Collaborative Research: Inferring admixture history in non-model organisms using local ancestry detection

当地质、气候或其他事件导致最近分化的物种重新引入彼此时，会发生什么？如果它们进化的基因差异不大，这两个物种可能会交配并产生杂交后代。物种间的杂交，曾经被认为是一种罕见的，大多数是无关紧要的现象，现在已经被记录在各种各样的物种对，包括棕色/北极熊，狗/狼，牛/野牛，甚至人类/尼安德特人。重要的是，在每一种情况下，至少有一些杂交后代是可行的和肥沃的，这是通过跟踪这些物种对之间的遗传交换来证明的。这些过去的杂交事件中的每一个都可以被认为是跨越物种障碍的自然实验。该项目将开发用于检测和分析跨物种移动的基因的工具。该工具的应用将集中在两个物种对过去的杂交一直特别重要。牛和野牛在20世纪初被牧场主故意杂交，因此大多数野牛携带牛的基因。棕熊和北极熊过去有过几次杂交，这种情况仍在发生。对这些物种对的分析将揭示哪些基因对跨物种的移动是难治的，哪些不是。这些信息将是了解任何感兴趣的物种对未来杂交的程度和后果的关键。将通过关注加州金熊奖和加州科学院的相关教育项目来接触公众、学生和职前教师。新的灵活的祖先推断工具将能够定位渗入的基因组区域，即使只有低覆盖率的DNA序列数据可用。该工具将结合复杂的人口统计学情景，例如混合物的多个脉冲，并将精确定位基因组中具有潜在进化意义的区域，这些区域由于频率高或缺乏混合祖先而具有潜在的进化意义。这一工具的应用，以两个物种对已知的混合物的历史将提供新的见解的过程中的物种形成和当地的适应，有可能告知管理实践，寻求限制混合祖先的人口，有针对性的保护。此外，该工具将满足对改进信号检测方法以推断进化过程的日益增长的需求，为研究界提供将基因组数据转化为科学推断的宝贵工具。该奖项反映了NSF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。

What happens when geological, climatic, or other events cause recently diverged species to be reintroduced to one another? If their evolved genetic differences are not great, the two species may mate and produce hybrid offspring. Between-species crossbreeding, once considered a rare and mostly inconsequential phenomenon, has now been documented in a wide variety of species pairs including brown/polar bears, dog/wolf, cow/bison, and even human/Neanderthal. Importantly, in each of these cases, at least some of the hybrid offspring were viable and fertile as evidenced by tracking genetic exchanges between these species pairs. Each of these past crossbreeding events can be considered a natural experiment across what were thought to be species barriers. This project will develop tools for detecting and analyzing genes that have moved across species. Application of the tool will focus on two species pairs for which past hybridization has been particularly important. Cows and bison were intentionally crossbred by ranchers in the early 1900s, such that most bison carry cow genes. Brown bears and polar bears had several episodes of past crossbreeding,and this continues to occur. Analysis of these species pairs will reveal which genes are refractory to movement across species and which are not. This information will be key to understanding the extent and consequences of future hybridization of any species pair of interest. Outreach to the public, students, and pre-service teachers will occur through a focus on the California Golden Bear and associated educational programs at the California Academy of Sciences. The new flexible ancestry inference tool will be capable of localizing introgressed genomic regions even when only low-coverage DNA sequence data are available. The tool will incorporate complex demographic scenarios, such as multiple pulses of admixture, and will pinpoint regions of the genome that are of potential evolutionary significance by virtue of being high frequency or devoid of admixed ancestry. The application of this tool to two species pairs with known admixture histories will provide new insights into the processes of speciation and local adaptation, with the potential to inform management practices that seek to limit admixed ancestry in populations that are targeted for conservation. In addition, the tool will satisfy the growing need for improved methods of signal detection to infer evolutionary processes, providing the research community with a valuable tool for transforming genomic data into scientific inference.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.