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

了解生命树中有机体之间的进化关系，对于了解地球上生命是如何进化的至关重要。通过解开这些相互关系，可以理解从疾病到饮食的各种生物现象的历史原因和后果。几十年的研究已经揭示了这棵树的许多区域，但仍然有许多关系鲜为人知。最近的技术进步现在使生物研究人员能够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树中这些复杂的分支模式。然而，关于基因组是如何在树的许多分枝事件中进化的，还有很多需要了解的地方。该项目将使用这些大型DNA序列数据集来研究链状灵长类动物和火蜥蜴的进化关系的分支模式。链状灵长类灵长类动物包含高度濒危的马达加斯加狐猴，火蜥蜴是一种多样化的两栖动物，通常被称为蝾螈。这两个非常不同的生物群体将被用来回答关于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的问题，即从整个基因组中提取哪些数据是最好的采样，以适当地推断生物在生命树中的位置。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职员工。这项研究将为这两个标志性生物的保护规划提供参考。此外，这项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宣传活动联系起来。这项研究项目将使用下一代DNA测序技术对链状灵长类动物和火蜥蜴的大部分基因组进行测序。这些数据将包括数百个处于正选择状态的基因座，以及数百个来自基因组中性进化部分的基因座。对这些数据的分析将探索将海量数据集用于系统发育重建的方法。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群体中，并包含对系统发育重建提出挑战的分支。研究人员将评估基因在正向选择下重建困难分支的表现。虽然分子系统发育学通常避免使用被选择的基因，但这些正选择基因的特性表明，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属性进行标注，从而提供了丰富的基因本体信息。研究人员将评估功能类基因在系统发育重建中的表现，以衡量特定功能类基因在恢复系统发育方面是否更好。总体而言，该项目的结果将为系统发育学界提供经验派生的解决方案，解决如何利用基因组数据来解决具有挑战性的系统发育问题。

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.