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

了解生命之树中生物之间的进化关系对于了解地球上的生命是如何进化的至关重要。通过解开这些相互关系，从疾病到饮食等生物现象的历史原因和后果就可以被理解。几十年的研究已经揭示了这棵树的许多区域，但仍然对许多关系知之甚少。最近的技术进步使生物学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，这些大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，还有很多有待研究。这个项目将使用这些大的DNA序列数据集来研究链猴灵长类动物进化关系的分支模式，链猴灵长类动物包括高度濒危的马达加斯加狐猴，以及蝾螈蝾螈，蝾螈是一种多样的两栖动物，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是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。这将有助于进化生物学家回答一个重要的问题，即从整个基因组中采集哪些数据是最好的，以正确地推断生命之树中的有机体位置。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，以及现有的教师。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，这项研究将与杜克狐猴中心和北卡罗来纳自然科学博物馆的公共宣传活动联系起来。该研究项目将使用下一代DNA序列技术对大部分链球菌灵长类动物和蝾螈基因组进行测序。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在系统发育重建中使用大量数据集的方法。系统发育重建将集中在那些表现出最近和快速物种辐射模式的群体中，并且包含对系统发育重建有挑战的分支。研究人员将评估基因在正选择下重建困难进化枝的表现。虽然在分子系统发育中通常避免使用选择下的基因，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系统发育信息的理想来源。正选择的基因座将被基因属性标注，从而提供大量的基因本体信息。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是否能更好地恢复系统发育。总的来说，这个项目的结果将为系统发育界提供经验推导的解决方案，如何使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.