Publications: Dr Mario Dos Reis Barros
Panchaksaram M, Freitas L, dos Reis M
(
2024
)
.
Bayesian Selection of Relaxed-Clock Models: Distinguishing between Independent and Autocorrelated Rates
.
Systematic Biology
Panchaksaram M, Freitas L, Dos Reis M
(
2024
)
.
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
.