Am Nat. 2019 Jun;193(6):755-772. doi: 10.1086/703055. Epub 2019 Apr 23.
The comparative method has long been a fundamental exploratory tool in evolutionary biology, but this venerable approach was revolutionized in 1985, when Felsenstein published "Phylogenies and the Comparative Method" in . This article forced comparative biologists to start thinking phylogenetically when conducting statistical analyses of correlated trait evolution rather than simply applying conventional statistical methods that ignore evolutionary relationships. It did so by introducing a novel analytical method (phylogenetically "independent contrasts") that required a phylogenetic topology with branch lengths and that assumed a Brownian motion model of trait evolution. Independent contrasts enabled comparative biologists to avoid the statistical dilemma of nonindependence of species values, arising from shared ancestry, but came at the cost of needing a detailed phylogeny and of accepting a specific model of character change. Nevertheless, this article not only revitalized comparative biology but even encouraged studies aimed at estimating phylogenies. Felsenstein's characteristically lucid and concise statement of the problem (illustrated with powerful graphics), coupled with an oncoming flood of new molecular data and techniques for estimating phylogenies, led Felsenstein's 1985 article to become the second most cited article in the history of this journal. Here we present a personal review of comparative biology before, during, and after Joe's article. For historical context, we append a perspective written by Joe himself that describes how his article evolved, unedited transcripts of reviews of his submitted manuscript, and a guide to some nontrivial calculations. These additional materials help emphasize that the process of science does not always occur gradually or predictably.
比较方法长期以来一直是进化生物学中的基本探索工具，但这种古老的方法在 1985 年发生了革命性的变化，当时 Felsenstein 在《. 中发表了“系统发育和比较方法”。这篇文章迫使比较生物学家在对相关性状进化进行统计分析时开始从系统发育角度思考问题，而不是简单地应用忽略进化关系的传统统计方法。它通过引入一种新颖的分析方法（系统发育“独立对比”）来实现这一点，该方法需要具有分支长度的系统发育拓扑结构，并假设性状进化的布朗运动模型。独立对比使比较生物学家能够避免由于共同祖先而导致物种值的非独立性的统计困境，但代价是需要详细的系统发育，并且需要接受特定的性状变化模型。尽管如此，这篇文章不仅使比较生物学焕发生机，甚至鼓励了旨在估计系统发育的研究。Felsenstein 对问题的清晰简洁的陈述（用强大的图形说明），再加上大量新的分子数据和估计系统发育的技术的到来，使得 Felsenstein 在 1985 年的文章成为该期刊历史上被引用第二多的文章。在这里，我们在 Joe 的文章之前、期间和之后展示了个人对比较生物学的回顾。为了历史背景，我们附上了 Joe 自己撰写的一篇观点文章，描述了他的文章是如何演变的，他提交的手稿的未经编辑的评论记录，以及一些非平凡计算的指南。这些附加材料有助于强调科学的过程并不总是逐渐或可预测地发生。
