Resolving Acuticulata (Metridioidea: Enthemonae: Actiniaria), a clade containing many invasive species of sea anemones
Data files
Jan 28, 2026 version files 1.68 GB
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Acri_ADK_10.contigs.fasta
3.65 MB
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Actisp_PML.contigs.fasta
6.48 MB
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Aipge_PJM_2.contigs.fasta
16.83 MB
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Aipgh_AD_21.contigs.fasta
7.72 MB
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Aipmt_FSBC.contigs.fasta
9.38 MB
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Aiptm_AD_16.contigs.fasta
12.05 MB
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Alics_196882.contigs.fasta
8.67 MB
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Alicsan_MAB_41.contigs.fasta
102.58 MB
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Antha_FI_64.contigs.fasta
13.18 MB
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Antha.contigs.fasta
7.04 MB
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Anthc_FI_Unid_22.contigs.fasta
6 MB
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Barta_BH_39.contigs.fasta
11.07 MB
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Bellsp_AD_28.contigs.fasta
22.42 MB
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Bolocfm_CAL_23.contigs.fasta
7.29 MB
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Bolom_198131.contigs.fasta
7.09 MB
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Bolomc_CAL_15.contigs.fasta
98.27 MB
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Bolomcm_CAL_16.contigs.fasta
103.56 MB
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Bolomcmu_CAL_23.contigs.fasta
69.61 MB
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Bolomcmur_MAB_48_2.contigs.fasta
9.24 MB
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Bunosp_CAL_23.contigs.fasta
91.38 MB
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Callp_AMNH.contigs.fasta
155.48 MB
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Callt_4.contigs.fasta
21.42 MB
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Cereh.contigs.fasta
20.89 MB
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Diadl_DART.contigs.fasta
5.87 MB
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Diadl_DL_CB.contigs.fasta
15.05 MB
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Diadn_N_91_1.contigs.fasta
11.03 MB
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Diadp_GAIL.contigs.fasta
90.18 MB
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Diadsp_FG_07.contigs.fasta
14.73 MB
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Diadspe_FG_20.contigs.fasta
9.32 MB
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Diadspec_MAND.contigs.fasta
4.93 MB
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Diadspeci_orange.contigs.fasta
89.19 MB
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Diadspecie_WS2.contigs.fasta
89.11 MB
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FI_36.contigs.fasta
14.29 MB
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FI_37.contigs.fasta
64.59 MB
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FI_38.contigs.fasta
84.10 MB
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FI_40.contigs.fasta
5.81 MB
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FI_532_2b.contigs.fasta
11.30 MB
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FI_532_6.contigs.fasta
52.39 MB
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FI_533_3.contigs.fasta
17.51 MB
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FI_73.contigs.fasta
7.77 MB
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Gonap_Norway.contigs.fasta
11.02 MB
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Isopf_FI_29.contigs.fasta
72.07 MB
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Neoam_26.contigs.fasta
12.31 MB
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Paipr.contigs.fasta
14.23 MB
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Parasp._ONIO.contigs.fasta
7.38 MB
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Phyls_CAL_06.contigs.fasta
14.46 MB
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Prots_Norway.contigs.fasta
92.51 MB
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Protsp_Blane.contigs.fasta
11.63 MB
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README.md
5.64 KB
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RedBrooding_FI_39.contigs.fasta
8.16 MB
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resolving_acuticulata_code.txt
27.74 KB
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Sagae_5_1.contigs.fasta
11.64 MB
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Triap_MAB_36.contigs.fasta
12.88 MB
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Verip_39.contigs.fasta
12.01 MB
Abstract
Acuticulata is a globally distributed group in the actiniarian superfamily Metridiodea comprised of taxa with ecological, economic, and scientific significance. Prominent members such as Exaiptasia diaphana and Diadumene lineata serve as model organisms for studying coral symbiosis, bleaching phenomena, and ecological invasions. Despite their importance, unresolved phylogenetic relationships and outdated taxonomic frameworks hinder a full understanding of the diversity and evolution of the taxa in this clade. In this study, we employ a targeted sequence-capture approach to construct a robust phylogeny for Acuticulata, addressing long-standing questions about familial monophyly and comparing the results to results from a more conventional, five-gene dataset. Specimens from previously underrepresented families and global regions, including the Falkland Islands, were included to elucidate evolutionary interrelationships and improve resolution. Our results support the monophyly of Aliciidae, Boloceroididae, Diadumenidae, Gonactiniidae, and Metridiidae. Our results highlight the need for taxonomic revision within the family Sagartiidae, as the specimens we included from this family were recovered in four distinct clades. Based on our results, we transfer Paraiptasia from Aiptasiidae to Sagartiidae.These findings emphasize the utility of genome-scale data for resolving phylogenetic ambiguities for morphologically problematic taxa and suggest a framework for future integrative taxonomic and ecological studies within Acuticulata.
https://doi.org/10.5061/dryad.vmcvdnd32
Description of the data and file structure
Actiniarian specimens were collected either by hand, while SCUBA diving, or via trawls. Specimens were identified using external polyp anatomy and preserved in 95% ethanol to ensure the integrity of molecular data. Twelve specimens from the Falkland Islands were collected by hand while SCUBA diving (maximum depth of 20m) during the 2019 research cruise for the “Fine Scaling of the Marine Management Area of the Falkland Islands” project. Collection data for each specimen is contained in Appendix 1.
DNA extraction was performed using the E.Z.N.A. Tissue DNA Kit (Omega Bio-Tek, Norcross, GA, USA) according to the manufacturer’s protocol, except with a reduced elution volume to increase concentration. The quality and quantity of extracted DNA were evaluated using a Qubit 2.0 fluorometer and a NanoDrop spectrophotometer, measuring DNA concentration (ng/μL). Specimens with remaining tissue have been deposited at the American Museum of Natural History (AMNH). Taxa sampled represent 75% of the acuticulate diversity at the family-level (9 of 12 valid families), and include several unidentified individuals collected from the Falkland Islands in 2019. No members of Haliactinidae Carlgren, 1949, Haliplanellidae Hand, 1956, nor Sagartiomorphidae Carlgren, 1934 were considered in the phylogenetic framework presented here.
Up to 1000 ng of DNA per sample was used for library preparations, which were conducted using the Kapa HyperPrep Kit (Kapa Biosciences, Wilmington, MA, USA), optimized for target capture. Universal Y-yoke oligonucleotide adapters and iTru dual-indexed primers were used as described in Glenn et al. Eleven libraries were pooled in equimolar ratios, each contributing approximately 100 ng, for a total of 1.3–2.3 μg of DNA per pool for target enrichment.
Target enrichment and sequencing were conducted at Arbor Biosciences (Ann Arbor, MI, USA). The hexacoral-v2 bait set used contained a total of 25,288 baits targeting 2,476 (1,127 UCE and 1,349 exon) loci. Target enrichment was conducted according to the MyBaits v.IV protocol with bait concentrations of 500 ng per reaction. Libraries were sequenced using 150bp paired-end sequencing on an Illumina NovaSeq platform.
Paired-end reads were trimmed to remove low-quality bases and adapters using TrimGalore. Trimmed reads were then assembled into contigs using SPAdes genome assembler v3.15.5. Data included are the resulting assembled contigs.
Files
The identification for the files is as follows:
Acri_ADK_10.contigs.fasta – Acricoactis brachyacontis
Actisp_PML.contigs.fasta – Actinothoe sp.
Aipge_PJM_2.contigs.fasta – Aiptasiogeton eruptaurantia
Aipgh_AD_21.contigs.fasta – Aiptasiogeton hyalinus
Aipmt_FSBC.contigs.fasta – Aiptasiomorpha texaensis
Aiptm_AD_16.contigs.fasta – Aiptasia mutabilis
Alics_196882.contigs.fasta – Alicia sansibarensis
Alicsan_MAB_41.contigs.fasta – Alicia sansibarensis
Antha.contigs.fasta – Antholoba achates
Antha_FI_64.contigs.fasta – Antholoba achates
Anthc_FI_Unid_22.contigs.fasta – Anthothoe chilensis
Barta_BH_39.contigs.fasta – Bartholomea annulata
Bellsp_AD_28.contigs.fasta – Bellactis lux
Bolocfm_CAL_23.contigs.fasta – Boloceroides sp.
Bolom_198131.contigs.fasta – Boloceroides sp.
Bolomc_CAL_15.contigs.fasta – Boloceroides sp.
Bolomcm_CAL_16.contigs.fasta – Bunodeopsis sp.
Bolomcmu_CAL_23.contigs.fasta – Boloceroides sp.
Bolomcmur_MAB_48_2.contigs.fasta – Boloceroides sp.
Bunosp_CAL_23.contigs.fasta – Bunodeopsis sp.
Callp_AMNH.contigs.fasta – Calliactis polypus
Callt_4.contigs.fasta – Calliactis tricolor
Cereh.contigs.fasta – Cereus herpetodes
Diadl_DART.contigs.fasta – Diadumene lineata
Diadl_DL_CB.contigs.fasta – Diadumene sp.
Diadn_N_91_1.contigs.fasta – Diadumene neozelanica
Diadp_GAIL.contigs.fasta – Diadumene paranaensis
Diadsp_FG_07.contigs.fasta – Diadumene sp.
Diadspe_FG_20.contigs.fasta – Aiptasiogeton sp.
Diadspec_MAND.contigs.fasta – Diadumene sp.
Diadspeci_orange.contigs.fasta – Diadumene sp.
Diadspecie_WS2.contigs.fasta – Diadumene neozelanica
FI_36.contigs.fasta – Isoparactis fionae
FI_37.contigs.fasta – Isoparactis fionae
FI_38.contigs.fasta – Isoparactis fionae
FI_40.contigs.fasta – Anthothoe chilensis
FI_532_2b.contigs.fasta – Anthothoe chilensis
FI_532_6.contigs.fasta – Anthothoe chilensis
FI_533_3.contigs.fasta – Antholoba achates
FI_73.contigs.fasta – Anthothoe chilensis
Gonap_Norway.contigs.fasta – Gonactinia prolifera
Isopf_FI_29.contigs.fasta – Isoparactis fionae
Neoam_26.contigs.fasta – Neoaiptasia morbilla
Paipr.contigs.fasta – Paraiptasia radiata
Parasp._ONIO.contigs.fasta – Acuticulata indet.
Phyls_CAL_06.contigs.fasta – Phyllodiscus semoni
Prots_Norway.contigs.fasta – Protanthea simplex
Protsp_Blane.contigs.fasta – Protanthea sp.
RedBrooding_FI_39.contigs.fasta – Sagartiidae sp.
Sagae_5_1.contigs.fasta – Cylista elegans
Triap_MAB_36.contigs.fasta – Triactis producta
Verip_39.contigs.fasta – Verrillactis paguri
resolving_acuticulata_code.txt - Code used for generating phylogenies
Code/software
See resolving_acuticulata_code.txt for details on the software used.
Actiniarian specimens were collected either by hand, while SCUBA diving, or via trawls. Specimens were identified using external polyp anatomy and preserved in 95% ethanol to ensure the integrity of molecular data. Twelve specimens from the Falkland Islands were collected by hand while SCUBA diving (maximum depth of 20m) during the 2019 research cruise for the “Fine Scaling of the Marine Management Area of the Falkland Islands” project. Collection data for each specimen is contained in Appendix 1.
DNA extraction was performed using the E.Z.N.A. Tissue DNA Kit (Omega Bio-Tek, Norcross, GA, USA) according to the manufacturer’s protocol, except with a reduced elution volume to increase concentration. The quality and quantity of extracted DNA were evaluated using a Qubit 2.0 fluorometer and a NanoDrop spectrophotometer, measuring DNA concentration (ng/μL). Specimens with remaining tissue have been deposited at the American Museum of Natural History (AMNH). Taxa sampled represent 75% of the acuticulate diversity at the family-level (9 of 12 valid families), and include several unidentified individuals collected from the Falkland Islands in 2019. No members of Haliactinidae Carlgren, 1949, Haliplanellidae Hand, 1956, nor Sagartiomorphidae Carlgren, 1934 were considered in the phylogenetic framework presented here.
Up to 1000 ng of DNA per sample was used for library preparations, which were conducted using the Kapa HyperPrep Kit (Kapa Biosciences, Wilmington, MA, USA), optimized for target capture. Universal Y-yoke oligonucleotide adapters and iTru dual-indexed primers were used as described in Glenn et al. Eleven libraries were pooled in equimolar ratios, each contributing approximately 100 ng, for a total of 1.3–2.3 μg of DNA per pool for target enrichment.
Target enrichment and sequencing were conducted at Arbor Biosciences (Ann Arbor, MI, USA). The hexacoral-v2 bait set used contained a total of 25,288 baits targeting 2,476 (1,127 UCE and 1,349 exon) loci. Target enrichment was conducted according to the MyBaits v.IV protocol with bait concentrations of 500 ng per reaction. Libraries were sequenced using 150bp paired-end sequencing on an Illumina NovaSeq platform.
Paired-end reads were trimmed to remove low-quality bases and adapters using TrimGalore. Trimmed reads were then assembled into contigs using SPAdes genome assembler v3.15.5.