Improved phylogenetic tools for gene content data

改进的基因内容数据系统发育工具

基本信息

  • 批准号:
    BB/E019005/1
  • 负责人:
  • 金额:
    $ 12.06万
  • 依托单位:
  • 依托单位国家:
    英国
  • 项目类别:
    Research Grant
  • 财政年份:
    2007
  • 资助国家:
    英国
  • 起止时间:
    2007 至 无数据
  • 项目状态:
    已结题

项目摘要

The traditional approach to constructing an evolutionary tree from molecular data is to obtain the sequence of nucleotides or amino acids that makes up a single gene, and build a tree that explains the differences in these sequences among species. Since the mid-90s, a large number of prokaryotic organisms (bacteria and archaea: single-celled organisms without a nucleus) have had their genomes sequenced. These data have suggested that the traditional approach is unreliable for two reasons. First, the sequence of a single gene may be quite short, so that statistical variability may limit the accuracy of a tree derived from a single gene. Second, different genes may genuinely have different evolutionary histories, because genes can be transferred between prokaryotic organisms, even when they are not closely related. An alternative approach exists. Genes can be rapidly gained and lost from the genome, and it is apparent that closely-related organisms tend to have similar patterns of presence and absence of genes. This suggests that we could use data on the presence and absence of genes to construct an evolutionary tree that reflects the overall history of the genome. There are many existing methods that attempt to do this. However, most either lack a sound theoretical justification and are known to give the wrong answer in some cases, or do not account for variability in the evolutionary process over time. A new method known as conditioned genome reconstruction has a sound theoretical justification and performs well even when the rates of gene gain and loss vary over time. We will develop new statistical methods that widen the range of genomes to which this method can be applied. However, as with most other gene content methods, conditioned genome reconstruction does not perform well for parasitic bacteria. This may be an artefact of the way that databases of gene presence/absence are constructed. We will explore this by comparisons across databases using different methods. Another explanation is that the problem is a consequence of increased loss rates of genes that are unnecessary for parasitic organisms that live inside other cells. For these parasites, many genes that are essential for life in the external environment may suddenly become unimportant and may be lost. This loss could occur independently in unrelated lineages of parasites, resulting in these lineages having similar gene content. We will determine whether this is the case by separately analyzing essential and dispensable sets of genes. Finally, we will determine whether our new methods are really better by simulating large and realistic sets of genome data, and comparing the performance of new and existing methods on these data. This work will increase our understanding of the evolution of whole genomes, and will provide new tools for the construction of evolutionary trees.
从分子数据中构建进化树的传统方法是获得构成单个基因的核苷酸或氨基酸的序列,并建造一棵树,解释了物种之间这些序列的差异。自90年代中期以来,大量的原核生物(细菌和古细菌:没有核的单细胞生物)对其基因组进行了测序。这些数据表明,传统方法是不可靠的,原因有两个。首先,单个基因的序列可能很短,因此统计变异性可能会限制从单个基因得出的树的准确性。其次,不同的基因可能确实具有不同的进化史,因为即使基因不密切相关,也可以在原核生物之间传递基因。存在另一种方法。基因可以从基因组中迅速获得并丢失,很明显,密切相关的生物往往具有相似的存在和不存在基因的模式。这表明我们可以使用有关存在基因的存在的数据来构建反映基因组整体历史的进化树。有许多现有方法试图这样做。但是,大多数人要么缺乏合理的理论理由,因此在某些情况下会给出错误的答案,或者不考虑随着时间的推移进化过程的变异性。一种称为条件基因组重建的新方法具有合理的理论理由,即使基因增益和损失的速率随时间变化,也可以很好地表现。我们将开发新的统计方法,以扩大可以应用此方法的基因组范围。但是,与大多数其他基因含量方法一样,条件基因组重建对寄生细菌的表现不佳。这可能是构建基因存在/不存在数据库的方式的人工制品。我们将使用不同的方法对数据库进行比较来探讨这一点。另一个解释是,问题是基因损失率提高的结果,这对于生活在其他细胞内的寄生生物是不必要的。对于这些寄生虫,许多对外部环境中生命必不可少的基因可能突然变得不重要并可能会丢失。这种损失可能在寄生虫的无关谱系中独立发生,从而导致这些谱系具有相似的基因含量。我们将通过分别分析基本基因集和可支配的基因组来确定这种情况。最后,我们将通过模拟大型基因组数据集,并比较这些数据上的新方法和现有方法的性能来确定我们的新方法是否真的更好。这项工作将增加我们对整个基因组进化的理解,并为建造进化树的建造提供新的工具。

项目成果

期刊论文数量(2)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
On the artefactual parasitic eubacteria clan in conditioned logdet phylogenies: heterotachy and ortholog identification artefacts as explanations.
  • DOI:
    10.1186/1471-2148-10-343
  • 发表时间:
    2010-11-09
  • 期刊:
  • 影响因子:
    3.4
  • 作者:
    Sangaralingam A;Susko E;Bryant D;Spencer M
  • 通讯作者:
    Spencer M
A phylogenetic mixture model for gene family loss in parasitic bacteria.
寄生细菌基因家族丢失的系统发育混合模型。
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Matthew Spencer其他文献

Integrating Theory and Hands-On Practice using Underwater Robotics in a Multidisciplinary Introductory Engineering Course
在多学科入门工程课程中使用水下机器人将理论与实践相结合
  • DOI:
    10.18260/1-2--28561
  • 发表时间:
    2017
  • 期刊:
  • 影响因子:
    0
  • 作者:
    Nancy K. Lape;L. Bassman;Christopher Clark;A. Dato;Angela M. Lee;Matthew Spencer;E. Spjut;L. Blake
  • 通讯作者:
    L. Blake
A Board and Projects for an FPGA/Microcontroller-Based Embedded Systems Lab
基于 FPGA/微控制器的嵌入式系统实验室的电路板和项目
Erasing a Gender Gap in Performance in a Multidisciplinary Introductory Engineering Course
消除多学科工程入门课程中的性别差距
Implementation of Competency-Based Learning in a Laboratory-Focused Analog Design Course
在以实验室为重点的模拟设计课程中实施基于能力的学习
Dynamic ensemble approach for estimating organic carbon using computational intelligence
使用计算智能估算有机碳的动态集成方法

Matthew Spencer的其他文献

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{{ truncateString('Matthew Spencer', 18)}}的其他基金

Scaling Trust: An Anthropology of Cyber Security (Renewal)
扩展信任:网络安全人类学(续订)
  • 批准号:
    MR/X023338/1
  • 财政年份:
    2024
  • 资助金额:
    $ 12.06万
  • 项目类别:
    Fellowship
Scaling Trust: An Anthropology of Cyber Security
扩大信任:网络安全人类学
  • 批准号:
    MR/S037373/1
  • 财政年份:
    2019
  • 资助金额:
    $ 12.06万
  • 项目类别:
    Fellowship
Dynamics of community composition
群落组成的动态
  • 批准号:
    NE/K00297X/1
  • 财政年份:
    2013
  • 资助金额:
    $ 12.06万
  • 项目类别:
    Research Grant
Collaborative Research: Continued Study of Physical Properties of the WAIS Divide Deep Core
合作研究:继续研究 WAIS 鸿沟深核的物理特性
  • 批准号:
    1043313
  • 财政年份:
    2011
  • 资助金额:
    $ 12.06万
  • 项目类别:
    Continuing Grant
Collaborative Research: Combined Physical Property Measurements at Siple Dome
合作研究:Siple Dome 的综合物理特性测量
  • 批准号:
    0917509
  • 财政年份:
    2008
  • 资助金额:
    $ 12.06万
  • 项目类别:
    Standard Grant
Collaborative Research: Combined Physical Property Measurements at Siple Dome
合作研究:Siple Dome 的综合物理特性测量
  • 批准号:
    0440447
  • 财政年份:
    2005
  • 资助金额:
    $ 12.06万
  • 项目类别:
    Standard Grant

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