BIOCOMPLEXITY: Hexapod Phylogenomics - Bringing Phylogenetic Supercomputing to the Masses

[120718]杨百翰大学（Brigham Young University）的一个跨学科研究团队获得了whitinga Biocomplexity in Environment: Genome-Enabled赠款，该团队结合了计算机科学、统计学和系统发育系统学方面的专业知识，以解决进化生物学、基因组学和计算生物学中的三个基本问题。(1)六足动物（昆虫及其相关分类群）之间的主要关系是什么？(2)相对于六足动物的多样性，线粒体基因组进化是如何发生的？(3)我们如何开发快速、并行的计算机算法来重建大型数据集的系统发育关系？为了回答这些问题，研究人员将对六足动物多样性中约2500个物种的12个核基因进行测序，总测序工作为3000万个碱基对。然后，他们将对代表每个六足动物目的主要谱系中的120个线粒体基因组进行测序，以在12个核基因的良好系统发育背景下检查线粒体基因组的进化。这代表了另外180万个核苷酸的序列。并行处理算法将被开发用于大核苷酸序列数据集的计算分析。研究结果将为了解六足动物多样性（对了解农业害虫、病媒等至关重要）、线粒体基因组进化（有助于了解基因重排的功能意义）和系统发育的平行方法提供一个框架。由于系统发育学正在成为研究人类疾病（包括感染和复杂疾病的遗传成分，如癌症和冠状动脉疾病）的工具，因此，根据不断增加的数据集准确、快速地重建系统发育关系的能力是在遗传变化和疾病风险因素之间建立联系的关键。研究人员将让本科生、研究生和博士后参与这项工作的每个阶段，并以出版物和信息网站的形式提供出口。michael Whiting, Keith Crandall, Mark Clement, Quin Snell， David WhitingA被授予杨百翰大学的一个跨学科研究团队，该团队结合了计算机科学，统计学和系统发育系统学方面的专业知识，以解决进化生物学，基因组学和计算生物学中的三个基本问题：1)六足动物（昆虫及其相关分类群）之间的主要关系是什么？2)相对于六足动物的多样性，线粒体基因组进化是如何发生的？3)我们如何开发快速、并行的计算机算法来重建大型数据集的系统发育关系？为了回答这些问题，研究人员将对六足动物多样性中约2500个物种的约12个基因进行测序，总测序工作为3000万碱基对。然后，他们将对大约120个线粒体基因组进行测序，这些线粒体基因组跨越主要谱系，代表每一个六足动物目，在我们已经建立的12个核基因的系统发育背景下，研究线粒体基因组的进化。这代表了另外180万个核苷酸的序列。最后，我们将开发用于核苷酸序列数据计算分析的并行算法。研究结果将为了解六足动物多样性（对了解农业害虫、病媒等至关重要）、线粒体基因组进化（有助于了解基因重排的功能意义）和系统发育的平行方法提供一个框架。由于系统发育学正在成为研究人类疾病（由于感染和复杂疾病的遗传成分，如癌症和冠状动脉疾病）的工具，因此准确和快速地重建系统发育关系的能力是在遗传变化和疾病风险因素之间建立联系的关键。研究人员将让本科生、研究生和博士后参与这项工作的每个阶段，并以出版物和信息网站的形式提供出口。

0120718WhitingA Biocomplexity in the Environment: Genome-Enabled grant has been awarded to an interdisciplinary team of researchers at the Brigham Young University that combines expertise in computer science, statistics, and phylogenetic systematics to address three fundamental questions in evolutionary biology, genomics, and computational biology. (1) What are the major relationships among Hexapods (insects and related taxa)? (2) How has mitochondrial genome evolution occurred relative to Hexapod diversity? (3) How can we develop fast, parallel computer algorithms to reconstruct phylogenetic relationships for large data sets? To answer these questions, the investigators will sequence about 2500 species across hexapod diversity for about 12 nuclear genes representing a total sequencing effort of 30 million base pairs. They will then sequence about 120 mitochondrial genomes across the major lineages representing each of the hexapod orders to examine mitochondrial genome evolution in the context of a well established phylogeny from the 12 nuclear genes. This represents another 1.8 million nucleotides of sequence. Parallel-processing algorithms will be developed for computational analysis of large nucleotide sequence data sets. The results will provide a framework for understanding Hexapod diversity (crucial for understanding agricultural pests, disease vectors, etc.), mitochondrial genome evolution (instrumental in understanding the functional significance of gene rearrangements), and easily available parallel approaches for phylogenetics. Because phylogenetics is becoming an instrumental tool in the study of human disease (both due to infection and the genetic component of complex diseases such as cancer and coronary artery disease), the ability to reconstruct phylogenetic relationships accurately and with great speed for ever-increasing data sets is key to making the link between genetic changes and disease risk factors. The investigators will heavily involve undergraduates, graduate students, and postdoctoral fellows in every phase of this work and provide outlets in the form of publications and informational websites.DEB-0120719Michael Whiting, Keith Crandall, Mark Clement, Quin Snell, David WhitingA grant has been awarded to an interdisciplinary team of researchers at the Brigham Young University that combines expertise in computer science, statistics, and phylogenetic systematics to address three fundamental questions in evolutionary biology, genomics, and computational biology: 1) What are the major relationships among Hexapods (insects and related taxa)? 2) How has mitochondrial genome evolution occurred relative to Hexapod diversity? And 3) how can we develop fast, parallel computer algorithms to reconstruct phylogenetic relationships for large data sets? To answer these questions, the investigators will sequence ~2500 species across hexapod diversity for ~12 genes representing a total sequencing effort of 30 million base pairs. They will then sequence ~120 mitochondrial genomes across the major lineages representing each of the hexapod orders to examine mitochondrial genome evolution in the context of our well established phylogeny from the 12 nuclear genes. This represents another 1.8 million nucleotides of sequence. Finally we will develop parallel algorithms for computational analysis of nucleotide sequence data. The results will provide a framework for understanding Hexapod diversity (crucial for understanding agricultural pests, disease vectors, etc.), mitochondrial genome evolution (instrumental in understanding the functional significance of gene rearrangements), and easily available parallel approaches for phylogenetics. Since phylogenetics is becoming an instrumental tool in the study of human disease (both due to infection and the genetic component of complex diseases such as cancer and coronary artery disease), the ability to reconstruct phylogenetic relationships accurately and with great speed for ever-increasing data sets is key to making the link between genetic changes and disease risk factors. The investigators will heavily involve undergraduates, graduate students, and postdoctoral fellows in every phase of this work and provide outlets in the form of publications and informational websites.