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

共域物种形成(没有地理隔离的物种形成)的概念历来被视为一个有争议的领域；然而，物种形成可以在基因流存在的情况下发生这一点正日益被接受(Coyne&Orr，2004)。同域物种形成的一个令人信服的例子是位于塔斯曼海小豪主岛的Howea Palms，大约1百万年前，通过新沉积的方解石土壤的殖民，Howea forsteriana从其姊妹分类群--Howea belmore ana的祖先--分化出来(Savolainen等人，2006年)。石灰性土壤似乎引起了底物诱导的Forsteriana开花时间的变化，导致了与H.belmore ana的生态分歧和生殖隔离(Savolainen等人，2006年；Dunning等人，2016)。这种土壤提供了显著的胁迫，包括水、盐度和pH(Savolainen等人，2006年；Papadulos等人，2013年)，并假设当地对这些胁迫的适应可能已经通过多效性或连锁不平衡直接影响了开花时间的改变(Savolainen等人，2006年；Dunning等人，2016)。使用详细的土壤化学分析和rna-seq数据，奥斯本等人。(在准备中)已经确定了可能解释Howea Palm物种形成的遗传机制的候选基因座，其基础是满足三个标准：1)拥有与土壤胁迫有关的功能。2)具有与开花时间有关的功能。3)适应性进化的证据。本项目旨在通过以下方法对这些候选基因进行研究：1)首先通过模式植物拟南芥和短柄短穗麦中同源基因的T-DNA敲除突变体，验证相关基因在东方海棠中具有逆境耐受性和/或开花时间功能。包括干旱、盐度和pH在内的非生物胁迫的分析将被用来检验基因敲除的表型效应。2)在此之后，该项目将试图通过将同源Howea基因插入到基因敲除突变体基因组中来挽救任何表现出土壤胁迫和/或开花时间影响的敲除突变体的表型。这对于确认Howea和模式物种之间的保守功能是必要的。3)通过前两个阶段确定的在Howea Palm中对胁迫耐性和适应起作用的任何基因座都可能对具有农业和园艺重要性的相关物种感兴趣，例如油棕榈树。使用Howea中应用的方法，该项目可能能够在这些具有胁迫耐受功能的相关物种中识别同源基因，由于气候变化的威胁，这一功能可能具有更高的意义。参考文献：Coyne，J.A.&Orr，H.A.2004。物种形成。Sinauer Associates Inc.，马萨诸塞州桑德兰2)Dunning LT，Hipman H，Baker WJ，Butlin RK，Devaux C，Hutton I，Igea J，Papadadulos AST，Quan X，Smadja CM等。2016年。共生棕榈树的生态物种形成：1.基因表达、选择和多效性。《进化生物学杂志》29：1472-1487。3)奥斯本等人。准备好了。4)Papadadulos，A.S.T.，Price，Z.，Devaux，C.，HipPerson，H.，Smadja，C.M.，Hutton，I.等人2013年。豪勋爵岛物种形成机制的比较分析。J·埃沃。比奥尔。26：733-745。5)Savolainen，V.，Anstett，M.C.，Lexer，C.，Hutton，I.，Clarkson，J.J.，Norup，M.V.等。2006年。海洋岛屿上棕榈树的共生物种形成。自然441：210-213。

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.