Collaborative Research: Reversing evolution to understand the genetic basis of species divergence

进化生物学最基本的任务之一是了解生物多样性是如何通过适应和物种形成而产生的。参与物种间适应或隔离的基因通常位于祖先基因顺序翻转的染色体区域。这些倒置的染色体区域阻断了亲缘关系密切的物种之间的基因交换，这使得它们内部的基因能够独立进化。目前尚不清楚这些关键基因是随机分布在倒位区域内，还是更可能出现在倒位区域的边缘或中心。克服逆序对遗传分析造成的障碍将使研究人员能够了解物种分化和适应的遗传基础。该项目将使用果蝇（果蝇）基因组编辑工具包来逆转进化过程的结果，并翻转分离伪果蝇和D. persimilis的大染色体倒位。这将允许对与这些倒转有关的重要物种差异特征进行前所未有的分析。通过与当地少数民族高中公立学校教师的合作，本研究还将对K-12教育和教师培训产生教育影响。此外，染色体倒位导致许多重要的人类疾病。了解关键序列所在的位置对开发这些疾病的治疗至关重要。一个重要的机制，使物种持续面对基因流是染色体倒位的存在。尽管染色体倒位被认为是杂合子中基因通量的不可渗透屏障，但它可以通过双交叉或非交叉基因转换来交换遗传物质。这些过程应该在倒温的中心区域更为普遍。因此，理论研究预测，相对于中心，因倒位而不同的物种之间的核苷酸差异应该在断点区域更高，并且适应性或生殖隔离基因也应该更有可能位于断点附近。使用群体遗传或比较基因组数据对第一种预测进行了测试，结果产生了一系列不一致的模式，表明理论模型可能过度简化了反转对重组的预期影响。另一方面，对第二种预测的测试是不可能进行的，因为反转减少或阻碍了杂交的重组，从而排除了对这些基因组区域的种间差异进行精细的遗传分析。为了克服这一限制，该项目将利用CRISPR/Cas9基因组编辑技术来恢复兄弟果蝇物种Drosophila pseudobscura和D. persimilis之间的两个固定倒置。将产生的菌株将用于生殖隔离因素（杂交雄性不育）的遗传作图，并用于一项实验性进化研究，该研究将测试染色体倒位是否以及在多大程度上促进杂交物种的持久性。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

One of the most fundamental quests of Evolutionary Biology is to understand how biodiversity arises through adaptation and speciation. Genes involved in adaptation or isolation between species are frequently located in regions of a chromosome where the ancestral gene order has flipped. These inverted chromosome regions block gene exchange between closely related species, which allows the genes inside them to evolve independently. It is not known whether those key genes are randomly spread inside the inversions or whether they are more likely found close to the edges or the center of those inverted regions. Circumventing the barriers to genetic analyses posed by inversions will allow researchers to learn the genetic basis of species divergence and adaptation. This project will use the Drosophila (fruit fly) genome editing toolkit to reverse the outcome of the evolutionary process and flip back the large chromosomal inversions that separate Drosophila pseudoobscura and D. persimilis. This will allow unprecedented analyses of important species divergence traits linked to these inversions. This research will also have educational impacts in K-12 education and teacher training via collaboration with public school teachers from local minority high schools. Moreover, chromosome inversions cause many important human diseases. Understanding where the critical sequences lie is fundamental to development of treatment of those diseases. An important mechanism that allows species to persist in the face of gene flow is the presence of chromosomal inversions. Although considered impermeable barriers to gene flux in heterozygotes, chromosomal inversions can exchange genetic material via double-crossovers or non-crossover gene conversion. Those processes should be more common in the central regions of inversions. Theoretical studies thus predict that nucleotide divergence between species differing by inversions should be higher at the breakpoint regions relative to the center, and that adaptive or reproductive isolation genes should also be more likely located towards the breakpoints. Tests of the first prediction have been conducted using population genetic or comparative genomic data, resulting in a range of inconsistent patterns suggesting that theoretical models may oversimplify the expected effects of inversions on recombination. Test of the second prediction, on the other hand, have been impossible to conduct because inversions reduce or impede recombination in hybrids, precluding fine scale genetic analysis of interspecific differences at those genomic regions. To overcome this limitation, this project will leverage CRISPR/Cas9 genome editing technology to revert two fixed inversions between the sibling fruit fly species Drosophila pseudoobscura and D. persimilis. The strains that will be generated will be used for genetic mapping of reproductive isolation factors (hybrid male sterility), and for an experimental evolution study that will test whether and how much chromosomal inversions facilitate the persistence of hybridizing species.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.