Is the tree of life the best metaphor, model or heuristic for phylogenetics?

Mindell (2013) [henceforth simply “Mindell”] has provided a claim that the Tree of Life (ToL) is still useful in phylogenetics as a model, a metaphor, and a heuristic. Here I examine all three of these claims. Mindell noted that what biologists have long discussed as the ToL is in fact reticulate, and always has been. He therefore objected to simplistic declarations that there is no ToL, in the sense of no recoverable phylogenetic history for recognized taxa. Mindell argued that a “tree with reticulations” is still basically a tree, and that the ToL therefore continues to be a useful metaphor, model, and heuristic for phylogenetics. Here, I argue an alternative point of view, in which a “tree with reticulations” is a network, and that therefore a network will be a better metaphor, model, and heuristic for phylogenetics, in the sense that it will be more inclusive and more powerful. This distinction between tree and network in the face of reticulations is not a semantic one. The tree met...

Mindell (2013) [以下简称“Mindell”] 提出，生命之树（Tree of Life, ToL）作为模型、隐喻与启发式方法，在系统发育学领域仍具有应用价值。本文将对该作者提出的这三类主张逐一展开检视。
Mindell指出，长期以来生物学家所讨论的生命之树，本质上具备网状演化特征，且始终如此。因此，他驳斥了“不存在已识别类群的可恢复系统发育历史”这一简化论断，即反对“不存在生命之树”的简单化声明。
Mindell主张，“带有网状结构的树”本质上仍属于树的范畴，因此生命之树作为系统发育学的隐喻、模型与启发式方法，依然具备实用价值。
本文则提出不同观点：“带有网状结构的树”实为演化网络，相较之下，演化网络作为系统发育学的隐喻、模型与启发式方法，具备更强的包容性与解释力，是更为合适的研究框架。
面对网状演化现象时，树与网络的区分并非语义层面的文字游戏。