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。涉及物种间适应或隔离的基因通常位于染色体上祖先基因顺序颠倒的区域。这些倒置的染色体区域阻止了密切相关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置区域内，还是更有可能在倒置区域的边缘或中心附近发现。绕过倒置带来的遗传分析障碍，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，并逆转分隔果蝇和果蝇的大型染色体倒置。这将使我们能够对与这些倒位相关的重要物种分化特征进行前所未有的分析。这项研究还将通过与当地少数民族高中的公立学校教师合作，在K-12教育和教师培训方面产生教育影响。此外，染色体倒置会导致许多重要的人类疾病。了解关键序列所在位置是开发这些疾病治疗方法的基础。允许物种在基因流动面前坚持下来的一个重要机制是染色体倒置的存在。虽然染色体倒置被认为是杂合子中基因流动的不可渗透的障碍，但它可以通过双交换或非交换基因转换来交换遗传物质。这些过程应该在反转的中心区域更为常见。因此，理论研究预测，不同倒位的物种之间的核苷酸分歧应该在断点区相对于中心更高，适应性或生殖隔离基因也更有可能位于断点处。对第一个预测的测试是使用群体遗传或比较基因组数据进行的，导致了一系列不一致的模式，这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，对第二个预测的检验是不可能进行的，因为倒置会减少或阻碍杂交后代的重组，从而无法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果蝇和拟黑果蝇之间的两个固定的倒置。将产生的菌株将用于生殖隔离因素(杂交雄性不育)的基因图谱，并将用于一项实验性进化研究，该研究将测试染色体倒置是否以及在多大程度上有助于杂交物种的持久性。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。

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.