Biology subjects

Bongaerts, P.

Publications and source records attributed to Bongaerts, P..

7 recordsLinked to original sources

bioRxiv2026

Spatial genotypic patterns within monospecific stands of a dominant coral revealed through photogrammetry-guided sampling.

Local and global stressors are driving declines in competitive reef-building corals and favouring stress-tolerant, weedy species. In many of these taxa, rapid asexual reproductive strategies promote the proliferation of existing genotypes at small spatial scales, potentially leading to the formation of monospecific stands ("carpets"). Such reproductive strategies raise concerns for the intraspecific diversity and resilience of future reefs. The genetic structure of these spatially dominant, weedy corals remains poorly understood, in part because densely aggregated colonies lack distinct boundaries, hindering the use of standard sampling designs. We employed a photogrammetry-guided, spatially explicit sampling approach to assess the genotypic diversity and genet distribution in the increasingly dominant scleractinian coral Madracis auretenra across three reef sites in Curacao. Cover of M. auretenra varied widely among sites and reef zones (4.1-26.2%). Genome-wide genotyping of 678 samples collected at 1-m intervals identified two genetically distinct lineages comprising 90% and 10% of the samples, with contrasting genotypic diversity (genet-to-ramet ratio Ng/N = 0.287 and 0.481, respectively). Monospecific stands (n = 20) usually contained multiple genotypes and occasionally even both lineages, but were typically dominated by a single genotype (mean 65.5%, minimum 42.3%). Simulated sampling demonstrated that combining monostands, patches, and isolated colonies would maximise captured genotypic diversity for restoration applications. Our results demonstrate that photogrammetry-guided sampling provides an effective, unbiased framework for population genetic studies of monostand-forming corals while revealing substantial genotypic diversity within a species that is becoming increasingly dominant on southern Caribbean reefs.

ecology↗

bioRxiv2025

Genetic structure of mesophotic and shallow Acropora aculeus on isolated atolls of Eastern Australia

Acropora is the most diverse and widespread coral genus in the world. Although known for its critical ecological role in shallow-water habitats, its abundance and diversity at upper mesophotic depths have only recently been uncovered. Consequently, little is known about the genetic structuring of mesophotic Acropora populations and their potential ecological and evolutionary relationships with shallow populations. Here, we present the first population genomic evaluation of the depth-generalist coral Acropora aculeus to assess genetic structuring across depths (10 and 40 m) and regions (the Great Barrier Reef (GBR) and the Western Coral Sea (WCS)). We observed strong geographic differentiation between regions, indicating the relative isolation of WCS atolls, with some gene flow occurring from WCS to the GBR, but rarely in the opposite direction. Conversely, we observed no geographic or depth-related genetic structuring within regions, although sample sizes limited the evaluation of local allelic patterns of depth structuring. Our results indicate that widespread connectivity within regions characterizes the broadcast spawning A. aculeus. The lack of depth differentiation should be explored to see whether the wide depth range of some species may be safeguarded against a rapidly changing climate.

genomics↗

bioRxiv2022

Global phylogenomic assessment of Leptoseris and Agaricia reveals substantial undescribed diversity at mesophotic depths

Mesophotic coral communities are increasingly gaining attention for the unique biological species they host, exemplified by the numerous mesophotic fish species that continue to be discovered. In contrast, many of the photosynthetic scleractinian corals observed at mesophotic depths are assumed to be depth-generalists, with very few species characterised as mesophotic-specialists. This presumed lack of a specialised community remains largely untested, as phylogenetic studies rarely include mesophotic samples and have long suffered from resolution issues associated with traditional sequence markers. Here, we used reduced-representation genome sequencing to provide a phylogenomic assessment of the two dominant mesophotic genera of plating corals in the Indo-Pacific and Western Atlantic, respectively, Leptoseris and Agaricia. While these genome-wide phylogenies broadly corroborated the morphological taxonomy, they also exposed substantial undescribed diversity (at least 24 molecular clades across the 8 species), including deep divergences within genera and current taxonomic species. Five of the eight focal species consisted of at least two sympatrically-occurring, genetically distinct clades, which were consistently detected across different methods. The repeated observation of genetically divergent clades associated with mesophotic depths highlights that there are many more mesophotic-specialist coral species than currently acknowledged, and that an urgent assessment of this largely unstudied biological diversity is warranted.

evolutionary biology↗

bioRxiv2021

Hidden in the deep: distinct benthic trajectories call for monitoring of mesophotic reefs

Long-term monitoring studies are central to coral reef ecology and conservation management. However, ongoing monitoring programs are almost exclusively focused on shallow depths, and it remains unclear to what extent those are representative of the whole ecosystem. Here, we present a temporal comparison (2012-2017) of directly adjacent shallow and mesophotic benthic communities across seven sites from the Great Barrier Reef and Western Coral Sea. We found a positive correlation initially between shallow and mesophotic coral cover, with higher cover at shallow depths. However, this correlation broke down after multiple disturbances, with coral cover declining only at shallow depths. Point-based tracking revealed the dynamic nature of mesophotic communities, with their consistent coral cover reflecting a net balance between substantial growth and mortality. Overall, the divergent trajectories highlight the urgency to expand monitoring efforts into mesophotic depths, to decipher the processes governing these habitats and enable better-informed management of the overall ecosystem.

ecology↗

bioRxiv2020

Cryptic diversity masks ecologically distinct coral species on tropical reefs

Coral reefs are the epitome of species diversity, yet the number of described scleractinian coral species, the framework-builders of coral reefs, remains moderate by comparison. DNA sequencing studies are rapidly challenging this notion by exposing a wealth of undescribed diversity, but the evolutionary and ecological significance of this diversity remains largely unclear. Here, we present an annotated genome for one of the most ubiquitous corals in the Indo-Pacific (Pachyseris speciosa), and uncover through a comprehensive genomic and phenotypic assessment that it comprises morphologically indistinguishable, but ecologically divergent cryptic lineages. Demographic modelling based on whole-genome resequencing disproved that morphological crypsis was due to recent divergence, and instead indicated ancient morphological stasis. Although the lineages occur sympatrically across shallow and mesophotic habitats, extensive genotyping using a rapid diagnostic assay revealed differentiation of their ecological distributions. Leveraging "common garden" conditions facilitated by the overlapping distributions, we assessed physiological and quantitative skeletal traits and demonstrated concurrent phenotypic differentiation. Lastly, spawning observations of genotyped colonies highlighted the potential role of temporal reproductive isolation in the limited admixture, with consistent genomic signatures in genes related to morphogenesis and reproduction. Overall, our findings demonstrate how ecologically and phenotypically divergent coral species can evolve despite morphological stasis, and provide new leads into the potential mechanisms facilitating such divergence in sympatry. More broadly, they indicate that our current taxonomic framework for reef-building corals may be scratching the surface of the ecologically relevant diversity on coral reefs, consequently limiting our ability to protect or restore this diversity effectively.

evolutionary biology↗

bioRxiv2020

Signatures of selection in the coral holobiont reveal complex adaptations to inshore environments driven by Holocene climate change

Climate change at the Pleistocene/Holocene boundary reshaped many coastal landscapes, and provides an opportunity to study recent adaptive processes in marine species and ecosystems including coral reefs. On the Great Barrier Reef (GBR) sea level rise flooded a vast shelf creating a distinct inshore region which now harbours extensive coral assemblages despite being subject to relatively high turbidity, freshwater input and thermal fluctuations. To investigate how the coral holobiont has adapted to these conditions we first generated a highly contiguous genome assembly for Acropora tenuis based on long-read sequencing, and then used shallow whole-genome resequencing of 148 Acropora tenuis colonies from five inshore locations to model demographic history, identify signatures of selection and profile symbiont communities. We show that corals from Magnetic Island, located in the central inshore region of the GBR, are genetically distinct from those 50-500km further north, reflecting a Pleistocene (250-600Kya) split, whereas photosymbiont genotypes differ between reefs in a pattern more likely to reflect contemporary (Holocene) conditions. We also identified loci in the coral host genome with signatures of positive selection in the northern population and used coalescent simulations to show that these are unlikely to be accounted for by demographic history. Genes at these loci have roles in a diverse range of processes that includes heterotrophic nutrition, osmotic regulation, skeletal development and the establishment and maintenance of symbiosis. Our results show that, in the case of A. tenuis holobionts from the inshore GBR, the genomes of both the coral host and the primary photosymbiont of have been significantly shaped by their environment and illustrate the complexity of adaptations that have occurred in response to past climate change.

genomics↗

bioRxiv2017

Symbiodinium genomes reveal adaptive evolution of functions related to symbiosis

Symbiosis between dinoflagellates of the genus Symbiodinium and reef-building corals forms the trophic foundation of the worlds coral reef ecosystems. Here we present the first draft genome of Symbiodinium goreaui (Clade C, type C1: 1.03 Gbp), one of the most ubiquitous endosymbionts associated with corals, and an improved draft genome of Symbiodinium kawagutii (Clade F, strain CS-156: 1.05 Gbp), previously sequenced as strain CCMP2468, to further elucidate genomic signatures of this symbiosis. Comparative analysis of four available Symbiodinium genomes against other dinoflagellate genomes led to the identification of 2460 nuclear gene families that show evidence of positive selection, including genes involved in photosynthesis, transmembrane ion transport, synthesis and modification of amino acids and glycoproteins, and stress response. Further, we identified extensive sets of genes for meiosis and response to light stress. These draft genomes provide a foundational resource for advancing our understanding Symbiodinium biology and the coral-algal symbiosis.

genomics↗