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Fossil Calibrations for the Arthropod Tree of Life

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Fossil Calibrations for the Arthropod Tree of Life bioRxiv preprint doi: https://doi.org/10.1101/044859; this version posted March 21, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. FOSSIL CALIBRATIONS FOR THE ARTHROPOD TREE OF LIFE Joanna M. Wolfe1*, Allison C. Daley2,3, David A. Legg3, Gregory D. Edgecombe4 1 Department of Earth, Atmospheric & Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA 2 Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK 3 Oxford University Museum of Natural History, Parks Road, Oxford OX1 3PZ, UK 4 Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK *Corresponding author: [email protected] ABSTRACT Fossil age data and molecular sequences are increasingly combined to establish a timescale for the Tree of Life. Arthropods, as the most species-rich and morphologically disparate animal phylum, have received substantial attention, particularly with regard to questions such as the timing of habitat shifts (e.g., terrestrialisation), genome evolution (e.g., gene family duplication and functional evolution), origins of novel characters and behaviours (e.g., wings and flight, venom, silk), biogeography, rate of diversification (e.g., Cambrian explosion, insect coevolution with angiosperms, evolution of crab body plans), and the evolution of arthropod microbiomes. We present herein a series of rigorously vetted calibration fossils for arthropod evolutionary history, taking into account recently published guidelines for best practice in fossil calibration. These are restricted to Palaeozoic and Mesozoic fossils, no deeper than ordinal taxonomic level, nonetheless resulting in 79 fossil calibrations for 101 clades. This work is especially timely owing to the rapid growth of molecular sequence data and the fact that many included fossils have been described within the last five years. This contribution provides a resource for systematists and other biologists interested in deep-time questions in arthropod evolution. KEYWORDS Arthropods; Fossils; Phylogeny; Divergence times ABBREVIATIONS AMNH, American Museum of Natural History; AMS, Australian Museum, Sydney; AUGD, University of Aberdeen; BGR, Bundesanstalt für Geowissenschaften und Rohstoffe, Berlin; BMNH, The Natural History Museum, London; CNU, Key Laboratory of Insect Evolutionary & Environmental Change, Capital Normal University, Beijing; DE, Ulster Museum, Belfast; ED, Ibaraki University, Mito, Japan; FMNH, Field Museum of Natural History; GMCB, Geological Museum of China, Beijing; GSC, Geological Survey of Canada; IRNSB, Institut Royal des Sciences Naturelles de Belgique, Brussels; KSU, Kent State University; Ld, Musée Fleury, Lodève, France; LWL, Landschaftsverband Westfalen- Lippe-Museum für Naturkunde, Münster; MACN, Museo Argentino de Ciencias Naturales, Buenos Aires; MB, Humboldt Museum für Naturkunde, Berlin; MBA, Humboldt Museum für Naturkunde, Berlin; MCNA, Museo de Ciencias Naturales de Álava, Vitoria-Gasteiz, Álava, Spain; MCZ, Museum of Comparative Zoology, Harvard University; MGSB, Museo Geologico del Seminario de Barcelona; MN, Museu Nacional, Rio de Janeiro; MNHN, Muséum national d'Histoire naturelle, Paris; NHMUK, The Natural History Museum, London; NIGP, Nanjing Institute of Geology and Palaeontology; NMS, National Museum of Scotland; OUM, Oxford University Museum of Natural History; PBM, Palaöbotanik Münster; PIN, Paleontological Institute, Moscow; PRI, Paleontological Research 1 bioRxiv preprint doi: https://doi.org/10.1101/044859; this version posted March 21, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Institution, Ithaca; ROM, Royal Ontario Museum; SM, Sedgwick Museum, University of Cambridge; SMNK, Staatliches Museum für Naturkunde, Karlsruhe; SMNS, Staatliches Museum für Naturkunde, Stuttgart; TsGM, F.N. Chernyshev Central Geologic Prospecting Research Museum, St. Petersburg; UB, University of Bonn; USNM, US National Museum of Natural History, Smithsonian Institution; UWGM, University of Wisconsin Geology Museum; YKLP, Yunnan Key Laboratory for Palaeobiology, Yunnan University; YPM, Yale Peabody Museum; ZPAL, Institute of Paleobiology, Polish Academy of Sciences, Warsaw. 1. Introduction Accurate and precise systematic placement and dating of fossils underpins most efforts to infer a chronology for the Tree of Life. Arthropods, as a whole or in part, have received considerable focus owing to their incredible morphological disparity, species richness, and (relative to much of the Tree of Life) excellent fossil record. A growing number of recent studies have constructed timetrees for arthropods as whole or for major groups therein (e.g., Bellec and Rabet, 2016; Bond et al., 2014; Bracken-Grissom et al., 2014, 2013; Djernæs et al., 2015; Fernández et al., 2015, 2014; Fernández and Giribet, 2015; Garrison et al., 2016; Garwood et al., 2014; Giribet and Edgecombe, 2013; Herrera et al., 2015; Klopfstein et al., 2015; Legendre et al., 2015; Malm et al., 2013; McKenna et al., 2015; Misof et al., 2014; Oakley et al., 2013; Rehm et al., 2011; Schwentner et al., 2013; Song et al., 2015; Sun et al., 2015; Thomas et al., 2013; Tsang et al., 2014; Wahlberg et al., 2013; Wiegmann et al., 2011; Wood et al., 2013; Xu et al., 2015; Zhu et al., 2015). These studies vary in how well they have adhered to best practices for selecting calibration fossils, as many previous calibrations assume that fossil taxonomy accurately reflects phylogeny. Compounding the issue is the expansion of divergence time studies for a variety of comparative questions far beyond systematics and biogeography, including habitat shifts (Letsch et al., 2016; Lins et al., 2012; Rota-Stabelli et al., 2013a; Yang et al., 2013), genome evolution (Cao et al., 2013; Schwarz et al., 2014; Starrett et al., 2013; Wissler et al., 2013; Yuan et al., 2016), origins of novel characters and behaviours (Rainford et al., 2014; Sanggaard et al., 2014; Wheat and Wahlberg, 2013), evolution of parasites and disease (Ibarra-Cerdeña et al., 2014; Palopoli et al., 2014; Rees et al., 2014; Zhou et al., 2014), rate of diversification and its relationship to morphology and ecology (Lee et al., 2013; Wiens et al., 2015), coevolution (Kaltenpoth et al., 2014; Wilson et al., 2013), conservation (Owen et al., 2015), and the use of arthropods as a model for methodological development (O’Reilly et al., 2015; Ronquist et al., 2012; Warnock et al., 2012; Zhang et al., 2015). Recent consensus on best practices for calibration fossil selection requires reference to specific fossil specimen(s), phylogenetic or morphological evidence justifying placement of the fossil, and stratigraphic and/or absolute dating information for the fossil (Parham et al., 2012). The importance of accurate phylogenetic knowledge of calibration fossils is underscored by recent controversies in dating the evolution of insects, where arguments hinge on the classification of particular ‘roachoid’ fossils on the stem lineage of Dictyoptera, with resulting differences on the order of 100 Myr (Kjer et al., 2015; Tong et al., 2015). With the explosion of taxonomic sampling in molecular phylogenies due to improvements in sequencing technology, improving the coverage of fossil calibrations is equally important. Recommendations include, for example, including as many as one fossil per ten extant OTUs for precise ages, with a varied distribution across lineages and clade depth (Bracken-Grissom et al., 2014). As a response, we have compiled an atlas of 79 rigorously scrutinized calibration fossils for 101 key nodes in arthropod phylogeny. These represent four basal ecdysozoan and arthropod clades, 17 chelicerates, 12 myriapods, 30 non-hexapod pancrustaceans, and 38 hexapod clades. Where possible, we favour clade topologies resulting from a phylogenetic analysis of the largest total dataset. If phylogenomic analysis of genomes or transcriptomes has been performed but conflicts 2 bioRxiv preprint doi: https://doi.org/10.1101/044859; this version posted March 21, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. with morphology, a strongly supported molecular result is presented (e.g., putative clades such as Oligostraca that do not yet have identified morphological autapomorphies). If, however, molecular phylogenies have been constructed with few genes (e.g., clades such as Peracarida) or with highly conflicting results (e.g., Arachnida), morphological results are given greater weight. Where relevant, we discuss clade names with respect to NCBI’s GenBank taxonomy (as recommended by the Fossil Calibrations Database: Polly et al., 2015), as this review is intended to be used by molecular biologists who are interested in dating the evolution of arthropod groups. As there are >1.2 million species of arthropods, our calibrations are limited to fossils from the Palaeozoic and Mesozoic. Many extant clades have their oldest fossils in Cenozoic ambers such as the Eocene Baltic amber but are predicted to be vastly older based on fossils
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