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无根系统发生网络。

Uprooted Phylogenetic Networks.

机构信息

LIGM (UMR 8049), UPEM, CNRS, ESIEE, ENPC, Université Paris-Est, 77454, Marne-la-Vallée, France.

School of Computing Sciences, University of East Anglia, Norwich, UK.

出版信息

Bull Math Biol. 2017 Sep;79(9):2022-2048. doi: 10.1007/s11538-017-0318-x. Epub 2017 Jul 31.

DOI:10.1007/s11538-017-0318-x
PMID:28762018
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5552900/
Abstract

The need for structures capable of accommodating complex evolutionary signals such as those found in, for example, wheat has fueled research into phylogenetic networks. Such structures generalize the standard model of a phylogenetic tree by also allowing for cycles and have been introduced in rooted and unrooted form. In contrast to phylogenetic trees or their unrooted versions, rooted phylogenetic networks are notoriously difficult to understand. To help alleviate this, recent work on them has also centered on their "uprooted" versions. By focusing on such graphs and the combinatorial concept of a split system which underpins an unrooted phylogenetic network, we show that not only can a so-called (uprooted) 1-nested network N be obtained from the Buneman graph (sometimes also called a median network) associated with the split system [Formula: see text] induced on the set of leaves of N but also that that graph is, in a well-defined sense, optimal. Along the way, we establish the 1-nested analogue of the fundamental "splits equivalence theorem" for phylogenetic trees and characterize maximal circular split systems.

摘要

需要能够容纳复杂进化信号的结构,例如在小麦中发现的那些信号,这推动了系统发育网络的研究。这些结构通过允许循环来概括系统发育树的标准模型,并以有根和无根的形式引入。与系统发育树或其无根版本相比,有根系统发育网络很难理解。为了帮助缓解这一问题,最近对它们的研究也集中在它们的“无根”版本上。通过关注这样的图和支撑无根系统发育网络的组合概念——分裂系统,我们表明,不仅可以从与分裂系统相关的 Buneman 图(有时也称为中值网络)获得所谓的(无根)1-嵌套网络 N,而且该图在一个定义明确的意义上是最优的。一路上,我们建立了系统发育树基本的“分裂等价定理”的 1-嵌套类似物,并描述了最大循环分裂系统。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/459e/5552900/727763603598/11538_2017_318_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/459e/5552900/3abbe1be4a9a/11538_2017_318_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/459e/5552900/5533d57b740c/11538_2017_318_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/459e/5552900/b9bcca79c023/11538_2017_318_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/459e/5552900/4d376a4a7430/11538_2017_318_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/459e/5552900/727763603598/11538_2017_318_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/459e/5552900/3abbe1be4a9a/11538_2017_318_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/459e/5552900/5533d57b740c/11538_2017_318_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/459e/5552900/b9bcca79c023/11538_2017_318_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/459e/5552900/4d376a4a7430/11538_2017_318_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/459e/5552900/727763603598/11538_2017_318_Fig5_HTML.jpg

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本文引用的文献

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On Unrooted and Root-Uncertain Variants of Several Well-Known Phylogenetic Network Problems.关于几个著名系统发育网络问题的无根和根不确定变体
Algorithmica. 2018;80(11):2993-3022. doi: 10.1007/s00453-017-0366-5. Epub 2017 Aug 22.
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Bounds for phylogenetic network space metrics.系统发育网络空间度量的边界。
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Quartets and unrooted phylogenetic networks.四重奏与无根系统发育网络。
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All that glisters is not galled.闪光的未必都是金子。
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