Biology subjects

Locatelli, N. S.

Publications and source records attributed to Locatelli, N. S..

5 recordsLinked to original sources

bioRxiv2026

Simulations reveal hybridization in Caribbean Acropora restoration poses low risk of genetic swamping but limited potential for adaptive introgression

Severe global declines in coral populations have driven growing demand for human intervention and restoration. One goal of restoration is to repopulate reef ecosystems through outplanting, which requires detailed understanding of target systems. However, long term ecological and reproductive data from interventions remain scarce. An exception to this are the critically endangered Caribbean corals, Acropora palmata and A. cervicornis, which have been central to restoration efforts in the region. These species serve as a unique case study due to the abundance of published data spanning ecology, and reproductive biology. In the wild, these species can cross to form an F1 hybrid, A. prolifera, though it is rarely used in restoration. It remains unclear whether A. prolifera is an evolutionary dead-end competing with its parents, or a potential bridge enabling genetic exchange via backcrossing. To evaluate benefits and risks of restoration among Caribbean Acropora, we developed a two-dimensional agent-based simulation using reproductive and ecological data to model realistic reef dynamics. Our model suggests the hybrid can facilitate introgression between parentals without outcompeting them. Yet, such introgression is too limited for large-scale or beneficial ancestry transfer except under ecologically unrealistic conditions or timescales significantly longer than those relevant for management. Thus, our model suggests that the risks of genetic swamping may be overstated, whereas hopes for adaptive introgression are also low, underscoring the value of simulations for generating long-term ecological and evolutionary insights relevant to coral restoration.

bioinformatics↗

bioRxiv2025

Heat-responsive dynamic shifts in alternative splicing of the coral Acropora cervicornis

Climate change has caused drastic declines in corals. As sessile organisms, response to shifting environmental conditions may include changes in gene expression, epigenetic modifications, or the microbiome, but as of yet, a common mechanism of stress response, alternative splicing (AS), has been underexplored in corals. Using short-term acute thermal stress assays, we investigated patterns of AS in the scleractinian coral Acropora cervicornis during response to and a subsequent overnight recovery phase from low (33), medium (35), and high (37) levels of heat stress. We find that 40% of the genomic gene set is subject to AS. Our findings demonstrate conserved and dynamic shifts in splicing profiles during the heat treatment and subsequent recovery phase. AS increased in response to heat stress and was primarily dominated by intron retention in specific classes of transcripts, including those related to splicing regulation itself. While AS returned to baseline levels post-exposure to low heat, AS persisted even after reprieve from higher levels of heat stress. Partial overlap of AS transcripts with differentially expressed genes suggests that AS may represent a distinct and previously underappreciated regulatory mechanism for thermal stress response in corals.

genomics↗

bioRxiv2024

Genomes of the Caribbean reef-building corals Colpophyllia natans, Dendrogyra cylindrus, and Siderastrea siderea

Corals populations worldwide are declining rapidly due to elevated ocean temperatures and other human impacts. The Caribbean harbors a high number of threatened, endangered, and critically endangered coral species compared to reefs of the larger Indo-Pacific. The reef corals of the Caribbean are also long diverged from their Pacific counterparts and may have evolved different survival strategies. Most genomic resources have been developed for Pacific coral species which may impede our ability to study the changes in genetic composition of Caribbean reef communities in response to global change. To help fill the gap in genomic resources, we used PacBio HiFi sequencing to generate the first genome assemblies for three Caribbean, reef-building corals, Colpophyllia natans, Dendrogyra cylindrus, and Siderastrea siderea. We also explore the genomic novelties that shape scleractinian genomes. Notably, we find abundant gene duplications of all classes (e.g., tandem and segmental), especially in S. siderea. This species has one of the largest genomes of any scleractinian coral (822Mb) which seems to be driven by repetitive content and gene family expansion and diversification. As the genome size of S. siderea was double the size expected of stony corals, we also evaluated the possibility of an ancient whole genome duplication using Ks tests and found no evidence of such an event in the species. By presenting these genome assemblies, we hope to develop a better understanding of coral evolution as a whole and to enable researchers to further investigate the population genetics and diversity of these three species.

evolutionary biology↗

bioRxiv2023

Genome assemblies and genetic maps highlight chromosome-scale macrosynteny in Atlantic acroporids

BackgroundCorals belong to the Cnidaria, an early branching phylum of metazoans. Over the course of their long evolutionary history, they have adapted to changing environments, such as rising sea levels and increasing ocean temperatures. While their history speaks to their evolutionary capacity, it is less clear how quickly they may respond to rapid changes. A critical aspect of adaptive capacity is the structure of their genome and the genetic diversity contained within. FindingsHere, we present chromosome-scale genome assemblies and genetic linkage maps of two critically endangered coral species, Acropora palmata and A. cervicornis, the two extant Atlantic acroporid corals. Genomes of both species were resolved into 14 chromosomes with comparable assembly sizes (A. palmata, 287Mb; A. cervicornis, 305Mb). Gene content, repeat content, gene collinearity and macrosynteny were largely preserved between the Atlantic acroporids but a 2.5 Mb inversion and 1.4 Mb translocation were detected between two of the chromosome pairs. Macrosynteny and gene collinearity decreased when comparing Atlantic with Pacific acroporids. Paracentric inversions of whole chromosome arms characterized A. hyacinthus, specifically. In the larger context of cnidarian evolution, the four acroporids and another scleractinian coral with chromosome-resolved genome assemblies retained six of 21 cnidarian ancestral linkage groups, while also privately sharing numerous ALG fission and fusion events compared to other distantly related cnidarians. Genetic linkage maps were built using a 30K genotyping array with 105 offspring in one family for A. palmata and 154 offspring across 16 families for A. cervicornis. The A. palmata consensus linkage map spans 1,013.42 cM and includes 2,114 informative markers. The A. cervicornis consensus map spans 927.36 cM across 4,859 markers. A. palmata and A. cervicornis exhibited similarly high sex-averaged genome-wide recombination rates (3.53 cM/Mb and 3.04 cM/Mb, respectively) relative to other animals. In our gamete-specific maps, we found pronounced sex-based differences in recombination, known as heterochiasmy, in this simultaneous hermaphrodite, with both species showing recombination rates 2-2.5X higher in eggs compared to sperm. ConclusionsThe genomic resources presented here are the first of their kind available for Atlantic coral species. These data sets revealed that adaptive capacity of endangered Atlantic corals is not limited by their recombination rates, with both species exhibiting high recombination rates and heterochiasmy. Nevertheless, the two sister species maintain high levels of macrosynteny and gene collinearity between them. The few large-scale rearrangements detected deserve further study as a potential cause of fertilization barriers between the species. Together, the assemblies and genetic maps presented here now enable genome-wide association studies and discovery of quantitative trait loci; tools that can aid in the conservation of these endangered corals.

evolutionary biology↗

bioRxiv2019

Population structure and clonal prevalence of scleractinian corals (Montipora capitata and Porites compressa) in Kaneohe Bay, Oahu

As the effects of anthropogenic climate change grow, mass coral bleaching events are expected to increase in severity and extent. Much research has focused on the environmental stressors themselves, symbiotic community compositions, and transcriptomics of the coral host. Globally, fine-scale population structure of corals is understudied. This study reports patterns of population structure and clonal prevalence found in Montipora capitata and Porites compressa in Kaneohe Bay, Oahu. Generated using ddRAD methods, genetic data reveals different patterns in each taxa despite them being exposed to the same environmental conditions. STRUCTURE and site-level pairwise FST analyses suggest population structure in M. capitata resembling isolation by distance. Mantel tests show strong, significant FST correlations in M. capitata in relation to geographic distance, water residence time, and salinity and temperature variability (range) at different time scales. STRUCTURE did not reveal strong population structure in P. compressa. FST correlation was found in P. compressa in relation to yearly average sea surface height. We also report high prevalence of clonal colonies in P. compressa in outer bay sites exposed to storms and high energy swells. Amongst only outer bay sites, 7 out of 23 sequenced individuals were clones of other colonies. Amongst all 47 sequenced P. compressa individuals, 8 were clones. Only one clone was detected in M. capitata. Moving forward, it is crucial to consider these preexisting patterns relating to genetic diversity when planning and executing conservation and restoration initiatives. Recognizing that there are differences in population structure and diversity between coral taxa, even on such small-scales, is important as it suggests that small-scale reefs must be managed by species rather than by geography.

ecology↗