Genomic analysis of complex speciation in Heliconius

最近的观点认为，新物种的进化（物种形成）可能是复杂的，基因组的不同部分在不同的时间分离，而不是一个由单一分裂组成的简单过程。甚至我们自己的物种也被认为是几百万年前与黑猩猩血统杂交的结果，尽管这一结论存在争议。最近的高通量基因组学技术现在允许在可能的非模式生物候选者中详细调查复杂的物种形成，例如蝴蝶。黑蛱蝶是一种引人注目的热带蝴蝶，颜色鲜艳，令鸟类厌恶。大多数种类的图案也模仿了其他的Heliconius或ithomiine蝴蝶。一些物种在地理种族或物种之间表现出显著的颜色模式差异，但另一些物种与密切相关的物种有着可疑的相似模式，这些模式可能是在物种形成后很久通过杂交获得的。杂交是常见的：35%的物种参与其中。在melpomene/silvaniform组中，几乎所有物种都在实验室和自然界中进行杂交和回交。这个迷人的系统为研究复杂物种形成的最新观点提供了一个极好的试验组。在这个项目中，我们将确定四个物种（Heliconius melpomene， H. numata， H. elevatus和H. timareta）最近交换部分基因组的程度。该项目汇集了英国和海外的蝴蝶生物学知识和最新的基因组技术，以了解导致物种起源和维持的遗传机制。我们建议结合新的高通量基因组技术（454和Solexa测序，以及Illumina基因分型阵列芯片）来绘制两个焦点物种，秘鲁的H. melpomene和H. numata的基因组区域。下一代测序技术将用于从两个物种获得大量的基因组序列数据，以鉴定数千种遗传标记（单核苷酸多态性，或SNPs）。随后，我们将使用这些snp来制作每个物种的高分辨率遗传图谱。然后，我们将对野生捕获的H. melpomene、H. numata、H. elevatus和H. timareta的标本进行基因分型。如果复杂的物种形成正在发生，我们预计会发现共享多态性的区域（表明最近交换的区域）和固定差异的“基因组岛”（表明可能围绕着差异选择基因的区域，如影响模仿、基因组不相容、配偶选择和生态适应的基因）。最近发现了一些东安第斯的分类群，它们与H. melpomene很接近，但仍与该物种不同。这一物种含有一些与另一物种H. cydno更相似的基因标记，但与该物种不同的是，它们经常共享H. melpomene的局部模仿颜色模式。我们预测这些形式通过杂交获得了它们的颜色图案，这是Heliconius中相对常见的现象。利用集中在这些基因周围的snp，我们将研究H. melpomene基因通过杂交转移到这些分离形式，从而形成新的杂交物种的可能性。这些SNPs也将允许研究H. melpomene和H. numata种族的颜色模式多态性。这项拟议的研究是Heliconius专家在英国多所大学，基因库（爱丁堡）和微阵列资源中心（剑桥）之间的合作。进一步的实验室/生物信息学支持将由马克斯·普朗克化学生态学研究所（德国）提供。到目前为止，全基因组研究仅限于果蝇和小鼠等几种模式生物。我们的建议概述了一种方法，首次使对野生热带生物的进化和物种形成的突破性全基因组理解成为可能。

Recent ideas suggest that evolution of new species (speciation) may be complex, whereby different parts of the genome separate at different times rather than a simple process consisting of a single split. Even our own species has been suggested to result from hybridization with chimpanzee lineages a few million years ago, although this conclusion is contested. Recent high-throughput genomics technologies now permit detailed investigation of complex speciation in likely non-model organism candidates, such as Heliconius butterflies. Heliconius are conspicuous warningly coloured tropical butterflies distasteful to birds. The patterns of most species also mimic those of other Heliconius or ithomiine butterflies. Some species show remarkable divergence in colour patterns between geographical races or species, but others share suspiciously similar patterns with closely related species, which they could have acquired via hybridization long after speciation. Hybridization is common: 35% of species are involved. In the melpomene/silvaniform group, almost all species are known to hybridize and backcross in both lab and in nature. This fascinating system provides an excellent test group for studying recent ideas about complex speciation. In this project, we will determine the extent to which four species (Heliconius melpomene, H. numata, H. elevatus and H. timareta) have recently exchanged parts of their genomes. This project brings together British and overseas knowledge of Heliconius butterfly biology and the latest genomic technologies to understand the genetic mechanisms that lead to the origin and maintenance of species. We propose to combine new high-throughput genomic technologies (454 and Solexa sequencing, and Illumina genotyping array chips) to map genomic regions in two focal species, H. melpomene and H. numata from Peru. Next generation sequencing technology will be used to obtain large amounts of genomic sequence data from the two species to identify thousands of genetic markers (single nucleotide polymorphisms, or SNPs). Subsequently, we will use these SNPs to produce high resolution genetic maps of each species. We will then genotype wild-caught specimens of H. melpomene, H. numata, H. elevatus and H. timareta. If complex speciation is occurring, we expect to find regions of shared polymorphism (indicating regions of recent exchange) and 'genomic islands' of fixed differences (indicating regions of older divergence probably surrounding sites of divergently selected genes such as those affecting mimicry, genomic incompatibility, mate choice, and ecological adaptations). A number of Eastern Andean taxa have recently been discovered that are close to H. melpomene, yet remain distinct from that species. The species contain some gene markers more similar to another species, H. cydno, but unlike that species they often share the local mimicry colour pattern of H. melpomene. We predict that these forms acquired their colour pattern via hybridization, which is a relatively common phenomenon in Heliconius. Using SNPs concentrated around these genes we will investigate the possibility that H. melpomene genes have been transferred to these segregate forms via hybridization, leading to the formation of new hybrid species. These SNPs will also allow investigation of colour pattern polymorphism in races of H. melpomene and H. numata The proposed research is a collaboration between Heliconius experts at a number of UK universities, The Gene Pool (Edinburgh), and the Centre for Microarray Resources (Cambridge). Further laboratory/bioinformatics support will be provided by the Max Planck Institute for Chemical Ecology (Germany). Up to now, whole-genome studies have been restricted to a few model organisms such as fruit flies and mice. Our proposal outlines a means of enabling ground breaking whole-genome understanding of evolution and speciation in a wild tropical organism for the first time.