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，地球的栖息地变化正在加速。人们对物种如何反应知之甚少，因为通常没有关于物种生活在哪里或它们过去是什么样子的详细历史记录。然而，来自自然历史博物馆的标本可以提供几十年前物种的快照。这个项目利用了博物馆从20世纪30年代到50年代无与伦比的北美和中美鸟类收藏。使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，历史田野笔记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发生了怎样的变化。将研究与推广相结合，一项国际重新调查努力将与eBird的公民科学专家合作，比较1933年至1955年间最初抽样的300个地点的鸟类物种。对15个历史收藏点进行的联合国际实地重新调查将提供专家收集的补充实地数据。这项研究的结果将为大陆范围内鸟类基因组和分布格局的变化提供前所未有的细节。这项工作的所有方面都将与一个本科生研究项目相结合，该项目将用最新的基因组学设备和技术培训下一代生物学家，这些设备和技术非常适合公共和私营部门。研究人员将评估20种栖息地在现代发生了戏剧性变化的局部鸟类的DNA变化。对历史和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由于当地灌木栖息地转变为灌溉农田而经历了范围扩大，以及高原针叶林物种是否由于生境碎片化而经历了遗传多样性的丧失。DNA将使用数千个保守的基因组锚来提取，这些锚可以捕获和恢复在较老的博物馆标本中发现的受损DNA。稍后的分析将把这些较小的片段缝合成较大的片段，以便对种群之间的多样性和连接性进行基因组分析，并进行时间点之间的比较。使用下一代测序技术的基因组研究，特别是使用保守元件，尚未研究脊椎动物如此浅层次的进化。这项研究将阐明保守的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作用。

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.