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生命之树历史树的树状结构。

The treeness of the tree of historical trees of life.

机构信息

UMR 7205 CNRS-MNHN-SU-EPHE « Institut de Systématique, Evolution et Biodiversité », département « Origines & Évolution », Muséum National d'Histoire Naturelle, Paris, France.

Musée d'Histoire Naturelle du Havre, Place du vieux marché, Le Havre, France.

出版信息

PLoS One. 2020 Jan 15;15(1):e0226567. doi: 10.1371/journal.pone.0226567. eCollection 2020.

DOI:10.1371/journal.pone.0226567
PMID:31940355
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6961905/
Abstract

This paper compares and categorizes historical ideas about trees showing relationships among biological entities. The hierarchical structure of a tree is used to test the global consistency of similarities among these ideas; in other words we assess the "treeness" of the tree of historical trees. The collected data are figures and ideas about trees showing relationships among biological entities published or drawn by naturalists from 1555 to 2012. They are coded into a matrix of 235 historical trees and 141 descriptive attributes. From the most parsimonious "tree" of historical trees, treeness is measured by consistency index, retention index and homoplasy excess ratio. This tree is used to create sets or categories of trees, or to study the circulation of ideas. From an unrooted network of historical trees, treeness is measured by the delta-score. This unrooted network is used to measure and visualize treeness. The two approaches show a rather good treeness of the data, with respectively a retention idex of 0.83 and homoplasy excess ratio of 0.74, on one hand, and a delta-score of 0.26 on the other hand. It is interpreted as due to vertical transmission, i.e. an inheritance of shared ideas about biological trees among authors. This tree of trees is then used to test categories previously made. For instance, cladists and gradists are « paraphyletic ». The branches of this tree of trees suggest new categories of tree-thinkers that could have been overlooked by historians or systematists.

摘要

本文比较和分类了历史上关于树木的观念，展示了生物实体之间的关系。树的层次结构用于检验这些观念之间相似性的整体一致性；换句话说，我们评估了历史树木之树的“树状结构”。收集的数据是 1555 年至 2012 年间由自然主义者发表或绘制的关于树木的图形和观念，展示了生物实体之间的关系。这些数据被编码为一个包含 235 棵历史树木和 141 个描述性属性的矩阵。从最简约的“历史树木之树”中，通过一致性指数、保留指数和同形过剩比来衡量树状结构。这棵树被用于创建树木的集合或类别，或研究观念的传播。从历史树木的无根网络中，通过 delta 分数来衡量树状结构。这个无根网络用于测量和可视化树状结构。这两种方法都显示了数据具有相当好的树状结构，分别为保留指数 0.83 和同形过剩比 0.74，另一方面，delta 分数为 0.26。这被解释为由于垂直传播，即作者之间对生物树的共同观念的继承。然后，使用这棵树木之树来检验之前创建的类别。例如，分支分类学家和渐变论者是“并系的”。这棵树木之树的分支暗示了新的树木思维者类别，这些类别可能被历史学家或系统分类学家忽视了。

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