Cryptic species and hybridisation in corals: challenges and opportunities for conservation and restoration

Abstract

Conservation and management of coral reef ecosystems will depend on accurate assessments of reef-building coral species diversity. However, the true diversity of corals may be obfuscated by the presence of cryptic species, which are likely much more pervasive than is currently recognised. Additionally, cryptic species may sometimes hybridize, resulting in gene introgression between species. Here, we investigate the prevalence of cryptic coral species via a structured literature review and find that over 50% of population genomic studies show evidence for divisions within taxonomically recognised species and that such closely-related taxa are often linked by gene flow. We find that cryptic taxa frequently segregate by environment, especially depth, and may differ by phenotypic characteristics including resilience to heat stress. This hidden biodiversity creates challenges for coral conservation and restoration planning that are not well appreciated, including hiding true population declines, biasing estimates for species’ phenotypic breadth, overestimating the resilience of species to stressors, yielding uncertainty in evolutionary dynamics inferred from past studies, and creating reproductive barriers that may limit mating between local and translocated corals. Increasing awareness that coral cryptic species with incomplete species boundaries are common and building this expectation into conservation and restoration plans is an important pathway forward. Rich opportunities for interdisciplinary collaboration among coral and speciation biologists could fill key knowledge gaps relevant to conservation. We detail recommendations for best practice and strategies for identifying cryptic taxa and hybrids and urge their consideration in all future studies on corals.

Contaminant or goldmine? In silico assessment of Symbiodiniaceae community using coral hologenomes

“…Hologenome data, or genome data generated from all interacting biotic components of a holobiont, have been proven useful for taxonomic and functional assessment of the prokaryotic microbial community in the holobionts of humans, other animals, and plants (Alberdi et al, 2022). In recent studies of coral holobionts, hologenome data are generated by sequencing genomic DNA extracted from coral tissues, enabling recovery of whole-genome sequences from the coral host, and assessment of the host genotype (Figure 1); see recent reviews (Voolstra et al, 2021a;Riginos et al, 2024) for more detail. These samples are dominated by the host DNA (e.g.…”