A pluralistic account of homology: adapting the models to the data.
A pluralistic account of homology: adapting the models to the data.
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DOI：
10.1093/molbev/mst228
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发表时间：
2014-03
影响因子：
10.7
通讯作者：
McInerney JO
中科院分区：
文献类型：
--
作者：
Haggerty LS;Jachiet PA;Hanage WP;Fitzpatrick DA;Lopez P;O'Connell MJ;Pisani D;Wilkinson M;Bapteste E;McInerney JO
定义同源基因在许多进化研究中很重要，但也提出了明显的问题。其中一些问题是概念性的，源于我们对基因如何进化的假设，另一些则是实际问题，取决于现有软件中实现的算法决策。因此，要使同源性研究取得进展，必须同时考虑本体论和认识论问题。特别是，定义同源基因不能仅仅在强树思维的经典假设下解决，根据该假设，基因以垂直下降和发散的严格树状方式进化，并且同源性检测问题主要是方法论的。基因同源性也可以从不同的角度来考虑，即基因作为“公共物品”进化，经历各种渐渗过程。在后一种情况下，定义同源基因就变成了设计适合数据实际复杂性以及这种复杂性如何产生的模型的问题，而不是试图将遗传数据拟合到某种先验的树状进化模型，这种做法不可避免地会导致大量信息的丢失。在这里，我们展示了当通过分析基因经常起源的公共产品思维进化过程来解决这些问题的更根本根源时，如何克服同源性检测方法所提出的问题的重要方面。这种思维承认系统发育和非系统发育的无根或多根网络中具有不同模式的不同类型的同源物。此外，我们将“家族相似性”定义为包括通过中间亲属相关的基因，从而将同源性的概念置于更广泛的进化关系背景中。最后，我们提出了采用这种对同源性和家族关系的多元解释的一些回报，这扩大了进化分析的范围，超出了传统的、但相对狭窄的焦点，而这种焦点是由基因进化的强烈的树形思维观点所允许的。
Defining homologous genes is important in many evolutionary studies but raises obvious issues. Some of these issues are conceptual and stem from our assumptions of how a gene evolves, others are practical, and depend on the algorithmic decisions implemented in existing software. Therefore, to make progress in the study of homology, both ontological and epistemological questions must be considered. In particular, defining homologous genes cannot be solely addressed under the classic assumptions of strong tree thinking, according to which genes evolve in a strictly tree-like fashion of vertical descent and divergence and the problems of homology detection are primarily methodological. Gene homology could also be considered under a different perspective where genes evolve as “public goods,” subjected to various introgressive processes. In this latter case, defining homologous genes becomes a matter of designing models suited to the actual complexity of the data and how such complexity arises, rather than trying to fit genetic data to some a priori tree-like evolutionary model, a practice that inevitably results in the loss of much information. Here we show how important aspects of the problems raised by homology detection methods can be overcome when even more fundamental roots of these problems are addressed by analyzing public goods thinking evolutionary processes through which genes have frequently originated. This kind of thinking acknowledges distinct types of homologs, characterized by distinct patterns, in phylogenetic and nonphylogenetic unrooted or multirooted networks. In addition, we define “family resemblances” to include genes that are related through intermediate relatives, thereby placing notions of homology in the broader context of evolutionary relationships. We conclude by presenting some payoffs of adopting such a pluralistic account of homology and family relationship, which expands the scope of evolutionary analyses beyond the traditional, yet relatively narrow focus allowed by a strong tree-thinking view on gene evolution.
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影响因子：
14.9
作者：
DURET, L;MOUCHIROUD, D;GOUY, M
通讯作者：
GOUY, M
影响因子：
4.3
作者：
Chen X;Zhang J
通讯作者：
Zhang J
DOI：
10.1098/rstb.2009.0040
发表时间：
2009-08-12
影响因子：
6.3
作者：
Dagan, Tal;Martin, William
通讯作者：
Martin, William
DOI：
10.1093/bioinformatics/btp348
发表时间：
2009-08-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Capella-Gutiérrez S;Silla-Martínez JM;Gabaldón T
通讯作者：
Gabaldón T
影响因子：
14.9
作者：
Corpet, F;Servant, F;Kahn, D
通讯作者：
Kahn, D