Does hybridisation promote tree species diversification in the Amazon?

亚马逊雨林拥有地球上最高的植物物种多样性，但产生这种最高多样性的机制仍然是个谜。阿尔弗雷德·拉塞尔·华莱士（Alfred Russell Wallace）首先提出了一个长期持有的观点，即这种多样性反映了物种在漫长的地质时期内由于最小灭绝而逐渐积累。然而，最近的研究指出，一些树木的新物种的快速和最近的形成有很大的贡献。Inga是这项提议的焦点，是这些最近进化辐射的典范，在过去的600万年里，在亚马逊和其他拉丁美洲雨林中进化了至少300个物种。此外，在亚马逊河流域，数百种树种可以在一公顷（多达300种）内共存，这种极高的地方多样性主要是由少数物种丰富的属（如印加）造成的。亚马逊森林整体和局部的高度多样性表明，它与其他物种丰富的系统有相似之处，在这些系统中，进化辐射--许多物种从一个祖先种群迅速崛起--产生了许多新的谱系。在这里，我们的目标是将Inga开发为亚马逊地区植物物种辐射的模型，建立动物以外的全球范例（例如达尔文雀、裂谷湖慈鲷）和一些地理上受限制的植物群（例如夏威夷银汉鱼），或非热带（例如安第斯羽扇豆）。特别是，我们将研究杂交的作用，物种群体之间的杂交，最近的研究表明，这是进化辐射的一个主要原因。杂交对进化辐射的影响还没有在热带树木中进行过研究，尽管它被广泛认为是植物进化中强大的创造力。杂交产生了形态和遗传上的新奇，影响了许多群体的物种形成率，在所有主要的适应性辐射事件中都是显而易见的，因为存在多个测序的基因组。在植物中，物种形成的一种机制，即多倍性或基因组大小加倍，通常与杂交有关，已知是特别重要的。虽然流行的观点是热带树种之间的杂交是非常罕见的，但这种观点受到最近DNA序列数据的挑战。在因加，杂交最近已被证明发生，尽管以前的报道物种互不育，和一些染色体计数已证明，无关的物种是多倍体。在这里，使用新的基因组技术，首次在亚马逊河流域的树木，我们的目标是测试的意义，杂交和多倍性在印加多样化。我们将使用目标捕获技术产生的810个基因的DNA序列，在所有300个印加物种中找到杂交和多倍体的特征。由于昆虫的食草动物的压力明显的结构，在精细的空间尺度上的当地印加社区，我们怀疑一个强大的选择性因素驱动印加物种之间的分歧可能是化学防御。因此，我们将在我们的目标捕获基因集中的113个化学防御基因区域中寻找选择的签名。然后，我们将产生多个人口的选择数量的广泛的印加物种的全基因组数据，以确定是否组的化学防御基因在杂交过程中一起转移在“连锁块”，从而促进物种之间的适应性变化的运动。最后，我们将使用我们的目标捕获数据来识别可能的多倍体Inga物种，并使用基因组测序来发现它们是否是杂交和基因组加倍的结果（异源多倍体）或基因组加倍而不杂交（同源多倍体）。这个项目将提高我们对亚马逊河流域树木多样性的大部分进化的理解，因为因加是其他物种丰富的树属的典范，这些树属具有高度的本地物种多样性，并经历了类似的近期进化。

The Amazon rain forest holds the highest diversity of plant species on Earth, but the mechanisms which gave rise to this superlative diversity remain enigmatic. A long-held view, first proposed by Alfred Russell Wallace, was that this diversity reflected gradual accumulation of species over long geological periods due to minimal extinction. However, more recent studies point to a large contribution of rapid and recent formation of new species of some groups of trees. Inga, the focus of this proposal, is an exemplar for these recent evolutionary radiations, having evolved at least 300 species in the last 6 million years in the Amazon and other Latin American rain forests. Moreover, in Amazonia hundreds of tree species can coexist in a single hectare (up to 300), and this extremely high local diversity is largely accounted for by a few species-rich genera such as Inga. The high overall and local diversity of Amazonian forests suggests parallels with other species-rich systems where evolutionary radiation - the rapid rise of many species from one ancestor population - produced many new lineages. Here, we aim to develop Inga as a model for plant species radiation in Amazonia, building global examples beyond animals (e.g. Darwin's finches, rift lake cichlid fishes) and a few plant groups that are geographically restricted (e.g. Hawaiian silverswords), or non-tropical (e.g. Andean lupins).In particular, we will investigate the role of hybridization, the interbreeding between groups of species, as recent work shows it is a major cause of evolutionary radiations. Hybridization's effect on evolutionary radiation has not yet been studied within tropical trees, despite being widely acknowledged as a powerful creative force in plant evolution. Hybridization generates morphological and genetic novelty, impacting the rate of speciation in many groups and is evident in all major adaptive radiation events for which multiple sequenced genomes exist. In plants, one mechanism of speciation, polyploidy or the doubling of genome size, which is often linked with hybridisation, is known to be particularly important. While the prevailing view has been that hybridization between tropical tree species is exceptionally rare, this view is challenged by recent DNA sequence data. In Inga, hybridization has been recently demonstrated to occur, despite prior reports of species intersterility, and a few chromosome counts have demonstrated that unrelated species are polyploid. Here, using new genomic techniques for the first time in Amazonian trees, we aim to test the significance of hybridization and polyploidy in Inga diversification. We will use DNA sequences for 810 genes generated by the target capture technique to find signatures of hybridisation and polyploidy across all 300 Inga species. Because insect herbivore pressure demonstrably structures local Inga communities at fine spatial scales, we suspect that a powerful selective factor driving divergence among Inga species may be chemical defences. We will therefore search for signatures of selection among 113 chemical defence gene regions in our target capture gene set. We will then generate whole-genome data for multiple populations of a select number of widespread Inga species to determine whether groups of chemical defence genes are transferred together during hybridization in 'linkage blocks', thereby facilitating the movement of adaptive variation between species. Finally, we will use our target capture data to identify possible polyploid Inga species and use genome sequencing to discover if they are the result of hybridisation and genome doubling (allopolyploidy) or genome doubling without hybridisation (autopolyploidy).This project will improve our understanding of the evolution of a large portion of Amazonian tree diversity, because Inga is an exemplar for other species-rich tree genera that have high local species diversity and underwent similar recent evolution.