Cargando…
Rooting Phylogenies and the Tree of Life While Minimizing Ad Hoc and Auxiliary Assumptions
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, a...
Autores principales: | , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
SAGE Publications
2018
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6196624/ https://www.ncbi.nlm.nih.gov/pubmed/30364468 http://dx.doi.org/10.1177/1176934318805101 |
_version_ | 1783364591003107328 |
---|---|
author | Caetano-Anollés, Gustavo Nasir, Arshan Kim, Kyung Mo Caetano-Anollés, Derek |
author_facet | Caetano-Anollés, Gustavo Nasir, Arshan Kim, Kyung Mo Caetano-Anollés, Derek |
author_sort | Caetano-Anollés, Gustavo |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-6196624 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | SAGE Publications |
record_format | MEDLINE/PubMed |
spelling | pubmed-61966242018-10-24 Rooting Phylogenies and the Tree of Life While Minimizing Ad Hoc and Auxiliary Assumptions Caetano-Anollés, Gustavo Nasir, Arshan Kim, Kyung Mo Caetano-Anollés, Derek Evol Bioinform Online Review 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. SAGE Publications 2018-10-20 /pmc/articles/PMC6196624/ /pubmed/30364468 http://dx.doi.org/10.1177/1176934318805101 Text en © The Author(s) 2018 http://www.creativecommons.org/licenses/by-nc/4.0/ This article is distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 License (http://www.creativecommons.org/licenses/by-nc/4.0/) which permits non-commercial use, reproduction and distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access pages (https://us.sagepub.com/en-us/nam/open-access-at-sage). |
spellingShingle | Review Caetano-Anollés, Gustavo Nasir, Arshan Kim, Kyung Mo Caetano-Anollés, Derek Rooting Phylogenies and the Tree of Life While Minimizing Ad Hoc and Auxiliary Assumptions |
title | Rooting Phylogenies and the Tree of Life While Minimizing Ad Hoc and Auxiliary Assumptions |
title_full | Rooting Phylogenies and the Tree of Life While Minimizing Ad Hoc and Auxiliary Assumptions |
title_fullStr | Rooting Phylogenies and the Tree of Life While Minimizing Ad Hoc and Auxiliary Assumptions |
title_full_unstemmed | Rooting Phylogenies and the Tree of Life While Minimizing Ad Hoc and Auxiliary Assumptions |
title_short | Rooting Phylogenies and the Tree of Life While Minimizing Ad Hoc and Auxiliary Assumptions |
title_sort | rooting phylogenies and the tree of life while minimizing ad hoc and auxiliary assumptions |
topic | Review |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6196624/ https://www.ncbi.nlm.nih.gov/pubmed/30364468 http://dx.doi.org/10.1177/1176934318805101 |
work_keys_str_mv | AT caetanoanollesgustavo rootingphylogeniesandthetreeoflifewhileminimizingadhocandauxiliaryassumptions AT nasirarshan rootingphylogeniesandthetreeoflifewhileminimizingadhocandauxiliaryassumptions AT kimkyungmo rootingphylogeniesandthetreeoflifewhileminimizingadhocandauxiliaryassumptions AT caetanoanollesderek rootingphylogeniesandthetreeoflifewhileminimizingadhocandauxiliaryassumptions |