Genomic analysis of complex speciation in Heliconius

Heliconius 复杂物种形成的基因组分析

• 批准号: BB/G008841/1
• 负责人: Chris Jiggins
• 金额: $ 4.65万
• 依托单位: University of Cambridge
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2009
• 资助国家: 英国
• 起止时间: 2009 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FG008841%2F1
• 关键词: Genomic; analysis; complex; speciation; Heliconius

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.

最近的想法表明，新物种（物种形成）的演变可能很复杂，因此基因组的不同部分在不同的时间分开，而不是由一个单一分裂组成的简单过程。即使是我们自己的物种也是由于几百万年前与黑猩猩血统杂交引起的，尽管这一结论是有争议的。现在，最近的高通量基因组学技术允许对可能非模型有机体（例如Heliconius蝴蝶）的复杂物种形成进行详细研究。 Heliconius是明显的警告性热带蝴蝶，对鸟类感到厌恶。大多数物种的模式也模仿了其他Heliconius或Ithomiine蝴蝶的模式。一些物种在地理种族或物种之间表现出显着的颜色模式差异，而另一些物种则与密切相关的物种具有可疑的类似模式，它们在物种物种后很久以来就可以通过杂交获得。杂交很常见：涉及35％的物种。在Melpomene/Silvaniform组中，几乎所有物种都在实验室和自然界中杂交和反向杂交。这个引人入胜的系统为研究有关复杂物种的最新想法提供了一个出色的测试小组。在这个项目中，我们将确定四个物种（Heliconius Melpomene，H。Numata，H。H. everatus和H. timareta）最近交换了其基因组的一部分。该项目汇集了英国和海外对Heliconius蝴蝶生物学的了解以及最新的基因组技术，以了解导致物种起源和维持的遗传机制。我们建议将新的高通量基因组技术（454和Solexa测序和Illumina Genotyping Array芯片）结合在一起，以绘制秘鲁的两个焦点物种H. Melpomene和H. numata的基因组区域。下一代测序技术将用于从这两个物种中获取大量基因组序列数据，以鉴定成千上万的遗传标记（单核苷酸多态性或SNP）。随后，我们将使用这些SNP产生每个物种的高分辨率遗传图。然后，我们将基因型的H. Melpomene，H。Numata，H。Everatus和H. Timareta的野生捕获的标本。如果发生复杂的物种形成，我们希望找到共享多态性的区域（表明最近交换的区域）和固定差异的“基因组岛”（表明较旧的差异的区域可能围绕着差异差异的位点，例如影响模拟物，基因组不相容性，伴侣选择，和生态适应的基因的基因，例如那些差异的区域。最近，已经发现了许多东部安第斯类群与梅尔托烯链球菌接近的分类单元，但与该物种保持不同。该物种包含某些基因标记物与其他物种H. cydno更相似，但与它们经常共享H. Melpomene的局部模仿颜色模式不同。我们预测这些形式通过杂交获得了它们的颜色模式，这是Heliconius中相对常见的现象。使用围绕这些基因的SNP，我们将通过杂交转移到这些隔离形式的梅洛烯基因基因的可能性，从而导致形成新的杂交物种。这些SNP还将允许研究梅尔托烯和H. numata种族中的颜色模式多态性。拟议的研究是许多英国大学的Heliconius专家之间的合作，Gene Pool（Edinburgh）（Edinburgh）和微阵列资源中心（Cambridge）之间的合作。 Max Planck化学生态学研究所（德国）将提供进一步的实验室/生物信息学支持。到目前为止，全基因组研究仅限于一些模型生物，例如果蝇和小鼠。我们的提议概述了首次使野生热带生物中对进化和物种形成的全基因组理解的一种方法。

项目成果

Genome-wide evidence for speciation with gene flow in Heliconius butterflies.

• DOI: 10.1101/gr.159426.113
• 发表时间: 2013-11
• 期刊: Genome research
• 影响因子: 7
• 作者: Martin SH;Dasmahapatra KK;Nadeau NJ;Salazar C;Walters JR;Simpson F;Blaxter M;Manica A;Mallet J;Jiggins CD
• 通讯作者: Jiggins CD

Major Improvements to the Heliconius melpomene Genome Assembly Used to Confirm 10 Chromosome Fusion Events in 6 Million Years of Butterfly Evolution.

• DOI: 10.1534/g3.115.023655
• 发表时间: 2016-01-15
• 期刊: G3 (Bethesda, Md.)
• 作者: Davey JW;Chouteau M;Barker SL;Maroja L;Baxter SW;Simpson F;Merrill RM;Joron M;Mallet J;Dasmahapatra KK;Jiggins CD
• 通讯作者: Jiggins CD

Adaptive introgression across species boundaries in Heliconius butterflies.

• DOI: 10.1371/journal.pgen.1002752
• 发表时间: 2012
• 期刊: PLoS genetics
• 影响因子: 4.5
• 作者: Pardo-Diaz C;Salazar C;Baxter SW;Merot C;Figueiredo-Ready W;Joron M;McMillan WO;Jiggins CD
• 通讯作者: Jiggins CD

Population genomics of parallel hybrid zones in the mimetic butterflies, H. melpomene and H. erato.

• DOI: 10.1101/gr.169292.113
• 发表时间: 2014-08
• 期刊: Genome research
• 影响因子: 7
• 作者: Nadeau NJ;Ruiz M;Salazar P;Counterman B;Medina JA;Ortiz-Zuazaga H;Morrison A;McMillan WO;Jiggins CD;Papa R
• 通讯作者: Papa R