Population genomics with pedigrees: new approaches for studying contemporary evolution

项目总结 现在有许多生态时间尺度上的表型进化的美丽例子。不过， 技术挑战和有限的时间基因组数据在知识上留下了巨大的差距 基因组水平上的短期进化动态。事实上，衡量自然种群的进化 实时仍然具有挑战性，拥有足够数据来研究当代遗传进化的系统正在 1~2成熟。这项拟议的工作将进化基因组学与长期的人口和系谱数据相结合，以 研究自然种群在短时间尺度上的进化。长期的、基于个人的研究 积累了数以千计的个体的表型、环境和健康数据 多代谱系为研究短期进化是如何发生的提供了独特的机会。特别是， 关于种群谱系的知识，种群中所有个体之间随着时间的推移的关系， 提供直接观察潜在等位基因频率变化的实际过程的能力。《少年派》 开发了佛罗里达灌木鸦(Aphelooma Coulescens)作为进化基因组学模型，通过添加 为一项长达50年的人口统计学研究提供了大量的基因组数据，并与其他团队建立了合作关系 类似的长期数据集。这项研究将沿着谱系追踪整个基因组的遗传，因为它是 在两个经典的研究系统中，几代人的重组使其分崩离析：佛罗里达灌木鸟和 放羊吧。阐明一个人的基因组是如何在其后代中世代分布的 世代为确定个体如何在一生中繁殖变异提供了一个强大的框架 成功预测个体对后代的遗传贡献的变异和等位基因频率的变化 并用于识别与适合度相关的基因组区域。该项目还将开发单倍型丢弃 模拟单倍型在家系中的孟德尔传递以测试短期选择的方法 并改进选择成分方法，以检验不同生活史阶段的选择。应用程序 佛罗里达灌木鸟的这些方法将增加对波动选择和生活的作用的理解- 在维持自然种群适应性遗传变异方面的历史权衡。此外，建议的 工作将通过以下方式量化移民对种群遗传多样性和适应能力的长期贡献 追踪特定移民单倍型在几代人中的频率和适合度影响。开发更多 有效利用血统信息的先进方法释放了前所未有的机会，直接 测量当代进化，研究进化生物学中的许多关键问题。建议数 框架为未来的进化和人类基因组研究勾勒出一种强大的方法。更好的 理解生态时间尺度上的进化为研究生物反应提供了有价值的见解 环境的快速变化，以及药物和农药耐药性的演变。

PROJECT SUMMARY There are now many beautiful examples of phenotypic evolution on ecological timescales. Nevertheless, technological challenges and limited availability of temporal genomic data have left a large gap in knowledge of short-term evolutionary dynamics at the genomic level. Indeed, measuring evolution of natural populations in real-time remains challenging, and systems with sufficient data to study contemporary genetic evolution are rare. The proposed work combines evolutionary genomics with long-term demographic and pedigree data to investigate the evolution of natural populations on short timescales. Long-term, individual-based studies that have accumulated extensive phenotypic, environmental, and fitness data for thousands of individuals on a multigenerational pedigree provide a unique opportunity to study how short-term evolution occurs. In particular, knowledge of the population pedigree, the relationships among all individuals in a population over time, provides the ability to observe directly the actual processes underlying allele frequency change. The PI developed the Florida Scrub-Jay (Aphelocoma coerulescens) as a model for evolutionary genomics by adding substantial genomic data to a 50-year demographic study and formed collaborations with other groups with similar long-term datasets. This study will track the inheritance of the entire genome down the pedigree, as it is broken up by recombination over the generations, in two classic study systems: the Florida Scrub-Jay and the Soay sheep. Elucidating how an individual's genome is distributed across its descendants from generation to generation provides a powerful framework for determining how individual variation in lifetime reproductive success predicts variation in individual genetic contributions to future generations and allele frequency change and for identifying genomic regions associated with fitness. This project will also develop haplotype-dropping methods that simulate Mendelian transmission of haplotypes down the pedigree to test for short-term selection and improve selection component methods to test for selection at different life-history stages. Application of these methods to the Florida Scrub-Jays will increase understanding of the role of fluctuating selection and life- history trade-offs in maintaining adaptive genetic variation in natural populations. Furthermore, the proposed work will quantify the long-term contributions of immigrants to population genetic diversity and fitness by tracing the frequency and fitness impact of specific immigrant haplotypes across generations. Developing more advanced methods that effectively use pedigree information unlocks unprecedented opportunities to directly measure contemporary evolution and study many key questions in evolutionary biology. The proposed framework outlines a powerful approach for future evolutionary and human genomics research. A better understanding of evolution on ecological time scales offers valuable insights to studies of organismal response to rapid environmental change, as well as the evolution of drug and pesticide resistance.