What Is an “Arachnid”? Consensus, Consilience, and Confirmation Bias in the Phylogenetics of Chelicerata

The basal phylogeny of Chelicerata is one of the opaquest parts of the animal Tree of Life, defying resolution despite application of thousands of loci and millions of sites. At the forefront of the debate over chelicerate relationships is the monophyly of Arachnida, which has been refuted by most a...

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Autores principales:	Prashant P. Sharma, Jesús A. Ballesteros, Carlos E. Santibáñez-López
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	Arthropoda circular reasoning investigator bias paleontology phylogenomics Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/3d05b801c9294d65940fe538392b82a5
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spelling	oai:doaj.org-article:3d05b801c9294d65940fe538392b82a52021-11-25T17:22:45ZWhat Is an “Arachnid”? Consensus, Consilience, and Confirmation Bias in the Phylogenetics of Chelicerata10.3390/d131105681424-2818https://doaj.org/article/3d05b801c9294d65940fe538392b82a52021-11-01T00:00:00Zhttps://www.mdpi.com/1424-2818/13/11/568https://doaj.org/toc/1424-2818The basal phylogeny of Chelicerata is one of the opaquest parts of the animal Tree of Life, defying resolution despite application of thousands of loci and millions of sites. At the forefront of the debate over chelicerate relationships is the monophyly of Arachnida, which has been refuted by most analyses of molecular sequence data. A number of phylogenomic datasets have suggested that Xiphosura (horseshoe crabs) are derived arachnids, refuting the traditional understanding of arachnid monophyly. This result is regarded as controversial, not least by paleontologists and morphologists, due to the widespread perception that arachnid monophyly is unambiguously supported by morphological data. Moreover, some molecular datasets have been able to recover arachnid monophyly, galvanizing the belief that any result that challenges arachnid monophyly is artefactual. Here, we explore the problems of distinguishing phylogenetic signal from noise through a series of in silico experiments, focusing on datasets that have recently supported arachnid monophyly. We assess the claim that filtering by saturation rate is a valid criterion for recovering Arachnida. We demonstrate that neither saturation rate, nor the ability to assemble a molecular phylogenetic dataset supporting a given outcome with maximal nodal support, is a guarantor of phylogenetic accuracy. Separately, we review empirical morphological phylogenetic datasets to examine characters supporting Arachnida and the downstream implication of a single colonization of terrestrial habitats. We show that morphological support of arachnid monophyly is contingent upon a small number of ambiguous or incorrectly coded characters, most of these tautologically linked to adaptation to terrestrial habitats.Prashant P. SharmaJesús A. BallesterosCarlos E. Santibáñez-LópezMDPI AGarticleArthropodacircular reasoninginvestigator biaspaleontologyphylogenomicsBiology (General)QH301-705.5ENDiversity, Vol 13, Iss 568, p 568 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Arthropoda circular reasoning investigator bias paleontology phylogenomics Biology (General) QH301-705.5
spellingShingle	Arthropoda circular reasoning investigator bias paleontology phylogenomics Biology (General) QH301-705.5 Prashant P. Sharma Jesús A. Ballesteros Carlos E. Santibáñez-López What Is an “Arachnid”? Consensus, Consilience, and Confirmation Bias in the Phylogenetics of Chelicerata
description	The basal phylogeny of Chelicerata is one of the opaquest parts of the animal Tree of Life, defying resolution despite application of thousands of loci and millions of sites. At the forefront of the debate over chelicerate relationships is the monophyly of Arachnida, which has been refuted by most analyses of molecular sequence data. A number of phylogenomic datasets have suggested that Xiphosura (horseshoe crabs) are derived arachnids, refuting the traditional understanding of arachnid monophyly. This result is regarded as controversial, not least by paleontologists and morphologists, due to the widespread perception that arachnid monophyly is unambiguously supported by morphological data. Moreover, some molecular datasets have been able to recover arachnid monophyly, galvanizing the belief that any result that challenges arachnid monophyly is artefactual. Here, we explore the problems of distinguishing phylogenetic signal from noise through a series of in silico experiments, focusing on datasets that have recently supported arachnid monophyly. We assess the claim that filtering by saturation rate is a valid criterion for recovering Arachnida. We demonstrate that neither saturation rate, nor the ability to assemble a molecular phylogenetic dataset supporting a given outcome with maximal nodal support, is a guarantor of phylogenetic accuracy. Separately, we review empirical morphological phylogenetic datasets to examine characters supporting Arachnida and the downstream implication of a single colonization of terrestrial habitats. We show that morphological support of arachnid monophyly is contingent upon a small number of ambiguous or incorrectly coded characters, most of these tautologically linked to adaptation to terrestrial habitats.
format	article
author	Prashant P. Sharma Jesús A. Ballesteros Carlos E. Santibáñez-López
author_facet	Prashant P. Sharma Jesús A. Ballesteros Carlos E. Santibáñez-López
author_sort	Prashant P. Sharma
title	What Is an “Arachnid”? Consensus, Consilience, and Confirmation Bias in the Phylogenetics of Chelicerata
title_short	What Is an “Arachnid”? Consensus, Consilience, and Confirmation Bias in the Phylogenetics of Chelicerata
title_full	What Is an “Arachnid”? Consensus, Consilience, and Confirmation Bias in the Phylogenetics of Chelicerata
title_fullStr	What Is an “Arachnid”? Consensus, Consilience, and Confirmation Bias in the Phylogenetics of Chelicerata
title_full_unstemmed	What Is an “Arachnid”? Consensus, Consilience, and Confirmation Bias in the Phylogenetics of Chelicerata
title_sort	what is an “arachnid”? consensus, consilience, and confirmation bias in the phylogenetics of chelicerata
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/3d05b801c9294d65940fe538392b82a5
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What Is an “Arachnid”? Consensus, Consilience, and Confirmation Bias in the Phylogenetics of Chelicerata

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