Graphical Methods for Visualizing Comparative Data on Phylogenies
Graphical Methods for Visualizing Comparative Data on Phylogenies
复制标题
系统发育比较数据可视化的图形方法
DOI：
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发表时间：
2014
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通讯作者：
L. Revell
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作者：
L. Revell
在过去的三十多年里，系统发育已经成为进化生物学的核心，系统发育比较方法的广度和复杂性的非凡扩展在这种增长中发挥了重要作用。在本章中，我将重点关注一个被忽视的领域：使用图形方法同时表示比较数据和树。由于这个研究领域在理论上非常广泛，我专注于我开发的新方法，或者其他人设计并由我实施的技术，作为我的R基因组软件包的一部分，phytools。我在本章中描述了各种方法，包括可用于映射重建的离散或连续的字符进化树的方法;将系统发育树投影到形态空间的技术;以及在全球或区域地理地图的背景下可视化系统发育的方法。在本章中，我的意图不仅仅是展示我开发的新方法。相反，我也投入了相当大的精力来详细介绍这些方法所需的算法和计算技术，希望本章将成为有兴趣在这一领域建立新的，更先进的方法和方法的研究人员的资源或起点。
Phylogenies have emerged as central in evolutionary biology over the past three decades or more, and an extraordinary expansion in the breadth and sophistication of phylogenetic comparative methods has played a large role in this growth. In this chapter, I focus on a somewhat neglected area: the use of graphical methods to simultaneously represent comparative data and trees. As this research area is theoretically very broad, I have concentrated on new methods developed by me, or techniques devised by others and implemented by me as part of my R phylogenetics package, phytools. I describe a variety of methods in this chapter, including approaches that can be used to map reconstructed discrete or continuous character evolution on trees; techniques for projecting phylogenetic trees into morphospace; and methods for visualizing phylogenies in the context of a global or regional geographic map. In this chapter, my intention is not merely to showcase new methods that I have developed. Rather, I have also dedicated considerable attention to detailing the algorithms and computational techniques required for these approaches with the hope that this chapter will become a resource or jumping-off point for researchers interested in building new, more advanced approaches and methods in this area.