DOI: 10.5061/dryad.xd2547dfb
title: Mimicry and mitonuclear discordance in nudibranchs: new insights from exon capture phylogenomics

description: 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 colour pattern.
 Chromodoris, a genus of colourful 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 i) demonstrate
 the efficacy of exon capture for recovering relationships among recently
 radiated invertebrate taxa, ii) employ genome-wide nuclear markers to test
 mimicry hypotheses in nudibranchs and iii) provide evidence for
 introgression and mitochondrial capture in nudibranchs.
description: Chromodoris westraliensis transcriptome:
 3.Chro_wes.Trinity.annotated.fa.gz Doriprismatica
 atromarginata transcriptome: 4.Dor_atro.Trinity.annotated.fa.gz
 Goniobranchus coi transcriptome:
 5.Gon_coi.Trinity.annotated.fa.gz Verconia verconis
 transcriptome: 8.Ver_ver.Trinity.annotated.fa.gz
 Hypselodoris saintvincentius transcriptome:
 9.Hyp_sain.Trinity.annotated.fa.gz Ardeadoris
 egretta transcriptome: 11.Ard_egr.Trinity.annotated.fa.gz
 Mexichromis festiva transcriptome:
 12.Mex_fes.Trinity.annotated.fa.gz Ceratosoma tenue
 transcriptome: 13.Cer_ten.Trinity.annotated.fa.gz
 Verconia norba transcriptome:
 23.Ver_nor.Trinity.annotated.fa.gz Chromodoris
 magnifica transcriptome: 24.Chr_mag.Trinity.annotated.fa.gz
 Felimida macfarlandi transcriptome:
 25.Fel_CAL.Trinity.annotated.fa.gz Actinocyclus
 verrucosus transcriptome: 26.Act_QLD.Trinity.annotated.fa.gz
 Goniobranchus fidelis transcriptome: Gon_fid.fa.gz
 Prodoris clavigera transcriptome (previously published data):
 19.Bathi.Trinity.annotated.fa.gz Doris
 kerguelenensis transcriptome (previously published data):
 20.Doris.Trinity.annotated.fa.gz Gene alignments (used
 to build individual gene trees for ASTRAL phylogeny):
 ChromEx3_Trim_aln.zip Concatenated alignment for ML
 tree: ChromEx3_Trim_concat.fasta Hybridization
 detection file: ChromEx3_filt.txt