Ecological speciation in palms on an oceanic island

两个多世纪以来，物种多样性的起源一直困扰着生物学家。查尔斯·达尔文认识到，由于地理隔离而导致的物种分化是物种形成的驱动力，但他也认为，在没有地理隔离的情况下，种群也可能分化成不同的物种，这种机制现在被称为同域物种形成。在过去的十年里，数学模型表明，同域物种形成在理论上是可能的，但在自然界中记录的例子非常少。今年早些时候，Savolainen及其同事（该提案的一些申请人）在对两种棕榈的案例研究中提供了同域物种形成的完整证据，howa forsteriana和H. belmoreana是遥远的Lord Howe岛（LHI）的特有物种（“海洋岛屿上棕榈树的同域物种形成”，Nature 441: 210-213, 2006）。在这里，我们建议将我们的研究带到更深的层次。我们的目标是在棕榈树的案例研究中记录物种分化的基因组结构和遗传基础，从而带来新的数据类型来测试同系分化的替代方案，并解开生态物种形成的机制，这些机制必须在这个独特的LHI系统中运作。LHI是一个面积不到12平方公里的亚热带小岛，位于澳大利亚东海岸580公里处。植物区系包括维管植物241种，其中特有种105种。在LHI上，地理隔离实际上是不可能的，因此它是一个理想的地点来测试同域物种形成的四个标准：1)物种的同域，2)姐妹关系，3)生殖隔离，4)早期的异域阶段是极不可能的。许多植物属，如棕榈树howa，在岛上由不止一种特有物种代表，这很可能是同域物种形成的产物。在我们之前对Howea棕榈树的实验中，我们发现物种分化的遗传特征表明，只有四个位点在两个物种之间的差异比中性条件下的预期更强烈，这些位点最有可能与同域物种形成过程中受分化选择影响的基因有关。为了在这个独特的岛屿系统中描述howa生态物种形成的基因组和遗传结构，我们将开展六项活动：a)使用更全面的AFLP基因组扫描，在Howea中鉴定出差异最大的标记位点和基因组中可能处于选择状态的区域b)使用这些差异位点作为BAC文库上的探针，表征可能包含与物种分化相关基因的kentia palm基因组部分（测试Gavrilets预测的只有少数位点参与Howea的物种形成）c)使用kentia palm的BACs序列作为模板。d)确定在两种棕榈树的基因组中，不同的基因组片段是集中的还是广泛分布的（验证Felsenstein关于物种形成的经典预测，即低重组促进了物种形成）。e)利用聚结模型和多位点，评估基因流动是否被中断，并估计在howa物种分化过程中中断的程度。f)与油棕的EST库进行比较，为选择下发现的任何orf提供可能的函数。

The origin of species diversity has challenged biologists for over two centuries. Charles Darwin recognised that allopatry, species divergence resulting from geographical isolation, is a driving force in speciation, but he also thought that populations could diverge into separate species in the absence of geographical isolation, a mechanism now called sympatric speciation. During the last decade, mathematical models have shown that sympatric speciation is theoretically possible, but extremely few examples have been documented in nature. Early this year, Savolainen and colleagues (some of the applicants of this proposal) provided complete evidence for sympatric speciation in a case study of two species of palm, Howea forsteriana and H. belmoreana, endemic of the remote Lord Howe Island (LHI) ('sympatric speciation in palms on an oceanic island', Nature 441: 210-213, 2006). Here we propose to take our research to a much deeper level. Our goal is to document the genomic architecture and genetic basis for species divergence in our case study of palms, thus bringing new types of data to test alternatives to divergence in sympatry and disentangle the mechanisms of ecological speciation that must have operated in this unique LHI system. LHI is a minute subtropical island of less than 12 km2, situated 580 km off the eastern coast of Australia. Its flora comprises 241 vascular plant species of which 105 are endemic. Geographic isolation is not realistically possible on LHI and thus it is an ideal site on which to test the four criteria for sympatric speciation: 1) species sympatry, 2) sister relationships, 3) reproductive isolation, and 4) that an earlier allopatric phase is highly unlikely. Numerous plant genera, like the palms Howea, are represented by more than one endemic species on the island, which may well be products of sympatric speciation. In our previous experiments of the Howea palms, we found that the genetic signature of species divergence indicated that only four loci differ more strongly between the two species than expected under neutrality and these are those most likely to be linked to genes subject to divergent selection during sympatric speciation. To characterise the genomic and genetic architecture underlying the ecological speciation of Howea in this unique island system, we will conduct six activities: a) Using a more comprehensive AFLP genome scan, identify in Howea the most divergent marker loci and so regions of the genome that may be under selection b) Using these divergent loci as probes on a BAC library, characterise portions of the kentia palm's genome that may contain genes involved in species divergence (testing Gavrilets' prediction of only a few loci being involved in speciation in Howea) c) Using the BACs sequences of the kentia palm as template, identify in the curly palm's genome homologous sequences and open reading frames (ORFs), which may contain the signature of positive selection d) Determine whether the divergent genomic segments are concentrated versus widely distributed in the genomes of the two palm species (testing Felsenstein's classic prediction of speciation being facilitated by low recombination). e) Using coalescence models and multiple loci, evaluate whether gene flow has been interrupted / and estimate the extent of disruption / during species divergence in Howea. f) In comparison with an EST library for the oil palm, provide possible functions for any ORFs found under selection.