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

职业：整合本科生研究、公民科学和博物馆基因组学，探索北美鸟类一个世纪的变化

• 批准号: 1652979
• 负责人: John McCormack
• 金额: $ 78.73万
• 依托单位: Occidental College
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-05-15 至 2025-04-30
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1652979&HistoricalAwards=false
• 关键词: CAREER; Integrating; undergraduate; research; citizen

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.

生命如何应对变化是生物学的关键问题之一。过去的100年见证了地球栖息地的加速变化。人们对物种如何应对这种情况知之甚少，因为通常没有详细的历史记录来记录物种生活的地方或它们过去的样子。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年代北美和中美洲鸟类的无与伦比的博物馆收藏。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，从历史现场记录中获得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发生变化。将研究与外联相结合，一项国际调查将与eBird的公民科学专家合作，对1933年至1955年间最初采样的300个地点的鸟类进行比较。对15个历史收集地点的联合国际实地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尺度上鸟类基因组和分布景观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研究项目相结合，该项目将培养下一代生物学家，使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种主要鸟类的DNA变化，这些鸟类的栖息地在现代发生了巨大变化。将历史样本与现代样本进行比较，将测试北美南部西部沿海低地的物种是否因原生刺灌木栖息地向灌溉农田的转变而经历了范围扩张，以及高地针叶林物种是否因栖息地破碎化而经历了遗传多样性的丧失。DNA提取将使用数千个保守的基因组锚点，这些锚点可以捕获并恢复在博物馆旧标本中发现的受损DNA。随后的分析将把这些小片段拼接成更大的片段，以便对种群之间的多样性和连通性进行基因组分析，并对不同时间点进行比较。使用下一代测序技术的基因组研究，特别是使用保守元素的研究，还没有在如此浅的尺度上研究脊椎动物的进化。这项研究将阐明保守的基因组片段在发现生境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。

项目成果

Museum genomics reveals the speciation history of Dendrortyx wood-partridges in the Mesoamerican highlands

博物馆基因组学揭示了中美洲高地 Dendrortyx 木鹧鸪的物种形成历史

• DOI: 10.1016/j.ympev.2019.03.017
• 发表时间: 2019
• 期刊: Molecular Phylogenetics and Evolution
• 影响因子: 4.1
• 作者: Tsai, Whitney L.E.;Mota-Vargas, Claudio;Rojas-Soto, Octavio;Bhowmik, Ravi;Liang, Emily Y.;Maley, James M.;Zarza, Eugenia;McCormack, John E.
• 通讯作者: McCormack, John E.

Cloudy with a chance of speciation: integrative taxonomy reveals extraordinary divergence within a Mesoamerican cloud forest bird

多云，有可能形成物种：综合分类法揭示了中美洲云林鸟类的非凡分化

• DOI: 10.1093/biolinnean/bly156
• 发表时间: 2018
• 期刊: Biological Journal of the Linnean Society
• 影响因子: 1.9
• 作者: Venkatraman, Madhvi X;Deraad, Devon A;Tsai, Whitney L;Zarza, Eugenia;Zellmer, Amanda J;Maley, James M;Mccormack, John E
• 通讯作者: Mccormack, John E

More than skin and bones: Comparing extraction methods and alternative sources of DNA from avian museum specimens

• DOI: 10.1111/1755-0998.13077
• 发表时间: 2020-09-01
• 期刊: MOLECULAR ECOLOGY RESOURCES
• 影响因子: 7.7
• 作者: Tsai, Whitney L. E.;Schedl, Margaret E.;McCormack, John E.
• 通讯作者: McCormack, John E.