Phylogenomics and the Developmental Genetics and Evolution of Butterfly Colour Patterns

进化发育生物学的一个目标是了解负责物种差异的发育机制。蝴蝶的颜色模式是一个有吸引力的模式系统发育遗传学和进化，因为它们是可变的，由简单的定义明确的二维亚基，并进行选择。蝴蝶属Junonia是一个重要的模式系统的颜色模式的发展，但几乎所有的数据来自一个物种，J. coenia没有考虑的变化和进化背景的属的其余部分。本研究计划的长期目标是（1）以Junonia属的42+种作为模型系统，了解基因组变化如何产生新的表型变异。猖獗的杂交发生在该属的部分地区，因此（2）我们也将使用Junonia来检查杂交和渐渗在多样化和适应中的作用，对比不同频率杂交的原因和影响。最后（3）我们将以蝴蝶和高海拔昆虫线粒体为例，研究杂交、渐渗和适应在多样化和适应性进化中的作用。短期目标包括：（1）对Junonia进行全基因组分析，建立一个全面的物种水平系统发育树，以重建该属成员之间的表型进化。(2)比较新大陆和旧大陆Junonia物种遗传变异的地理模式，重点是研究不足的旧大陆分支，显示杂交的初步证据，让人想起在新大陆观察到的。(3)重建入侵的时间进程和路线，传播，杂交，和渗入的J. villida谱系（以及可能的其他Junonia谱系）进入新世界。(4)评估有丝分裂基因组和完整的核rRNA重复序列作为下一代DNA条形码的候选者。(5)包括高海拔和低海拔物种的蝴蝶、蛾和石蛾分支中线粒体对高海拔适应的特征模式。(6)测试预测的mesoevolutionary理论，即类群与季节性多型性将有升高的物种形成率和增加表型多样性，通过进行基因组重建的蝴蝶分支包含物种都有和没有季节性多型性和比较率之间的谱系。重要性：该计划将蝴蝶颜色图案的基因组学和发育遗传学与其生态和进化背景相结合，提供了对进化新奇性的遗传基础以及这些过程对产生生物多样性的贡献的见解。更广泛的影响：该计划培训HQP在evo-devo，基因组学，进化生物学和昆虫学。开发新技术并在这些领域提供令人兴奋的结果，HQP配备了基础和应用研究，医疗保健和教育职业的基本技能。

A goal of evolutionary developmental biology is to understand developmental mechanisms responsible for species differences. Butterfly color patterns are an attractive model system for developmental genetics and evolution because they are variable, consist of simple well-defined 2-dimensional subunits, and undergo selection. The butterfly genus Junonia is an important model system for colour pattern development, but nearly all data comes from one species, J. coenia without considering the variation and evolutionary context of the rest of the genus. The long-term goals of this research program are (1) to understand how genomic changes create new phenotypic variation using the 42+ species of the genus Junonia as a model system. Rampant hybridization occurs in portions of the genus, so (2) we will also use Junonia to examine the role of hybridization and introgression in diversification and adaptation, contrasting the causes and effects of different frequencies of hybridization. Finally (3) we will examine the roles of hybridization, introgression, and adaptation in diversification and adaptive evolution, using butterflies and high elevation insect mitochondria as case studies. Short-term objectives include: (1) Conducting a phylogenomic analysis of Junonia to create a comprehensive species-level phylogenetic tree to reconstruct phenotypic evolution among members of this genus. (2) Comparing biogeographic patterns of genetic variation in New and Old World Junonia species, focused on poorly studied Old World clades showing preliminary evidence of hybridization reminiscent of that observed in the New World. (3) Reconstructing the time course and routes of invasion, dispersal, hybridization, and introgression of the J. villida lineage (as well as possibly other Junonia lineages) into the New World. (4) Evaluating mitogenomes and complete nuclear rRNA repeats as candidates for next generation DNA barcodes. (5) Characterizing patterns of mitochondrial adaptation to high elevation in butterfly, moth, and caddisfly clades including both high and low elevation species. (6) Testing a prediction of mesoevolutionary theory, that taxa with seasonal polyphenism will have elevated speciation rates and increased phenotypic diversity, by conducting phylogenomic reconstruction of butterfly clades containing species both with and without seasonal polyphenism and comparing rates between lineages. Significance: This program unifies the genomics and developmental genetics of butterfly colour patterns with their ecological and evolutionary context, providing insights into the genetic basis of evolutionary novelties and the contributions of these processes to generating biodiversity. Broader impacts: This program trains HQP in evo-devo, genomics, and evolutionary biology, and entomology. Developing new techniques and providing exciting results in these fields, HQP are equipped with essential skills for careers in basic and applied research, healthcare, and education.