CAREER: Integrating undergraduate research, citizen science, and museum genomics to explore a century of change in North American birds

生命如何应对变化是生物学的关键问题之一。在过去的100年里，我们目睹了地球上栖息地的加速变化。关于物种如何对此做出反应，我们知之甚少，因为通常没有详细的历史记录来记录物种在哪里生活，或者它们过去是什么样的。然而，自然历史博物馆的标本可以提供几十年前物种的快照。该项目利用了20世纪30年代至50年代无与伦比的北美和中美洲鸟类博物馆收藏。利用可以从这些标本中提取DNA的新技术，研究人员将比较历史和现代样本，以了解鸟类的基因组如何随着栖息地的变化而变化。此外，历史野外记录中的鸟类目击记录将与公民科学家收集的数千份现代观察记录进行比较，以确定鸟类的地理分布如何变化。将研究与推广相结合，一项国际重新调查工作将与eBird的公民科学专家合作，对1933年至1955年期间最初采样的300个地点的鸟类物种进行比较。对15个历史采集点进行的国际联合实地考察将提供专家收集的补充实地数据。这项研究的结果将提供前所未有的细节，在大陆规模的鸟类基因组和分布景观的变化。工作的各个方面将与本科研究计划相结合，该计划将培养下一代生物学家，他们拥有最新的基因组学设备和技术，非常适合公共和私营部门。研究人员将评估20种重点鸟类的DNA变化，这些鸟类的栖息地在现代已经发生了巨大的变化。历史与现代样本的比较将测试北美南部西部沿海低地的物种是否经历了由于原生thornsrub栖息地转换为灌溉农田而导致的范围扩张，以及高地针叶林物种是否经历了由于栖息地破碎而导致的遗传多样性丧失。DNA将使用数千个保守的基因组锚来提取，这些锚可以捕获和检索在旧博物馆标本中发现的受损DNA。随后的分析将把这些较小的片段拼接成较大的片段，从而可以对种群之间的多样性和连通性进行基因组分析，并在时间点之间进行比较。使用下一代测序技术的基因组研究，特别是使用保守元件，还没有在脊椎动物中如此浅的尺度上研究进化。这项研究将阐明保守基因组片段在发现栖息地退化和其他人类影响对野生生物基因组的影响方面的效用。

How life responds to change is one of the key questions in biology. The last 100 years have witnessed habitat changes to the planet at an accelerating pace. Very little is known about how species respond to this, because there are usually no detailed historical records of where species lived or what they were like in the past. Specimens from natural history museums, however, can provide a snapshot in time of what species were like decades ago. This project takes advantage of an unparalleled museum collection of North and Middle American birds from the 1930s to 1950s. Using new technology that can extract DNA from these specimens, the researchers will compare historic and modern samples to understand how the genomes of birds have changed in response to changes to their habitats. Additionally, records of bird sightings from the historical field notes will be compared to thousands of modern observation records collected by citizen scientists to determine how the geographic distributions of birds have changed. Combining research with outreach, an international resurvey effort will work with citizen-science experts at eBird to compare bird species at 300 sites originally sampled between 1933 and 1955. Joint, international field resurveys of 15 historic collecting sites will provide complementary on-the-ground data collected by experts. Results of this research will provide unprecedented detail to changes in the genomic and distributional landscape of birds at a continental scale. All facets of the work will be integrated with an undergraduate research program that will train the next generation of biologists with the latest genomics equipment and techniques well-suited to both the public and private sector. The researchers will assess changes in the DNA of 20 focal bird species whose habitats have been dramatically altered in modern times. The comparisons of historical to modern samples will test whether species in the western coastal lowlands of southern North America have experienced range expansion due to the conversion of native thornscrub habitat to irrigated cropland, and whether highland conifer forest species have experienced loss of genetic diversity due to habitat fragmentation. DNA will be extracted using thousands of conserved genomic anchors that can capture and retrieve the damaged DNA found in older museum specimens. Later analysis will stitch these smaller fragments into larger pieces, allowing for genomic analysis of diversity and connectivity among populations and comparison between time points. Genomic research using next-generation sequencing techniques, particularly using conserved elements, has yet to study evolution at such a shallow scale in vertebrates. This research will clarify the utility of conserved genomic fragments in discovering the impact of habitat degradation and other human influences on the genomes of wild organisms.