28 Tel: +61 2 9351 5591 29 30 Word count: Abstract -247 words, Importance -140 words, Main text -5930 words 31 32 Running title: Punctuated evolution of myxoma virus. 33 2 ABSTRACT 34 Myxoma virus (MYXV) has been evolving in a novel host species -European rabbits -in 35 Australia since 1950. Previous studies of viruses sampled from 1950 to 1999 revealed a 36 remarkably clock-like evolutionary process across all Australian lineages of MYXV. Through 37 an analysis of 49 newly generated MYXV genome sequences isolated in Australia between 38 2008 and 2017 we show that MYXV evolution in Australia can be characterized by three 39 lineages, one of which exhibited a greatly elevated rate of evolutionary change and a 40 dramatic break-down of temporal structure. Phylogenetic analysis revealed that this 41 apparently punctuated evolutionary event occurred between 1996 and 2012. The branch 42 leading to the rapidly evolving lineage contained a relatively high number of non-43 synonymous substitutions, and viruses in this lineage reversed a mutation found in the 44 progenitor standard laboratory strain (SLS) and all previous sequences that disrupts the 45 reading frame of the M005L/R gene. Analysis of genes encoding proteins involved in DNA 46 synthesis or RNA transcription did not reveal any mutations likely to cause rapid evolution. 47 Although there was some evidence for recombination across the MYXV phylogeny, this was 48 not associated with the increase in evolutionary rate. The period from 1996 to 2012 saw 49 significant declines in wild rabbit numbers, due to the introduction of rabbit hemorrhagic 50 disease and prolonged drought in south-eastern Australia, followed by the partial recovery 51 of populations. We therefore suggest that a rapidly changing environment for virus 52 transmission changed the selection pressures faced by MYXV and altered the course of 53 virus evolution. 54 55 IMPORTANCE 56 The co-evolution of myxoma virus (MYXV) and European rabbits in Australia is one of the 57 most important natural 'experiments' in evolutionary biology, providing insights into virus 58 adaptation to new hosts and the evolution of virulence. Previous studies of MYXV evolution 59 have also shown that the virus evolves both relatively rapidly and in a strongly clock-like 60 manner. Using newly acquired MYXV genome sequences from Australia we show that the 61 virus has experienced a dramatic change in evolutionary behavior over the last 20 years, 62 with a break-down in clock-like structure, the appearance of a rapidly evolving virus 63 lineage, and the accumulation of multiple non-synonymous and indel mutations. We 64 suggest that this punctuated evolutionary event likely reflects a change in selection 65