Biology subjects

Baums, I.

Publications and source records attributed to Baums, I..

7 recordsLinked to original sources

bioRxiv2026

High relatedness in sexually produced restoration cohorts of the endangered elkhorn coral, Acropora palmata

Climate change is driving the decline of coral populations around the world such that many are unlikely to recover without human intervention. Assisted sexual reproduction is one intervention proposed to enhance genetic diversity and support population recovery, yet its genetic outcomes remain poorly quantified. We evaluated genome-wide relatedness and genetic diversity in 168 restoration genets of the endangered Caribbean coral Acropora palmata, including 153 sexually produced offspring derived from multi-parent batch and biparental crosses. We detected high relatedness within multi-parent batch cross cohorts, with many genets comprising only one or a few full-sibling groups, indicating highly unequal parental contributions. Nucleotide diversity was lower in one batch cross cohort relative to founder populations, but the absolute difference was small and runs of homozygosity were relatively short indicating that inbreeding depression is not yet a concern. These patterns suggest that common larval propagation approaches can successfully generate large numbers of new genets but underscore the need to manage inbreeding risk, especially in small breeding stocks such as the Caribbean Acropora spp. Specifically, our results highlight the need for comprehensive genetic management to integrate assisted sexual reproduction into coral restoration, including parentage tracking, broodstock rotation, and relatedness-informed outplanting designs.

genomics↗

bioRxiv2026

Comparative somatic genomics reveals divergent development of cell lineages across scleractinian corals

Somatic mutations may drive adaptation and aging across diverse life forms, yet their role remains poorly understood in many early-branching animals. Here, we compare somatic mutation accumulation in the robust coral Orbicella faveolata with previous findings in the complex coral Acropora palmata. Whole-genome sequencing revealed high fixation of somatic genetic variants in O. faveolata, particularly in older, interior regions of colonies--contrasting with A. palmata. These patterns suggest distinct cell population dynamics between clades, indicating a segregated, mammal-like germline in O. faveolata, whereas such a germline remains undetected in A. palmata. This underscores the diversity of somatic evolutionary mechanisms across scleractinian corals.

genomics↗

bioRxiv2025

Mosaic accumulation of somatic genetic variation and estimates of age in the long-lived reef-building coral Acropora palmata

Somatic genetic variation (SOGV), accumulating during an organisms lifetime, was traditionally viewed as detrimental rather than adaptive due to links with cancer and senescence. However, in modular organisms like corals, deleterious mutations can be purged at the cellular or polyp level, while adaptive mutations may rise in frequency as polyps create genetically distinct modules. Quantifying the somatic genetic landscape in corals is necessary to understand the role these mutations may have in coral and clonal animal development and evolution. Here, we catalog somatic genetic variation in eight Acropora palmata colonies from Curacao. Whole genomes were sequenced (70-100x depth), documenting mutation variant allele frequency shifts as genets aged. Large numbers of SOGVs were observed in six- to ten-year-old colonies, and inferred mutation rates were used to age a genet of uncertain age to almost a century old. Although mutations were not fixed at the polyp or branch levels, i.e. they always displayed frequencies <0.5 as expected at mutating homozygous sites, their allele frequencies followed a power-law distribution, similar to aging human tissues. No signs of positive selection were found; instead SOGVs in the colony of uncertain age were under purifying selection. In one colony, mutations in 28 samples from along a branch were analyzed using a SNP microarray. Contrary to expectations, genetic and physical distances were unrelated. This observation together with the observed lack of fixation may be explained by a large stem cell population, the de-differentiation or dormancy of stem cells, the contribution of strong purifying selection, or a combination of the previously mentioned. Our findings provide a neutral framework against which to test for module-level selection of genetic variation in corals, explore the relationship between physical and genetic distance within a colony, and apply a somatic genetic clock to colonies of Acropora palmata. This work provides necessary fundamental insights into the landscape of somatic mutations in reef-building coral, highlighting the importance of studying these mutations as they may contribute to genetic diversity and adaptability in colonial animals.

genomics↗

bioRxiv2025

Assisted gene flow yields Acropora palmata corals with robust physiological performance under warmer water temperatures in a land-based nursery

Assisted gene flow (AGF) is a conservation approach that facilitates the spread of alleles and may accelerate the recovery of genetically depauperate cohorts. The threatened Caribbean coral Acropora palmata is approaching regional extinction within the western Atlantic partly due to increasing water temperatures associated with global climate change. Previously, AGF was conducted by crossing gametes collected from three regions (Curacao - CU, Florida - FL, and Puerto Rico - PR) characterized by contrasting temperature regimes and low gene flow between them. Here, we tested the thermal tolerance of these AGF cohorts in comparison to purebred Florida and Curacao cohorts. Exposure to high temperatures resulted in few physiological changes, likely because the corals hosted the thermally tolerant algal symbiont, Durusdinium trenchii. However, the FL x FL cohort was the most sensitive to the high temperatures with a significant reduction in net photosynthesis and maximum electron transport rate under this treatment. Like the phenotypic responses, gene expression changes in response to heat stress were muted overall. Consequently, there was little power to detect correlations between genotype and phenotype. Relative to mid-parent values, CUxFL AGF cohorts showed 26 overexpressed and 48 underexpressed genes. Differentially expressed genes included known stress responders. Importantly, hybrid crosses harbored 879 private alleles that were previously not recovered in representative genets from Florida and thus carry important conservation value. These findings suggest that AGF corals not only carry novel alleles but also represent novel gene expression patterns.

ecology↗

bioRxiv2020

STAGdb: a 30K SNP genotyping array and Science Gateway for Acropora corals and their dinoflagellate symbionts

Standardized identification of genotypes is necessary in animals that reproduce asexually and form large clonal populations such as coral. We developed a high-resolution hybridization-based genotype array coupled with an analysis workflow and database for the most speciose genus of coral, Acropora, and their symbionts. We designed the array to co-analyze host and symbionts based on bi-allelic single nucleotide polymorphisms (SNP) markers identified from genomic data of the two Caribbean Acropora species as well as their dominant dinoflagellate symbiont, Symbiodinium fitti. SNPs were selected to resolve multi-locus genotypes of host (called genets) and symbionts (called strains), distinguish host populations and determine ancestry of the coral hybrids in Caribbean acroporids. Pacific acroporids can also be genotyped using a subset of the SNP loci and additional markers enable the detection of symbionts belonging to the genera Breviolum, Cladocopium, and Durusdinium. Analytic tools to produce multi-locus genotypes of hosts based on these SNP markers were combined in a workflow called the Standard Tools for Acroporid Genotyping (STAG). In the workflow the users data is compared to the database of previously genotyped samples and generates a report of genet identification. The STAG workflow and database are contained within a customized Galaxy environment (https://coralsnp.science.psu.edu/galaxy/), which allows for consistent identification of host genet and symbiont strains and serves as a template for the development of arrays for additional coral genera. STAG data can be used to track temporal and spatial changes of sampled genets necessary for restoration planning as well as be applied to downstream genomic analyses.

genetics↗

bioRxiv2019

What drives phenotypic divergence among coral clonemates?

Evolutionary rescue of populations depends on their ability to produce phenotypic variation that is heritable and adaptive. DNA mutations are the best understood mechanisms to create phenotypic variation, but other, less well-studied mechanisms exist. Marine benthic foundation species provide opportunities to study these mechanisms because many are dominated by isogenic stands produced through asexual reproduction. For example, Caribbean acroporid corals are long lived and reproduce asexually via breakage of branches. Fragmentation is often the dominant mode of local population maintenance. Thus, large genets with many ramets (colonies) are common. Here, we observed phenotypic variation in stress response within genets following the coral bleaching events in 2014-and 2015 caused by high water temperatures. This was not due to genetic variation in their symbiotic dinoflagellates (Symbiodinium fitti) because each genet of this coral species typically harbors a single strain of S. fitti. Characterization of the microbiome via 16S tag sequencing did not provide evidence for a central role of microbiome variation in determining bleaching response. Instead, epigenetic changes were significantly correlated with the hosts genetic background, the position of the sampled polyps within the colonies (e.g. branch versus base of colony), and differences in the colonies condition during the bleaching event. We conclude that microenvironmental differences in growing conditions led to long-term changes in the way the ramets methylated their genomes contributing to, but not fully explaining, the differential bleaching response. This research provides novel data to understanding intra-genet variability in stress phenotypes of sessile marine species.

evolutionary biology↗

bioRxiv2018

Genomic variants among threatened Acropora corals

Genomic sequence data for non-model organisms are increasingly available requiring the development of efficient and reproducible workflows. Here, we develop the first genomic resources and reproducible workflows for two threatened members of the reef-building coral genus Acropora. We generated genomic sequence data from multiple samples of the Caribbean A. cervicornis (staghorn coral) and A. palmata (elkhorn coral), and predicted millions of nucleotide variants among these two species and the Pacific A. digitifera. A subset of predicted nucleotide variants were verified using restriction length polymorphism assays and proved useful in distinguishing the two Caribbean Acroporids and the hybrid they form (\"A. prolifera\"). Nucleotide variants are freely available from the Galaxy server (usegalaxy.org), and can be analyzed there with computational tools and stored workflows that require only an internet browser. We describe these data and some of the analysis tools, concentrating on fixed differences between A. cervicornis and A. palmata. In particular, we found that fixed amino acid differences between these two species were enriched in proteins associated with development, cellular stress response and the hosts interactions with associated microbes, for instance in the Wnt pathway, ABC transporters and superoxide dismutase. Identified candidate genes may underlie functional differences in the way these threatened species respond to changing environments. Users can expand the presented analyses easily by adding genomic data from additional species as they become available.\n\nArticle SummaryWe provide the first comprehensive genomic resources for two threatened Caribbean reef-building corals in the genus Acropora. We identified genetic differences in key pathways and genes known to be important in the animals response to the environmental disturbances and larval development. We further provide a list of candidate loci for large scale genotyping of these species to gather intra- and interspecies differences between A. cervicornis and A. palmata across their geographic range. All analyses and workflows are made available and can be used as a resource to not only analyze these corals but other non-model organisms.

genomics↗