Environmental stress, adaptation and speciation: phenomics and functional genomics in recently evolved palm species

The concept of sympatric speciation (speciation without geographic isolation) has historically been viewed as an area of controversy; however, it is becoming increasingly accepted that speciation can occur in the presence of gene flow (Coyne & Orr, 2004). One convincing example of sympatric speciation is that of the Howea palms, located on the tiny Lord Howe Island in the Tasman Sea, where Howea forsteriana diverged from its sister taxa, the ancestor to Howea belmoreana, around 1 Myr ago, through colonisation of newly deposited calcarenite soils (Savolainen et al., 2006). Calcareous soils appear to have caused a substrate-induced change in flowering time in H. forsteriana, leading to ecological divergence and reproductive isolation from H. belmoreana (Savolainen et al., 2006; Dunning et al., 2016). Such soils provide significant stresses, including water, salinity and pH (Savolainen et al., 2006; Papadopulos et al., 2013), and it is hypothesised that local adaptation to these stresses may have directly influenced flowering time alteration through pleiotropy or linkage disequilibrium (Savolainen et al., 2006; Dunning et al., 2016). Using detailed soil chemistry analysis and RNA-seq data, Osborne et al. (in prep) have identified candidate loci which may explain the genetic mechanism of speciation in the Howea palms, based on fulfilment of three criteria: 1)Possession of a function related to soil stresses. 2)Possession of a function relating to flowering time. 3)Evidence of adaptive evolution. This project will aim to investigate these candidate loci through the following methods: 1)The genes of interest will first be validated as possessing stress tolerance and/or flowering time function in H. forsteriana, through T-DNA knockout mutants of orthologous genes in the model plant species Arabidopsis thaliana and Brachypodium distachyon. Assays of abiotic stresses including drought, salinity and pH will be used to examine the phenotypic effects of knockouts. 2)Following this, the project will attempt to rescue the phenotypes of any knockout mutants displaying an effect of soil stress and/or flowering time, through insertion of the orthologous Howea genes into the knockout mutant genome. This is necessary to confirm conserved function between Howea and the model species. 3)Any loci identified through the first two stages as playing a role in stress tolerance and adaptation in Howea palms may be of interest in related species with agricultural and horticultural importance, such as the oil palm. Using the methods applied in Howea, the project may be able to identify orthologous genes in these related species with stress tolerance function, which could have heightened significance due to the threats posed by climate change. References: 1)Coyne, J.A. & Orr, H.A. 2004. Speciation. Sinauer Associates Inc., Sunderland, MA. 2)Dunning LT, Hipperson H, Baker WJ, Butlin RK, Devaux C, Hutton I, Igea J, Papadopulos AST, Quan X, Smadja CM et al. 2016. Ecological speciation in sympatric palms: 1. Gene expression, selection and pleiotropy. Journal of Evolutionary Biology 29: 1472-1487. 3)Osborne et al. In prep. 4)Papadopulos, A.S.T., Price, Z., Devaux, C., Hipperson, H., Smadja, C.M., Hutton, I. et al. 2013. A comparative analysis of the mechanisms underlying speciation on Lord Howe Island. J. Evol. Biol. 26: 733-745. 5)Savolainen, V., Anstett, M.C., Lexer, C., Hutton, I., Clarkson, J.J., Norup, M.V. et al. 2006. Sympatric speciation in palms on an oceanic island. Nature 441: 210-213.