Linquist Stefan, Cottenie Karl, Elliott Tyler A, Saylor Brent, Kremer Stefan C, Gregory T Ryan
Department of Philosophy, University of Guelph, Guelph, Ontario, Canada, N1G 2W1.
Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada, N1G 2W1.
Mol Ecol. 2015 Jul;24(13):3232-42. doi: 10.1111/mec.13219. Epub 2015 Jun 15.
A promising recent development in molecular biology involves viewing the genome as a mini-ecosystem, where genetic elements are compared to organisms and the surrounding cellular and genomic structures are regarded as the local environment. Here, we critically evaluate the prospects of ecological neutral theory (ENT), a popular model in ecology, as it applies at the genomic level. This assessment requires an overview of the controversy surrounding neutral models in community ecology. In particular, we discuss the limitations of using ENT both as an explanation of community dynamics and as a null hypothesis. We then analyse a case study in which ENT has been applied to genomic data. Our central finding is that genetic elements do not conform to the requirements of ENT once its assumptions and limitations are made explicit. We further compare this genome-level application of ENT to two other, more familiar approaches in genomics that rely on neutral mechanisms: Kimura's molecular neutral theory and Lynch's mutational-hazard model. Interestingly, this comparison reveals that there are two distinct concepts of neutrality associated with these models, which we dub 'fitness neutrality' and 'competitive neutrality'. This distinction helps to clarify the various roles for neutral models in genomics, for example in explaining the evolution of genome size.
分子生物学领域最近一项有前景的进展是将基因组视为一个微型生态系统，其中基因元件被比作生物，而周围的细胞和基因组结构被视为局部环境。在此，我们批判性地评估了生态中性理论（ENT）这一生态学中流行模型在基因组层面的应用前景。这种评估需要概述群落生态学中围绕中性模型的争议。特别是，我们讨论了将ENT既用作群落动态解释又用作零假设的局限性。然后我们分析了一个将ENT应用于基因组数据的案例研究。我们的核心发现是，一旦明确了ENT的假设和局限性，基因元件就不符合其要求。我们进一步将ENT在基因组层面的这种应用与基因组学中另外两种更常见的依赖中性机制的方法进行比较：木村的分子中性理论和林奇的突变风险模型。有趣的是，这种比较揭示了与这些模型相关的两种不同的中性概念，我们将其称为“适合度中性”和“竞争中性”。这种区分有助于阐明中性模型在基因组学中的各种作用，例如在解释基因组大小的进化方面。
