Professor Rob Lanfear
Areas of expertise
- Phylogeny And Comparative Analysis 060309
- Molecular Evolution 060409
- Population, Ecological And Evolutionary Genetics 060411
- Bioinformatics 060102
- Genomics 060408
- Speciation And Extinction 060311
Research interests
Our work is motivated by the desire to understand molecular evolution, from the origin of mutations in individuals to their fixation in evolving lineages. To achieve this, we combine comparative methods, field work, genome sequencing, and evolutionary theory with the development of new methods and software.
Reading the history of mutations in individual plants
We are working on new methods to meausure and understand mutations that accumulate within individual plants. As most organisms grow they accumulate somatic mutations - changes to the genome that persist in the body's tissues. In plants, somatic mutations can be heritable and this has huge implications for plant ecology and evolution, as well as agriculture and plant industry. We are developing empirical methods to identify, map, and date the entire history of somatic mutations across the genome of an individual plant. This is an exciting area of research that combines beautiful field work with cutting-edge genome sequencing methods to illuminate a fascinating and underexplored area of biology. We are actively building collaborations and recruiting students in this area, so if you are interested, please get in touch.
Understanding the causes and consequences of molecular evolution
Why do some species evolve faster than others? Do rates of molecular evolution drive rates of speciation? What proportion of genomic changes are adaptive, deleterious, or neutral? Questions like these are fundamental to our understanding of evolution, genomics, and biodiversity. To answer them, we wrangle together large databases of genetic, environmental, and life-history information for whole clades of organisms (e.g. mammals, birds, plants), and use them to test hypotheses about the causes and consequences of molecular evolution. These broad scale comparative approaches are extremely rewarding, allowing important glimpses into some of the most important causes and consequences of molecular evolution.
Making robust inferences from DNA datasets
Developing software and writing code is great fun, if you enjoy that sort of thing. The biggest ongoing software project in the lab is PartitionFinder, which is a piece of software for model selection in phylogenetics. We are also developing tools to better understand phylogenetic trees (RWTY), and to analyse the behaviour of scientists by looking at both distributions of published P-values (pcurver) and aspects of gender bias. Our primary languages are Python and R, and all of our code is open source. To see all of lab's software projects, please see Rob's GitHub page.
Biography
I grew up in England. My BSc and honors were in Ecology, my MSc was in Artificial Intelligence, and my PhD (at the University of Sussex in the UK) was in developmental biology. After a short postdoc attempting and failing to edit shrimp genomes at University College London, I switched gears to focus on my growing interest in molecular evolution and phylogenetics. In 2008 I moved the ANU as a postdoc, where I remained for 6 years. I then took up a permanent position as a Senior Lecturer in Genomics at Macquarie University in Sydney, and moved back to the ANU at the first opportunity in 2016. I now focus on a range of topics including molecular evolution, somatic mutation, phylogentics, comparative methods, and bioinformatics.
Publications
- Lanfear, R, Schalamun, M, Kainer, D et al. 2019, 'MinIONQC: fast and simple quality control for MinION sequencing data', Bioinformatics, vol. 35, no. 3, pp. 523-525pp.
- Schalamun, M, Nagar, R, Kainer, D et al. 2019, 'Harnessing the MinION: An example of how to establish long-read sequencing in a laboratory using challenging plant tissue from Eucalyptus pauciflora', Molecular Ecology Resources, vol. 19, no. 1, pp. 77-89pp.
- Lanfear, R 2018, 'Do plants have a segregated germline?', PLoS Biology, vol. 16, no. 5, pp. 1-13pp.
- Hua, X & Lanfear, R 2018, 'The influence of non-random species sampling on macroevolutionary and macroecological inference from phylogenies', Methods in Ecology and Evolution, vol. 9, no. 5, pp. 1353-1362pp.
- Whitehead, M, Lanfear, R, Mitchell, R et al 2018, 'Plant Mating Systems Often Vary Widely Among Populations', Frontiers in Ecology and Evolution, vol. 6, no. 38, pp. 1-9pp.
- Whitehead, M, Lanfear, R, Mitchell, R et al 2018, 'Plant Mating Systems Often Vary Widely Among Populations', Frontiers in Ecology and Evolution, vol. 6, no. 38, pp. 1-9pp.
- Tagliacollo, A & Lanfear, R 2018, 'Estimating Improved Partitioning Schemes for Ultraconserved Elements', Genome Biology and Evolution, vol. 35, no. 7, pp. 1798-1811pp.
- Wang, W, Kainer, D, Morales-Suarez, A et al 2018, 'Assembly of chloroplast genomes with long- and short-read data: A comparison of approaches using Eucalyptus pauciflora as a test case', BMC Genomics, vol. 19, no. 977, pp. 1-15.
- Peters, R, Krogmann, L, Mayer, C et al 2017, 'Evolutionary History of the Hymenoptera', Current Biology, vol. 27, no. 7, pp. 1013-1018.
- Lanfear, R, Frandsen, P, Wright, A et al 2017, 'PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses', Molecular Biology and Evolution, vol. 34, no. 3, pp. 772-773pp.
- Warren, D, Geneva, A & Lanfear, R 2017, 'RWTY (R We There Yet): An R Package for Examining Convergence of Bayesian Phylogenetic Analyses', Molecular Biology and Evolution, vol. 34, no. 4, pp. 1016-1020pp.
- Medina Guzman, I, Langmore, N, Lanfear, R et al 2017, 'The evolution of clutch size in hosts of avian brood parasites', The American Naturalist, vol. 190, no. 5, pp. E113-E123.
- Lanfear, R, Hua, X & Warren, D 2016, 'Estimating the Effective Sample Size of Tree Topologies from Bayesian Phylogenetic Analyses', Genome Biology and Evolution, vol. 8, no. 8, pp. 2319-2332pp.
- James, J, Lanfear, R & Eyre-Walker, A 2016, 'Molecular Evolutionary Consequences of Island Colonization', Genome Biology and Evolution, vol. 8, no. 6, pp. 1876-1888pp.
- Barton, K, Hiener, B, Winckelmann, A et al. 2016, 'Broad activation of latent HIV-1 in vivo', Nature Communications, vol. 7, no. 12731, pp. 12731-12731.
- Nabholz, B, Lanfear, R & Fuchs, J 2016, 'Body mass-corrected molecular rate for bird mitochondrial DNA', Molecular Ecology, vol. 25, no. 18, pp. 4438-4449.
- Kjer, K, Ware, J, Rust, J et al 2015, 'Response to Comment on "phylogenomics resolves the timing and pattern of insect evolution"', Science, vol. 349, no. 6247, pp. 487c-487c.
- Roche, D, Kruuk, L, Lanfear, R et al 2015, 'Public Data Archiving in Ecology and Evolution: How Well Are We Doing?', PLoS Biology, vol. 13, no. 11, pp. e1002295-e1002295.
- Head, M, Holman, L, Lanfear, R et al 2015, 'The Extent and Consequences of P-Hacking in Science', PLoS Biology, vol. 13, no. 3, pp. e1002106-e1002106.
- Bromham, L, Hua, X, Lanfear, R et al 2015, 'Exploring the Relationships between Mutation Rates, Life History, Genome Size, Environment, and Species Richness in Flowering Plants', The American Naturalist, vol. 185, no. 4, pp. 507-524.
- Frandsen, P, Calcott, B, Mayer, C et al. 2015, 'Automatic selection of partitioning schemes for phylogenetic analyses using iterative k-means clustering of site rates', BMC Evolutionary Biology (now BMC Ecology and Evolution), vol. 15, no. 1, pp. 13-13.
- Kainer, D & Lanfear, R 2015, 'The Effects of Partitioning on Phylogenetic Inference', Molecular Biology and Evolution, vol. 32, no. 6, pp. 1611-1627.
- Holman, L, Head, M, Lanfear, R et al 2015, 'Evidence of experimental bias in the life sciences: Why we need blind data recording', PLoS Biology, vol. 13, no. 7, pp. e1002190-e1002190.
- Kainer, D, Lanfear, R, Foley, W et al 2015, 'Genomic approaches to selection in outcrossing perennials: focus on essential oil crops', Theoretical and Applied Genetics, vol. 128, no. 12, pp. 2351-2365pp.
- Duchene, S & Lanfear, R 2015, 'Phylogenetic Uncertainty Can Bias the Number of Evolutionary Transitions Estimated From Ancestral State Reconstruction Methods', Journal of Experimental Zoology, vol. 324, no. 6, pp. 517-524.
- Cooke, J, Lanfear, R, Downing, A et al 2015, 'The unusual occurrence of green algal balls of Chaetomorpha linum on a beach in Sydney, Australia', Botanica Marina, vol. 58, no. 5, pp. 401-407.
- Lanfear, R, Kokko, H & Eyre-Walker, A 2014, 'Population size and the rate of evolution', Trends in Ecology and Evolution, vol. 29, no. 1, pp. 33-41.
- Misof, B, Liu, S, Meusemann, K et al. 2014, 'Phylogenomics resolves the timing and pattern of insect evolution', Science, vol. 346, no. 6210, pp. 763-767.
- Roche, D, Lanfear, R, Binning, S et al 2014, 'Troubleshooting Public Data Archiving: Suggestions to Increase Participation', PLoS Biology, vol. 12, no. 1, pp. e1001779-e1001779.
- Lanfear, R, Calcott, B, Kainer, D et al. 2014, 'Selecting optimal partitioning schemes for phylogenomic datasets', BMC Evolutionary Biology (now BMC Ecology and Evolution), vol. 14, no. 82, pp. 1-14.
- 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, vol. 6, no. 1, pp. 161-169.
- Catullo, R, Lanfear, R, Doughty, P et al. 2014, 'The biogeographical boundaries of northern Australia: evidence from ecological niche models and a multi- locus phylogeny of Uperoleia toadlets ( Anura: Myobatrachidae)', Journal of Biogeography, vol. 41, no. 4, pp. 659-672.
- Duchene, S, Lanfear, R & Ho, S 2014, 'The impact of calibration and clock-model choice on molecular estimates of divergence times', Molecular Phylogenetics and Evolution, vol. 78, no. 1, pp. 277-289.
- Lanfear, R & Pennell, M 2014, 'Open access is worth considering: a reply to Agrawal', Trends in Plant Science, vol. 19, no. 6, pp. 340-341.
- Misof, B, Liu, S, Meusemann, K et al 2014, 'Phylogenomics resolves the timing and pattern of insect evolution', Science, vol. 346, no. 6210, pp. 763-767.
- Jones, T, Fanson, K, Lanfear, R et al 2014, 'Gender differences in conference presentations: A consequence of self-selection?', PeerJ, vol. 2, pp. e627-e627.
- Lehtonen, J & Lanfear, R 2014, 'Generation time, life history and the substitution rate of neutral mutations', Biology Letters, vol. 10, no. 11, pp. 20140801-20140801.
- Padovan, A, Lanfear, R, Keszei, A et al 2013, 'Differences in gene expression within a striking phenotypic mosaic Eucalyptus tree that varies in susceptibility to herbivory', BMC Plant Biology, vol. 13, no. 1, pp. 1-12.
- Webb, H, Lanfear, R, Hamill, J et al 2013, 'The Yield of Essential Oils in Melaleuca alternifolia (Myrtaceae) Is Regulated through Transcript Abundance of Genes in the MEP Pathway', PLOS ONE (Public Library of Science), vol. 8, no. 3, pp. e60631-e60631.
- Lanfear, R, Ho, S, Davies, T et al. 2013, 'Taller plants have lower rates of molecular evolution', Nature Communications, vol. 4, pp. 1879-1879.
- Holman, L, Lanfear, R & d'Ettorre, P 2013, 'The evolution of queen pheromones in the ant genus Lasius', Journal of Evolutionary Biology, vol. 26, no. 7, pp. 1549-1558.
- Bromham, L, Cowman, P & Lanfear, R 2013, 'Parasitic plants have increased rates of molecular evolution across all three genomes', BMC Evolutionary Biology (now BMC Ecology and Evolution), vol. 13, no. 126, pp. 126-126.
- Bromham, L, Lanfear, R, Cassey, P et al 2012, 'Reconstructing past species assemblages reveals the changing patterns and drivers of extinction through time', Proceedings of the Royal Society of London Series B: Biological Sciences, vol. 279, no. 1744, pp. 4024-4032.
- Skroblin, A, Lanfear, R, Cockburn, A et al 2012, 'Inferring population connectivity across the range of the purple-crowned fairy-wren (Malurus coronatus) from mitochondrial DNA and morphology: Implications for conservation management', Australian Journal of Zoology, vol. 60, no. 3, pp. 199-209.
- Skroblin, A, Lanfear, R, Cockburn, A et al 2012, 'Inferring population connectivity across the range of the purple-crowned fairy-wren (Malurus coronatus) from mitochondrial DNA and morphology: Implications for conservation management', Australian Journal of Zoology, vol. 60, no. 3, pp. 199-209.
- Lanfear, R, Ho, S & Ho, S 2012, 'Mito-communications', Mitochondrial DNA, vol. 23, no. 2, pp. 154-156.
- Lanfear, R & Ho, S 2012, 'Mito-communications', Mitochondrial DNA, vol. 23, no. 2, pp. 154-156.
- Ho, S & Lanfear, R 2012, 'Calibrating mitochondrial rates in marine invertebrates', Mitochondrial DNA, vol. 23, no. 4, pp. 321-321.
- Lanfear R, Calcott B, Ho SYW, and Guindon S, 2012. 'PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses.' Molecular Biology and Evolution.
- Webb, H, Kulheim, C, Lanfear, R et al 2011, 'The regulation of quantitative variation of foliar terpenes in medicinal tea tree Melaleuca alternifolia', IUFRO Tree Biotechnology Conference, ed. Dario Grattapaglia, BMC Proceedings, Unknown, pp. 1-3pp.
- Ho, S, Lanfear, R, Bromham, L et al 2011, 'Time-dependent rates of molecular evolution', Molecular Ecology, vol. 20, no. 15, pp. 3087-3101.
- Lanfear, R 2011, 'The local-clock permutation test: a simple test to compare rates of molecular evolution on phylogenetic trees', Evolution, vol. 65, no. 2, pp. 606-611.
- Ho, S, Lanfear, R, Phillips, M et al. 2011, 'Bayesian estimation of substitution rates from ancient DNA sequences with low information content', Systematic Biology, vol. 60, no. 3, pp. 366-374.
- Ho, S, Lanfear, R, Bromham, L et al 2011, 'Time-dependent rates of molecular evolution', Molecular Ecology, vol. 20, no. 15, pp. 3087-3101.
- Lanfear, R & Bromham, L 2011, 'Estimating phylogenies for species assemblages: A complete phylogeny for the past and present native birds of New Zealand', Molecular Phylogenetics and Evolution, vol. 61, no. 3, pp. 958-963.
- Goldie, X, Lanfear, R & Bromham, L 2011, 'Diversification and the rate of molecular evolution: no evidence of a link in mammals', BMC Evolutionary Biology (now BMC Ecology and Evolution), vol. 11, no. 1, pp. 286-286.
- Lanfear, R, Bromham, L & Ho, S 2011, 'Reply to Englund: Molecular evolution and diversification:Counting species is better than counting nodes when the phylogeny is unknown', PNAS - Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 17, pp. E85-E86.
- Fritsch, C, Lanfear, R & Ray, R 2010, 'Rapid evolution of a novel signalling mechanism by concerted duplication and divergence of a BMP ligand and its extracellular modulators', Development Genes and Evolution, vol. 220, no. 9-10, pp. 235-250.
- Lanfear, R, Ho, S, Love, D et al 2010, 'Mutation rate is linked to diversification in birds', PNAS - Proceedings of the National Academy of Sciences of the United States of America, vol. 107, no. 47, pp. 20423-20428.
- Ho, S & Lanfear, R 2010, 'Ancient mitogenome from an unknown hominin', Mitochondrial DNA, vol. 21, no. 5, pp. 147-148.
- Bourlat, S, Rota-Stabelli, O, Lanfear, R et al. 2009, 'The mitochondrial genome structure of Xenoturbella bocki (phylum Xenoturbellida) is ancestral within the deuterostomes', BMC Evolutionary Biology (now BMC Ecology and Evolution), vol. 9, no. 1, pp. 1-14.
- Ho, S & Lanfear, R 2010, 'Distinctive characteristics of post-mortem damage in human mitochondrial DNA', Mitochondrial DNA, vol. 21, no. 2, pp. 33-35.
- Thomas, J, Welch, J, Lanfear, R et al 2010, 'A Generation Time Effect on the Rate of Molecular Evolution in Invertebrates', Molecular Biology and Evolution, vol. 27, no. 5, pp. 1173-1180.
- Lanfear, R & Ho, S 2010, 'Understanding the origin of doubly uniparental inheritance in bivalves', Mitochondrial DNA, vol. 21, no. 3-4, pp. 57-58.
- Lanfear, R 2010, 'Are the Deuterostome Posterior Hox Genes a Fast-Evolving Class?', in Jean S. Deutsch (ed.), Hox Genes: Studies from the 20th to the 21st Century, Landes Bioscience/Springer Science+Business Media, USA, pp. 111-121.
- Ho, S & Lanfear, R 2010, 'Improved characterisation of among-lineage rate variation in cetacean mitogenomes using codon-partitioned relaxed clocks', Mitochondrial DNA, vol. 21, no. 3-4, pp. 138-146.
- Lanfear, R, Welch, J & Bromham, L 2010, 'Watching the clock: Studying variation in rates of molecular evolution between species', Trends in Ecology and Evolution, vol. 25, no. 9, pp. 495-503.
- Lanfear, R & Ho, S 2010, 'MtZoa - a new mitochondrial protein replacement matrix for metaozan phylogenetics', Mitochondrial DNA, vol. 21, no. 1, pp. 1-4.
- Ho, S & Lanfear, R 2009, 'The influence of altitude on mitochondrial evolution in mammals', Mitochondrial DNA, vol. 20, no. 4, p. 66.
- Lanfear, R & Ho, S 2009, 'Mitochondrial evolution in tuatara', Mitochondrial DNA, vol. 20, no. Issue 2 & 3 2009, p. 1.
- Lanfear, R & Ho, S 2009, 'Mitochondrial genome of the thylacine', Mitochondrial DNA, vol. 20, no. 2, p. 1.
- Ho, S & Lanfear, R 2009, 'Two migration routes for the first Americans', Mitochondrial DNA, vol. 20, no. 4, p. 66.
- Ho, S & Lanfear, R 2009, 'Mitochondrial phylogeography of house mice', Mitochondrial DNA, vol. 20, no. 4, pp. 65-68.
- Pueyo, J, Lanfear, R & Couso, J 2008, 'Ancestral Notch-mediated segmentation revealed in the cockroach Periplaneta americana', PNAS - Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 43, pp. 16614-16619.
- Lanfear, R & Bromham, L 2008, 'Statistical Tests between Competing Hypotheses of Hox Cluster Evolution', Systematic Biology, vol. 57, no. 5, pp. 708-718.
- Lanfear, R, Thomas, J, Welch, J et al 2007, 'Metabolic rate does not calibrate the molecular clock', PNAS - Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 39, pp. 15388-15393.
Projects and Grants
Grants information is drawn from ARIES. To add or update Projects or Grants information please contact your College Research Office.
- IQ-TREE for ultra-large genomic data (Secondary Investigator)
- Understanding somatic mutation in plants: new methods, new software, new data (Primary Investigator)
- Mosaicism, somatic mutation, and environmental change in long-lived plants (Primary Investigator)