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Population genomics for symbiotic anthozoans: can reduced representation approaches be used for taxa without reference genomes?

Heredity volume 128, pages 338–351 (2022)Cite this article

Subjects

Abstract

Population genetic studies of symbiotic anthozoans have been historically challenging because their endosymbioses with dinoflagellates have impeded marker development. Genomic approaches like reduced representation sequencing alleviate marker development issues but produce anonymous loci, and without a reference genome, it is unknown which organism is contributing to the observed patterns. Alternative methods such as bait-capture sequencing targeting Ultra-Conserved Elements are now possible but costly. Thus, RADseq remains attractive, but how useful are these methods for symbiotic anthozoan taxa without a reference genome to separate anthozoan from algal sequences? We explore this through a case-study using a double-digest RADseq dataset for the sea anemone Bartholomea annulata. We assembled a holobiont dataset (3854 loci) for 101 individuals, then used a reference genome to create an aposymbiotic dataset (1402 loci). For both datasets, we investigated population structure and used coalescent simulations to estimate demography and population parameters. We demonstrate complete overlap in the spatial patterns of genetic diversity, demographic histories, and population parameter estimates for holobiont and aposymbiotic datasets. We hypothesize that the unique combination of anthozoan biology, diversity of the endosymbionts, and the manner in which assembly programs identify orthologous loci alleviates the need for reference genomes in some circumstances. We explore this hypothesis by assembling an additional 21 datasets using the assembly programs pyRAD and Stacks. We conclude that RADseq methods are more tractable for symbiotic anthozoans without reference genomes than previously realized.

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Fig. 1: Sample localities and genetic cluster plots for the corkscrew sea anemone Bartholomea annulata.
Fig. 2: Models used in FSC2 to understand the demographic processes leading to the two-population pattern of diversification in the corkscrew anemone Bartholomea annulata across the Tropical Western Atlantic.
Fig. 3: Genetic clustering results (K = 2) from 21 de novo ddRADseq dataset assemblies for the corkscrew anemone Bartholomea annulata compiled using pyRAD v3.0.66 and Stacks v2.55.

Data availability

All files and raw data are available on Dryad (https://doi.org/10.5061/dryad.kkwh70s6p).

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Acknowledgements

We are grateful to Erich Bartels, Annelise del Rio, Jose Diaz, Dan Exton, Lisle Gibbs, Natalie Hamilton, Alex Hunter, Anna Klompen, Jason Macrander, Spencer Palombit, Stephen Ratchford, Nancy Sheridan, Nuno Simoes, Jill Titus, Cory Walter, Eric Witt, Clay Vondriska, and the Operation Wallacea dive staff for assistance in the field and laboratory. We also thank Jordan Satler, Megan Smith, and Bryan Carstens for bioinformatic assistance and advice regarding fastsimcoal2 analyses and model selection. Paul Blischak and Theo Cavinto provided valuable bioinformatics assistance separating holobiont from aposymbiotic RADseq loci. Bellairs Research Station, the Bermuda Institute of Ocean Science, Cape Eleuthera Institute, CARMABI, Coral View Dive Center, Gerace Research Centre, the Honduran Coral Reef Foundation, Mote Marine Laboratory, Smithsonian Tropical Research Institute, and the University of the Virgin Islands provided valuable logistical support in the field. Specimens were collected from throughout the Tropical Western Atlantic under permits: SE/A-88- 15, PPF/DGOPA-127/14, CZ01/9/9, FKNMS-2012-155, SAL-12-1432A-SR, STT037-14, 140408, MAR/FIS/17, and 19985. This research was supported by funding from a National Science Foundation-Doctoral Dissertation Improvement Grant DEB-1601645 and Florida Fish and Wildlife Conservation Commission awards to B.M.T. & M.D. Operation Wallacea, American Philosophical Society, International Society for Reef Studies Graduate Fellowship, PADI Foundation Grant, and American Museum of Natural History Lerner Gray Funds supported field research for B.M.T. Additional funding was provided through the Trautman Fund of the OSU Museum of Biological Diversity, The Ohio State University, and National Science Foundation DEB-1257796 to MD.

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  1. Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA

    Benjamin M. Titus

  2. Dauphin Island Sea Lab, Dauphin Island, AL, USA

    Benjamin M. Titus

  3. Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA

    Benjamin M. Titus & Marymegan Daly

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BMT and MD conceived the study and collected samples, BMT conducted laboratory work and analyzed the data. BMT and MD wrote and edited the manuscript.

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Correspondence to Benjamin M. Titus.

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Titus, B.M., Daly, M. Population genomics for symbiotic anthozoans: can reduced representation approaches be used for taxa without reference genomes?. Heredity 128, 338–351 (2022). https://doi.org/10.1038/s41437-022-00531-3

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  • DOI: https://doi.org/10.1038/s41437-022-00531-3

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