Characterizing coral reef biodiversity: genetic species delimitation in brachyuran crabs of Palmyra Atoll, Central Pacific

Abstract

Coral reefs are highly threatened ecosystems, yet there are numerous challenges in conducting inventories of their vanishing biodiversity, partly because many taxa remain difficult to detect and describe. Genetic species delimitation methods provide a standardized means for taxonomic classification including of cryptic, rare, or elusive groups, but results can vary by analytical method and genetic marker. In this study, a combination of morphological and genetic identification methods was used to estimate species richness and identify taxonomic units in true crabs (Infraorder Brachyura; n = 200) from coral reefs of Palmyra Atoll, Central Pacific. Genetic identification was based on matches between mitochondrial 16S ribosomal RNA (16S rRNA) and/or cytochrome c oxidase subunit I (COI) sequences to GenBank data, while morphological work relied on the taxonomic literature. Broad agreement in the number of candidate species delimited by genetic distance thresholds and tree-based approaches was found, although the multi-rate Poisson tree process (mPTP) was less appropriate for this dataset. The COI sequence data identified 30–32 provisional species and the 16S data revealed 34–35. The occurrence of 10 families, 20 genera, and 19 species of brachyurans at Palmyra was corroborated by at least two methods. Diversity levels within Chlorodiella laevissima indicated possible undescribed or cryptic species in currently lumped taxa. These results illustrate the efficacy of DNA sequences in identifying organisms and detecting cryptic variation, and underscore the importance of using appropriate genetic markers and multiple species delimitation analyses, with applications for future species descriptions.

Keywords:

• General mixed Yule-coalescent
• Poisson tree process
• automated barcode gap discovery
• Palmyra Atoll National Wildlife Refuge

Acknowledgments

The authors thank Seth Wollney and Ramon Perez for assistance with lab work. ARMS were deployed and recovered under NOAA’s National Coral Reef Monitoring Plan (NCRMP), which is funded by the Coral Reef Conservation Program (CRCP) and the Pacific Islands Fisheries Science Center. The authors are deeply grateful to the Editor and anonymous reviewers whose comments greatly improved the paper. The findings and conclusions in this article are those of the authors and do not necessarily represent the views of the U.S. Fish and Wildlife Service.

Disclosure statement

On behalf of all authors, the corresponding author states that there is no conflict of interest.

Additional information

Funding

Funding for this project was provided by the Lerner Gray Fund for Marine Research of the American Museum of Natural History (to JAS) and the Professional Staff Congress of the City University of New York (to ENM).