The unbearable uncertainty of panarthropod relationships.

Phylogeny royalsocietypublishing.org/journal/rsbl The unbearable uncertainty of panarthropod relationships Ruolin Wu1,2, Davide Pisani1,3 and Philip C. J. Donoghue1,2 1 Research Cite this article: Wu R, Pisani D, Donoghue PCJ. 2023 The unbearable uncertainty of panarthropod relationships. Biol. Lett. 19: 20220497. https://doi.org/10.1098/rsbl.2022.0497 Received: 29 October 2022 Accepted: 1 December 2022 Subject Areas: palaeontology Keywords: Panarthropoda, Tactopoda, Lobopodia, Protarthropoda, phylogeny, topology testing Author for correspondence: Ruolin Wu e-mail: Electronic supplementary material is available online at https://doi.org/10.6084/m9.figshare. c.6340227. Bristol Palaeobiology Group, 2School of Earth Sciences and 3School of Biological Sciences, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, UK RW, 0000-0002-6782-873X; DP, 0000-0003-0949-6682; PCJD, 0000-0003-3116-7463 Panarthropoda, the clade comprising the phyla Onychophora, Tardigrada and Euarthropoda, encompasses the largest majority of animal biodiversity. The relationships among the phyla are contested and resolution is key to understanding the evolutionary assembly of panarthropod bodyplans. Molecular phylogenetic analyses generally support monophyly of Onychophora and Euarthropoda to the exclusion of Tardigrada (Lobopodia hypothesis), which is also supported by some analyses of morphological data. However, analyses of morphological data have also been interpreted to support monophyly of Tardigrada and Euarthropoda to the exclusion of Onychophora (Tactopoda hypothesis). Support has also been found for a clade of Onychophora and Tardigrada that excludes Euarthropoda (Protarthropoda hypothesis). Here we show, using a diversity of phylogenetic inference methods, that morphological datasets cannot discriminate statistically between the Lobopodia, Tactopoda and Protarthropoda hypotheses. Since the relationships among the living clades of panarthropod phyla cannot be discriminated based on morphological data, we call into question the accuracy of morphology-based phylogenies of Panarthropoda that include fossil species and the evolutionary hypotheses based upon them. 1. Introduction Euarthropods (Chelicerata, Myriapoda and Pancrustacea—also referred to as Arthropoda [1]) dominate animal biodiversity but the origin of their bodyplans remains unclear due to the uncertainty of phylogenetic relationships with their nearest living relatives. Euarthropods are members of Ecdysozoa, a clade composed of Scalidophora (Kinorhyncha, Lorcifera and Priapulida), Nematoida (Nematoda and Nematomorpha) and Panarthropoda (Euarthropoda, Onychophora and Tardigrada). Conventionally, molecular [2–6] and some morphological [7–13] phylogenetic analyses have supported the Lobopodia hypothesis (=Arthropoda of [1]) in which Euarthropoda and Onychophora are closest relatives; however, this has been challenged by morphologybased phylogenetic analyses that instead support a sister-group relationship between Euarthropoda and Tardigrada (Tactopoda hypothesis) [10,14–20]. The Protarthropoda hypothesis (a clade of onychophorans and tardigrades) is a third rival that has been supported by both molecular [21,22] and morphological [19,23] data. These competing hypotheses impact upon attempts to resolve the relationships of fossil and living ecdysozoans and, consequently, result in contrasting scenarios for the evolutionary assembly of panarthropod bodyplans. Since support for Tactopoda is rooted in morphology and attempts to resolve bodyplan evolution require integrated phylogenetic analysis of living and fossil taxa, here we explore support for these competing phylogenetic hypotheses © 2023 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited. To determine whether morphological datasets can discriminate among the three competing phylogenetic hypotheses, we analysed morphological datasets that have been used previously to support them [9,13,18] using parsimony, maximum likelihood and Bayesian methods of phylogenetic inference. Within these frameworks, we explored the sensitivity of the optimal topologies to the data on which the hypotheses are based. We did this by constraining the phylogenetic analyses to the Tactopoda, Lobopodia and Protarthropoda hypotheses. We evaluated statistical support for these competing topologies using Kishino-Hasegawa (KH) [24], Shimodaira-Hasegawa (SH) [25], approximately unbiased (AU) tests [26] and Bayes factors (BFs) implemented using the stepping stone method [27] or harmonic mean [28]. These tests determine whether, given the data and the model, phylogenetic hypotheses can be distinguished from one another. This approach is particularly important in morphological and palaeontological datasets because of their comparatively small size relative to molecular datasets and the expectation that decisiveness correlates with dataset size [29]. (a) Datasets A diversity of morphological datasets have been used to resolve panarthropod relationships, but most of these are members of three dataset families, two supporting Lobopodia, the other supporting Tactopoda. As exemplar Lobopodia-supporting datasets, we used Legg et al. [9] (henceforth ’Legg dataset’), updated from Legg et al. [8] and Rota-Stabelli et al. [22], and Aria et al. [9] (henceforth ’Aria dataset’), modified from Aria [25]. The Legg dataset is composed of 311 taxa and 753 characters, including 90 extant euarthropods, two extant onychophorans and two extant tardigrades, plus Caenorhabditis and Priapulus as outgroup taxa. The Aria dataset is composed of 111 taxa and 276 characters, including 36 extant euarthropods, plus Nematoda and Priapulida as the outgroup; the clades of onychophorans and tardigrades are distinguished as ’Onychophora’ and ’Tardigrada’. As an exemplar Tactopoda-supporting dataset, we used Yang et al. [18], updated from Yang et al. [17] and Smith & Ortega-Hernandez [16] (henceforth ’Yang dataset’). The Yang dataset is composed of 50 taxa and 95 characters, including two extant euarthropods, three extant onychophorans and five extant tardigrades, plus Tubiluchus troglodytes as an outgroup. (b) Phylogenetic methods To control for the impact of competing phylogenetic inference methods, we used PAUP* 4.0 [30] to perform parsimony analyses; Iqtree 2.1.3 [31] to perform maximum-likelihood analyses; and MrBayes v. 3.2.7a [32] to perform Bayesian analyses. For parsimony, characters are unordered and equally weighted. For maximum likelihood, we used the Mk + FQ + R3 model for (c) Topology tests and model selection method In an attempt to discriminate among the competing hypotheses, we first conducted unconstrained phylogenetic analyses of the morphological datasets using each of the phylogenetic inference methods. We then u (...truncated)