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

Quattrini, Andrea M., Faircloth, Brant C., Dueñas, Luisa F., Bridge, Tom C.L., Brugler, Mercer R., Calixto-Botía, Iván F., DeLeo, Danielle M., Forêt, Sylvain, Herrera, Santiago, Lee, Simon M.Y., Miller, David J., Prada, Carlos, Rádis-Baptista, Gandhi, Ramírez-Portilla, Catalina, Sánchez, Juan A., Rodríguez, Estefanía, and McFadden, Catherine S. (2018) Universal target-enrichment baits for anthozoan (Cnidaria) phylogenomics: new approaches to long-standing problems. Molecular Ecology Resources, 18 (2). pp. 281-295.

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Abstract

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 similar to 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.

Item ID: 53432
Item Type: Article (Refereed Research - C1)
Keywords: coral, exon, phylogeny, target-capture, ultraconserved element, UCE
Copyright Information: © 2017 John Wiley & Sons Ltd.
ISSN: 1755-0998
Funders: National Science Foundation, Division of Environmental Biology (NSF-DEB), HIMB Pauley Program, Gulf of Mexico Research, Marine Institute's Shiptime Programme
Projects and Grants: NSF-DEB 1457817, NSF-DEB 1457581
Date Deposited: 03 May 2018 12:06
FoR Codes: 06 BIOLOGICAL SCIENCES > 0604 Genetics > 060411 Population, Ecological and Evolutionary Genetics @ 50%
06 BIOLOGICAL SCIENCES > 0603 Evolutionary Biology > 060301 Animal Systematics and Taxonomy @ 50%
SEO Codes: 96 ENVIRONMENT > 9608 Flora, Fauna and Biodiversity > 960805 Flora, Fauna and Biodiversity at Regional or Larger Scales @ 100%
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