Molecular Evolution and Phylogenetic Analyses
Addendum: A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology.
Rambaut A, Holmes EC, O'Toole Á, Hill V, McCrone JT, Ruis C, du Plessis L & Pybus OG (2021) Nature microbiology 6, 415.
Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST.
Baele G, Lemey P, Rambaut A & Suchard, MA (2017) Bioinformatics 33, 1798?1805.
Exploring the temporal structure of heterochronous sequences using TempEst.
Rambaut A, Lam TT, Carvalho LM & Pybus OG (2016) Virus Evolution 2, vew007.
The effects of sampling strategy on the quality of reconstruction of viral population dynamics using Bayesian skyline family coalescent methods: A simulation study.
Hall MD, Woolhouse M & Rambaut A (2016) Virus Evolution 2, vew003.
πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios.
Bielejec F, Lemey P, Carvalho LM, Baele G, Rambaut A & Suchard MA (2014) BMC Bioinfomatics 15, 133.
BEAST 2: A Software Platform for Bayesian Evolutionary Analysis.
Bouckaert R, Heled J, Kühnert D, Vaughan, Wu C-H, Xie D, Suchard MA, Rambaut A & Drummond AJ (2014) PLoS Comput Biol 10, e1003537.
Bayesian phylogenetics with BEAUti and the BEAST 1.7.
Drummond AJ, Suchard MA, Dong Xie & Rambaut A (2012) Mol Biol Evol 29, 1969-1973.
BEAGLE: a common application programming inferface and high-performance computing library for statistical phylogenetics.
Ayres D, Darling A, Zwickl D, Beerli P, Holder M, Lewis P, Huelsenbeck JP, Ronquist F, Swofford D, Cummings MP, Rambaut A & Suchard MA (2012) Syst Biol 61, 170-173.
Using Time-Structured Data to Estimate Evolutionary Rates of Double-Stranded DNA Viruses.
Firth C, Kitchen A, Shapiro A, Suchard MA, Holmes EC & Rambaut A (2010) Mol Biol Evol 27, 2038-2051.
Phylogeography takes a relaxed random walk in continuous space and time.
Lemey P, Rambaut A, Welch JJ & Suchard MA (2010) Mol Biol Evol 27, 1877-1886.
A generation time effect on the rate of molecular evolution in invertebrates.
Thomas JA, Welch JJ, Lanfear R & Bromham L (2010) Mol Biol Evol 27, 1173-1180.
Quantifying adaptive evolution in the Drosophila immune system: a high throughput approach.
Obbard DJ, Welch JJ, Kim K-W & Jiggins FM (2009) PLoS Genetics 5, e1000698.
Bayesian Phylogeography Finds Its Roots.
Lemey P, Rambaut A, Drummond AJ & Suchard MA (2009) PLoS Comput Biol 5, e1000520.
Conjugation genes are common throughout the genus Rickettsia and are transmitted horizontally.
Weinert, LA, Welch JJ & Jiggins FM (2009) Proc Roy Soc B 276, 3619-3627.
Inferring selection in the Anopheles gambiae species complex: an example from immune-related serine protease inhibitors.
Obbard DJ, Welch JJ & Little TJ (2009) Malaria Journal 8, 117.
Many-Core Algorithms for Statistical Phylogenetics.
Suchard MA & Rambaut A (2009) Bioinformatics 25, 1370-1376.
Reduced effectiveness of selection caused by a lack of recombination on the dot chromosome of Drosophila americana.
Betancourt AJ, Welch JJ & Charlesworth B (2009) Current Biology 19, 655-660.
Accommodating the effect of ancient DNA damage on inferences of demographic histories.
Rambaut A, Ho SYW, Drummond AJ & Shapiro B (2008) Mol Biol Evol 26, 245-248.
Divergence and polymorphism under the nearly neutral theory of molecular evolution.
Welch JJ, Eyre-Walker A & Waxman D (2008) J Mol Evol 67, 418-26.
Evolutionary genomics of host adaptation in vesicular stomatitis virus (VSV).
Remold SK, Rambaut A & Turner PE (2008) Mol Biol Evol 25, 1138-1147.
Correlates of substitution rate variation in mammalian protein-coding sequences.
Welch JJ, Bininda-Emonds ORP & Bromham L (2008) BMC Evol Biol 8, 53.
Metabolic rate does not calibrate the molecular clock.
Lanfear R, Thomas JA, Welch JJ, Brey T & Bromham L (2007) Proc Natl Acad Sci USA 104, 15388-15393.
The influence of body size and net diversification rate on molecular evolution during the radiation of animal phyla .
Fontanillas E, Welch JJ, Thomas JA & Bromham L (2007) BMC Evol Biol 7, 95.
Bayesian estimation of sequence damage in ancient DNA.
Ho SYW, Heupink TH, Rambaut A & and Shapiro B (2007) Mol Biol Evol 24, 1416-1422.
Estimating the genomewide rate of adaptive protein evolution in Drosophila.
Welch JJ (2006) Genetics 173, 821-837.
There is no universal molecular clock for invertebrates, but rate variation does not scale with body size.
Thomas JA, Welch JJ, Woolfit M & Bromham L (2006) Proc Natl Acad Sci USA 103, 7366-7371.
The nature of heterotachy.
Lockhart P, Novis P, Milligan B, Riden J, Rambaut A & Larkum T (2006) Mol Biol Evol 23, 40-45.
A dissection of volatility in yeast.
Stoletzki N, Welch JJ, Hermisson J & Eyre-Walker A (2005) Mol Biol Evol 22, 2022-2026.
Rise and fall of the Beringian steppe bison.
Shapiro B, Drummond AJ, Rambaut A, Wilson M, Sher A, Pybus OG, Gilbert MTP, Barnes I, Binladen J, Willerslev E, Hansen A, Baryshnikov GF, Burns J, Davydov S, Driver J, Gubin SV, Harington CR, Keddie G, Kosintsev P, Kunz ML, Martin LD, Stephenson R, Storer J, Tedford R, Vorobiev A, Zimov S & Cooper A (2004) Science 306, 1561-1565.
Testing the relationship between morphological and molecular rates of change along phylogenies.
Bromham L, Woolfit M, Lee MS & Rambaut A (2002) Evolution 56, 1921-1930.
Flight of the dodo.
Shapiro B, Sibthorpe D, Rambaut A, Austin J, Wragg GM, Bininda-Emonds OR, Lee PL & Cooper A (2002) Science 295, 1683.
Human origins and ancient human DNA.
Cooper A, Rambaut A, Macaulay V, Willerslev E, Hansen AJ & Stringer C (2001) Science 292, 1655-1656.
Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution.
Cooper A, Lalueza-Fox C, Anderson S, Rambaut A, Austin J & Ward R (2001) Nature 409, 704-707.
Phylogeny, genome evolution, and host specificity of single-stranded RNA bacteriophage (Family Leviviridae).
Bollback JP & Huelsenbeck JP (2001) J Mol Evol 52, 117-128.
Testing the Cambrian explosion hypothesis by using a molecular dating technique.
Bromham L, Rambaut A, Fortey R, Cooper A & Penny D (1998) Proc Natl Acad Sci USA 95, 12386-12389.
Determinants of rate variation in mammalian DNA sequence evolution.
Bromham L, Rambaut A & Harvey PH (1996) J Mol Evol 43, 610-621.
Isolation and sequence analysis of a cDNA encoding the c subunit of a vacuolar-type H(+)-ATPase from the CAM plant Kalanchoe daigremontiana.
Bartholomew DM, Rees DJ, Rambaut A & Smith JA (1996) Plant Mol Biol 31, 435-442.
Andrew Rambaut, 2007