Mimicry and mitonuclear discordance in nudibranchs: new insights from exon capture phylogenomics

Kara K S Layton* (Corresponding Author), Jose I. Carvajal, Nerida G. Wilson

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

8 Citations (Scopus)
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Phylogenetic inference and species delimitation can be challenging in taxonomic groups that have recently radiated and where introgression produces conflicting gene trees, especially when species delimitation has traditionally relied on mitochondrial data and color pattern. Chromodoris, a genus of colorful and toxic nudibranch in the Indo‐Pacific, has been shown to have extraordinary cryptic diversity and mimicry, and has recently radiated, ultimately complicating species delimitation. In these cases, additional genome‐wide data can help improve phylogenetic resolution and provide important insights about evolutionary history. Here, we employ a transcriptome‐based exon capture approach to resolve Chromodoris phylogeny with data from 2,925 exons and 1,630 genes, derived from 15 nudibranch transcriptomes. We show that some previously identified mimics instead show mitonuclear discordance, likely deriving from introgression or mitochondrial capture, but we confirm one “pure” mimic in Western Australia. Sister–species relationships and species‐level entities were recovered with high support in both concatenated maximum likelihood (ML) and summary coalescent phylogenies, but the ML topologies were highly variable while the coalescent topologies were consistent across datasets. Our work also demonstrates the broad phylogenetic utility of 149 genes that were previously identified from eupulmonate gastropods. This study is one of the first to (a) demonstrate the efficacy of exon capture for recovering relationships among recently radiated invertebrate taxa, (b) employ genome‐wide nuclear markers to test mimicry hypotheses in nudibranchs and (c) provide evidence for introgression and mitochondrial capture in nudibranchs.
Original languageEnglish
Pages (from-to)11966-11982
Number of pages17
JournalEcology and Evolution
Issue number21
Early online date17 Sept 2020
Publication statusPublished - Nov 2020

Bibliographical note

Open access via the Wiley Jisc Agreement

Funding Information
Gorgon Barrow Island Net Conservation Benefits Fund
The University of Western Australia
Malacological Society of Australasia

We are grateful to our collaborators who have contributed specimens to this work, including David Mullins, Gary Cobb, Greg Rouse, Karen Cheney, Kate Dawson, Lisa Kirkendale, Terry Farr, and Terry Gosliner. We also thank Elizabeth Kools for coordinating K.K.S.L's tissue sampling at the California Academy of Sciences and for sending specimens for this work. We sincerely thank Alison Devault and Jakob Enk from Arbor Biosciences for logistical support and advice, and Greg Rouse, Joel Huey, and Josefin Stiller for feedback on data analysis. Funding for this project comes from the Gorgon Project's Barrow Island Net Conservation Benefits Fund, The University of Western Australia, and the Malacological Society of Australasia. K.K.S.L. was supported by a University Postgraduate Award for International Students (UPAIS) and an RTP International Fees Offset scholarship (RTPFI) administered by the University of Western Australia, as well as a postgraduate doctoral scholarship from the Natural Sciences and Engineering Research Council of Canada (NSERC). Here we provide permit details for newly collected specimens that do not derive from Layton et al. (2018). Specimens from Western Australia were collected under permits from the Department of Parks and Wildlife, including a regulation 17 licence to collect fauna for scientific purposes (SF010218, SF010710) and a regulation 4 exemption to collect marine invertebrates within Ningaloo Marine Park (CE005306). Specimens from Queensland were collected under permits from the Department of Agriculture, Fisheries and Forestry (Permit #: 183990). Specimens from Victoria were collected under permits from the Department of Environment, Land, Water and Planning (Permit #: 10007853). The specimen from California was collected under a permit from California Department of Fish and Wildlife (Permit #: 4564).


  • exon capture
  • mimicry
  • mitonuclear discordance
  • nudibranchia
  • phylogemics
  • speciation
  • Nudibranchia
  • phylogenomics


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