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相互重新引入时会发生什么？如果它们进化的遗传差异不是很大，这两个物种可能交配并产生杂交后代。物种间杂交曾经被认为是一种罕见且大多无关紧要的现象，现在已在多种物种对中得到记录，包括棕熊/北极熊、狗/狼、牛/野牛，甚至人类/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且可繁殖的，正如通过跟踪这些物种对之间的遗传交换所证明的那样。过去的每一次杂交事件都可以被视为跨越被认为是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基因转移的工具。该工具的应用将集中于过去的杂交特别重要的两个物种对。 1900 年代初，牧场主有意将奶牛和野牛杂交，因此大多数野牛都带有奶牛基因。棕熊和北极熊过去曾发生过几次杂交，而且这种情况仍在继续发生。对这些物种对的分析将揭示哪些基因难以跨物种移动，哪些基因则不然。这些信息对于了解任何感兴趣的物种对未来杂交的程度和后果至关重要。将通过关注加州金熊奖和加州科学院的相关教育项目来向公众、学生和职前教师进行宣传。即使只有低覆盖率的 DNA 序列数据可用，新的灵活祖先推断工具也能够定位渗入的基因组区域。该工具将结合复杂的人口统计场景，例如混合的多个脉冲，并将查明由于频率高或缺乏混合祖先而具有潜在进化意义的基因组区域。该工具应用于具有已知混合历史的两个物种对，将为物种形成和当地适应过程提供新的见解，并有可能为旨在限制目标种群中混合血统的管理实践提供信息。此外，该工具将满足对改进信号检测方法以推断进化过程日益增长的需求，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，并被认为值得支持通过使用基金会的智力优点和更广泛的影响审查标准进行评估。

项目成果

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

阿拉斯加北极地区出土的更新世草原野牛（Bison priscus）骨骼的详细生活史

• DOI: 10.1016/j.quascirev.2020.106578
• 发表时间: 2020-12
• 期刊: Quaternary Science Reviews
• 影响因子: 4
• 作者: Funck, Juliette;Heintzman, Peter D.;Murray, Gemma G.R.;Shapiro, Beth;McKinney, Holly;Huchet, Jean;Bigelow, Nancy;Druckenmiller, Patrick;Wooller, Matthew J.
• 通讯作者: Wooller, Matthew J.

Ancient Hybridization with an Unknown Population Facilitated High-Altitude Adaptation of Canids

古代与未知种群的杂交促进了犬科动物的高海拔适应

• DOI: 10.1093/molbev/msaa113
• 发表时间: 2020-05
• 期刊: Molecular Biology and Evolution
• 影响因子: 10.7
• 作者: Wang, Ming;Wang, Sheng;Li, Yan;Jhala, Yadvendradev;Thakur, Mukesh;Otecko, Newton O;Si, Jing;Chen, Hong;Shapiro, Beth;Nielsen, Rasmus;et al
• 通讯作者: et al

An annotated draft genome for the Andean bear, Tremarctos ornatus

安第斯熊 Tremarctos ornatus 的注释基因组草图

• DOI: 10.1093/jhered/esab021
• 发表时间: 2021-04
• 期刊: Journal of Heredity
• 影响因子: 3.1
• 作者: Saremi, Nedda F;Oppenheimer, Jonas;Vollmers, Christopher;O’Connell, Brendan;Milne, Shard A;Byrne, Ashley;Yu, Li;Ryder, Oliver A;Green, Richard E;Shapiro, Beth
• 通讯作者: Shapiro, Beth

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

百万年前的 DNA 揭示了猛犸象的基因组历史

• DOI: 10.1038/s41586-021-03224-9
• 发表时间: 2020-08-11
• 期刊: Nature
• 影响因子: 64.8
• 作者: Tom van der Valk;P. Pečnerová;D. Díez;Anders Bergström;Jonas Oppenheimer;S. Hartmann;G. Xenikoudakis;Jessica A. Thomas;Marianne Dehasque;Ekin Sağlıcan;Fatma Rabia Fidan;I. Barnes;Shanlin Liu;M. Somel;P. Heintzman;P. Nikolskiy;B. Shapiro;P. Skoglund;M. Hofreiter;A. Lister;A. Götherström;L. Dalén
• 通讯作者: L. Dalén

A polar bear paleogenome reveals extensive ancient gene flow from polar bears into brown bears

北极熊古基因组揭示了从北极熊到棕熊的广泛古代基因流

• DOI: 10.1038/s41559-022-01753-8
• 发表时间: 2022-06-16
• 期刊: Nature Ecology & Evolution
• 影响因子: 16.8
• 作者: Ming;Gemma G. R. Murray;D. Mann;P. Groves;A. Vershinina;Megan A. Supple;J. Kapp;Russell B. Corbett;S. Crump;I. Stirling;K. Laidre;M. Kunz;L. Dalén;R. Green;B. Shapiro
• 通讯作者: B. Shapiro