信息理论、进化创新与可进化性。
Information theory, evolutionary innovations and evolvability.
机构信息
Institute of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland
Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
出版信息
Philos Trans R Soc Lond B Biol Sci. 2017 Dec 5;372(1735). doi: 10.1098/rstb.2016.0416.
Abstract
How difficult is it to 'discover' an evolutionary adaptation or innovation? I here suggest that information theory, in combination with high-throughput DNA sequencing, can help answer this question by quantifying a new phenotype's information content. I apply this framework to compute the phenotypic information associated with novel gene regulation and with the ability to use novel carbon sources. The framework can also help quantify how DNA duplications affect evolvability, estimate the complexity of phenotypes and clarify the meaning of 'progress' in Darwinian evolution.This article is part of the themed issue 'Process and pattern in innovations from cells to societies'.
摘要
“发现”一种进化适应或创新有多难？我在这里提出，信息论结合高通量 DNA 测序，可以通过量化新表型的信息含量来帮助回答这个问题。我将这个框架应用于计算与新基因调控和利用新碳源相关的表型信息。该框架还可以帮助量化 DNA 重复如何影响可进化性，估计表型的复杂性，并澄清达尔文进化中“进步”的含义。本文是“从细胞到社会的创新过程和模式”专题的一部分。
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2
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3
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PLoS Comput Biol. 2015 Aug 7;11(8):e1004329. doi: 10.1371/journal.pcbi.1004329. eCollection 2015 Aug.
4
The fitness value of information.信息的适应值。
Oikos. 2010 Feb;119(2):219-230. doi: 10.1111/j.1600-0706.2009.17781.x.
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8
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