Collaborative Research: Species tree reconstruction using neutral and non-neutral phylogenomic data.

合作研究：使用中性和非中性系统发育数据重建物种树。

• 批准号: 1354610
• 负责人: Anne Yoder
• 金额: $ 39.05万
• 依托单位: Duke University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-09-15 至 2017-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1354610&HistoricalAwards=false
• 关键词: Collaborative; Research; Species; tree; reconstruction

Understanding the evolutionary relationships among organisms within the Tree of Life is essential for learning how life has evolved on Earth. By unraveling these interrelationships, the historical causes and consequences of biological phenomena ranging from disease to diet can be understood. Decades of research has shed light on many regions of the Tree, but still, many relationships are poorly understood. Recent technological advancements now allow biological researchers to collect DNA sequence data from the genomes of organisms on an unprecedented scale, and these massive data have the potential to untangle these difficult branching patterns in the Tree of Life. However, much remains to be learned about how genomes evolve across the many branching events of the Tree. This project will use these large DNA sequence data sets to study the branching patterns of evolutionary relationships in Strepsirrhine primates, a group that contains the highly endangered lemurs of Madagascar, and salamandrid salamanders, a diverse group of amphibians most commonly known as the newts. These two very different organismal groups will be used to answer questions about how different types of genes evolve at the molecular level as the lineages that contain them diversify and split over time. This will help evolutionary biologists answer the important question of which data from across the genome is best sampled to properly infer the organismal placement in the Tree of Life. This project will involve participants across multiple levels of education, including undergraduate, graduate, and postdoctoral researchers, as well as established faculty. This research will inform conservation planning of these two iconic organisms. Additionally the research will link with public outreach activities at the Duke Lemur Center and the North Carolina Museum of Natural Science. This research project will use next generation DNA sequence technology to sequence large portions of strepsirrhine primates and salamandrid salamanders genomes. These data will include hundreds of loci under positive selection as well as hundreds of loci from neutrally evolving parts of the genome. Analyses of these data will explore the ways in which massive data sets can be used in phylogeny reconstruction. The phylogenetic reconstruction will be focused within groups which have exhibited patterns of recent and rapid species radiations and contain branches that have challenged phylogenetic reconstruction. The researchers will assess the performance of genes under positive selection in reconstructing difficult clades. While the use of genes under selection is something typically avoided in molecular phylogenetics, properties of these positive-selection loci suggest that they may be an ideal source of phylogenetic information for the most challenging of branches. The loci under positive-selection will be annotated by gene properties thereby providing a tremendous wealth of gene ontology information. The researchers will assess the performance of functional classes of genes in phylogeny reconstruction to gauge whether particular functional classes of genes are better at recovering phylogeny. Overall, the results of this project will provide empirically-derived solutions to the phylogenetics community for how a genomic data can be used to solve challenging phylogenetic questions.

了解生命树中生物体之间的进化关系对于学习生命在地球上的发展至关重要。通过揭示这些相互关系，可以理解生物学现象的历史原因和后果，从疾病到饮食不等。数十年的研究已经揭示了树的许多地区，但仍然对许多关系知之甚少。 现在的技术进步现在允许生物学研究人员以前所未有的规模从生物体的基因组中收集DNA序列数据，并且这些大量数据有可能解开生命树中这些困难的分支模式。但是，关于基因组如何在树的许多分支事件中演变而来的尚待了解。该项目将使用这些大型DNA序列数据集来研究链球链球菌灵长类动物中进化关系的分支模式，该小组包含马达加斯加的高度濒危诱捕性，以及Salamandrid Salamanders，Salamandrid Salamanders，这是一群最常见的两栖动物。这两个截然不同的生物基将用于回答有关不同类型基因在分子水平上如何发展的问题，因为包含它们随时间的谱系多样化和分裂。 这将有助于进化生物学家回答一个重要的问题，即最好对整个基因组中的数据进行采样以正确地推断生命树中的生物体位置。该项目将涉及多个教育的参与者，包括本科生，研究生和博士后研究人员以及已建立的教师。这项研究将为这两个标志性生物提供保护计划。 此外，这项研究将与杜克狐猴中心和北卡罗来纳州自然科学博物馆的公共外展活动联系在一起。 该研究项目将使用下一代DNA序列技术来对大部分链球链吡欣灵长类动物和salamandrid salamanders基因组进行测序。 这些数据将包括数百个基因座在正选择下以及数百个基因组的基因座，来自基因组的中性部分。这些数据的分析将探讨可以在系统发育重建中使用大量数据集的方式。系统发育重建将集中在表现出最近和快速物种辐射模式的组中，并包含挑战系统发育重建的分支。研究人员将评估在重建困难进化枝中阳性选择下基因的性能。尽管在分子系统发育学中通常避免了选择基因的使用，但这些正选择基因座的特性表明它们可能是最具挑战性分支的系统发育信息的理想来源。基因选择下的基因座将由基因性质注释，从而提供大量基因本体学信息。研究人员将评估系统发育重建中基因功能类别的性能，以衡量特定的功能类别基因是否更好地恢复系统发育。总体而言，该项目的结果将为系统发育学界提供凭经验衍生的解决方案，以解决基因组数据如何用于解决具有挑战性的系统发育问题。