Short-term Visitor

Synthesising methods and data to understand the mutational processes that shape genomes

PI(s): Robert Lanfear (Australian National University)
Start Date: 15-Jun-2012
End Date: 8-Sep-2013
Keywords: mutation, evolutionary genetics, phylogenetics, evolutionary theory
Mutation is one of the most fundamentally important sources of variation between living organisms, and understanding the causes and consequences of mutation is central to evolutionary biology. However, we still know relatively little about how and why mutational processes vary between taxa. This is critical because understanding mutation is central to how we use and interpret DNA sequence data, and there is a growing reliance upon such data across the biological sciences. Studies on model organisms have led to a detailed knowledge of the biochemical causes of mutation in a handful of taxa. However, we lack methods with which to exploit this knowledge in order to understand mutation in a broader framework. I will synthesise the results from model organism studies with novel statistical and phylogenetic methods. These methods will use DNA sequence data to estimate biologically meaningful parameters that relate directly to particular mutational processes. I will integrate these methods with large DNA, life-history and protein structure datasets to test specific hypotheses about the causes and consequences of mutation. This work will significantly extend our current understanding of how and why mutational processes vary between taxa, generate novel insights from existing data, and spur the development of more appropriate methods of DNA sequence analysis across the biological sciences.

Related products

Publications
  • The Effects of Partitioning on Phylogenetic Inference D. Kainer and R. Lanfear. 2015, The Effects of Partitioning on Phylogenetic Inference, Molecular Biology and Evolution
  • Domestication and the Mitochondrial Genome: Comparing Patterns and Rates of Molecular Evolution in Domesticated Mammals and Birds and Their Wild Relatives C. Moray, R. Lanfear and L. Bromham. 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, volume 6, issue 1, pp. 161-169
  • Generation time, life history and the substitution rate of neutral mutations J. Lehtonen and R. Lanfear. 2014, Generation time, life history and the substitution rate of neutral mutations, Biology Letters, volume 10, issue 11, pp. 20140801-20140801
  • Phylogenomics resolves the timing and pattern of insect evolution B. Misof, S. Liu, K. Meusemann, R. S. Peters, A. Donath, C. Mayer, P. B. Frandsen, J. Ware, T. Flouri, R. G. Beutel, O. Niehuis, M. Petersen, F. Izquierdo-Carrasco, T. Wappler, J. Rust, A. J. Aberer, U. Aspock, H. Aspock, D. Bartel, A. Blanke, S. Berger, A. Bohm, T. R. Buckley, B. Calcott, J. Chen, F. Friedrich, M. Fukui, M. Fujita, C. Greve, P. Grobe, S. Gu, Y. Huang, L. S. Jermiin, A. Y. Kawahara, L. Krogmann, M. Kubiak, R. Lanfear, H. Letsch, Y. Li, Z. Li, J. Li, H. Lu, R. Machida, Y. Mashimo, P. Kapli, D. D. McKenna, G. Meng, Y. Nakagaki, J. L. Navarrete-Heredia, M. Ott, Y. Ou, G. Pass, L. Podsiadlowski, H. Pohl, B. M. von Reumont, K. Schutte, K. Sekiya, S. Shimizu, A. Slipinski, A. Stamatakis, W. Song, X. Su, N. U. Szucsich, M. Tan, X. Tan, M. Tang, J. Tang, G. Timelthaler, S. Tomizuka, M. Trautwein, X. Tong, T. Uchifune, M. G. Walzl, B. M. Wiegmann, J. Wilbrandt, B. Wipfler, T. K. F. Wong, Q. Wu, G. Wu, Y. Xie, S. Yang, Q. Yang, D. K. Yeates, K. Yoshizawa, Q. Zhang, R. Zhang, W. Zhang, Y. Zhang, J. Zhao, C. Zhou, L. Zhou, T. Ziesmann, S. Zou, Y. Li, X. Xu, Y. Zhang, H. Yang, J. Wang, J. Wang, K. M. Kjer and X. Zhou. 2014, Phylogenomics resolves the timing and pattern of insect evolution, Science, volume 346, issue 6210, pp. 763-767
  • Population size and the rate of evolution Robert Lanfear, Hanna Kokko and Adam Eyre-Walker. 2014, Population size and the rate of evolution, Trends in Ecology & Evolution, volume 29, issue 1, pp. 33-41
  • Selecting optimal partitioning schemes for phylogenomic datasets Robert Lanfear, Brett Calcott, David Kainer, Christoph Mayer and Alexandros Stamatakis. 2014, Selecting optimal partitioning schemes for phylogenomic datasets, BMC Evol Biol, volume 14, issue 1, pp. 82
  • Taller plants have lower rates of molecular evolution Robert Lanfear, Simon Y. W. Ho, T. Jonathan Davies, Angela T. Moles, Lonnie Aarssen, Nathan G. Swenson, Laura Warman, Amy E. Zanne and Andrew P. Allen. 2013, Taller plants have lower rates of molecular evolution, Nat Comms, volume 4, pp. 1879