The Lanfear Lab @ANU Molecular Evolution and Phylogenetics

Lab members are shown in bold

2018

MinIONQC: fast and simple quality control for MinION sequencing data
Lanfear R, Schalamun M, Kainer D, Wang W, Schwessinger B (2018) Bioinformatics bty654
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Do plants have a segregated germline?
Lanfear R (2018) PLOS Biology 16(5):e2005439
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The influence of non‐random species sampling on macroevolutionary and macroecological inference from phylogenies
Hua X, Lanfear R (2018) Molecular Biology and Evolution 34(4):1016-1020
PDF      Zenodo  
Estimating Improved Partitioning Schemes for Ultraconserved Elements
Tagliacollo VA, Lanfear R (2018) Molecular Biology and Evolution in press
PDF      GitHub data   GitHub method  
Plant Mating Systems Often Vary Widely Among Populations
Whitehead MR, Lanfear R, Mitchell RJ, Karron JD (2018) Frontiers in Ecology and Evolution 6:38
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2017

The Evolution of Clutch Size in Hosts of Avian Brood Parasites
Medina I, Langmore NE, Lanfear R, Kokko H (2017) The American Naturalist 190(5):E112-E123
PDF      Data Dryad  
Evolutionary history of the Hymenoptera
Peters RS, Krogmann L, Mayer C, Donath A, Gunkel S, Meusemann K, Kozlov A, Podsiadlowski L, Petersen M, Lanfear R, Diez PA, Heraty J, Kjer KM, Klopfstein S, Meier R, Polidori C, Schmitt T, Liu S, Zhou X, Wappler T, Rust J, Misof B, Niehuis O (2017) Current Biology 27(7):1013-1018
PDF      Mendeley Data  
RWTY (R We There Yet): an R package for examining convergence of Bayesian phylogenetic analyses
Warren DL, Geneva AJ, Lanfear R (2017) Molecular Biology and Evolution 34(4):1016-1020
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2016

PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses
Lanfear R, Frandsen PB, Wright AM, Senfeld T, Calcott B. (2016) Molecular Biology and Evolution 34(3):772-773
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Estimating the Effective Sample Size of tree topologies from Bayesian phylogenetic analyses
Lanfear R, Hua X, Warren DL. (2016) Genome Biology and Evolution 8(8):2319-2332
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Molecular Evolutionary Consequences of Island Colonization
James EJ, Lanfear R, Eyre-Walker A. (2016) Genome Biology and Evolution 8(6):1876-1888
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Body mass‐corrected molecular rate for bird mitochondrial DNA.
Nabholz B, Lanfear R, Fuchs J. (2016) Molecular Ecology 25(18):4438-4449
PDF      DataDryad  
Broad activation of latent HIV-1 in vivo
Barton K, Hiener B, Winckelmann A, Rasmussen TA, Shao W, Byth K, Lanfear R, Solomon A, McMahon J, Harrington S, Buzon M. (2016) Nature Communications 7: 12731
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2015

Public Data Archiving in Ecology and Evolution: How Well Are We Doing?
Roche DG, Kruuk LE, Lanfear R, Binning SA. (2015) PLoS Biology 13(11): e1002295
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The unusual occurrence of green algal balls of Chaetomorpha linum on a beach in Sydney, Australia
Cooke J, Lanfear R, Downing A, Gillings MR, Poore AGB, Goodwin ID, Waldron LS, Phillips A, Metti Y, Bulbert MW (2015) Botanica marina 58(5): 401-407
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Response to Comment on “Phylogenomics resolves the timing and pattern of insect evolution
Kjer KM, Ware JL, Rust J, Wappler T, Lanfear R, Jermiin LS, Zhou X, Aspöck H, Aspöck U, Beutel RG, Blanke R, Donath A, Flouri T, Frandsen PB, Kapli P, Kawahara AY, Letsch H, Mayer C, McKenna DD, Meusemann K, Niehuis O, Peters RS, Wiegmann BM, Yeates DK, von Reumont BM, Stamatakis A, Misof B (2015) Science 349(6247): 487
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Genomic approaches to selection in outcrossing perennials: focus on essential oil crops
Kainer D, Lanfear R, Foley WJ, Külheim C (2015) Theoretical and Applied Genetics 128(12): 2351-2365
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Evidence of Experimental Bias in the Life Sciences: Why We Need Blind Data Recording
Holman L, Head ML, Lanfear R, Jennions MD (2015) PLOS Biology 13(7): e1002190
PDF      DataDryad   Zenodo  
Phylogenetic uncertainty can bias the number of evolutionary transitions estimated from ancestral state reconstruction methods
Duchêne S, Lanfear R (2015) Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 324(6): 517-524
PDF      GitHub  
The effects of partitioning on phylogenetic inference
Kainer D, Lanfear R (2015) Molecular Biology and Evolution 32(6): 1611-1627
PDF      figshare  
Molecular Rate Variation (Molecular Clocks)
Lanfear R (2015) Encyclopedia of Scientific Dating Methods 596-597
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Exploring the relationships between mutation rates, life history, genome size, environment and species richness in flowering plants
Bromham L, Hua X, Lanfear R, Cowman PF (2015) American Naturalist 185(4): 507-524
PDF      DataDryad  
Automatic selection of partitioning schemes for phylogenetic analyses using iterative k-means clustering of site rates
Frandsen PB, Calcott B, Mayer C, Lanfear R (2015) BMC Evolutionary Biology 15:13
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The Extent and Consequences of P-Hacking in Science
Head ML, Holman L, Lanfear R, Kahn AT, Jennions MD (2015) PLOS Biology 13(3): e1002106
PDF      DataDryad  

2014

Generation time, life history, and the substitution rate of neutral mutations
Lehtonen J, Lanfear R (2014) Biology Letters 10:20140801.
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Phylogenomics resolves the timing and pattern of insect evolution
Misof B, … Lanfear R, (34th/101 authors), … Zhou X (2014) Science 346:763-767
   DataDryad  
Gender differences in conference presentations: a consequence of self-selection?
Jones TM, Fanson KV, Lanfear R, Symonds MRE, Higgie M (2014) PeerJ e627
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Open access is worth considering: a reply to Agrawal
Lanfear R, Pennell MW (2014) Trends in Plant Science 19(6):340
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The impact of clock-model choice on molecular estimates of divergence times
Duchêne S, Lanfear R, Ho SYW (2014) Molecular Phylogenetics and Evolution 78:277-289
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Population size and the rate of evolution
Lanfear R, Eyre-Walker A, Kokko H (2014) Trends in Ecology and Evolution 29(1):33-41
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Selecting optimal partitioning schemes for phylogenomic datasets
Lanfear R*, Calcott B*, Kainer D, Mayer C, Stamatakis A (2014) BMC Evolutionary Biology 14:82
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Domestication and the mitochondrial genome: comparing patterns and rates of molecular evolution in domesticated mammals and birds and their wild relatives
Moray C, Lanfear R, Bromham L (2014) Genome biology and evolution 6(1):161-169
PDF      DataDryad  
Troubleshooting public data archiving: suggestions to increase participation.
Roche DG, Lanfear R, Binning SA, Haff TM, Schwanz LE, Cain KE, Kokko H, Jennions MD, Kruuk LEB (2014) PLOS Biology 12(1):e1001779
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The biogeographical boundaries of northern Australia: evidence from ecological niche models and a multi-locus phylogeny of Toadlets (Uperoleia: Myobatrachidae)
Catullo RA, Lanfear R, Doughty P, Keogh JS (2014) Journal of Biogeography 41(4):659-672
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2013

Parasitic plants have increased rates of molecular evolution across all three genomes
Bromham L, Cowman P, Lanfear R (2013) BMC Evolutionary Biology 13:126
PDF      DataDryad  
Taller plants have lower rates of molecular evolution
Lanfear R, Ho SYW, Davies TJ, Moles AT, Aarssen L, Swenson NG, Warman L, Zanne A, Allen AP (2013) Nature Communications 4:1879
PDF      DataDryad  
Differences in gene expression within a striking phenotypic mosaic Eucalyptus tree that varies in susceptibility to herbivory
Padovan A, Lanfear R, Keszei A, Foley WJ, Külheim C (2013) BMC Plant Biology 13:29
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The evolution of queen pheromones in the ant genus Lasius
Holman L, Lanfear R, d’Ettorre P (2013) Journal of Evolutionary Biology 26(7):1549–1558
PDF      DataDryad  
The yield of essential oils in Melaleuca alternifolia (Myrtaceae) is regulated through transcript abundance of genes in the MEP pathway
Webb H, Lanfear R, Foley W, Kulheim C (2013) PLOS ONE 8(3):e60631 PDF  

2012

PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses
Lanfear R, Calcott B, Ho SYW, Guindon S (2012) Molecular Biology and Evolution 29(6):1695–1701
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Inferring population connectivity across the range of the purple-crowned fairy-wren (Malurus coronatus) from mitochondrial DNA and morphology: implications for conservation management
Skroblin A, Lanfear R, Cockburn A, Legge S (2012) Australian Journal of Zoology 60(3):199–209
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Reconstructing past species assemblages reveals the changing patterns and drivers of extinction through time
Bromham L, Lanfear R, Cassey P, Gibb G, Cardillo M (2012) Proceedings of the Royal Society B: Biological Sciences 279:4024–4032
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Mito-communications: (i) Calibrating mitochondrial rates in marine invertebrates; (ii) Untangling the evolutionary processes that shape plant mitochondrial genomes
Ho SYW and Lanfear R (2012) Mitochondrial DNA 23(4):321–322
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Mito-communications: (i) Mitochondrial mutation rates in the water flea Daphnia pulex; (ii) Selection against pathogenic mutations in human mitogenomes; (iii) Mother’s curse: Mitochondria cause problems for male flies
Lanfear R and Ho SYW (2012) Mitochondrial DNA 23(2):154–156
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2011

Estimating phylogenies for species assemblages: a complete phylogeny for the past and present native birds of New Zealand
Lanfear R and Bromham L (2011) Molecular Phylogenetics and Evolution 61(3):958–963
PDF      GeneFinder.py  
Diversification and the rate of molecular evolution: no evidence of a link in mammals.
Goldie X, Lanfear R, and Bromham L (2011) BMC Evolutionary Biology 11:286
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Time-dependent rates of molecular evolution
Ho SYW, Lanfear R, Bromham L, Phillips MJ, Soubrier J, Rodrigo A, Cooper A (2011) Molecular Ecology 20(15):3087–3101
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Reply to Englund: Molecular evolution and diversification: counting species is better than counting nodes when the phylogeny is unknown
Lanfear R, Bromham L, Ho SYW (2011) PNAS 108(17):E85–E86.
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Bayesian estimation of substitution rates from ancient DNA sequences with low information content
Ho SYW, Lanfear R, Phillips MJ, Barnes I, Thomas JA, Kolokotronis S-O, and Shapiro B (2011) Systematic Biology 60(3):366–375
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Mito-communications: (i) Adding insult to injury: Transmissible cancer captures host mitochondrial genomes; (ii) Evolutionary diversification of birds in the Cretaceous
Lanfear R and Ho SYW (2011) Mitochondrial DNA 22(3):39–40
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2010

Watching the clock: studying variation in rates of molecular evolution between species.
Lanfear R, Welch JJ, and Bromham L (2010) Trends in Ecology and Evolution 25(9):495–503
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Mutation rate is linked to diversification in birds
Lanfear R, Ho SYW, Love D, and Bromham L (2010) PNAS 107(47):20423–20428.
PDF      Alignments
The local-clock permutation test: A simple test to compare rates of molecular evolution on phylogenetic trees.
Lanfear R (2010) Evolution 65(2):606–611.
PDF      DataDryad
Rapid Evolution of a Novel Signalling Mechanism by Concerted Duplication and Divergence of a BMP Ligand and its Extracellular Modulators
Fritsch C, Lanfear R, and Ray R (2010) Development Genes and Evolution 220(9-10):235–250.
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Improved characterisation of among-lineage rate variation in cetacean mitogenomes using codon-partitioned relaxed clocks
Ho SYW and Lanfear R (2010) Mitochondrial DNA 21(3–4):138–146
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A generation time effect on the rate of molecular evolution in invertebrates
Thomas JA*, Welch JJ*, Lanfear R, and Bromham L (2010) Molecular Biology and Evolution 27(5):1173-1180
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Are the Deuterostome Posterior Hox genes a Fast-Evolving Class?
Lanfear R (2010) In: Deutsch, J. Hox Genes’ Studies from the 20th to the 21st Century. London: Landes Bioscience.
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Mito-communications: (i) Ancient mitogenome from an unknown hominin; (ii) Population dynamics of cave bears in the Pleistocene; (iii) Mutational processes differ significantly between closely related nematodes
Ho SYW and Lanfear R (2010) Mitochondrial DNA 21(5):147–148
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Mito-communications: (i) Understanding the origin of doubly uniparental inheritance in bivalves; (ii) Mitogenomic sequence from an ancient polar bear
Lanfear R and Ho SYW (2010) Mitochondrial DNA21(3-4):138–146
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Mito-communications: (i) Distinctive characteristics of postmortem damage in human mitochondrial DNA; (ii) Time-dependent molecular rates in human mitogenomes; (iii) The role of mito-nuclear interactions in F2 hybrid breakdown
Ho SYW and Lanfear R (2010) Mitochondrial DNA 21(2):33–35
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Mito-communications: (i) MtZoa – a new mitochondrial protein replacement matrix for metaozan phylogenetics; (ii) Evolutionary constraints on mitochondrial DNA depend on the locomotive demands of the host; (iii) Longevity, mutation rates, and the evolution of avian mitochondrial DNA; (iv) Population mitogenomics of extinct species; (v) Tracking the demographic history of seals using mitochondrial DNA
Lanfear R and Ho SYW (2010) Mitochondrial DNA 21(1):1–4
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2009

The mitochondrial genome structure of Xenoturbella bocki is ancestral within the deuterostomes
Bourlat SJ, Rota-Stabelli O, Lanfear R, and Telford MJ (2009) BMC Evolutionary Biology 9:107
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Mito-communications: (i) Mitochondrial phylogeography of house mice; (ii) Two migration routes for the first Americans; (iii) The influence of altitude on mitochondrial evolution in mammals; (iv) Extreme organization; (v) The effective population size of mitochondrial DNA
Ho SYW and Lanfear R (2009) Mitochondrial DNA 20(4):65–68
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Mito-communications: (i) Age-related selection in mitochondrial genomes; (ii) Mitochondrial evolution in tuatara; (iii) Mitochondrial genome of the thylacine
Lanfear R and Ho SYW (2009) Mitochondrial DNA20(2-3)27–28
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2008

Ancestral Notch-mediated Segmentation Revealed in the Cockroach P. americana
Pueyo JI*, Lanfear R*, Couso JP (2008) PNAS 105(43):16614–16619
PDF      Appendices   Commentary  
Statistical Tests Between Competing Hypotheses of Hox Cluster Evolution
Lanfear R and Bromham L (2008) Sytstematic Biology 57(5):708–718
PDF      Appendices   Python Script   F1000  

2007

Metabolic rate does not calibrate the molecular clock
Lanfear R, Thomas JA, Welch JJ, Brey T, Bromham L (2007) PNAS 104(39):15388–15393
PDF      Appendix1   Appendix2   F1000  

* denotes equal first authors