Likelihood phylogenetic analyses of morphology do not generally integrate uncertainty in inferring evolutionary history: A response to Brown et al. Proceedings of the Royal Society B: Biological Sciences, 284 (1864),[20171636].

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., others, 2017a. Parsimony and maximum-likelihood phylogenetic analyses of morphology do not generally integrate uncertainty in inferring evolutionary history: a response to Brown et al. Proc. R. Soc. B Biol. Sci. 284, 20171636.

Puttick, M.N., O’Reilly, J.E., Tanner, A.R., Fleming, J.F., Clark, J., Holloway, L., Lozano-Fernandez, J., Parry, L.A., Tarver, J.E., Pisani, D., others, 2017b. Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data. Proc. R. Soc. B Biol. Sci. 284, 20162290.


Tarver, J.E., Dos Reis, M., Mirarab, S., Moran, R.J., Parker, S., O’Reilly, J.E., King, B.L., O’Connell, M.J., Asher, R.J., Warnow, T., others, 2016. The interrelationships of placental mammals and the limits of phylogenetic inference. Genome Biol. Evol. 8,

O’Reilly, J.E., Donoghue, P.C., 2016. Tips and nodes are complementary not competing approaches to the calibration of molecular clocks. Biol. Lett. 12, 20150975.

O’Reilly, J.E., Puttick, M.N., Parry, L., Tanner, A.R., Tarver, J.E., Fleming, J., Pisani, D., Donoghue, P.C., 2016. Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data. Biol. Lett. 12, 20160081.


O’Reilly, J.E., Dos Reis, M., Donoghue, P.C., 2015. Dating tips for divergence-time estimation. Trends Genet. 31, 637–650.

PhD Thesis

My PhD thesis is available here as a PDF (17.4 Mb).