Collaborative Research: ABI Innovation: RUI: Quantifying biogeographic history: a novel model-based approach to integrating data from genes, fossils, specimens, and environments

森林生态系统覆盖了美国陆地面积的三分之一，是重要的经济和文化资源。未来的森林管理取决于对其历史动态的了解。例如，在最后一次冰河时代之后，随着环境条件变得更加有利，包括树木在内的许多物种通常向北迁移，导致种群规模和地理范围发生了巨大变化。关于这些转移的基本生物学问题包括：(i)植物如何在种子传播能力有限的情况下跨越很远的距离在新的地点建立起来；（ii）物种作为群落或个体同步传播的程度如何；（iii）哪些物种移动最快，为什么移动；（iv）在最后一个冰河时期物种居住在哪里？传统上，科学家们使用三种类型的数据之一来解决这些问题：博物馆和植物标本馆的标本与当代环境数据相匹配，保存最近和过去变化印记的DNA序列，以及化石记录中物种的存在，包括沉积在湖泊沉积物中的古代花粉。然而，基于单一数据类型的研究并不能完全解决上述问题，这主要是由于缺乏综合的计算方法和基础设施。这项研究将开发方法和软件，首次将三种主要数据类型和现有理论连贯地结合起来，以提供对物种生物地理历史的更全面的理解。每种类型的数据都有不同的优点和缺点；利用每一种方法的优势，可以最大限度地利用有关物种范围变化的全部信息。所开发的方法将提供利用“大数据”所需的基础设施，并使有关物种历史动态的重大长期问题取得科学进展，这将服务于各种科学界。这项工作也符合国家利益，通过促进对自然环境的未来研究来促进繁荣和福利，自然环境是重要的文化和经济资源。通过使用这些新方法获得的知识有助于为自然资源（即森林和草原）和功能生态系统的管理提供信息，并确定对环境压力具有复原力或可能包含有助于物种适应的独特遗传资源的地理区域。这些新的计算方法将在一个开放源代码的、在线的、文档化的、透明的代码开发系统中产生，任何人都可以与之交互，并通过两个强调参与者多样性的互动研讨会进行交互。该项目还将通过在多个教育层面产生更广泛的影响来推进科学教育：1)与一个已建立的K-12教育项目合作，教授生态概念；2)设计一个基于课程的本科生研究体验；3)在两个植物园制作教育视频和展览，总访问量达到200万人次；4)为早期职业科学家和学生提供培训和指导。尽管数据的可靠性和准确性不断提高，第四纪物种范围变化的问题仍然存在激烈的争论。这场争论部分是由于用于重建生物地理历史的主要数据类型（即化石和推断的古植被，当前和后预测的物种分布模型，以及当前和古代基因组数据）的已知的、实质性的局限性和偏见而引起的。从不同的方法推断出的关于范围移动的速度和避难所位置的过去研究的相互矛盾的结果已经减缓了几十年来古生态学的进展。该项目将开发全面的、统计上强大的信息工具，以连贯地整合不同的、迄今为止不相关的数据类型和模型的信息内容，以推断物种的遗传、人口和生物地理历史。这项研究的目的是建立信息基础设施，帮助科学家利用跨越空间和时间的多种来源的信息来(a)更好地估计关键的人口统计学参数，(b)生成冰川后物种分布图，以及(c)解释每种数据类型的不确定性。该框架植根于近似贝叶斯计算，但有附加模块，将建立在最先进的生物地理推断。信息方面的改进将分增加新颖性和数据整合的四个阶段进行，每个阶段都有具体的产出。信息学的进展将通过分析模拟数据和现有的经验数据集来评估计算效率和有效性，这些数据集是针对一种基础树种，绿灰，宾夕法尼亚白蜡树。这项研究将帮助许多领域的科学家从基因组学、环境建模和古数据的方法和数据库的持续复兴中获得最大的收益，以帮助更好地了解过去物种的动态（人口增长率、长距离分散、生物速度等），这在空间和时间分辨率上是以前无法实现的。科学界将通过开源、社区开发和GitHub上的编码，以及两个实践研讨会，参与模型和软件设计。该项目的结果可以在https://github.com/orgs/TIMBERhub.This网站上找到。该奖项反映了美国国家科学基金会的法定使命，并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，被认为值得支持。

Forest ecosystems cover a third of the land area of the United States and are a significant economic and cultural resource. Managing forests for the future depends on knowledge of their historical dynamics. For example, after the last Ice Age many species, including trees, generally moved north as environmental conditions became more favorable, leading to large changes in population size and geographic range. Fundamental biological questions about these shifts include: (i) how do plants establish in new locations across great distances in spite of having limited seed dispersal abilities, (ii) to what degree do species travel synchronously as communities or individually, (iii) which species moved the fastest and why, and (iv) where did species reside during the last Ice Age? Traditionally scientists have used one of three types of data to address these questions: specimens from museums and herbaria matched with contemporary environmental data, DNA sequences that hold imprints of recent and past changes, and species' presence in the fossil record including ancient pollen deposited in lake sediments. However, studies based on single data types have not been able to fully resolve the aforementioned questions, largely due to lack of integrative computational methods and infrastructure. This research will develop methods and software that, for the first time, coherently combine the three main data types and existing theory to provide a more comprehensive understanding of species' biogeographic history. Each type of data has different strengths and weaknesses; utilizing the strengths of each will make best use of the total information on species' range shifts. The methods developed will provide the infrastructure needed to leverage "big data" and enable scientific progress on significant, long-standing questions about species historical dynamics, which will serve a variety of scientific communities. This work also serves the national interest, advancing prosperity and welfare by enabling future studies of natural environments which are an important cultural and economic resource. Knowledge gained by using these new methods can help inform management of natural resources (i.e. forests and grasslands) and functioning ecosystems, and identify geographic regions that are resilient to environmental stress or may contain unique genetic resources to help species adapt. These new computational methods will be produced in an open-source, online, documented, and transparent code development system with which anyone can interact, as well as through two interactive workshops that will emphasize participant diversity. This project will also advance science education through broader impacts at multiple educational levels by i) partnering with an established K-12 educational program to teach ecological concepts, ii) designing a course-based undergraduate research experience, iii) producing educational videos and exhibits at two botanical gardens that collectively reach two million visitors, and iv) providing training and mentoring to early career scientists and students. Despite continued improvements in data reliability and accuracy, questions about Quaternary species range shifts remain hotly debated. This debate is fueled in part by known, substantial limitations and biases of the primary data types used to reconstruct biogeographic history (i.e., fossils and inferred paleo-vegetation, current and hindcast species distribution models, and current and ancient genomic data). Conflicting results from past studies regarding the speed of range shifts and location of refugia inferred from different approaches have slowed progress in paleoecology for decades. This project will develop comprehensive, statistically robust informatic tools to coherently integrate the information content of disparate and heretofore disconnected data types and models for inferring species' genetic, demographic, and biogeographic history. The objective of this research is to build informatic infrastructure that will help scientists leverage information from multiple sources spanning space and time to (a) better estimate key demographic parameters, (b) generate maps of species distributions post-glaciation, and (c) account for uncertainty from each data type. The framework is rooted in Approximate Bayesian Computation but with additional modules that will build on the state-of-the-art in biogeographic inference. The informatic improvements will occur in four stages of increasing novelty and data integration, with specific outputs at each stage. The informatic advances will be evaluated for computational efficiency and effectiveness through analyses of both simulated data and an existing empirical dataset for a foundational tree species, green ash, Fraxinus pennsylvanica. This research will help scientists from many fields make the most benefit from the ongoing renaissance in methods and databases in genomics, environmental modeling, and paleo-data to help achieve better understanding of past species' dynamics (demographic growth rates, long distance dispersal, biotic velocities, etc.) at a spatial and temporal resolution that was previously unachievable. The scientific community will be involved in model and software design via open source, community development and coding on GitHub, and two hands-on workshops. Results from this project can be found online at https://github.com/orgs/TIMBERhub.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.