20220112

Aleta Quinn

doi:10.3998/ptpbio.16039257.0011.017

Abstract

I analyze recent debates between proponents of concatenation versus coalescence in phylogenetic inference. I argue that concatenation is the latest manifestation of a paradigm weaving through phylogenetics that has focused on a successive series of models thought to be justified by the “principle of total evidence.” I analyze the principle of total evidence as the main philosophical strand linking parsimony versus likelihood (1980s), character congruence versus consensus trees (1990s), and concatenation versus coalescence (2000–10s). My hope is to provide a foothold for philosophers to engage with contemporary phylogenetics, in the face of the discipline’s bewildering and rapidly expanding array of computational models. The basic idea of total evidence—include all data that is relevant to an analysis, that has signal with respect to the problem at hand—is extremely attractive at an intuitive level. However, the general intuition is less clear in the case that all relevant data are included in the overall study, but no single method employs the total dataset in one inferential step. Moreover, simulation studies demonstrate that there are cases in which excluding some data, even when that data provides signal, leads to a better result by a particular method. Each of these points is explored through analysis of the historical and contemporary debates.

Highlights

Sterner and Lidgard (2018) urge that philosophers of phylogenetics move beyond the “systematics wars”, referring to the 1960s–80s debates between numerical taxonomists, evolutionary taxonomists, and phylogenetic systematists
My intent is to illuminate the present state of the field of phylogenetics by tracing the use of one particular philosophical argument, “total evidence”, through several distinct scientific debates
I analyze the principle of total evidence as the main philosophical strand linking parsimony versus likelihood (Section 2: Kluge), character congruence versus consensus trees (3: Nixon and Carpenter), and concatenation versus coalescence (4: Gatesy)

Summary

Introduction

Sterner and Lidgard (2018) urge that philosophers of phylogenetics move beyond the “systematics wars”, referring to the 1960s–80s debates between numerical taxonomists, evolutionary taxonomists, and phylogenetic systematists. For example Talavera and Castresana (2007) found that omitting uncertain sections of gene alignments can lead to better inference of phylogenetic trees These uncertain sequences, when analyzed independently, converged on the correct phylogenetic tree when given enough time and data. Coalescence-based methods use the signal provided by discordant gene trees to infer species trees (Liu et al 2015) or to estimate species boundaries (Yang and Rannala 2010; Yang 2015). They suggest (rather unconvincingly) that the particular method of screening sequences would perform better if more realistic models of evolution were applied to the situations in question This issue is not relevant to my arguments, which only require that omitting data in some situations (not all) leads to a better result. I hope that this may prove useful to readers of this special issue, and I welcome comments—philosophers well know how difficult it can be to define basic terms

Kluge on Total Evidence

Nixon and Carpenter on Character Congruence

Gatesy on Hidden Support

Cladists on Parsimony

Supertree methods Taxonomic congruence methods

Literature cited