系统地理学的新途径
New Routes to Phylogeography
摘要：
系统地理学方法的目的是从遗传数据中推断迁移趋势和采样谱系的历史。生物地理学的应用是广泛的，在病原体的背景下，包括传播历史的重建和爆发的起源和出现。基于自下而上的群体遗传学模型的系统地理推断在计算上是昂贵的，因此基于离散性状进化的更快的替代方案已经变得流行。在本文中，我们证明了基于离散性状模型的迁移率和根位置的推断是非常不可靠的，并且对有偏抽样非常敏感。为了解决这个问题，我们引入了BASTA（BASTA结构化聚结近似），这是一种在BEAST 2中实现的新方法，它将基于结构化聚结的方法的准确性与处理不仅仅是少数群体所需的计算效率相结合。我们通过调查埃博拉病毒的人畜共患病传播，说明了模型选择不佳对地理分析的潜在严重影响。尽管结构化结合分析正确地推断出连续的人类埃博拉疫情是由大量未抽样的非人类宿主人群传播的，但离散性状分析令人难以置信地得出结论，未被发现的人际传播使病毒在过去四十年中持续存在。随着基因组学在传染病的控制和预防方面发挥越来越重要的作用，地理学推断为传播历史提供强有力的见解至关重要。
英文摘要：
Phylogeographic methods aim to infer migration trends and the history of sampled lineages from genetic data. Applications of phylogeography are broad, and in the context of pathogens include the reconstruction of transmission histories and the origin and emergence of outbreaks. Phylogeographic inference based on bottom-up population genetics models is computationally expensive, and as a result faster alternatives based on the evolution of discrete traits have become popular. In this paper, we show that inference of migration rates and root locations based on discrete trait models is extremely unreliable and sensitive to biased sampling. To address this problem, we introduce BASTA (BAyesian STructured coalescent Approximation), a new approach implemented in BEAST2 that combines the accuracy of methods based on the structured coalescent with the computational efficiency required to handle more than just few populations. We illustrate the potentially severe implications of poor model choice for phylogeographic analyses by investigating the zoonotic transmission of Ebola virus. Whereas the structured coalescent analysis correctly infers that successive human Ebola outbreaks have been seeded by a large unsampled non-human reservoir population, the discrete trait analysis implausibly concludes that undetected human-to-human transmission has allowed the virus to persist over the past four decades. As genomics takes on an increasingly prominent role informing the control and prevention of infectious diseases, it will be vital that phylogeographic inference provides robust insights into transmission history.
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