SG: Inferring phylogenies under ancestral population structure

SG：推断祖先种群结构下的系统发育

• 批准号: 1949268
• 负责人: Michael DeGiorgio
• 金额: $ 16.31万
• 依托单位: Florida Atlantic University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-08-01 至 2023-02-28
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1949268&HistoricalAwards=false
• 关键词: SG; Inferring; phylogenies; under; ancestral

Accurate estimation of population and species relationships from genetic data is essential for understanding the evolutionary history of everything from influenza viruses to humans. However, as genetic datasets rapidly grow in size due to technological advances, a number of hurdles arise when trying to estimate such relationships. Though many methods have been developed to address these challenges, one source of error that is not accounted for by available methods is non-random mating in ancient populations. Because individuals generally do not mate randomly, and because population and species relationships are used to answer diverse research questions from basic science to epidemiology, addressing this source of error is critical. The primary goal of this project is to design statistical methods for estimating population and species relationships that account for non-random mating in ancient populations, thereby increasing the accuracy of estimation. Moreover, it is of high priority that both the scientific community and the public are engaged in the advances of this project. To this end, the researchers will make all approaches developed during this project freely available for use by the wider scientific community. Also, the researchers will work with K-12 students in hands-on activities for learning why and how to build population and species relationships through the Penn State Science-U program. Finally, the researchers will engage indigenous peoples as part of the Summer internship for INdigenous peoples in Genomics (SING) Workshop which examines the use of genomic data in science and society.Ancestral structure, which has been uncovered in many diverse species, can skew gene tree frequencies, thereby hindering the performance of methods for estimating species trees. This research seeks to develop novel likelihood methods that can infer phylogenies under such scenarios, and apply these methods to test evolutionary hypotheses about ancestral structure and gene flow in several model and non-model organisms. The model organisms considered will be mouse, yeast, and mosquito, for which previous studies have observed skewed gene tree frequencies that were attributed to gene flow through hybridization, but may instead be the result of ancestral structure. The researchers will also apply these methods to a non-model coral system, which is of particular interest because morphological and fossil data provide evidence of hybridization, suggesting that this system may exhibit skewed gene tree frequencies. Application to these systems will serve to elucidate and refine knowledge of the events shaping the evolution of these lineages.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.

根据遗传数据准确估计种群和物种关系，对于理解从流感病毒到人类的一切事物的进化史至关重要。然而，由于技术进步，基因数据集的规模迅速扩大，在试图估计这种关系时，会出现一些障碍。虽然已经开发了许多方法来解决这些挑战，但现有方法无法解释的一个错误来源是古代种群中的非随机交配。因为个体通常不是随机交配的，而且种群和物种关系被用来回答从基础科学到流行病学的各种研究问题，解决这个错误的来源是至关重要的。这个项目的主要目标是设计统计方法来估计种群和物种关系，以说明古代种群的非随机交配，从而提高估计的准确性。此外，科学界和公众都参与这一项目的进展，这是高度优先的。为此，研究人员将免费提供在该项目期间开发的所有方法，供更广泛的科学界使用。此外，研究人员将在实践活动中与K-12的学生合作，学习为什么以及如何通过宾夕法尼亚州立大学的科学-U计划建立种群和物种关系。最后，研究人员将把土著人民作为夏季基因组学实习(SING)讲习班的一部分，该讲习班审查基因组数据在科学和社会中的使用。在许多不同物种中发现的原始结构可能会扭曲基因树的频率，从而阻碍估计物种树的方法的性能。这项研究寻求开发新的似然方法，可以在这种情况下推断系统发育，并应用这些方法来测试几个模式生物和非模式生物中关于祖先结构和基因流动的进化假说。被考虑的模式生物将是老鼠、酵母和蚊子，以前的研究已经观察到基因树频率的扭曲，这些基因树频率被归因于通过杂交的基因流动，但可能是祖先结构的结果。研究人员还将把这些方法应用于非模型珊瑚系统，这一点特别令人感兴趣，因为形态和化石数据提供了杂交的证据，表明该系统可能显示出基因树频率的扭曲。对这些系统的应用将有助于阐明和完善对塑造这些线的演变的事件的知识。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

Spatiotemporal fluctuations of population structure in the Americas revealed by a meta‐analysis of the first decade of archaeogenomes

考古基因组第一个十年的荟萃分析揭示了美洲人口结构的时空波动

• DOI: 10.1002/ajpa.24673
• 发表时间: 2022
• 期刊: American Journal of Biological Anthropology
• 作者: Campelo dos Santos, Andre Luiz;Lavalle Sullasi, Henry Socrates;Gokcumen, Omer;Lindo, John;DeGiorgio, Michael
• 通讯作者: DeGiorgio, Michael

Maximum Likelihood Estimation of Species Trees from Gene Trees in the Presence of Ancestral Population Structure

• DOI: 10.1093/gbe/evaa022
• 发表时间: 2020-02-01
• 期刊: GENOME BIOLOGY AND EVOLUTION
• 影响因子: 3.3
• 作者: Koch，Hillary;DeGiorgio，Michael
• 通讯作者: DeGiorgio，Michael

VolcanoFinder: Genomic scans for adaptive introgression

• DOI: 10.1371/journal.pgen.1008867
• 发表时间: 2019-07
• 期刊: PLoS Genetics
• 影响因子: 4.5
• 作者: D. Setter;S. Mousset;Xiaoheng Cheng;R. Nielsen;Michael Degiorgio;J. Hermisson

Learning the properties of adaptive regions with functional data analysis

通过功能数据分析学习自适应区域的属性

• DOI: 10.1371/journal.pgen.1008896
• 发表时间: 2020
• 期刊: PLOS Genetics
• 影响因子: 4.5
• 作者: Mughal, Mehreen R.;Koch, Hillary;Huang, Jinguo;Chiaromonte, Francesca;DeGiorgio, Michael
• 通讯作者: DeGiorgio, Michael