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

合作研究：使用当地血统检测推断非模式生物的混合历史

• 批准号: 1754451
• 负责人: Beth Shapiro
• 金额: $ 51.55万
• 依托单位: University of California-Santa Cruz
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-06-01 至 2023-05-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1754451&HistoricalAwards=false
• 关键词: Collaborative; Research; Inferring; admixture; history

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.

当地质、气候或其他事件导致最近分化的物种彼此重新引入时会发生什么？如果它们进化出的遗传差异不大，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、几乎无关紧要的现象，现在已经在各种各样的物种对中被记录下来，包括棕熊/北极熊、狗/狼、牛/野牛，甚至人/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存活和可生育的，这一点通过跟踪这些物种对之间的遗传交换得到了证明。这些过去的杂交事件中的每一个都可以被认为是一次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转移的基因的工具。该工具的应用将侧重于过去的杂交对特别重要的两个物种对。牛和野牛是20世纪初牧场主故意杂交的，因此大多数野牛携带奶牛基因。棕熊和北极熊过去有过几次杂交，而且这种情况还在继续发生。对这些物种对的分析将揭示哪些基因不能跨物种移动，哪些不能。这些信息将是理解任何感兴趣的物种对未来杂交的程度和后果的关键。通过重点关注加州金熊和加州科学院的相关教育项目，将向公众、学生和职前教师进行宣传。新的灵活的祖先推断工具将能够定位导入的基因组区域，即使只有低覆盖率的DNA序列数据可用。该工具将纳入复杂的人口统计学场景，如多个混合脉冲，并将精确定位基因组中具有潜在进化意义的区域，这些区域具有高频或没有混合祖先的优点。将这一工具应用于具有已知混合历史的两个物种对，将为物种形成和局部适应过程提供新的见解，有可能为试图限制目标保护种群的混合祖先的管理做法提供参考。此外，该工具将满足对改进的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理的宝贵工具。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

项目成果

A detailed life history of a pleistocene steppe bison (Bison priscus) skeleton unearthed in Arctic Alaska

• DOI: 10.1016/j.quascirev.2020.106578
• 发表时间: 2020-12-01
• 期刊: QUATERNARY SCIENCE REVIEWS
• 影响因子: 4
• 作者: Funck, Juliette;Heintzman, Peter D.;Wooller, Matthew J.
• 通讯作者: Wooller, Matthew J.

Glacial ice supports a distinct and undocumented polar bear subpopulation persisting in late 21st-century sea-ice conditions

• DOI: 10.1126/science.abk2793
• 发表时间: 2022-06-17
• 期刊: SCIENCE
• 影响因子: 56.9
• 作者: Laidre, Kristin L.;Supple, Megan A.;Shapiro, Beth
• 通讯作者: Shapiro, Beth

Dire wolves were the last of an ancient New World canid lineage

• DOI: 10.1038/s41586-020-03082-x
• 发表时间: 2021-01
• 期刊: Nature
• 影响因子: 64.8
• 作者: Angela R. Perri;Kieren J. Mitchell;A. Mouton;Sandra Álvarez-Carretero;A. Hulme-Beaman;J. Haile;A. Jamieson;J. Meachen;Audrey T. Lin;B. Schubert;C. Ameen;E. Antipina;P. Bover;Selina Brace;Alberto Carmagnini;Christian Carøe;J. A. Samaniego Castruita;J. Chatters;K. Dobney;Mario dos Reis;A. Evin;P. Gaubert;Shyam Gopalakrishnan;Graham Gower;Holly Heiniger;K. Helgen;J. Kapp;P. Kosintsev;Anna Linderholm;A. Ozga;Samantha Presslee;Alexander T. Salis;Nedda F. Saremi;Colin J. Shew;K. Skerry;Dmitry E Taranenko;M. Thompson;M. Sablin;Y. Kuzmin;M. Collins;Mikkel-Holger S. Sinding;M. Gilbert;A. Stone;B. Shapiro;B. Van Valkenburgh;R. Wayne;G. Larson;A. Cooper;L. Frantz

Debating Conservation: Developing Critical Thinking Skills in Introductory Biology Classes

辩论保护：在生物学入门课程中培养批判性思维能力

• DOI: 10.24918/cs.2023.1
• 发表时间: 2023
• 期刊: CourseSource
• 作者: Orland, Chloé;Ballare, Kimberly M.;Garcia-Vedrenne, Ana E.;Palacios Mejia, Maura;Wayne, Robert K.;Shapiro, Beth
• 通讯作者: Shapiro, Beth

Million-year-old DNA sheds light on the genomic history of mammoths

• DOI: 10.1038/s41586-021-03224-9
• 发表时间: 2021-02-17
• 期刊: NATURE
• 影响因子: 64.8
• 作者: van der Valk, Tom;Pecnerova, Patricia;Dalen, Love
• 通讯作者: Dalen, Love