Tree thinking for all biology: the problem with reading phylogenies as ladders of progress

Abstract

Phylogenies are increasingly prominent across all of biology, especially as DNA sequencing makes more and more trees available. However, their utility is compromised by widespread misconceptions about what phylogenies can tell us, and improved "tree thinking" is crucial. The most-serious problem comes from reading trees as ladders from "left to right"--many biologists assume that species-poor lineages that appear "early branching" or "basal" are ancestral--we call this the "primitive lineage fallacy". This mistake causes misleading inferences about changes in individual characteristics and leads to misrepresentation of the evolutionary process. The problem can be rectified by considering that modern phylogenies of present-day species and genes show relationships among evolutionary cousins. Emphasizing that these are extant entities in the 21(st) century will help correct inferences about ancestral characteristics, and will enable us to leave behind 19(th) century notions about the ladder of progress driving evolution.

Ancestral traits and specializations in the flowers of the basal grade of living angiosperms

“…In terms of parsimony, if the sister group of all other members of a larger clade (such as Amborella in trees where it is sister to all other angiosperms) has features that differ from those in the rest of the larger clade, and outgroup information is lacking, it is equivocal whether these features are apomorphic or plesiomorphic for the larger clade (such as angiosperms as a whole). In other words, "basal" does not necessarily mean "primitive" (Crisp & Cook, 2005;Omland & al., 2008). However, if features are shared by a series of two or more clades that branch off successively below the bulk of the larger clade to which they belong, making up a basal grade (such as Amborella, Nymphaeales, and Austrobaileyales in Fig.…”

Why coelacanths are not ‘living fossils’

“…However, the phylogenetic paradigm, also called 'tree-thinking' point of view [49], has encountered difficulties in spreading outside the community of evolutionary researchers [50,51]. The most common misunderstanding of tree-thinking and evolution is the remnant misinterpretation of biodiversity as a 'ladder of progress' [52], a concept that originated in the preevolutionist idea of scala naturae that came from antiquity as it appeared in Figure 1. Comparison of extant and selected extinct actinistians, commonly known as coelacanths.…”

Where Do I Come From? Using Student’s Mitochondrial DNA to Teach About Phylogeny, Molecular Clocks, and Population Genetics

“…Using the freeware program MEGA (Tamura et al 2011) to examine the world mtDNA tree, students can understand the concept of roots and clades, different ways to represent a tree, and how rotating internal nodes does not change the tree topology or evolutionary history. With these kinds of exercises, students can get around the common misconceptions of the "great chain of Being" (Gregory 2008) in which living species (in this case, individuals) are ranked lowest or highest and the "main line and side tracks" misconception (Gregory 2008;Omland et al 2008) where evolutionary history is interpreted as a progressive process with a superior distinctive "end point" at the end of the main line.…”

“…During the third lab (data analysis and phylogenetic reconstruction), while students were building basic phylogenetic trees and manipulating trees in Mega (Tamura et al 2011;Tamura et al 2007; see "ESM 3"), they should be turning to questions related to "tree-thinking" (Baum et al 2005;Gregory 2008;Omland et al 2008). Our main goal during this discussion was to make students aware of main misconceptions on phylogenetic interpretation and help them understand how patterns of migration (phylogeography) could be acquired from data (students were also provided with copies of Fig.…”