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 Genomics2024
Bayesian Selection of Relaxed-Clock Models: Distinguishing between Independent and Autocorrelated RatesPanchaksaram M, Freitas L and dos Reis M
Systematic Biology, Oxford University Press (Oup)
21-11-2024
Bayesian Selection of Relaxed-clock Models: Distinguishing Between Independent and Autocorrelated Rates.Panchaksaram M, Freitas L and Dos Reis M
Systematic Biology
01-11-2024
2022
Dating Microbial Evolution with MCMCtreedos Reis M
In Methods in Molecular Biology, Springer Nature 3-22.
10-09-2022
Receptor deorphanization in an echinoderm reveals kisspeptin evolution and relationship with SALMFamide neuropeptidesEscudero Castelán N, Semmens DC, Guerra LAY, Zandawala M, dos Reis M, Slade SE, Scrivens JH, Zampronio CG, Jones AM, Mirabeau O and Elphick MR
Bmc Biology, Biomed Central vol. 20 (1)
24-08-2022
2021
A Species-Level Timeline of Mammal Evolution Integrating Phylogenomic DataÁlvarez-Carretero S, Tamuri AU, Battini M, Nascimento FF, Carlisle E, Asher RJ, Yang Z, Donoghue PCJ and dos Reis M
Nature, Springer Science and Business Media Llc
22-12-2021
A Mutation–Selection Model of Protein Evolution under Persistent Positive SelectionTamuri AU and dos Reis M
Molecular Biology and Evolution, Oxford University Press (Oup) vol. 39 (1)
25-10-2021
Nectar-feeding bats and birds show parallel molecular adaptations in sugar metabolism enzymesPotter 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
Current Biology, Elsevier vol. 31 (20), 4667-4674.e6.
02-09-2021
Dietary Diversification and Specialization in Neotropical Bats Facilitated by Early Molecular Evolution.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
Mol Biol Evol vol. 38 (9), 3864-3883.
23-08-2021
Pedigree-based and phylogenetic methods support surprising
patterns of mutation rate and spectrum in the gray mouse
lemurCampbell CR, Tiley GP, Poelstra JW, Hunnicutt KE, Larsen PA, Lee H-J, Thorne JL, dos Reis M and Yoder AD
Heredity, Springer Nature [Academic Journals On Nature.Com]
16-07-2021
Bayesian Phylogenomic DatingÁlvarez-Carretero S and dos Reis M
In The Molecular Evolutionary Clock 221-249.
19-01-2021
Dire wolves were the last of an ancient New World canid lineagePerri 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.
Nature, Springer Nature vol. 591 (7848), 87-91.
13-01-2021
2020
Molecular Clocks without Rocks: New Solutions for Old ProblemsTiley GP, Poelstra JW, dos Reis M, Yang Z and Yoder AD
Trends in Genetics, Elsevier
22-07-2020
2019
Phylogenomics reveals the evolutionary timing and pattern of butterflies and mothsKawahara 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
Proceedings of The National Academy of Sciences, Proceedings of The National Academy of Sciences, 201907847-201907847.
21-10-2019
Phylogenomic Resolution of the Cetacean Tree of Life Using Target Sequence Capture.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
Systematic Biology, Oxford University Press (Oup)
21-10-2019
Bayesian Molecular Clock Dating Using Genome-Scale Datasets.Dos Reis M and Yang Z
Methods Mol Biol vol. 1910, 309-330.
06-07-2019
Rapid morphological evolution in placental mammals post-dates the origin of the crown groupHalliday TJD, dos Reis M, Tamuri AU, Ferguson-Gow H, Yang Z and Goswami A
Proceedings of The Royal Society B: Biological Sciences, Royal Society, The
06-03-2019
Bayesian estimation of species divergence times using correlated quantitative charactersÁlvarez-Carretero S, Goswami A, Yang Z and dos Reis M
Systematic Biology, Oxford University Press (Oup)
28-02-2019
2018
Constraining uncertainty in the timescale of angiosperm evolution and the veracity of a Cretaceous Terrestrial RevolutionBarba-Montoya J, dos Reis M, Schneider H, Donoghue P and Yang Z
New Phytologist, Wiley
05-02-2018
Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Casedos Reis M, Gunnell GF, Barba-Montoya J, Wilkins A, Yang Z and Yoder AD
Systematic Biology
12-01-2018
2017
A biologist’s guide to Bayesian phylogenetic analysisNascimento FF, dos Reis M and Yang Z
Nature Ecology and Evolution, Nature Publishing Group vol. 1, 1446-1454.
21-09-2017
Comparison of different strategies for using fossil calibrations to generate the time prior in Bayesian molecular clock datingBarba-Montoya J, Dos Reis M and Yang Z
Mol Phylogenet Evol vol. 114, 386-400.
11-07-2017
An evaluation of different partitioning strategies for Bayesian estimation of species divergence timesAngelis K, Álvarez-Carretero S, dos Reis M and Yang Z
Systematic Biology
04-07-2017
RelTime rates collapse to a strict clock when estimating the timeline of animal diversification.Lozano-Fernandez J, dos Reis M, Donoghue PCJ and Pisani D
Genome Biol Evol
25-04-2017
2016
Finding direction in the search for selectionThiltgen G, dos Reis M and Goldstein RA
Journal of Molecular Evolution, Springer Verlag (Germany)
02-12-2016
Geogenetic patterns in mouse lemurs (genus Microcebus) reveal the ghosts of Madagascar's forests past.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
Proc Natl Acad Sci U S A vol. 113 (29), 8049-8056.
19-07-2016
Notes on the birth-death prior with fossil calibrations for Bayesian estimation of species divergence timesdos Reis M
Philosophical Transactions of The Royal Society of London: Biological Sciences, Royal Society, The
20-06-2016
The Interrelationships of Placental Mammals and the Limits of Phylogenetic InferenceTarver 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
Genome Biology and Evolution, Oxford University Press (Oup) vol. 8 (2), 330-344.
05-01-2016
2015
Bayesian molecular clock dating of species divergences in the genomics erados Reis M, Donoghue PCJ and Yang Z
Nature Reviews Genetics, Springer Nature vol. 17 (2), 71-80.
21-12-2015
Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescalesdos Reis M, Thawornwattana Y, Angelis K, Telford MJ, Donoghue PCJ and Yang Z
Current Biology, Elsevier vol. 25 (22), 2939-2950.
22-10-2015
Dating Tips for Divergence-Time EstimationO’Reilly JE, dos Reis M and Donoghue PCJ
Trends in Genetics, Elsevier vol. 31 (11), 637-650.
01-10-2015
The impact of ancestral population size and incomplete lineage sorting on Bayesian estimation of species divergence timesAngelis K and Dos Reis M
Current Zoology, Oxford University Press (Oup) vol. 61 (5), 874-885.
01-10-2015
How to calculate the non-synonymous to synonymous rate ratio of protein-coding genes under the Fisher–Wright mutation–selection frameworkdos Reis M
Biology Letters, The Royal Society vol. 11 (4)
01-04-2015
2014
Characterization of the Uncertainty of Divergence Time Estimation under Relaxed Molecular Clock Models Using Multiple LociZhu T, Dos Reis M and Yang Z
Systematic Biology, Oxford University Press (Oup) vol. 64 (2), 267-280.
11-12-2014
A Beginners Guide to Estimating the Non-synonymous to Synonymous Rate Ratio of all Protein-Coding Genes in a GenomeJeffares DC, Tomiczek B, Sojo V and dos Reis M
Methods in Molecular Biology, Springer Nature vol. 1201, 65-90.
07-10-2014
A Penalized-Likelihood Method to Estimate the Distribution of Selection Coefficients from Phylogenetic DataTamuri AU, Goldman N and dos Reis M
Genetics, Oxford University Press (Oup) vol. 197 (1), 257-271.
01-05-2014
Bayesian Estimation of Nonsynonymous/Synonymous Rate Ratios for Pairwise Sequence ComparisonsAngelis K, dos Reis M and Yang Z
Molecular Biology and Evolution, Oxford University Press (Oup) vol. 31 (7), 1902-1913.
18-04-2014
The Impact of the Rate Prior on Bayesian Estimation of Divergence Times with Multiple LociDos Reis M, Zhu T and Yang Z
Systematic Biology, Oxford University Press (Oup) vol. 63 (4), 555-565.
21-03-2014
Molecular Evolutionary Characterization of a V1R Subfamily Unique to Strepsirrhine PrimatesYoder AD, Chan LM, dos Reis M, Larsen PA, Campbell CR, Rasoloarison R, Barrett M, Roos C, Kappeler P, Bielawski J and Yang Z
Genome Biology and Evolution, Oxford University Press (Oup) vol. 6 (1), 213-227.
06-01-2014
Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammalsdos Reis M, Donoghue PCJ and Yang Z
Biology Letters, The Royal Society vol. 10 (1)
01-01-2014
2013
Why Do More Divergent Sequences Produce Smaller Nonsynonymous/Synonymous Rate Ratios in Pairwise Sequence Comparisons?dos Reis M and Yang Z
Genetics, Oxford University Press (Oup) vol. 195 (1), 195-204.
01-09-2013
2012
The unbearable uncertainty of Bayesian divergence time estimationDOS REIS M and Ziheng Y
Journal of Systematics and Evolution, Wiley vol. 51 (1), 30-43.
25-12-2012
Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogenydos Reis M, Inoue J, Hasegawa M, Asher RJ, Donoghue PCJ and Yang Z
Proceedings of The Royal Society B, The Royal Society vol. 279 (1742), 3491-3500.
23-05-2012
Estimating the Distribution of Selection Coefficients from Phylogenetic Data Using Sitewise Mutation-Selection ModelsTamuri AU, dos Reis M and Goldstein RA
Genetics, Oxford University Press (Oup) vol. 190 (3), 1101-1115.
01-03-2012
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 populationsHOFINGER BJ, RUSSELL JR, BASS CG, BALDWIN T, Dos REIS M, HEDLEY PE, LI Y, MACAULAY M, WAUGH R, HAMMOND‐KOSACK KE and KANYUKA K
Molecular Ecology, Wiley vol. 20 (17), 3653-3668.
01-07-2011
Approximate Likelihood Calculation on a Phylogeny for Bayesian Estimation of Divergence Timesdos Reis M and Yang Z
Molecular Biology and Evolution, Oxford University Press (Oup) vol. 28 (7), 2161-2172.
10-02-2011
2010
Charting the Host Adaptation of Influenza Virusesdos Reis M, Tamuri AU, Hay AJ and Goldstein RA
Molecular Biology and Evolution, Oxford University Press (Oup) vol. 28 (6), 1755-1767.
25-11-2010
Statistical Properties of the Branch-Site Test of Positive SelectionYang Z and dos Reis M
Molecular Biology and Evolution, Oxford University Press (Oup) vol. 28 (3), 1217-1228.
18-11-2010
Analysis of the Albumin/α-Fetoprotein/Afamin/Group specific component gene family in the context of zebrafish liver differentiationNoël ES, dos Reis M, Arain Z and Ober EA
Gene Expression Patterns, Elsevier vol. 10 (6), 237-243.
13-05-2010
2009
Identifying Changes in Selective Constraints: Host Shifts in InfluenzaTamuri AU, dos Reis M, Hay AJ and Goldstein RA
Plos Computational Biology, Public Library of Science (Plos) vol. 5 (11)
01-11-2009
Using Non-Homogeneous Models of Nucleotide Substitution to Identify Host Shift Events: Application to the Origin of the 1918 ‘Spanish’ Influenza Pandemic Virusdos Reis M, Hay AJ and Goldstein RA
Journal of Molecular Evolution, Springer Nature vol. 69 (4)
29-09-2009
2008
Estimating Translational Selection in Eukaryotic Genomesdos Reis M and Wernisch L
Molecular Biology and Evolution, Oxford University Press (Oup) vol. 26 (2), 451-461.
25-11-2008
2006
Archaeology and evolution of transfer RNA genes in the Escherichia coli genomeWithers M, Wernisch L and dos Reis M
Rna, Cold Spring Harbor Laboratory vol. 12 (6), 933-942.
17-04-2006
2004
Solving the riddle of codon usage preferences: a test for translational selectiondos Reis M, Savva R and Wernisch L
Nucleic Acids Research, Oxford University Press (Oup) vol. 32 (17), 5036-5044.
23-09-2004
2003
Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K‐12 genomedos Reis M, Wernisch L and Savva R
Nucleic Acids Research, Oxford University Press (Oup) vol. 31 (23), 6976-6985.
01-12-2003
Churchill, a Zinc Finger Transcriptional Activator, Regulates the Transition between Gastrulation and NeurulationSheng G, dos Reis M and Stern CD
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
£460,301 BBSRC Biotechnology and Biological Sciences Research Council
29-11-2024 - 28-11-2027
Efficient Bayesian phylogenomic dating with new models of trait evolution and rich diversities of living and fossil speciesMario dos Reis
£203,910 BBSRC Biotechnology and Biological Sciences Research Council
01-10-2020 - 31-05-2024