Abstract
Phylogenetic methods unearth evolutionary history when supported by three starting points of reason: (1) the continuity axiom begs the existence of a “model” of evolutionary change, (2) the singularity axiom defines the historical ground plan (phylogeny) in which biological entities (taxa) evolve, and (3) the memory axiom demands identification of biological attributes (characters) with historical information. Axiom consequences are interlinked, making the retrodiction enterprise an endeavor of reciprocal fulfillment. In particular, establishing direction of evolutionary change (character polarization) roots phylogenies and enables testing the existence of historical memory (homology). Unfortunately, rooting phylogenies, especially the “tree of life,” generally follow narratives instead of integrating empirical and theoretical knowledge of retrodictive exploration. This stems mostly from a focus on molecular sequence analysis and uncertainties about rooting methods. Here, we review available rooting criteria, highlighting the need to minimize both ad hoc and auxiliary assumptions, especially argumentative ad hocness. We show that while the outgroup comparison method has been widely adopted, the generality criterion of nesting and additive phylogenetic change embodied in Weston rule offers the most powerful rooting approach. We also propose a change of focus, from phylogenies that describe the evolution of biological systems to those that describe the evolution of parts of those systems. This weakens violation of character independence, helps formalize the generality criterion of rooting, and provides new ways to study the problem of evolution.
| Original language | English (US) |
|---|---|
| Journal | Evolutionary Bioinformatics |
| Volume | 14 |
| DOIs | |
| State | Published - Oct 1 2018 |
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Keywords
- Character polarization
- Weston rule
- ontogenetic criterion
- outgroup comparison
- phylogenetic analysis
- protein structure
- proteomes
ASJC Scopus subject areas
- Ecology, Evolution, Behavior and Systematics
- Genetics
- Computer Science Applications
Cite this
Rooting Phylogenies and the Tree of Life While Minimizing Ad Hoc and Auxiliary Assumptions. / Caetano-Anolles, Gustavo; Nasir, Arshan; Kim, Kyung Mo; Caetano-Anollés, Derek.
In: Evolutionary Bioinformatics, Vol. 14, 01.10.2018.Research output: Contribution to journal › Review article
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TY - JOUR
T1 - Rooting Phylogenies and the Tree of Life While Minimizing Ad Hoc and Auxiliary Assumptions
AU - Caetano-Anolles, Gustavo
AU - Nasir, Arshan
AU - Kim, Kyung Mo
AU - Caetano-Anollés, Derek
PY - 2018/10/1
Y1 - 2018/10/1
N2 - Phylogenetic methods unearth evolutionary history when supported by three starting points of reason: (1) the continuity axiom begs the existence of a “model” of evolutionary change, (2) the singularity axiom defines the historical ground plan (phylogeny) in which biological entities (taxa) evolve, and (3) the memory axiom demands identification of biological attributes (characters) with historical information. Axiom consequences are interlinked, making the retrodiction enterprise an endeavor of reciprocal fulfillment. In particular, establishing direction of evolutionary change (character polarization) roots phylogenies and enables testing the existence of historical memory (homology). Unfortunately, rooting phylogenies, especially the “tree of life,” generally follow narratives instead of integrating empirical and theoretical knowledge of retrodictive exploration. This stems mostly from a focus on molecular sequence analysis and uncertainties about rooting methods. Here, we review available rooting criteria, highlighting the need to minimize both ad hoc and auxiliary assumptions, especially argumentative ad hocness. We show that while the outgroup comparison method has been widely adopted, the generality criterion of nesting and additive phylogenetic change embodied in Weston rule offers the most powerful rooting approach. We also propose a change of focus, from phylogenies that describe the evolution of biological systems to those that describe the evolution of parts of those systems. This weakens violation of character independence, helps formalize the generality criterion of rooting, and provides new ways to study the problem of evolution.
AB - Phylogenetic methods unearth evolutionary history when supported by three starting points of reason: (1) the continuity axiom begs the existence of a “model” of evolutionary change, (2) the singularity axiom defines the historical ground plan (phylogeny) in which biological entities (taxa) evolve, and (3) the memory axiom demands identification of biological attributes (characters) with historical information. Axiom consequences are interlinked, making the retrodiction enterprise an endeavor of reciprocal fulfillment. In particular, establishing direction of evolutionary change (character polarization) roots phylogenies and enables testing the existence of historical memory (homology). Unfortunately, rooting phylogenies, especially the “tree of life,” generally follow narratives instead of integrating empirical and theoretical knowledge of retrodictive exploration. This stems mostly from a focus on molecular sequence analysis and uncertainties about rooting methods. Here, we review available rooting criteria, highlighting the need to minimize both ad hoc and auxiliary assumptions, especially argumentative ad hocness. We show that while the outgroup comparison method has been widely adopted, the generality criterion of nesting and additive phylogenetic change embodied in Weston rule offers the most powerful rooting approach. We also propose a change of focus, from phylogenies that describe the evolution of biological systems to those that describe the evolution of parts of those systems. This weakens violation of character independence, helps formalize the generality criterion of rooting, and provides new ways to study the problem of evolution.
KW - Character polarization
KW - Weston rule
KW - ontogenetic criterion
KW - outgroup comparison
KW - phylogenetic analysis
KW - protein structure
KW - proteomes
UR - http://www.scopus.com/inward/record.url?scp=85060297414&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85060297414&partnerID=8YFLogxK
U2 - 10.1177/1176934318805101
DO - 10.1177/1176934318805101
M3 - Review article
AN - SCOPUS:85060297414
VL - 14
JO - Evolutionary Bioinformatics
JF - Evolutionary Bioinformatics
SN - 1176-9343
ER -