Unexpected diversity of Isidoides (Anthozoa: Octocorallia: Isidoidae) revealed by morphology and phylogenomic analysis with descriptions of three new species

Yu Xu^1,†, Jaret P. Bilewitch^2,†, Eric Pante^3,4,†,$, Zifeng Zhan¹, Sadie Mills², Malcolm R. Clark² and Kuidong Xu^1,5,$

¹ Laboratory of Marine Organism Taxonomy and Phylogeny, Shandong Province Key Laboratory of Marine Biodiversity and Bio-resource Sustainable Utilization, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China ² New Zealand Institute of Earth Science Ltd (NZIES), 301 Evans Bay Parade, Wellington 6021, New Zealand ³ Univ Brest, CNRS, IRD, Ifremer, UMR 6539, LEMAR, Plouzané, France ⁴ Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 43 rue Cuvier, CP 26, 75005 Paris, France ⁵ University of Chinese Academy of Sciences, Beijing 100049, China

^$ Corresponding authors: Eric Pante (eric.pante@cnrs.fr), Kuidong Xu (kxu@qdio.ac.cn) ^† These authors contributed equally to this work

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This repository contains code and references to the rawdata necessary to replicate the analyses in Xu et al 2026. To assemble UCEs from raw fastq.gz, start with the snp_pipeline folder, and perform steps 0 to 6 (derived form Erickson et al 2021 and github.com/Lavarchus); fork to phylogenetic/Workflow_UCE.htmlfor the next steps of the assembly; this part is based on the phyluce tutorial 1). For detecting SNPs, perform steps 7-18 from snp_pipeline. snp_config_filescontains the files necessary to run the snp_pipelinescripts. The pipeline is optimised for HPC with slurm.