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，而不是一个简单的过程，包括一个单一的分裂。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，尽管这一结论受到质疑。最近的高通量基因组学技术现在允许详细调查复杂的物种形成可能的非模式生物候选人，如Heliconius蝴蝶。Heliconius是一种引人注目的热带蝴蝶，颜色警告鸟类。大多数物种的模式也模仿其他Heliconius或ithomiine蝴蝶的模式。一些物种在地理种族或物种之间的颜色模式上表现出显着的差异，但其他物种与密切相关的物种共享可疑的相似模式，它们可能在物种形成后很久通过杂交获得。杂交很常见：35%的物种都参与其中。在melpomene/silvaniform组中，几乎所有的物种都已知在实验室和自然界中杂交和回交。这个迷人的系统为研究复杂物种形成的最新想法提供了一个很好的测试组。在这个项目中，我们将确定的程度，四个物种（Heliconius melpomene，H。numata，H. elevatus和H. timareta）最近交换了部分基因组。该项目汇集了英国和海外的Heliconius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。我们建议结合联合收割机新的高通量基因组技术（454和Solexa测序，和Illumina基因分型阵列芯片）来绘制两个重点物种的基因组区域，H。melpomene和H.来自秘鲁的numata。下一代测序技术将用于从这两个物种中获得大量的基因组序列数据，以识别数千个遗传标记（单核苷酸多态性或SNP）。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。然后我们将对野生的H。melpomene，H. numata，H. elevatus和H.蒂马雷塔。如果复杂的物种形成正在发生，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”（表明可能围绕分歧选择基因的位点的较老分歧区域，例如影响拟态的基因，基因组不相容性，配偶选择和生态适应）。最近发现了一些与H.但仍与该物种不同。该物种含有一些与另一物种H. cydno，但与该物种不同的是，它们经常分享H的局部模仿颜色模式。美波美我们预测这些形式通过杂交获得了它们的颜色模式，这是赫里康纽斯中相对常见的现象。利用这些基因周围的SNPs，我们将研究H。melpomene基因已通过杂交转移到这些分离形式中，导致新杂交物种的形成。这些SNPs也将允许调查的颜色模式多态性的种族H。melpomene和H. numata拟议的研究是Heliconius专家在英国一些大学，基因库（爱丁堡）和微阵列资源中心（剑桥）之间的合作。马克斯·普朗克化学生态学研究所（德国）将提供进一步的实验室/生物信息学支助。到目前为止，全基因组研究仅限于少数模式生物，如果蝇和小鼠。我们的提案概述了一种方法，首次实现了对野生热带生物进化和物种形成的突破性全基因组理解。

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