English
 
User Manual Privacy Policy Disclaimer Contact us
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT
 
 
DownloadE-Mail
  Rooting phylogenies and the tree of life while minimizing Ad Hoc and auxiliary assumptions

Caetano-Anollés, G., Nasir, A., Kim, K. M., & Caetano-Anollés, D. (2018). Rooting phylogenies and the tree of life while minimizing Ad Hoc and auxiliary assumptions. Evolutionary Bioinformatics, 14, 1-21. doi:10.1177/1176934318805101.

Item is

Basic

show hide
Item Permalink: http://hdl.handle.net/21.11116/0000-0002-6C03-2 Version Permalink: http://hdl.handle.net/21.11116/0000-0002-6C04-1
Genre: Journal Article

Files

show Files
hide Files
:
1176934318805101.pdf (Publisher version), 975KB
Name:
1176934318805101.pdf
Description:
-
Visibility:
Public
MIME-Type / Checksum:
application/pdf / [MD5]
Technical Metadata:
Copyright Date:
-
Copyright Info:
-

Creators

show
hide
 Creators:
Caetano-Anollés, Gustavo, Author
Nasir, Arshan, Author
Kim, Kyung Mo, Author
Caetano-Anollés, Derek1, Author              
Affiliations:
1Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_1445635              

Content

show
hide
Free keywords: Character polarization; phylogenetic analysis; protein structure; proteomes; outgroup comparison; Weston rule; ontogenetic criterion; UNIVERSAL TREE; MOLECULAR FUNCTIONS; MAXIMUM-LIKELIHOOD; EVOLUTIONARY TREES; PROTEIN WORLD; PARSIMONY; GENE; NETWORKS; DOMAINS; CHARACTERS
 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.

Details

show
hide
Language(s): eng - English
 Dates: 2018-01-252018-09-052018-10-202018-10
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: -
 Identifiers: DOI: 10.1177/1176934318805101
 Degree: -

Event

show

Legal Case

show

Project information

show hide
Project name : National Science Foundation
Grant ID : OISE-1132791
Funding program : -
Funding organization : -
Project name : United States Department of Agriculture
Grant ID : ILLU-802-909
Funding program : -
Funding organization : -
Project name : United States Department of Agriculture
Grant ID : ILLU-483-625
Funding program : -
Funding organization : -
Project name : Higher Education Commission Start-up Research Grant Program
Grant ID : 21-519/SRGP/RD/HEC/2014
Funding program : -
Funding organization : -
Project name : Collaborative Genome Program - Ministry of Oceans and Fisheries, Korea
Grant ID : 20140428
Funding program : -
Funding organization : -
Project name : NSF postdoctoral fellowship
Grant ID : 1523549
Funding program : -
Funding organization : -

Source 1

show
hide
Title: Evolutionary Bioinformatics
Source Genre: Journal
 Creator(s):
Affiliations:
Publ. Info: London, England : Sage Publications Ltd.
Pages: 1176934318805101 Volume / Issue: 14 Sequence Number: - Start / End Page: 1 - 21 Identifier: Other: 1176-9343
CoNE: https://pure.mpg.de/cone/journals/resource/1176-9343