Molecular Evolution and Bioinformatics Unit, Department of Biology, National University of Ireland Maynooth, County Kildare, Ireland.
Biol Direct. 2011 Aug 23;6:41. doi: 10.1186/1745-6150-6-41.
It is becoming increasingly difficult to reconcile the observed extent of horizontal gene transfers with the central metaphor of a great tree uniting all evolving entities on the planet. In this manuscript we describe the Public Goods Hypothesis and show that it is appropriate in order to describe biological evolution on the planet. According to this hypothesis, nucleotide sequences (genes, promoters, exons, etc.) are simply seen as goods, passed from organism to organism through both vertical and horizontal transfer. Public goods sequences are defined by having the properties of being largely non-excludable (no organism can be effectively prevented from accessing these sequences) and non-rival (while such a sequence is being used by one organism it is also available for use by another organism). The universal nature of genetic systems ensures that such non-excludable sequences exist and non-excludability explains why we see a myriad of genes in different combinations in sequenced genomes. There are three features of the public goods hypothesis. Firstly, segments of DNA are seen as public goods, available for all organisms to integrate into their genomes. Secondly, we expect the evolution of mechanisms for DNA sharing and of defense mechanisms against DNA intrusion in genomes. Thirdly, we expect that we do not see a global tree-like pattern. Instead, we expect local tree-like patterns to emerge from the combination of a commonage of genes and vertical inheritance of genomes by cell division. Indeed, while genes are theoretically public goods, in reality, some genes are excludable, particularly, though not only, when they have variant genetic codes or behave as coalition or club goods, available for all organisms of a coalition to integrate into their genomes, and non-rival within the club. We view the Tree of Life hypothesis as a regionalized instance of the Public Goods hypothesis, just like classical mechanics and euclidean geometry are seen as regionalized instances of quantum mechanics and Riemannian geometry respectively. We argue for this change using an axiomatic approach that shows that the Public Goods hypothesis is a better accommodation of the observed data than the Tree of Life hypothesis.
将观察到的水平基因转移的程度与将地球上所有进化实体统一在一个大树下的核心隐喻相协调变得越来越困难。在本文中，我们描述了公共物品假说，并表明它适合描述地球上的生物进化。根据这一假说，核苷酸序列（基因、启动子、外显子等）仅仅被视为商品，通过垂直和水平转移从一个生物体传递到另一个生物体。公共物品序列的定义是具有以下属性：很大程度上不可排除（没有生物体可以有效地阻止其访问这些序列）和非竞争性（当一个生物体使用这样的序列时，另一个生物体也可以使用它）。遗传系统的普遍性确保了存在不可排除的序列，不可排除性解释了为什么我们在测序基因组中看到了无数不同组合的基因。公共物品假说有三个特点。首先，DNA 片段被视为公共物品，可供所有生物体整合到其基因组中。其次，我们期望出现 DNA 共享机制和基因组中 DNA 入侵防御机制的进化。第三，我们预计不会看到一个全球树状模式。相反，我们预计会出现局部树状模式，这些模式是由基因的共同起源和通过细胞分裂的基因组垂直遗传的组合产生的。事实上，虽然基因在理论上是公共物品，但在现实中，一些基因是可排除的，特别是当它们具有变体遗传密码或表现为联盟或俱乐部物品时，可以供联盟中的所有生物体整合到它们的基因组中，并且在俱乐部内部是无竞争的。我们将生命之树假说视为公共物品假说的区域化实例，就像经典力学和欧几里得几何分别被视为量子力学和黎曼几何的区域化实例一样。我们使用公理方法来证明这一变化，该方法表明，公共物品假说比生命之树假说更能适应观察到的数据。
