IIBR Informatics: Unlocking the incredible potential for museum specimens to yield DNA

IIBR 信息学：释放博物馆标本产生 DNA 的巨大潜力

• 批准号: 2029955
• 负责人: Christopher Raxworthy
• 金额: $ 77.58万
• 依托单位: American Museum Natural History
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-15 至 2024-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2029955&HistoricalAwards=false
• 关键词: IIBR; Informatics; Unlocking; incredible; potential

Traditional museum specimens (e.g., skins, skeletons, dry- and fluid-preserved specimens), once considered poor sources of DNA, are now becoming recognized as a potential vast biological resource for historical DNA (hDNA), that provide an unparalleled record of biodiversity spanning the last 200 years. In particular, the advent of high-throughput sequencing platforms (using short DNA fragments) now provides a more efficient means of sampling the hDNA genome. However, hDNA’s potential has hardly yet been explored, with current procedures for DNA extraction often relying on approaches tested on few individuals and optimized for specific projects. Consequently, outcomes of most extraction efforts still often lead to unusable sequence data, or otherwise, high sequencing errors, missing data, and/or contamination. This project will develop efficient and open-source protocols for yielding usable genome-scale molecular data from typical traditional museum specimens, based on rigorous comparative experiments of existing and novel DNA extraction methods, using time-series collections at the American Museum of Natural History (AMNH). Broader societal impacts include conservation (using museum specimens to document historical trends in populations and emerging diseases), forensics (providing improved methods for accurate species identification of biological material), and genomics (documenting genetic change over the past 200 years).Project outcomes will determine optimal tissue sources and extraction methods for hDNA, develop improved methods for reverse crosslinking of formalin-fixed DNA, and provide a deeper understanding of how DNA degrades due to exposure to formalin, alcohol, tissue buffers, and archival storage time. This project will also develop new approaches for bioinformatic processing of hDNA, to better detect contamination, evaluate the effects of hDNA on phylogenetic inference, and improve the utility of hDNA in all aspects of comparative biology. The application of reliable bioinformatic processing pipelines produced from this study will scale-up the availability of genetic research resources by at least 100-fold (e.g., at AMNH, 120,000 current DNA tissue samples compared to 20 million biological museum vouchers). The availability of DNA from historical museum specimens will also allow the genetics and epigenetics of extinct species and populations to be studied and provide exciting new opportunities to determine how genetic diversity has changed during the Anthropocene. Results of the project will be provided at https://www.amnh.org/research.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.

传统的博物馆标本（例如，皮肤、骨骼、干燥和液体保存的标本），曾经被认为是DNA的贫乏来源，现在正被认为是历史DNA（hDNA）的潜在巨大生物资源，它提供了过去200年来无与伦比的生物多样性记录。特别是，高通量测序平台（使用短DNA片段）的出现现在提供了一种更有效的方法来采样的hDNA基因组。然而，人类DNA的潜力几乎还没有被探索，目前的DNA提取程序通常依赖于在少数人身上测试并针对特定项目进行优化的方法。因此，大多数提取努力的结果仍然经常导致不可用的序列数据，或者高测序错误、缺失数据和/或污染。该项目将开发有效和开源的协议，用于从典型的传统博物馆标本中产生可用的基因组规模的分子数据，基于现有和新型DNA提取方法的严格比较实验，使用美国自然历史博物馆（AMNH）的时间序列藏品。更广泛的社会影响包括保护（利用博物馆标本记录人口和新出现疾病的历史趋势）、法医学（提供用于生物材料的准确物种鉴定的改进方法）和基因组学（记录过去200年的遗传变化）。项目成果将确定人类DNA的最佳组织来源和提取方法，开发福尔马林固定DNA反向交联的改进方法，并提供了一个更深入的了解如何DNA降解，由于暴露于福尔马林，酒精，组织缓冲液，和档案储存时间。该项目还将开发用于hDNA生物信息学处理的新方法，以更好地检测污染，评估hDNA对系统发育推断的影响，并提高hDNA在比较生物学各个方面的实用性。本研究产生的可靠生物信息处理管道的应用将使遗传研究资源的可用性扩大至少100倍（例如，在AMNH，120，000个当前的DNA组织样本与2000万个生物博物馆代金券相比）。从历史博物馆标本中获得DNA也将使人们能够研究灭绝物种和种群的遗传学和表观遗传学，并为确定人类世期间遗传多样性如何变化提供令人兴奋的新机会。该项目的结果将在www.example.com上提供https://www.amnh.org/research.This奖项反映了NSF的法定使命，并被认为值得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来支持。

项目成果

Widespread reticulate evolution in an adaptive radiation

适应性辐射中广泛的网状进化

• DOI: 10.1093/evolut/qpad011
• 发表时间: 2023
• 期刊: Evolution
• 影响因子: 3.3
• 作者: DeBaun, Dylan;Rabibisoa, Nirhy;Raselimanana, Achille P.;Raxworthy, Christopher J.;Burbrink, Frank T.
• 通讯作者: Burbrink, Frank T.

Phylogenomic Analysis of the Parrots of the World Distinguishes Artifactual from Biological Sources of Gene Tree Discordance

对世界鹦鹉的系统发育分析区分了基因树不一致的人工来源和生物来源

• DOI: 10.1093/sysbio/syac055
• 发表时间: 2022
• 期刊: Systematic Biology
• 影响因子: 6.5
• 作者: Smith, Brian Tilston;Merwin, Jon;Provost, Kaiya L.;Thom, Gregory;Brumfield, Robb T.;Ferreira, Mateus;Mauck, III, William M.;Moyle, Robert G.;Wright, Timothy F.;Joseph, Leo
• 通讯作者: Joseph, Leo

Genomes of the extinct Bachman’s warbler show high divergence and no evidence of admixture with other extant Vermivora warblers

• DOI: 10.1016/j.cub.2023.05.058
• 发表时间: 2023-06
• 期刊: Current Biology
• 影响因子: 9.2
• 作者: Andrew W. Wood;Zachary A. Szpiech;I. Lovette;Brian Tilston Smith;D. P. Toews

Ultraconserved elements-based phylogenomic systematics of the snake superfamily Elapoidea, with the description of a new Afro-Asian family

• DOI: 10.1016/j.ympev.2022.107700
• 发表时间: 2023-01-06
• 期刊: MOLECULAR PHYLOGENETICS AND EVOLUTION
• 影响因子: 4.1
• 作者: Das, Sunandan;Greenbaum, Eli;Merila, Juha
• 通讯作者: Merila, Juha

Changes in parrot diversity after human arrival to the Caribbean

• DOI: 10.1073/pnas.2301128120
• 发表时间: 2023-10-10
• 期刊: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• 影响因子: 11.1
• 作者: Oswald，Jessica A.;Smith，Brian Tilston;LeFebvre，Michelle J.
• 通讯作者: LeFebvre，Michelle J.