NSFDEB-NERC: Integrating Computational, Phenotypic, and Population-Genomic Approaches to Reveal Processes of Cryptic Speciation and Gene Flow in Madagascars Mouse Lemurs

人类和所有其他物种一样，需要一个健康的环境才能茁壮成长，并最终生存下来。生物多样性-在某一特定生境中的各种动植物-是任何环境健康的关键因素。然而，我们看到，生物多样性目前正受到极大的威胁，这主要来自人类的影响，如砍伐森林和气候变化。为了准确衡量这一威胁的性质，科学家必须建立商定的方法，以识别物种的分布和丰度，以及物种形成的机制，即物种形成。这是一项复杂的任务，因为物种形成通常是由生物，地质和气候力量的复杂交叉驱动的。为了应对这一挑战，该项目将使用一种综合方法，结合计算机科学，实地观察和基因组分析，以揭示通过物种形成产生和维持生物多样性的过程。该项目将侧重于马达加斯加的一个地区，那里的生境破碎化正在威胁着独特和不可替代的生物多样性的生存。除了产生关于驱动和界定物种形成过程的重要新知识外，该项目还将包括对不同教育水平的学生进行培训和指导。这项培训对于增强下一代保护科学家的能力至关重要，以便他们能够减轻当今和未来几年世界面临的环境挑战。这项研究的重点是鼠狐猴，这是世界上最小的灵长类动物，是马达加斯加特有的。这些灵长类动物具有特殊的生物学意义，因为它们在形态和生态学上相似，但在遗传上高度不同。物种之间的这种表型相似性和遗传分歧模式已在整个生命树中观察到，通常被称为神秘物种多样性。神秘物种令物种形成生物学家感到困惑，因为它们物种身份的指标对人眼来说是隐藏的，从而挑战了我们准确测量受威胁生物多样性的能力。该项目旨在开发和应用一种新的和可推广的方法来理解鼠狐猴的物种形成机制，以及一般的神秘物种辐射。该项目建立在目前的研究基础上，该研究表明鼠狐猴是高度物种化的，经历了与更新世气候周期一致的谱系多样化的突发事件。该项目的主要成果将是：（1）开发用于确定谱系之间遗传交换的幅度、方向和速率的计算工具;（2）对生态学、新陈代谢和感官交流在抑制物种间繁殖方面的作用有独特的理解;（3）在种间繁殖发生的情况下，该项目将阐明基因组结构在损害杂交个体生殖潜力方面的作用。该研究将利用强大的计算创新来估计不同谱系之间的基因交换模式，跟踪和监测小型夜间哺乳动物的新技术，以及应用长读测序技术生成基因组资源的方法。最终，这项研究将有助于区分自然与人为气候变化的影响，以评估地球生物多样性的健康状况。该奖项反映了NSF的法定使命，并被认为值得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。

Human beings, like all other species, require a healthy environment in order to thrive and, ultimately, survive. Biodiversity — the variety of plants and animals in a given habitat — is the key factor in the health of any environment. We see that biodiversity is presently under extreme threat, however, largely from human impacts such as deforestation and climate change. In order to accurately gauge the nature of that threat, it is essential that scientists establish agreed-upon methods for recognizing the distribution and abundance of species, as well as the mechanism, known as speciation, by which they are formed. This is a complicated task because speciation is usually driven by a complex intersection of biological, geological, and climatological forces. To address this challenge, the project will use an integrated approach that combines computer science, field observation, and genomic analysis to reveal the processes that generate and maintain biodiversity via speciation. The project will focus on an area of Madagascar where habitat fragmentation is threatening the survival of unique and irreplaceable biodiversity. In addition to generating important new knowledge about the processes that drive and delimit speciation, the project will include training and mentorship of students across a range of educational levels. This training is critical for empowering the next generation of conservation scientists so that they can mitigate the environmental challenges that the world faces today and in the years to come.The research focuses on mouse lemurs, which are the world's smallest primates and are unique to Madagascar. These primates are of special biological interest given that they are morphologically and ecologically similar but are genetically highly distinct. This pattern of phenotypic similarity and genetic divergence among species has been observed across the tree of life and is generally referred to as cryptic species diversity. Cryptic species are perplexing to speciation biologists because the indicators of their species identity are hidden to the human eye, thus challenging our ability to accurately measure threatened biodiversity. This project aims to develop and apply a novel and generalizable approach for understanding speciation mechanisms in mouse lemurs specifically, and cryptic species radiations generally. The project builds on current research that indicates that mouse lemurs are highly speciose having experienced episodic bursts of lineage diversification consistent with the climatic cycles of the Pleistocene. Key outcomes of the project will be (1) the development of computational tools for identifying the magnitude, direction, and rate of genetic exchange among lineages, (2) a unique understanding of the roles of ecology, metabolism, and sensory communication for inhibiting reproduction among species, and (3) in those cases where interspecific reproduction occurs, the project will illuminate the role of genomic architecture in compromising the reproductive potential of hybrid individuals. The research will leverage powerful computational innovations for estimating patterns of gene exchange among diverging lineages, new technologies for tracking and monitoring small nocturnal mammals, and methods for applying long-read sequencing technologies for generating genomic resources. Ultimately, this research will help differentiate the effects of natural versus anthropogenic climate change for assessing the health of earth's biodiversity.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.