Publications: Dr Mario Dos Reis Barros

Panchaksaram M, Freitas L, dos Reis M ( 2025 ) . Bayesian Selection of Relaxed-clock Models: Distinguishing Between Independent and Autocorrelated Rates . Systematic Biology

dos Reis M ( 2022 ) . Dating Microbial Evolution with MCMCtree . Methods in Molecular Biology , vol. 2569 , Springer Nature

Escudero Castelán N, Semmens DC, Guerra LAY, Zandawala M, dos Reis M, Slade SE, Scrivens JH, Zampronio CG et al. ( 2022 ) . Receptor deorphanization in an echinoderm reveals kisspeptin evolution and relationship with SALMFamide neuropeptides . BMC Biology vol. 20 , ( 1 )

Álvarez-Carretero S, Tamuri AU, Battini M, Nascimento FF, Carlisle E, Asher RJ, Yang Z, Donoghue PCJ et al. ( 2021 ) . A Species-Level Timeline of Mammal Evolution Integrating Phylogenomic Data . Nature

Tamuri AU, dos Reis M ( 2021 ) . A Mutation–Selection Model of Protein Evolution under Persistent Positive Selection . Molecular Biology and Evolution vol. 39 , ( 1 )

Potter JHT, Drinkwater R, Davies KTJ, Nesi N, Lim MCW, Yohe LR, Chi H, Zhang X et al. ( 2021 ) . Nectar-feeding bats and birds show parallel molecular adaptations in sugar metabolism enzymes . Current Biology vol. 31 , ( 20 ) 4667 - 4674.e6 .

Potter JHT, Davies KTJ, Yohe LR, Sanchez MKR, Rengifo EM, Struebig M, Warren K, Tsagkogeorga G et al. ( 2021 ) . Dietary Diversification and Specialization in Neotropical Bats Facilitated by Early Molecular Evolution . Mol Biol Evol vol. 38 , ( 9 ) 3864 - 3883 .

Campbell CR, Tiley GP, Poelstra JW, Hunnicutt KE, Larsen PA, Lee H-J, Thorne JL, dos Reis M et al. ( 2021 ) . Pedigree-based and phylogenetic methods support surprising patterns of mutation rate and spectrum in the gray mouse lemur . Heredity

Álvarez-Carretero S, dos Reis M ( 2021 ) . Bayesian Phylogenomic Dating . The Molecular Evolutionary Clock ,

Perri AR, Mitchell KJ, Mouton A, Álvarez-Carretero S, Hulme-Beaman A, Haile J, Jamieson A, Meachen J et al. ( 2021 ) . Dire wolves were the last of an ancient New World canid lineage . Nature vol. 591 , ( 7848 ) 87 - 91 .

Tiley GP, Poelstra JW, dos Reis M, Yang Z, Yoder AD ( 2020 ) . Molecular Clocks without Rocks: New Solutions for Old Problems . Trends in Genetics

McGowen MR, Tsagkogeorga G, Álvarez-Carretero S, Dos Reis M, Struebig M, Deaville R, Jepson PD, Jarman S et al. ( 2019 ) . Phylogenomic Resolution of the Cetacean Tree of Life Using Target Sequence Capture . Systematic Biology

Kawahara AY, Plotkin D, Espeland M, Meusemann K, Toussaint EFA, Donath A, Gimnich F, Frandsen PB et al. ( 2019 ) . Phylogenomics reveals the evolutionary timing and pattern of butterflies and moths . Proceedings of the National Academy of Sciences201907847 - 201907847 .

Dos Reis M, Yang Z ( 2019 ) . Bayesian Molecular Clock Dating Using Genome-Scale Datasets . Methods Mol Biol vol. 1910 , 309 - 330 .

Halliday TJD, dos Reis M, Tamuri AU, Ferguson-Gow H, Yang Z, 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

Álvarez-Carretero S, Goswami A, Yang Z, dos Reis M ( 2019 ) . Bayesian estimation of species divergence times using correlated quantitative characters . Systematic Biology

dos Reis M ( 2018 ) . Fossil-free dating . Nature Ecology and Evolution

Barba-Montoya J, dos Reis M, Schneider H, Donoghue P, Yang Z ( 2018 ) . Constraining uncertainty in the timescale of angiosperm evolution and the veracity of a Cretaceous Terrestrial Revolution . New Phytologist

dos Reis M, Gunnell GF, Barba-Montoya J, Wilkins A, Yang Z, 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

Nascimento FF, dos Reis M, Yang Z ( 2017 ) . A biologist’s guide to Bayesian phylogenetic analysis . Nature Ecology and Evolution vol. 1 , 1446 - 1454 .

Barba-Montoya J, Dos Reis M, 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 .

Angelis K, Álvarez-Carretero S, dos Reis M, Yang Z ( 2017 ) . An evaluation of different partitioning strategies for Bayesian estimation of species divergence times . Systematic Biology

Lozano-Fernandez J, dos Reis M, Donoghue PCJ, Pisani D ( 2017 ) . RelTime rates collapse to a strict clock when estimating the timeline of animal diversification . Genome Biol Evol

Thiltgen G, dos Reis M, Goldstein RA ( 2016 ) . Finding direction in the search for selection . Journal of Molecular Evolution

Yoder AD, Campbell CR, Blanco MB, Dos Reis M, Ganzhorn JU, Goodman SM, Hunnicutt KE, Larsen PA et al. ( 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 .

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

Tarver JE, Dos Reis M, Mirarab S, Moran RJ, Parker S, O'Reilly JE, King BL, O'Connell MJ et al. ( 2016 ) . The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference . Genome Biology and Evolution vol. 8 , ( 2 ) 330 - 344 .

dos Reis M, Donoghue PCJ, Yang Z ( 2015 ) . Bayesian molecular clock dating of species divergences in the genomics era . Nature Reviews Genetics vol. 17 , ( 2 ) 71 - 80 .

dos Reis M, Thawornwattana Y, Angelis K, Telford MJ, Donoghue PCJ, Yang Z ( 2015 ) . Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales . Current Biology vol. 25 , ( 22 ) 2939 - 2950 .

O’Reilly JE, dos Reis M, Donoghue PCJ ( 2015 ) . Dating Tips for Divergence-Time Estimation . Trends in Genetics vol. 31 , ( 11 ) 637 - 650 .

Angelis K, Dos Reis M ( 2015 ) . The impact of ancestral population size and incomplete lineage sorting on Bayesian estimation of species divergence times . Current Zoology vol. 61 , ( 5 ) 874 - 885 .

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 vol. 11 , ( 4 )

Zhu T, Dos Reis M, Yang Z ( 2014 ) . Characterization of the Uncertainty of Divergence Time Estimation under Relaxed Molecular Clock Models Using Multiple Loci . Systematic Biology vol. 64 , ( 2 ) 267 - 280 .

Jeffares DC, Tomiczek B, Sojo V, dos Reis M ( 2014 ) . A Beginners Guide to Estimating the Non-synonymous to Synonymous Rate Ratio of all Protein-Coding Genes in a Genome . Methods in Molecular Biology vol. 1201 , 65 - 90 .

Tamuri AU, Goldman N, dos Reis M ( 2014 ) . A Penalized-Likelihood Method to Estimate the Distribution of Selection Coefficients from Phylogenetic Data . Genetics vol. 197 , ( 1 ) 257 - 271 .

Angelis K, dos Reis M, Yang Z ( 2014 ) . Bayesian Estimation of Nonsynonymous/Synonymous Rate Ratios for Pairwise Sequence Comparisons . Molecular Biology and Evolution vol. 31 , ( 7 ) 1902 - 1913 .

Dos Reis M, Zhu T, Yang Z ( 2014 ) . The Impact of the Rate Prior on Bayesian Estimation of Divergence Times with Multiple Loci . Systematic Biology vol. 63 , ( 4 ) 555 - 565 .

Yoder AD, Chan LM, dos Reis M, Larsen PA, Campbell CR, Rasoloarison R, Barrett M, Roos C et al. ( 2014 ) . Molecular Evolutionary Characterization of a V1R Subfamily Unique to Strepsirrhine Primates . Genome Biology and Evolution vol. 6 , ( 1 ) 213 - 227 .

dos Reis M, Donoghue PCJ, Yang Z ( 2014 ) . Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals . Biology Letters vol. 10 , ( 1 )

dos Reis M ( 2013 ) . Population genetics and substitution models of adaptive evolution . Abstract: java.sql.Clob org.hibernate.engine.jdbc.WrappedClob java.io.Serializable , Notes: 24 pages, 4 figures and 1 table. Manuscript written between January and April 2010 ,

dos Reis M, Yang Z ( 2013 ) . Why Do More Divergent Sequences Produce Smaller Nonsynonymous/Synonymous Rate Ratios in Pairwise Sequence Comparisons? . Genetics vol. 195 , ( 1 ) 195 - 204 .

DOS REIS M, Ziheng Y ( 2012 ) . The unbearable uncertainty of Bayesian divergence time estimation . Journal of Systematics and Evolution vol. 51 , ( 1 ) 30 - 43 .

dos Reis M, Inoue J, Hasegawa M, Asher RJ, Donoghue PCJ, Yang Z ( 2012 ) . Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny . Proceedings of the Royal Society B vol. 279 , ( 1742 ) 3491 - 3500 .

Tamuri AU, dos Reis M, Goldstein RA ( 2012 ) . Estimating the Distribution of Selection Coefficients from Phylogenetic Data Using Sitewise Mutation-Selection Models . Genetics vol. 190 , ( 3 ) 1101 - 1115 .

HOFINGER BJ, RUSSELL JR, BASS CG, BALDWIN T, Dos REIS M, HEDLEY PE, LI Y, MACAULAY M et al. ( 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 vol. 20 , ( 17 ) 3653 - 3668 .

dos Reis M, Yang Z ( 2011 ) . Approximate Likelihood Calculation on a Phylogeny for Bayesian Estimation of Divergence Times . Molecular Biology and Evolution vol. 28 , ( 7 ) 2161 - 2172 .

dos Reis M, Tamuri AU, Hay AJ, Goldstein RA ( 2010 ) . Charting the Host Adaptation of Influenza Viruses . Molecular Biology and Evolution vol. 28 , ( 6 ) 1755 - 1767 .

Yang Z, dos Reis M ( 2010 ) . Statistical Properties of the Branch-Site Test of Positive Selection . Molecular Biology and Evolution vol. 28 , ( 3 ) 1217 - 1228 .

Noël ES, dos Reis M, Arain Z, 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 vol. 10 , ( 6 ) 237 - 243 .

Tamuri AU, dos Reis M, Hay AJ, Goldstein RA ( 2009 ) . Identifying Changes in Selective Constraints: Host Shifts in Influenza . PLOS Computational Biology vol. 5 , ( 11 )

dos Reis M, Hay AJ, 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 vol. 69 , ( 4 )

dos Reis M, Wernisch L ( 2008 ) . Estimating Translational Selection in Eukaryotic Genomes . Molecular Biology and Evolution vol. 26 , ( 2 ) 451 - 461 .

Withers M, Wernisch L, dos Reis M ( 2006 ) . Archaeology and evolution of transfer RNA genes in the Escherichia coli genome . RNA vol. 12 , ( 6 ) 933 - 942 .

dos Reis M, Savva R, Wernisch L ( 2004 ) . Solving the riddle of codon usage preferences: a test for translational selection . Nucleic Acids Research vol. 32 , ( 17 ) 5036 - 5044 .

dos Reis M, Wernisch L, 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 vol. 31 , ( 23 ) 6976 - 6985 .

Sheng G, dos Reis M, Stern CD ( 2003 ) . Churchill, a Zinc Finger Transcriptional Activator, Regulates the Transition between Gastrulation and Neurulation . Cell vol. 115 , ( 5 ) 603 - 613 .