Adaptive Evolution of Gene Expression and Alternative Splicing

单个基因通常通过组装原始DNA序列中的不同成分来编码许多蛋白质。这些蛋白质具有不同的功能。因此，基因产生的蛋白质的数量和类型，即基因调控，是生物体功能的重要方面。研究人员将研究适应不同温度环境的果蝇自然种群的整个基因组。通过比较这些种群的基因调控，他们将了解随着生物体适应环境，基因调控是如何变化的。该项目将提供对基因调控进化的原因、机制和后果的异常完整的看法。它还将告知昆虫如何适应新的环境。因此，他们还将了解限制农业害虫或病媒昆虫地理范围的因素。该项目的更广泛影响包括对青年科学家的广泛培训，包括科学界代表性不足群体的成员。该项目还将加强美国研究人员与非洲同行之间的科学联系。最后，该小组将提高公众在线可用科学参考材料的质量。果蝇黑腹果蝇起源于非洲温暖地区；这项研究侧重于三个平行的适应较冷气候的实例。该项目包括收集三对适应温暖和寒冷的种群的RNA序列数据，这些种群涵盖了这三个气候转变。通过将群体遗传框架应用于该数据集，可以识别最可能由局部适应驱动的基因表达和选择性剪接的群体差异。热适应和冷适应种群之间的杂交将允许这些变化被归类为受影响基因顺式编码的或由另一基因反式编码的。对于顺式编码的适应性表达或剪接进化，遗传变异模式可以阐明自然选择作用模式的关键细节。研究人员将使用现有的种群基因组数据来测试选择是有利于新的突变还是有利于现有的遗传变异。该项目还需要对每个种群对的耐冷性差异进行基因图谱绘制。将作图结果、现有数据的群体基因组分析和上述RNA测序结果相结合，将通过基因调控的顺式作用变化确定值得注意的局部适应候选基因。探索遗传适应和热环境之间的接口将测试基因调控变化是否改变或维持祖先的调控，以及这种变化是否导致基因调控网络对干扰的缓冲能力较弱。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

A single gene often encodes numerous proteins by assembling different components from the original DNA sequence. These proteins have different functions. Thus, the number and type of proteins produced from a gene, i.e., gene regulation, are important aspects of how an organism functions. The investigators will look across the whole genome in natural populations of the fruit fly that have adapted to different temperature environments. By comparing gene regulation among these populations, they will learn how gene regulation changes as organisms adapt to their environment. The project will provide an unusually complete view of the causes, mechanisms, and consequences of the evolution of gene regulation. It will also inform how insects adapt to novel environments. Thus, they will also learn about the factors that limit the geographic ranges of insects that are agricultural pests or disease vectors. Broader impacts of this project include extensive training of young scientists, including members of underrepresented groups in science. The project will also strengthen scientific connections between U.S. researchers and their counterparts in Africa. Finally, the team will improve the quality of scientific reference material available to the public online.The fruit fly Drosophila melanogaster originated from warm regions of Africa; this research focuses on three parallel instances of adaptation to colder climates. The project includes the collection of RNA sequence data from three pairs of warm- and cold-adapted populations that encompass these three climate transitions. By applying a population genetic framework to this data set, population differences in gene expression and alternative splicing that were most likely driven by local adaptation can be identified. Crosses between warm- and cold-adapted populations will allow these changes to be classified as either cis-encoded at the affected gene, or trans-encoded by another gene. For cis-encoded cases of adaptive expression or splicing evolution, patterns of genetic variation can illuminate key details of natural selection's mode of action. Researchers will use existing population genomic data to test whether selection favored new mutations or standing genetic variation. The project also entails the genetic mapping of cold tolerance differences for each population pair. The combination of mapping results, population genomic analysis of existing data, and the above RNA sequencing results will identify notable candidate genes for local adaptation via cis-acting changes in gene regulation. Probing the interface between genetic adaptation and the thermal environment will test whether gene regulatory changes alter or maintain ancestral regulation, and whether such changes result in gene regulatory networks that are less buffered against perturbation.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.