Publications

Bromham L, Duchêne S, Hua, X, Ritchie A, Duchêne DA, Ho SYW (2017) Bayesian molecular dating: opening up the black box. Biological Reviews, DOI: 10.1111/brv.12390 PDF

Bromham L (2017) Curiously the same: swapping tools between linguistics and evolutionary biology. Biology & Philosophy DOI 10.1007/s10539-017-9594-y Read Online  Preprint

Duchêne DA, Hua X, Bromham L (2017) Phylogenetic estimates of diversification rate are affected by molecular rate variation. Journal of Evolutionary Biology doi: 10.1111/jeb.13148 PDF

Cardillo M, Weston PH, Reynolds ZKM, Olde PM, Mast AR, Moriarty Lemmon E, Lemmon AR, Bromham L (2017) The phylogeny and biogeography of Hakea (Proteaceae) reveals the role of biome shifts in a continental plant radiation. Evolution 17(8): 1928–1943 DOI: 10.1111/evo.13276  PDF Commentary

Hua X, Bromham L (2017) Darwinism for the genomic age: connecting mutation to diversification. Frontiers in Genetics 8:12. doi: 10.3389/fgene.2017.00012 PDF

Bromham L, Dinnage R, Hua X (2016) Interdisciplinary research has consistently lower funding success. Nature 534: 684–687 PDF  Suppl.Info  Data  FigS1

Day E, Hua X, Bromham L. (2016) Is specialization an evolutionary dead-end? Testing for differences in speciation, extinction and trait transition rates across diverse phylogenies of specialists and generalists. Journal of Evolutionary Biology, DOI: 10.1111/jeb.12867 PDF Supplementary Information

Hua X, Bromham L. (2016) Phylometrics: An R package for detecting macroevolutionary patterns, using phylogenetic metrics and backward tree simulation. Methods in Ecology and Evolution, 32 (10):2633-2645. DOI: 10.1111/2041-210X.12531 PDF  R package

Moray C, Goolsby E, Bromham L (2016) The phylogenetic association between salt tolerance and heavy metal hyperaccumulation in angiosperms. Evolutionary Biology   43: 119-130 doi:10.1007/s11692-015-9355-2 PDF Supplementary1 supplementary2

Bromham L, Hua X, Cardillo M (2016) Detecting macroevolutionary self-destruction from phylogenies. Systematic Biology 65: 109-127 doi: 10.1093/sysbio/syv062 PDF Data

Bromham L (2016) Testing hypotheses in macroevolution. Studies in History and Philosophy of Science 55: 47-59 PDF

Bromham L (2016) An introduction to molecular evolution and phylogenetics. Oxford University Press, Oxford. ISBN 978-0-19-873636-3

Hua X, Cowman PF, Warren D, Bromham L (2015) Longevity is linked to mitochondrial mutation rates in rockfish: a test using Poisson regression. Molecular Biology and Evolution doi: 10.1093/molbev/msv137 PDF

Bromham L (2015) Evolutionary change: nothing stands still in biology. p129-154 in “Change! Combining analytic approaches with street wisdom” Ed G. Bammer. ANU Press.  PDF Website

Duchene D, Bromham L (2015) Molecular dating of evolutionary events. In: Rink WJ, Thompson JW, editors. Encyclopedia of Scientific Dating Methods: Springer Netherlands. p. 593-6. PDF Website

Moray C, Hua X , Bromham L (2015) Salt tolerance is evolutionarily labile in a diverse set of angiosperm families. BMC Evolutionary Biology 15:90 PDF  supplementary files Data

Cardillo M, Bromham L, Greenhill SJ (2015)  Links between language diversity and species richness can be confounded by spatial autocorrelation. Proceedings of the Royal Society of London B 282: 20142986. PDF

Bromham L, Hua X, Fitzpatrick TG, Greenhill SJ (2015)  Rate of language evolution is affected by population size. Proceedings of the National Academy of Sciences USA 112(7):  2097–2102  PDF

Bromham L, Hua X, Lanfear R, Cowman PF (2015) Exploring the relationships between mutation rates, life history, genome size, environment and species richness in flowering plants. American Naturalist 185: 507 PDF Data

Bromham L (2015)  What is a gene for? Biology & Philosophy  31(1), 103-123 DOI 10.1007/s10539-014-9472-9 PDF Reply Commentary

Saslis-Lagoudakis CH, Hua X, Bui E, Moray C, Bromham L (2015) Predicting species’ tolerance to salinity and alkalinity using distribution data and geochemical modelling: a case study using Australian grasses. Annals of Botany  115 (3): 343-351, doi: 10.1093/aob/mcu248 PDF

Bromham L (2014) Macroevolutionary patterns of salt tolerance in angiosperms. Annals of Botany, 115 (3): 333-341. doi: 10.1093/aob/mcu229  PDF

Saslis-Lagoudakis CH, Moray C, Bromham L (2014) Evolution of salt tolerance in angiosperms: a phylogenetic approach. in “Plant ecology and evolution in harsh environments” eds Nishanta Rajakaruna, Robert S. Boyd, Tanner B. Harris. Nova Publishing,Hauppauge, NY ISBN-13: 978-1633219557 PDF Website

Bromham L, Bennett TH (2014) Salt tolerance evolves more frequently in C4 grass lineages. Journal of Evolutionary Biology 27(3):653–659 doi: 10.1111/jeb.12320 PDF

Moray C, Lanfear R, Bromham L (2014) Domestication and the Mitochondrial Genome: Comparing Patterns and Rates of Molecular Evolution in Domesticated Mammals and Birds and Their Wild Relatives. Genome Biology and Evolution 6(1):161-169 PDF Data

Bromham L, Saslis-Lagoudakis CH, Bennett TH, Flowers TJ (2013) Soil alkalinity and salt tolerance: adapting to multiple stresses. Biology Letters 9(5) 20130642 PDf

Bennett TH, Flowers TJ, Bromham L (2013) Repeated evolution of salt-tolerance in grasses. Biology Letters 9(2):20130029 PDF

Bromham L (2013) Molecular evolution: rates (Advanced: 3.0) In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net/ DOI: 10.1002/9780470015902.a0001802.pub3

Bromham L, Cowman PF, Lanfear R (2013) Parasitic plants have increased rates of molecular evolution across all three genomes. BMC Evolutionary Biology 13:126 Doi:12610.1186/1471-2148-13-126).PDF Data

Bromham L (2013) Molecular Evolution: Patterns and Rates. (4.0) In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net/ [DOI: 10.1002/9780470015902.a0001799.pub4]

Duchene D, Bromham L (2013) Rates of molecular evolution and diversification in plants: chloroplast substitution rates correlate with species richness in the Proteaceae. BMC Evolutionary Biology 13:65 DOI:10.1186/1471-2148-13-65 PDF

Sauquet H, Ho SYW, Gandolfo MA, Jordan GJ, Wilf P, Cantrill DJ, Bayly MJ, Bromham L, Brown GK, Carpenter RJ, Lee DM, Murphy DJ, Sniderman JMK, Udovicic F (2012) Testing the Impact of Calibration on Molecular Divergence Times Using a Fossil-Rich Group: The Case of Nothofagus (Fagales). Systematic Biology 61(2):289-313 PDF Data

Bromham L, Lanfear R, Cassey P, Gibb G, Cardillo M (2012) Reconstructing past species assemblages reveals the changing patterns and drivers of extinction through time. Proceedings of the Royal Society B: Biological Sciences 279(1744):4024-4032 PDF

Lanfear R, Bromham L, Ho SY (2011) Molecular evolution and diversification: Counting species is better than counting nodes when the phylogeny is unknown. Proceedings of the National Academy of Sciences 108(17):E85-E86
PDF

Lanfear R, Bromham L (2011) Estimating phylogenies for species assemblages: a complete phylogeny for the past and present native birds of New Zealand. Molecular Phylogeny Evolution 61:958–963 PDF

Goldie X, Lanfear R, Bromham L (2011) Diversification and the rate of molecular evolution: no evidence of a link in mammals. BMC Evolutionary Biology 11:286 PDF

Ho SYW, Lanfear R, Bromham L, Phillips MJ, Soubrier J, Rodrigo AG, Cooper A (2011) Time-dependent rates of molecular evolution. Molecular Ecology 20 (15): 3087-3101 PDF

Bromham L (2011) The Small Picture Approach to the Big Picture: Using DNA Sequences to Investigate the Diversification of Animal Body Plans. In: “Major Transitions Revisited”, eds Calcott and Sterelny, Vienna Series in Theoretical Biology, MIT Press. ISBN-13: 978-0-262-01524-0 PDF

Bromham L (2011) The genome as a life history character: why rate of molecular evolution varies between mammal species. Philosophical Transactions of the Royal Society: Biological Sciences. 366:2503-2513 PDF

Bromham L (2011) Wandering drunks and general lawlessness in biology: does diversity and complexity tend to increase in evolutionary systems? Biology & Philosophy 26(6): 915-933 DOI: 10.1007/s10539-011-9259-1 PDF

Lanfear R, Ho SYW, Love D, Bromham L (2010) Mutation rate is linked to diversification in birds. Proceedings of the National Academy of Sciences USA 107: 20423-2042 PDF

Lanfear R, Welch JJ, Bromham L (2010) Watching the clock: Studying variation in rates of molecular evolution between species. Trends in Ecology and Evolution 25: 495-503 PDF

Thomas JA, Welch JJ, Lanfear R, Bromham L (2010) A generation time effect on the rate of molecular evolution in invertebrates. Mol. Biol. Evol 27:1173-1180 PDF

Flowers TJ, Galal HK, Bromham L (2010) Evolution of halophytes: multiple origins ofsalt tolerance in land plants. Functional Plant Biology. 37 (7) 604–612 PDF

Brennan R, Burrows J, Bell M, Bromham L, Csurhes P, Lenarczyk A, Sverndal, J, Klintenstedt J, Pender M, Burrows S (2010) Strains of Epstein-Barr virus infecting multiple sclerosis patients. Multiple Sclerosis. 16(6): 643-651 doi:10.1177/1352458510364537 PDF

Bromham L (2009) Why do species vary in their rate of molecular evolution? Biology Letters 5:401-404 PDF

Bromham L (2009) Does nothing in evolution make sense except in the light of population genetics? Biology & Philosophy 24: 387-403 PDF

Bromham L (2009) Putting the ‘bio’ into bioinformatics Biology Letters 5:391-393 PDF

Bromham L (2009) Darwin would have loved DNA: celebrating Darwin 200 Biology Letters 5:503-505 PDF

Bromham L (2008) Reading the story in DNA: a beginner’s guide to molecular evolution. Oxford University Press. ISBN 978-0-19-929091-8 PrintBook eBook

Welch JJ, Bininda-Emonds ORP, Bromham L (2008) Correlates of substitution rate variation in mammalian protein-coding sequences. BMC Evolutionary Biology 8:53. PDF data

Lanfear R, Bromham L. (2008) Statistical Tests Between Competing Hypotheses of Hox Cluster Evolution. Systematic Biology 57:708-718 PDF

Bromham L (2008) Teaching evolutionary biology in schools to foster active learning. School Science Review 90:57-63 PDF

Lanfear R, Thomas JA, Welch JJ, Bromham L (2007) Metabolic rate does not calibrate the molecular clock. Proceedings of the National Academy of Sciences USA 104:15388-15393 PDF Supplementary Info

Bromham L, Cardillo M (2007) Primates follow the “Island Rule”: implications for interpreting Homo floresiensis. Biology Letters 3(4):398-400 PDF Supplementary Info

Fontanillas E, Welch J, Thomas J, Bromham L (2007) The influence of body size and net diversification rate on molecular evolution during the radiation of animal phyla. BMC Evolutionary Biology 7:95 PDF

Thomas JA, Welch JJ, Woolfit M, Bromham L (2006) There is no universal molecular clock for invertebrates, but rate variation does not scale with body size. Proceedings of the national Academy of Sciences USA 103 (19):7366-7371 PDF

Bromham L (2006) Molecular dates for the Cambrian Explosion: is the light at the end of the tunnel an oncoming train? Palaeontologia Electronica 9(1):2E PDF

Bromham L, Oprandi P. (2006) Evolution online: developing active and blended learning by using a virtual learning environment in an introductory biology course. Journal of Biological Education 41(1):21-25 PDF

Welch JJ, Bromham L (2005) Molecular dating when rates vary. Trends in Ecology and Evolution 20(6):320-327 PDF

Bromham L, Leys R (2005) Sociality, population size and rate of molecular evolution. Molecular Biology and Evolution 22(6):1393–1402 PDF

Welch JJ, Fontanillas E, Bromham L (2005) Molecular dates for the “Cambrian Explosion”: the influence of prior assumptions. Systematic Biology 54(4):13–19 PDF

Wanninger A, Koop D, Bromham L, Noonan E, Degnan BM (2005) Nervous and muscle system development in Phascolion strombus (Sipuncula). Development Genes and Evolution 215(10):509-518 PDF

Woolfit M, Bromham L (2005) Population size and the rate of molecular evolution on islands. Proceedings of the Royal Society London B 272(1578):2277-82 PDF

Bromham L, Woolfit M (2004) Explosive radiations and the reliability of molecular clocks: island endemic radiations as a test case. Systematic Biology 53(5):758-766 PDF

Burrows JM, Bromham L, Woolfit M, Piganeau G, Tellam J, Connolly G, Webb N, Poulsen L, Cooper L, Burrows SR (2004) Selection pressure-driven evolution of the Epstein-Barr Virus-encoded oncogene LMP1 in virus isolates from Southeast Asia. Journal of Virology 78(13):7131-7137 PDF

Bromham L, Eyre-Walker A, Smith NH, Maynard Smith J (2003) Mitochondrial Steve: paternal inheritance of mitochondria in humans. Trends in Ecology and Evolution 18(1):2-4 PDF

Bromham L, Penny D (2003) The modern molecular clock. Nature Reviews Genetics 4:216-224 PDF

Bromham L, Cardillo M (2003) Testing the link between the latitudinal gradient in species richness and rates of molecular evolution. Journal of Evolutionary Biology 16:200-207 PDF

Cardillo M, Huxtable JS, Bromham L (2003) Geographic range size, life history and rates of diversification in Australian mammals. Journal of Evolutionary Biology 16:282–288 PDF

Woolfit M, Bromham L (2003) Increased rates of sequence evolution in endosymbiotic bacteria and fungi with small effective population sizes. Molecular Biology and Evolution 20(9):1545–1555 PDF

Bromham L (2003) What can DNA tell us about the Cambrian Explosion? Integrative and Comparative Biology 43(1): 148-156 PDF

Bromham L (2003) Molecular clocks and explosive radiations. Journal of Molecular Evolution 57:S13-S20 PDF

Bromham L (2002) Molecular clocks in reptiles: Life history influences rate of molecular evolution. Molecular Biology and Evolution 19:302-309 PDF

Bromham L (2002) The human zoo: endogenous retroviruses in the human genome. Trends in Ecology and Evolution 17:91-97 PDF

Bromham L, Woolfit M, Lee MSY, Rambaut A (2002) Testing the relationship between morphological and molecular rates of change along phylogenies. Evolution 56:1921-1930 PDF

Bromham L (2002) Searching for Pax in hydromedusa. Trends in Evolution and Ecology 17(1):11-12 PDF

Bromham L, Waxman D (2002) Phage lambda takes the first exit. Trends in Evolution and Ecology 17(4):160 PDF

Bromham L (2002) Slow as Molasses: a new gene in Drosophila. Trends in Evolution and Ecology 17(10): 454 PDF

Cardillo M, Bromham L (2001) Body size and risk of extinction in Australian mammals. Conservation Biology 15(5): 1435-1440 PDF

Bromham L, Clark F, McKee JJ (2001) Discovery of a novel mouse type-C retrovirus through bioinformatic analysis. Journal of Virology 75(6):3053-3057 PDF

Bromham L (2001) Evolution by leaps and bounds. Trends in Ecology and Evolution 16(3):125 PDF

Bromham L (2001) Molecular evolution: patterns and rates. Encyclopedia of Life Sciences, Macmillan Publishing, London

Bromham LD (2000) Molecular evolution: rates. Encyclopedia of Life Sciences, Macmillan Publishing, London.

Bromham L, Penny D, Hendy M, Rambaut A (2000) The power of relative rates tests depends on the data. Journal of Molecular Evolution 50(3):296-301 PDF

Bromham LD, Hendy MD (2000) Can fast early rates reconcile molecular dates to the Cambrian explosion? Proceedings of the Royal Society London B 267:1041-1047 PDF

Hanger JJ, Bromham LD, McKee JJ, O’Brien TM, Robinson WF (2000) The nucleotide sequence of koala (Phascolarctos cinereus) retrovirus (KoRV): a novel type-C retrovirus related to gibbon ape leukemia virus (GALV). Journal of Virology 74:4264-4272 PDF

Bromham L (2000) Conservation and mutability in molecular evolution. Trends in Ecology and Evolution 15(9):355 PDF

Bromham L, Phillips MJ, Penny D (1999) Growing up with dinosaurs: molecular dates and the mammalian radiation. Trends in Ecology and Evolution 14(4):113-118 PDF

Bromham L, Penny D, Phillips MJ (1999) Molecular dates and the mammalian radiation. Trends in Ecology and Evolution 14(7):278 PDF

Bromham L, Cardillo M, Elgar MA, Bennet AF (1999) The effects of grazing by stock on the ground invertebrate fauna of remnant woodlands. Australian Journal of Ecology 24:199-207 PDF

Bromham LD, Degnan B (1999) Hemichordates and deuterostome evolution: robust molecular phylogenetic support for a hemichordate+echinoderm clade. Evolution & Development 1(3):166-171 PDF

Bromham L, Rambaut A, Fortey RA, Cooper A, Penny D (1998) Testing the Cambrian explosion hypothesis using a new molecular dating technique. Proceedings of the National Academy of Sciences USA 95:12386-12389 PDF

Rambaut A, Bromham L (1998) Estimating divergence dates from molecular sequences. Molecular Biology and Evolution 15:442-448 PDF

Bromham LD (1998) Combining molecular and palaeontological data to defuse the Cambrian explosion. Geol Soc NZ Misc Publ 97:7-10

Cardillo M, Bromham L (1998) Terrestrial mammals: Britain and Europe. In: DM Macdonald, GM Mace, SP Rushton (eds) Proposals for the future monitoring of British mammals. Joint Nature Conservation Committee & Dept. of the Environment, Transport and the Regions, London.

Purvis A, Bromham L (1997) Estimating the transition/transversion ratio from independent pairwise comparisons with an assumed phylogeny. Journal of Molecular Evolution 44:112-119

Bromham L, Harvey PH (1996) Naked mole-rats on the move. Current Biology 6(9):1082-1083 PDF

Bromham L, Rambaut A, Harvey PH (1996) Determinants of rate variation in mammalian DNA sequence evolution. Journal of Molecular Evolution 43:610-621 PDF

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