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Mol Ecol Resour. 2018 Mar;18(2):281-295. doi: 10.1111/1755-0998.12736. Epub 2017 Dec 6.

Universal target-enrichment baits for anthozoan (Cnidaria) phylogenomics: New approaches to long-standing problems.

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Department of Biology, Harvey Mudd College, Claremont, CA, USA.
Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA.
Departamento de Ciencias Biológicas-Facultad de Ciencias, Laboratorio de Biología Molecular Marina (BIOMMAR), Universidad de los Andes, Bogotá, Colombia.
Queensland Museum Network, Townsville, QLD, Australia.
Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia.
Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA.
Biological Sciences Department, NYC College of Technology, City University of New York, Brooklyn, NY, USA.
Department of Animal Ecology and Systematics, Justus Liebig Universität, Giessen, Germany.
Department of Biological Sciences, Florida International University, North Miami, FL, USA.
Biology Department, Temple University, Philadelphia, PA, USA.
Research School of Biology, Australian National University, Canberra, ACT, Australia.
Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA.
State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macao, China.
Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA.
Institute for Marine Sciences, Federal University of Ceara, Fortaleza, CE, Brazil.


Anthozoans (e.g., corals, anemones) are an ecologically important and diverse group of marine metazoans that occur from shallow to deep waters worldwide. However, our understanding of the evolutionary relationships among the ~7,500 species within this class is hindered by the lack of phylogenetically informative markers that can be reliably sequenced across a diversity of taxa. We designed and tested 16,306 RNA baits to capture 720 ultraconserved element loci and 1,071 exon loci. Library preparation and target enrichment were performed on 33 taxa from all orders within the class Anthozoa. Following Illumina sequencing and Trinity assembly, we recovered 1,774 of 1,791 targeted loci. The mean number of loci recovered from each species was 638 ± 222, with more loci recovered from octocorals (783 ± 138 loci) than hexacorals (475 ± 187 loci). Parsimony informative sites ranged from 26 to 49% for alignments at differing hierarchical taxonomic levels (e.g., Anthozoa, Octocorallia, Hexacorallia). The per cent of variable sites within each of three genera (Acropora, Alcyonium, and Sinularia) for which multiple species were sequenced ranged from 4.7% to 30%. Maximum-likelihood analyses recovered highly resolved trees with topologies matching those supported by other studies, including the monophyly of the order Scleractinia. Our results demonstrate the utility of this target-enrichment approach to resolve phylogenetic relationships from relatively old to recent divergences. Redesigning the baits with improved affinities to capture loci within each subclass will provide a valuable toolset to address systematic questions, further our understanding of the timing of diversifications and help resolve long-standing controversial relationships in the class Anthozoa.


UCE; coral; exon; phylogeny; target-capture; ultraconserved element

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