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

Abstract

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.

Highly diversified mitochondrial genomes provide new evidence for interordinal relationships in the Arachnida

“…Most orders have an ancient origin dated back to the Carboniferous, Devonian or Silurian periods (Dunlop & Selden, 2009). Interordinal relationships in the Arachnida have been debated for over a century (reviewed by Wheeler & Hayashi, 1998 and Sharma et al., 2021) and researchers have reached little consensus using both morphological (Giribet et al., 2002; Shultz, 2007; Wheeler & Hayashi, 1998) and molecular approaches (Ballesteros & Sharma, 2019; Giribet et al., 2002; Sharma et al., 2014; Wheeler & Hayashi, 1998). The monophyly of Arachnida is controversial, accepted by some arachnologists (Howard et al., 2020; Lozano‐Fernandez et al., 2019; Shultz, 2007), yet rejected by others (reviewed by Sharma et al., 2021).…”

“…Interordinal relationships in the Arachnida have been debated for over a century (reviewed by Wheeler & Hayashi, 1998 and Sharma et al., 2021) and researchers have reached little consensus using both morphological (Giribet et al., 2002; Shultz, 2007; Wheeler & Hayashi, 1998) and molecular approaches (Ballesteros & Sharma, 2019; Giribet et al., 2002; Sharma et al., 2014; Wheeler & Hayashi, 1998). The monophyly of Arachnida is controversial, accepted by some arachnologists (Howard et al., 2020; Lozano‐Fernandez et al., 2019; Shultz, 2007), yet rejected by others (reviewed by Sharma et al., 2021). Furthermore, the monophyly of subclass Acari is unresolved (reviewed by Dunlop & Alberti, 2007), even by multiple phylogenomic efforts, recovered by analyses using genome sequences (Lozano‐Fernandez et al., 2019) or rejected by genome and transcriptome sequences (Ballesteros & Sharma, 2019; Ontano et al., 2021, 2022; Regier et al., 2010; Richart et al., 2016; Sharma et al., 2014).…”

Mitogenomics supports the monophyly of Mysidacea and Peracarida (Malacostraca)

“…However, the present analysis still suffers from taxon sampling of Tanaidacea and Cumacea. It also shows that the criticisms of morphological data sets expressed by Sharma et al (2021) -primarily referred to Arachnida-are certainly unjustified (at least) with regard to Malacostraca.…”

Phylogenomic, Biogeographic, and Evolutionary Research Trends in Arachnology

“…In a paper titled "What Is an "Arachnid"? Consensus, Consilience, and Confirmation Bias in the Phylogenetics of Chelicerata" [1], Prashant Sharma and colleagues review the systematics of the group we refer to as arachnids. They focus on the evidence for arachnid monophyly; it seems to be weak at best and seems to have been repeatedly confirmed through biased interpretations of hypotheses and the evidence in their support.…”