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: 1355000
• 负责人: David Weisrock
• 金额: $ 59.72万
• 依托单位: University of Kentucky Research Foundation
• 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 2020-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1355000&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.

了解生命之树内生物之间的进化关系对于了解地球上生命如何进化至关重要。通过阐明这些相互关系，可以理解从疾病到饮食等生物现象的历史原因和后果。数十年的研究已经揭示了树的许多区域，但仍然对许多关系知之甚少。 最近的技术进步现在允许生物研究人员以前所未有的规模从生物体基因组中收集 DNA 序列数据，这些海量数据有可能解开生命之树中这些困难的分支模式。然而，关于基因组如何在树的许多分支事件中进化，还有很多东西有待了解。该项目将利用这些大型 DNA 序列数据集来研究链球菌灵长类动物（包括高度濒危的马达加斯加狐猴）和蝾螈（一种最常见的两栖类蝾螈）进化关系的分支模式。这两个截然不同的生物群体将被用来回答不同类型的基因如何在分子水平上进化的问题，因为包含它们的谱系随着时间的推移而多样化和分裂。 这将帮助进化生物学家回答一个重要问题：整个基因组中的哪些数据最适合采样，以正确推断生物体在生命之树中的位置。该项目将涉及多个教育层次的参与者，包括本科生、研究生和博士后研究人员以及现有教师。这项研究将为这两种标志性生物的保护规划提供信息。 此外，该研究还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起来。 该研究项目将使用下一代 DNA 测序技术对链球菌灵长类动物和蝾螈的大部分基因组进行测序。 这些数据将包括正选择下的数百个基因座以及来自基因组中性进化部分的数百个基因座。对这些数据的分析将探索如何将大量数据集用于系统发育重建。系统发育重建将集中在那些表现出近期和快速物种辐射模式并包含挑战系统发育重建的分支的群体内。研究人员将评估正选择下基因在重建困难进化枝时的表现。虽然在分子系统发育学中通常避免使用选择基因，但这些正选择位点的特性表明它们可能是最具挑战性的分支的系统发育信息的理想来源。正选择下的基因座将通过基因特性进行注释，从而提供大量的基因本体信息。研究人员将评估基因功能类别在系统发育重建中的表现，以判断特定功能类别的基因是否能够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基于经验的解决方案，以了解如何使用基因组数据来解决具有挑战性的系统发育问题。