Dr Mario dos Reis
Reader in Statistical Phylogenetics
School of Biological and Behavioural Sciences
Queen Mary University of London
Queen Mary University of London
Research
Phylogenetics, Molecular Evolution, Genomics, Population Genetics
Interests
Dr. dos Reis research focuses on the development of statistical methods to understand species evolution through time and how this has shaped patterns of species diversity. Research topics of interest include methods to use genomic data to reconstruct timetrees, methods to measure the strength of natural selection in proteins, and methods to model trait evolution.Publications
Publications of specific relevance to the Centre for Evolutionary and Functional Genomics2022
dos Reis M (2022). Dating Microbial Evolution with MCMCtree. Methods in Molecular Biology 3-22. 10-09-2022
Escudero Castelán N, Semmens DC, Guerra LAY, Zandawala M, dos Reis M, Slade SE, Scrivens JH, Zampronio CG, Jones AM, Mirabeau O and Elphick MR (2022). Receptor deorphanization in an echinoderm reveals kisspeptin evolution and relationship with SALMFamide neuropeptides. BMC Biology, BioMed Central vol. 20 (1) 24-08-2022
2021
Álvarez-Carretero S, Tamuri AU, Battini M, Nascimento FF, Carlisle E, Asher RJ, Yang Z, Donoghue PCJ and dos Reis M (2021). A Species-Level Timeline of Mammal Evolution Integrating Phylogenomic Data. Nature, Springer Science and Business Media LLC 22-12-2021
Tamuri AU and dos Reis M (2021). A mutation-selection model of protein evolution under persistent positive selection. Molecular Biology and Evolution, Oxford University Press (OUP) vol. 39 (1) 25-10-2021
Potter JHT, Drinkwater R, Davies KTJ, Nesi N, Lim MCW, Yohe LR, Chi H, Zhang X, Levantis I, Lim BK, Witt CC, Tsagkogeorga G, Dos Reis M, Liu Y, Furey W, Whitley MJ, Aksentijevic D, Dávalos LM and Rossiter SJ (2021). Nectar-feeding bats and birds show parallel molecular adaptations in sugar metabolism enzymes. Current Biology, Elsevier vol. 31 (20), 4667-4674.e6. 02-09-2021
Potter JHT, Davies KTJ, Yohe LR, Sanchez MKR, Rengifo EM, Struebig M, Warren K, Tsagkogeorga G, Lim BK, Dos Reis M, Dávalos LM and Rossiter SJ (2021). Dietary Diversification and Specialization in Neotropical Bats Facilitated by Early Molecular Evolution. Mol Biol Evol vol. 38 (9), 3864-3883. 23-08-2021
Campbell CR, Tiley GP, Poelstra JW, Hunnicutt KE, Larsen PA, Lee H-J, Thorne JL, dos Reis M and Yoder AD (2021). Pedigree-based and phylogenetic methods support surprising
patterns of mutation rate and spectrum in the gray mouse
lemur. Heredity, Springer Nature [academic journals on nature.com] 16-07-2021
Álvarez-Carretero S and dos Reis M (2021). Bayesian Phylogenomic Dating. The Molecular Evolutionary Clock 221-249. 19-01-2021
Perri AR, Mitchell KJ, Mouton A, Álvarez-Carretero S, Hulme-Beaman A, Haile J, Jamieson A, Meachen J, Lin AT, Schubert BW, Ameen C, Antipina EE, Bover P, Brace S, Carmagnini A, Carøe C, Samaniego Castruita JA, Chatters JC, Dobney K, dos Reis M, et al. (2021). Dire wolves were the last of an ancient New World canid lineage. Nature, Springer Nature vol. 591 (7848), 87-91. 13-01-2021
2020
Tiley GP, Poelstra JW, dos Reis M, Yang Z and Yoder AD (2020). Molecular Clocks without Rocks: New Solutions for Old Problems. Trends in Genetics, Elsevier 22-07-2020
2019
Kawahara AY, Plotkin D, Espeland M, Meusemann K, Toussaint EFA, Donath A, Gimnich F, Frandsen PB, Zwick A, dos Reis M, Barber JR, Peters RS, Liu S, Zhou X, Mayer C, Podsiadlowski L, Storer C, Yack JE, Misof B and Breinholt JW (2019). Phylogenomics reveals the evolutionary timing and pattern of butterflies and moths. Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, 201907847-201907847. 21-10-2019
McGowen MR, Tsagkogeorga G, Álvarez-Carretero S, Dos Reis M, Struebig M, Deaville R, Jepson PD, Jarman S, Polanowski A, Morin PA and Rossiter SJ (2019). Phylogenomic Resolution of the Cetacean Tree of Life Using Target Sequence Capture. Systematic Biology, Oxford University Press (OUP) 21-10-2019
Dos Reis M and Yang Z (2019). Bayesian Molecular Clock Dating Using Genome-Scale Datasets. Methods Mol Biol vol. 1910, 309-330. 06-07-2019
Halliday TJD, dos Reis M, Tamuri AU, Ferguson-Gow H, Yang Z and Goswami A (2019). Rapid morphological evolution in placental mammals post-dates the origin of the crown group. Proceedings of the Royal Society B: Biological Sciences, Royal Society, The 06-03-2019
Álvarez-Carretero S, Goswami A, Yang Z and dos Reis M (2019). Bayesian estimation of species divergence times using correlated quantitative characters. Systematic Biology, Oxford University Press (OUP) 28-02-2019
2018
dos Reis M (2018). Fossil-free dating. Nature Ecology and Evolution, Nature Publishing Group 02-04-2018
Barba-Montoya J, dos Reis M, Schneider H, Donoghue P and Yang Z (2018). Constraining uncertainty in the timescale of angiosperm evolution and the veracity of a Cretaceous Terrestrial Revolution. New Phytologist, Wiley 05-02-2018
dos Reis M, Gunnell GF, Barba-Montoya J, Wilkins A, Yang Z and Yoder AD (2018). Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case. Systematic Biology 12-01-2018
2017
Nascimento FF, dos Reis M and Yang Z (2017). A biologist’s guide to Bayesian phylogenetic analysis. Nature Ecology and Evolution, Nature Publishing Group vol. 1, 1446-1454. 21-09-2017
Barba-Montoya J, Dos Reis M and Yang Z (2017). Comparison of different strategies for using fossil calibrations to generate the time prior in Bayesian molecular clock dating. Mol Phylogenet Evol vol. 114, 386-400. 11-07-2017
Angelis K, Álvarez-Carretero S, dos Reis M and Yang Z (2017). An evaluation of different partitioning strategies for Bayesian estimation of species divergence times. Systematic Biology 04-07-2017
Lozano-Fernandez J, dos Reis M, Donoghue PCJ and Pisani D (2017). RelTime rates collapse to a strict clock when estimating the timeline of animal diversification. Genome Biol Evol 25-04-2017
2016
Thiltgen G, dos Reis M and Goldstein RA (2016). Finding direction in the search for selection. Journal of Molecular Evolution, Springer Verlag (Germany) 02-12-2016
Yoder AD, Campbell CR, Blanco MB, Dos Reis M, Ganzhorn JU, Goodman SM, Hunnicutt KE, Larsen PA, Kappeler PM, Rasoloarison RM, Ralison JM, Swofford DL and Weisrock DW (2016). Geogenetic patterns in mouse lemurs (genus Microcebus) reveal the ghosts of Madagascar's forests past. Proc Natl Acad Sci U S A vol. 113 (29), 8049-8056. 19-07-2016
dos Reis M (2016). Notes on the birth-death prior with fossil calibrations for Bayesian estimation of species divergence times. Philosophical Transactions of the Royal Society of London: Biological Sciences, Royal Society, The 20-06-2016
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 PCJ and Pisani D (2016). The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference. Genome Biology and Evolution, Oxford University Press (OUP) vol. 8 (2), 330-344. 05-01-2016
2015
dos Reis M, Donoghue PCJ and Yang Z (2015). Bayesian molecular clock dating of species divergences in the genomics era. Nature Reviews Genetics, Springer Nature vol. 17 (2), 71-80. 21-12-2015
dos Reis M, Thawornwattana Y, Angelis K, Telford MJ, Donoghue PCJ and Yang Z (2015). Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales. Current Biology, Elsevier vol. 25 (22), 2939-2950. 22-10-2015
O’Reilly JE, dos Reis M and Donoghue PCJ (2015). Dating Tips for Divergence-Time Estimation. Trends in Genetics, Elsevier vol. 31 (11), 637-650. 01-10-2015
Angelis K and Dos Reis M (2015). The impact of ancestral population size and incomplete lineage sorting on Bayesian estimation of species divergence times. Current Zoology, Oxford University Press (OUP) vol. 61 (5), 874-885. 01-10-2015
dos Reis M (2015). How to calculate the non-synonymous to synonymous rate ratio of protein-coding genes under the Fisher–Wright mutation–selection framework. Biology Letters, The Royal Society vol. 11 (4) 01-04-2015
2014
Zhu T, Dos Reis M and Yang Z (2014). Characterization of the Uncertainty of Divergence Time Estimation under Relaxed Molecular Clock Models Using Multiple Loci. Systematic Biology, Oxford University Press (OUP) vol. 64 (2), 267-280. 11-12-2014
Jeffares DC, Tomiczek B, Sojo V and dos Reis M (2014). A Beginners Guide to Estimating the Non-synonymous to Synonymous Rate Ratio of all Protein-Coding Genes in a Genome. 07-10-2014
Tamuri AU, Goldman N and dos Reis M (2014). A Penalized-Likelihood Method to Estimate the Distribution of Selection Coefficients from Phylogenetic Data. Genetics, Oxford University Press (OUP) vol. 197 (1), 257-271. 01-05-2014
Angelis K, dos Reis M and Yang Z (2014). Bayesian Estimation of Nonsynonymous/Synonymous Rate Ratios for Pairwise Sequence Comparisons. Molecular Biology and Evolution, Oxford University Press (OUP) vol. 31 (7), 1902-1913. 18-04-2014
Dos Reis M, Zhu T and Yang Z (2014). The Impact of the Rate Prior on Bayesian Estimation of Divergence Times with Multiple Loci. Systematic Biology, Oxford University Press (OUP) vol. 63 (4), 555-565. 21-03-2014
Yoder AD, Chan LM, dos Reis M, Larsen PA, Campbell CR, Rasoloarison R, Barrett M, Roos C, Kappeler P, Bielawski J and Yang Z (2014). Molecular Evolutionary Characterization of a V1R Subfamily Unique to Strepsirrhine Primates. Genome Biology and Evolution, Oxford University Press (OUP) vol. 6 (1), 213-227. 06-01-2014
dos Reis M, Donoghue PCJ and Yang Z (2014). Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals. Biology Letters, The Royal Society vol. 10 (1) 01-01-2014
2013
dos Reis M and Yang Z (2013). Why Do More Divergent Sequences Produce Smaller Nonsynonymous/Synonymous Rate Ratios in Pairwise Sequence Comparisons? Genetics, Oxford University Press (OUP) vol. 195 (1), 195-204. 01-09-2013
2012
DOS REIS M and Ziheng Y (2012). The unbearable uncertainty of Bayesian divergence time estimation. Journal of Systematics and Evolution, Wiley vol. 51 (1), 30-43. 25-12-2012
dos Reis M, Inoue J, Hasegawa M, Asher RJ, Donoghue PCJ and Yang Z (2012). Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proceedings of the Royal Society B, The Royal Society vol. 279 (1742), 3491-3500. 23-05-2012
Tamuri AU, dos Reis M and Goldstein RA (2012). Estimating the Distribution of Selection Coefficients from Phylogenetic Data Using Sitewise Mutation-Selection Models. Genetics, Oxford University Press (OUP) vol. 190 (3), 1101-1115. 01-03-2012
2011
HOFINGER BJ, RUSSELL JR, BASS CG, BALDWIN T, Dos REIS M, HEDLEY PE, LI Y, MACAULAY M, WAUGH R, HAMMOND‐KOSACK KE and KANYUKA K (2011). An exceptionally high nucleotide and haplotype diversity and a signature of positive selection for the eIF4E resistance gene in barley are revealed by allele mining and phylogenetic analyses of natural populations. Molecular Ecology, Wiley vol. 20 (17), 3653-3668. 01-07-2011
dos Reis M and Yang Z (2011). Approximate Likelihood Calculation on a Phylogeny for Bayesian Estimation of Divergence Times. Molecular Biology and Evolution, Oxford University Press (OUP) vol. 28 (7), 2161-2172. 10-02-2011
2010
dos Reis M, Tamuri AU, Hay AJ and Goldstein RA (2010). Charting the Host Adaptation of Influenza Viruses. Molecular Biology and Evolution, Oxford University Press (OUP) vol. 28 (6), 1755-1767. 25-11-2010
Yang Z and dos Reis M (2010). Statistical Properties of the Branch-Site Test of Positive Selection. Molecular Biology and Evolution, Oxford University Press (OUP) vol. 28 (3), 1217-1228. 18-11-2010
Noël ES, dos Reis M, Arain Z and Ober EA (2010). Analysis of the Albumin/α-Fetoprotein/Afamin/Group specific component gene family in the context of zebrafish liver differentiation. Gene Expression Patterns, Elsevier vol. 10 (6), 237-243. 13-05-2010
2009
Tamuri AU, dos Reis M, Hay AJ and Goldstein RA (2009). Identifying Changes in Selective Constraints: Host Shifts in Influenza. PLOS Computational Biology, Public Library of Science (PLoS) vol. 5 (11) 01-11-2009
dos Reis M, Hay AJ and Goldstein RA (2009). Using Non-Homogeneous Models of Nucleotide Substitution to Identify Host Shift Events: Application to the Origin of the 1918 ‘Spanish’ Influenza Pandemic Virus. Journal of Molecular Evolution, Springer Nature vol. 69 (4) 29-09-2009
2008
dos Reis M and Wernisch L (2008). Estimating Translational Selection in Eukaryotic Genomes. Molecular Biology and Evolution, Oxford University Press (OUP) vol. 26 (2), 451-461. 25-11-2008
2006
Withers M, Wernisch L and dos Reis M (2006). Archaeology and evolution of transfer RNA genes in the Escherichia coli genome. RNA, Cold Spring Harbor Laboratory vol. 12 (6), 933-942. 17-04-2006
2004
dos Reis M, Savva R and Wernisch L (2004). Solving the riddle of codon usage preferences: a test for translational selection. Nucleic Acids Research, Oxford University Press (OUP) vol. 32 (17), 5036-5044. 23-09-2004
2003
dos Reis M, Wernisch L and Savva R (2003). Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K‐12 genome. Nucleic Acids Research, Oxford University Press (OUP) vol. 31 (23), 6976-6985. 01-12-2003
Sheng G, dos Reis M and Stern CD (2003). Churchill, a Zinc Finger Transcriptional Activator, Regulates the Transition between Gastrulation and Neurulation. Cell, Elsevier vol. 115 (5), 603-613. 01-11-2003
Grants
Grants of specific relevance to the Centre for Evolutionary and Functional GenomicsEfficient computational technologies to resolve the Timetree of Life: from ancient DNA to species-rich phylogeniesMario Dos Reis Barros
£460,301 BBSRC Biotechnology and Biological Sciences Research Council (16-07-2024 - 15-07-2027)
Efficient Bayesian phylogenomic dating with new models of trait evolution and rich diversities of living and fossil speciesMario Dos Reis Barros
£203,910 BBSRC Biotechnology and Biological Sciences Research Council (01-10-2020 - 31-05-2024)