Not just corals and fishes: distribution modelling and management of dark diversity on coral reefs

人类的压力正日益重塑生物圈，给生物多样性和生态系统功能带来可怕的后果（IPBES, 2019）。扭转生物多样性下降和限制环境破坏的全球集体行动一直受到阻碍，因为缺乏强有力的生态变化指标，无法帮助针对脆弱的生态系统和评估政策决定的有效性。然而，使用DNA测序的下一代生物监测方法现在提供了创建强大而快速的生态变化指标的机会（Bohan等人，2017；Dornelas等人，2019）。DNA测序能够快速估计整个生态系统的生物组成和功能属性。它包括从环境样本中大量提取DNA，然后根据通用标记对众多分类群和功能基因进行大规模扩增和鉴定（Leray和Knowlton, 2015； Ransome等人，2017）。这些方法产生了大量的数据，但由于缺乏标准化的分析管道，无法生成用于政策框架的指标，因此仍然受到限制。珊瑚礁提供了一个理想的系统，可以继续发展用于生态系统监测的大量环境DNA分析，并将其应用于循证政策。珊瑚礁特别容易受到许多正在影响所有生态系统的加速全球变化驱动因素的影响，因此提供了未来可能变化幅度的早期指标（Hoegh et al., 2017）。它们受到全球威胁和优先考虑（Wear等人，2016年）-因此确保了公众和政府的强烈关注，它们拥有地球上最大的海洋物种多样性，包括巨大的神秘多样性（Pandolf等人，2003年；Jackson等人，2014年；Hughes等人，2017年）-因此为传统生物监测提供了一个具有挑战性的系统。该项目将与史密森学会全球ARMS计划（https://naturalhistory.si.edu/research/global-arms-program）合作，使用来自隐藏珊瑚礁分类群的大量样本的测序数据来开发全球珊瑚礁的尖端物种分布模型。该项目将：开发工具，从细胞色素c氧化酶亚基I （COI）基因区域和其他分类标记基因中更好地量化多样性，这些基因在全球生物多样性记录中起着关键作用；利用现有方法量化多样性膨胀，并解决当前的局限性，例如假基因对物种划分的影响（Tay等人，2017；Brandt等人，2019），利用跨越太平洋100多个珊瑚礁地点的现有数据集，开发隐礁分类群的联合分布模型，以阐明关键物种的相互作用；利用底栖生物群落数据和卫星衍生数据集，利用模型探索功能和组成生态属性（例如威胁和保护行动）的可能驱动因素的作用；并制定指标，为监测、管理和保护生态系统的政策建议提供信息。

Human pressures are increasingly reshaping the biosphere with dire consequences for biodiversity and ecosystem functioning (IPBES, 2019). Collective global action to reverse declines in biodiversity and limit environmental damage have been hindered by a lack of robust indicators of ecological change that can help target vulnerable ecosystems and evaluate the effectiveness of policy decisions. However, next-generation biomonitoring approaches using DNA sequencing now provide the opportunity to create a powerful and rapid indicator of ecological change (Bohan et al., 2017; Dornelas et al., 2019). DNA sequencing enables rapid estimates of the biological composition and functional attributes of whole ecosystems. It consists of the bulk extraction of DNA from environmental samples, followed by the mass amplification and identification of a multitude of taxa, and functional genes based on universal markers (Leray and Knowlton, 2015; Ransome et al., 2017). These approaches produce enormous quantities of data but remain limited by the lack of standardised analytical pipelines that can generate metrics for use in policy frameworks. Coral reefs provide an ideal system in which to continue development of bulk environmental DNA analysis for ecosystem monitoring, and its application to evidence-based policy. Coral reefs are exceptionally vulnerable to many of the accelerating global drivers of change which are impacting all ecosystems - so providing an early indicator of the magnitude of future change possible (Hoegh et al., 2017). They are globally threatened and prioritised (Wear et al., 2016) - so ensuring strong public and government attention, and they harbour the greatest diversity of marine species on the planet, including vast cryptic diversity (Pandolf et al., 2003; Jackson et al., 2014; Hughes et al., 2017) - so providing a challenging system for traditional biomonitoring. This project will use sequencing data from bulk samples of cryptic reef taxa to develop cutting-edge species distribution models across global reefs in collaboration with the Smithsonian Institute Global ARMS Program (https://naturalhistory.si.edu/research/global-arms-program) the project will: develop tools to better quantify diversity from the cytochrome c oxidase subunit I (COI) gene region, and other taxonomic marker genes, which play pivotal roles in the global effort to document biodiversity; quantify the inflation of diversity using available methods and tackle current limitations, such as the influence of pseudogenes on species delimitation (Tay et al., 2017; Brandt et al., 2019) develop joint distribution models of cryptic reef taxa to elucidate key species interactions, using an existing dataset that spans more than 100 reef sites across the Pacific; use models to explore the role of possible drivers of functional and compositional ecological attributes (e.g. threats and conservation actions) using benthic community data and satellite-derived datasets; and develop metrics to inform policy recommendations for the monitoring, management and conservation of ecosystems.