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Mitogenomics reveals low variation within a trigeneric complex of black corals from the North Pacific Ocean

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Abstract

A 2013 study revealed that three morphologically distinct antipatharian genera (Dendrobathypathes, Lillipathes, Parantipathes) from the eastern North Pacific (ENP) are genetically indistinguishable using three mitochondrial and four nuclear markers (7,203 bp). To investigate whether this lack of molecular variability extends beyond three mitochondrial genes, we sequenced the complete mitogenome of a single representative within each genus. Dendrobathypathes was the only specimen from the 2013 study containing high molecular weight (HMW) DNA. In terms of geographic proximity to the ENP, the closest Lillipathes and Parantipathes yielding HMW DNA were from the central North Pacific near Hawai'i. Based on cox3-IGR-cox1, Lillipathes and Parantipathes each contained two variable sites and thus were not equivalent substitutes for specimens from the ENP. Nonetheless, variation was extremely low when comparing the mitogenomes, with 32 variable positions across 17,687 bp. Pairwise comparisons revealed 18 (Dendrobathypathes and Parantipathes) and 23 (Lillipathes and Parantipathes; Lillipathes and Dendrobathypathes) variable sites. An ML-based phylogenetic reconstruction using 13 protein-coding genes and two rRNAs revealed that the three North Pacific genera grouped in a clade with Atlantic Dendrobathypathes, while Atlantic Parantipathes spp. formed a sister clade. Previous research hypothesized that hybridization with subsequent introgression was responsible for the lack of variability among genera. Due to uniparental inheritance and lack of recombination, mtDNA cannot identify hybrids; however, finding Pacific Parantipathes grouping with Dendrobathypathes and Lillipathes rather than Atlantic Parantipathes suggests that the trigeneric complex has a unique evolutionary history. If high-resolution nuclear markers support hybridization, it will be important to elucidate the molecular mechanism that maintains three distinct morphological forms occurring in sympatry.

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Availability of data and material

Mitogenomic data are available in GenBank under accession numbers MZ520327 (Parantipathes cf. larix USNM-1404491), MZ520328 (Lillipathes cf. wingi USNM-1457355), and MZ520329 (Dendrobathypathes boutillieri USNM-1070762). The phylogenetic tree is available in TreeBASE under study number S28972.

Code availability

Our MitoFinder code is included under “Materials and methods.”

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Acknowledgements

The data in this paper were analyzed as part of a Molecular Ecology Techniques course (BIOL B499) at the University of South Carolina Beaufort. Sequencing was conducted at the New York Genome Center using funds provided to MRB through a Cycle 47 PSC-CUNY Research Award (#69191-00-47). Financial support was provided to MRB by the Port Royal Sound Foundation and to the Ocean Genome Legacy Center of Northeastern University by a grant from the National Fish and Wildlife Foundation. Resources purchased with funds from the NSF FSML program (DBI 1722553, to Northeastern University) were used to generate data for this manuscript. MRB is a Research Associate at the American Museum of Natural History and the Smithsonian Institution’s National Museum of Natural History and gratefully acknowledges these affiliations.

Funding

- Cycle 47 PSC-CUNY Research Award (#69191–00-47) for DNA sequencing to MRB. - Port Royal Sound Foundation to MRB. - National Fish and Wildlife Foundation to the Ocean Genome Legacy Center of Northeastern University. - NSF FSML program (DBI 1722553) to Northeastern University.

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Conceived of study: MRB. DNA extraction, DNA quantification, and shipping samples: HJAM, DLD. Data analysis: YMBB, IW, KMN, JJR, KM, KMC, SS, SNM, MSB, JAF, ANW, KEM, TN, HP, MRB. Data interpretation: YMBB, IW, JH, DTP, MRB. Submitted data to GenBank: YMBB, IW, JJR, KM, KMC, MRB. Significant intellectual contributions: JH, DTP. Wrote original draft of manuscript: YMBB, IW, JH, HJAM, MRB. Revised manuscript: all authors.

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Correspondence to Mercer R. Brugler.

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Yessenia M. Bledsoe-Becerra, Iesha S. Whittaker, Katherine Medina Naranjo, Jicayla Johnson-Rosemond, Kristen H. Mullins, Karena M. Cunningham, Suchir Shetty, Samuel N. Messinides, Melinda S. Behney, Jessica A. Fehsal, Ashley N. Watson, Kaitlyn E. McKnight, and Teresa W. Nasiadka are undergraduates.

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Bledsoe-Becerra, Y.M., Whittaker, I.S., Horowitz, J. et al. Mitogenomics reveals low variation within a trigeneric complex of black corals from the North Pacific Ocean. Org Divers Evol 22, 343–353 (2022). https://doi.org/10.1007/s13127-021-00537-5

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