DOI: 10.5061/dryad.dncjsxm47
title: Data for: Ancient gene linkages support ctenophores as sister to other animals

description: A central question in evolutionary biology is whether sponges or
 ctenophores (comb jellies) are the sister group to all other animals.
 These alternative phylogenetic hypotheses imply different scenarios for
 the evolution of complex neural systems and other animal-specific
 traits1–6. Conventional phylogenetic approaches based on morphological
 characters and increasingly extensive gene sequence collections have not
 been able to definitively answer this question7–11. Here we develop
 chromosome-scale gene linkage, also known as synteny, as a novel
 phylogenetic character for resolving this question12. We report new
 chromosome-scale genomes for a ctenophore and two marine sponges, and for
 three unicellular relatives of animals (a choanoflagellate, a filasterean
 amoeba, and an ichthyosporean) that serve as outgroups for phylogenetic
 analysis. Remarkably, we find ancient syntenies that are conserved between
 animals and their close unicellular relatives. Ctenophores and unicellular
 eukaryotes share ancestral metazoan patterns while sponges, bilaterians,
 and cnidarians share derived chromosomal rearrangements. Conserved
 syntenic characters unite sponges with bilaterians, cnidarians, and
 placozoans in a monophyletic clade to the exclusion of ctenophores,
 placing ctenophores as the sister group to all other animals. The patterns
 of synteny shared by sponges, bilaterians, and cnidarians are the result
 of rare and irreversible chromosome fusion-and-mixing events that provide
 robust and unambiguous phylogenetic support for the ctenophore-sister
 hypothesis. These findings provide a new framework for resolving deep,
 recalcitrant phylogenetic problems and have implications for our
 understanding of animal evolution. 1. Ryan, J. F. et al. The genome of the
 ctenophore Mnemiopsis leidyi and its implications for cell type evolution.
 Science 342, 1242592 (2013). 2. Halanych, K. M. The ctenophore lineage is
 older than sponges? That cannot be right! Or can it? J. Exp. Biol. 218,
 592–597 (2015). 3. Jékely, G., Paps, J. & Nielsen, C. The
 phylogenetic position of ctenophores and the origin(s) of nervous systems.
 Evodevo 6, 1 (2015). 4. Ryan, J. F. & Chiodin, M. Where is my
 mind? How sponges and placozoans may have lost neural cell types. Philos.
 Trans. R. Soc. Lond. B Biol. Sci. 370, 20150059– (2015). 5. Moroz, L. L.
 et al. The ctenophore genome and the evolutionary origins of neural
 systems. Nature 510, 109–114 (2014). 6. Burkhardt, P. Ctenophores and the
 evolutionary origin(s) of neurons. Trends Neurosci. 45, 878–880 (2022). 7.
 Philippe, H. et al. Phylogenomics revives traditional views on deep animal
 relationships. Curr. Biol. 19, 706–712 (2009). 8. Simion, P. et al. A
 Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister
 Group to All Other Animals. Curr. Biol. 27, 958–967 (2017). 9. Dunn, C. W.
 et al. Broad phylogenomic sampling improves resolution of the animal tree
 of life. Nature 452, 745–749 (2008). 10. Whelan, N. V. et al. Ctenophore
 relationships and their placement as the sister group to all other
 animals. Nat. Ecol. Evol. 1, 1737–1746 (2017). 11. Li, Y., Shen, X.-X.,
 Evans, B., Dunn, C. W. & Rokas, A. Rooting the animal tree of
 life. Mol. Biol. Evol. 38, 4322–4333 (2021). 12. Simakov, O. et al. Deeply
 conserved synteny and the evolution of metazoan chromosomes. Sci. Adv. 8,
 eabi5884 (2022).
description: This dataset is a collection of <em>de
 novo</em>-assembled and already-published genomes, and supplementary
 analyses/results complementing the main and supplementary figures of this
 manuscript.
description: The software necessary to perform these analyses,
 <em>odp</em>, is included in the linked Zenodo release. No
 proprietary software is required to open any of these files.