Biology subjects

Toonen, R. J.

Publications and source records attributed to Toonen, R. J..

17 recordsLinked to original sources

bioRxiv2026

Regional connectivity and viability selection in a range-expanding marine species

Identifying spatial and temporal patterns of connectivity among populations is fundamental to marine ecology, evolutionary biology, and fisheries management. Yet, due to large population sizes and low genetic differentiation among populations, empirical quantification of population connectivity across a species entire range has not been achieved for an open-coast marine organism. Here, we leverage experimental transcriptomics to develop a genotyping-in-thousands by sequencing (GT-seq) panel to support assignment of recruits of the kelp forest gastropod, Kellets whelk (Kelletia kelletii), collected across the species biogeographic range. Over a three-year period, we identified high self-recruitment in the historical range (100%) and low self-recruitment in the expanded range (10.53 - 13.73%). Additionally, self-recruitment within the expanded range generally increased with recruit age, from 27.14% at 0.93 years to 43.40% at 1.93 years, indicating that the locally spawned individuals were more likely to survive to older ages than migrants from the historical range. Together, these results reveal limited self-recruitment in the expanded range and suggest that a post-settlement selective filter contributes to differential survival in a high gene flow marine system.

evolutionary biology↗

bioRxiv2025

Proteomic insights into the photobiology of the Hawaiian rice coral Montipora capitata in response to decreased light intensity

Reef-building corals are sessile marine organisms that inhabit a wide range of light habitats along depth gradients. As coral biology is often studied in the context of global change and changing temperatures, knowledge gaps persist in our understanding of the molecular and cellular pathways involved in the responses to other factors than temperature, such as light intensity, which decreases exponentially in the water column and gradually changes the environment. To fill this gap, we tested the response of the Hawaiian rice coral Montipora capitata to decreased light intensity in a field experiment in K[a]neohe Bay, Oahu, Hawaii, using Data-Independent Acquisition (DIA) proteomics. There was a significant effect of light intensity on both the coral and zooxanthellae proteomes. In the M. capitata host, 69 proteins differed significantly in abundance between light levels after two years. The 50 proteins identified as significantly more abundant in the control condition were mostly involved in mRNA and RNA processing, pointing toward a positive correlation between metabolic activity, growth rates and increased light levels. The 19 proteins identified as significantly more abundant in the shade treatment were associated with calcium transport and with the structure of key cellular components, such as cell membrane and cytoskeleton. By contrast, zooxanthellae showed only minor changes in protein abundances, with photosynthesis proteins more abundant in the shade treatment and enzymes involved in fatty acid metabolism more abundant in the control treatment. Overall, these findings establish a baseline for our understanding of the cellular and metabolic processes driving Montipora capitatas acclimatization potential to different light intensities.

ecology↗

bioRxiv2025

Demographic insights for coral restoration

O_LICoral reef decline has prompted a global surge in reef restoration initiatives. The success of initiatives that aim to sustain coral populations or assemblages will depend on demographic principles. Restoration strategies generally follow two demographic pathways: supplemental approaches, which increase population numbers through the repeated addition of recruits, fragments, or adults, without fundamentally altering long-term population dynamics; and structural approaches, which enhance vital rates-growth, survival, or reproduction- through changes that modify the demographic processes governing population growth on a sustained basis, either extrinsically (e.g., herbivory, habitat protection) or intrinsically (e.g., assisted evolution). Some interventions, such as supplemental feeding, may temporarily improve vital rates but still function as supplemental approaches because benefits persist only while interventions continue. C_LIO_LIWe synthesized 28 coral matrix population models spanning morphologically diverse coral species from the Caribbean, Hawaii, and the Great Barrier Reef to quantify supplemental and structural changes needed to increase population growth. C_LIO_LIResults highlight two consistent demographic leverage points for which population growth was most sensitive: (1) survival of reproductive adults and (2) successful recruitment. Improving adult survival or recruitment by 20% through structural means produced a 5% increase in population growth rate across population on average, assuming the whole population was affected. By contrast through supplemental means, the same increase required [~]100 recruit outplants or 5-10 adult outplants per 1,000 individuals in a population annually. For large populations typical of restoration targets (105-107 individuals), this translates to 103 adult and 104 recruit outplants per year--levels rarely logistically or economically feasible. C_LIO_LIThese findings yield two key implications. First, supplemental interventions are inefficient for large populations and demand sustained, large-scale effort, even when they temporarily enhance growth or survival. Second, strategies enhancing vital rates across broad geographic areas represent the most effective means of boosting coral abundance, including habitat protection, alleviation of environmental stressors, and interventions which promote long-term survival and recruitment. Our demographic framework underscores that if the restoration goal is sustained increases in coral cover, success depends less on repeated supplements and more on interventions that produce lasting improvements in vital rates. C_LI

ecology↗

bioRxiv2025

Growth rate and adaptive capacity, not just thermal tolerance, are critical for long-term coral persistence under climate change

It is widely assumed that corals with a narrower thermal tolerance and greater bleaching susceptibility are at most risk under anthropogenic climate change. Using a simple eco-evolutionary model, we investigate coral reef futures under climate change through a factorial approach, across millions of simulations. We find that, while corals with low thermal tolerance are indeed at greatest risk of population collapse in the short term, coral population persistence beyond 2050 is instead primarily determined by the maximum population growth rate and additive genetic variance. Anthropogenic climate change exceeds the thermal tolerance of all corals, so adaptive capacity and the ability to rapidly recover from disturbance are critical for long-term persistence. As a result, it is plausible that branching corals could fare better than slower growing, stress-tolerant counterparts in the long term, but only if they can weather the greater acute threats over the coming decades. Since the response timescale of corals to climate change varies considerably across taxa, and due to the particular importance of genetic variance in facilitating evolutionary adaptation, sustainable restoration approaches should aim to conserve a broad range of coral species and genotypes, rather than aiming to optimise one particular trait.

ecology↗

bioRxiv2024

Shifts in Coral Reef Holobiont Communities in the High-CO2 Marine Environment of Iotorishima Island

Ocean acidification (OA), driven by rising atmospheric CO2, presents a serious threat to marine biodiversity, especially within coral reef ecosystems. Natural analogue sites, such as the high-pCO2 seep at I[o]torishima Island in Japan, offer insights into future conditions. This study investigated the holobiont communities of Symbiodiniaceae and bacteria in the zoantharian Palythoa tuberculosa at I[o]torishima and compared them to specimens from control sites in Okinawa and Hawaii. Using amplicon sequencing of the dinoflagellate internal transcribed spacer 2 (ITS2) region of ribosomal DNA and microbial 16S rRNA gene, we detected significant shifts in both Symbiodiniaceae and bacterial communities under high-pCO2 conditions at I[o]torishima. Specifically, P. tuberculosa at the seep site had reduced Symbiodiniaceae diversity, predominatly featuring Cladocopium C1 and C3 types. Additionally, its bacterial communities showed lower richness with distinct taxonomic profiles, including increased levels of Mollicutes and Vibrio spp. These results highlight the potentially adverse effects of OA on hexacoral holobionts and emphasize the need for detailed, high-resolution studies across various holobiont species and geographic locations. The shifts observed specifically in Symbiodiniaceae and bacterial communities at the I[o]torishima Seep suggest that holobionts may exhibit plasticity in response to environmental stress, which has implications for resilience and adaptation of zoantharians and other reef organisms amid climate change. This research provides crucial baseline data for predicting future coral reef compositions in an OA-affected world.

microbiology↗

bioRxiv2024

Shading does not lower thermal tolerance in the coral Montipora capitata: implications for conservation intervention

Marine heatwaves trigger severe coral bleaching events that result in dramatic losses of coral reefs worldwide. An increasingly common method used to mitigate coral bleaching is to shade portions of reefs. However, as shaded corals become less exposed to environmental stress, shading has also been hypothesized to lower their thermal tolerance, which would be detrimental for their survival. Here, we investigated how long-term shading modifies the response of Montipora capitata to both light and temperature stressors. After two years of growth, we used the Coral Bleaching Automated Stress System (CBASS) to compare responses of 73% shaded and unshaded corals during 1) temperature stress under ambient light, 2) temperature stress under low light, and 3) ambient temperature with light stress. Results show that shaded corals are less resistant than control ones to light stress and to heat stress under high light, but not to heat stress under low light, where no difference was detected. We further demonstrate that low light intensity during heat stress reduces the decline of photosynthetic efficiency when compared to heat stress at ambient light, regardless of the light history of the coral colonies. Our data support light-mediated stress, both independent of and synergistic with heat-induced stress, and suggest that light and heat stresses trigger different molecular and cellular pathways. We hereby confirm the benefits of coral shading under both short- and long-term temperature stress, and underline the importance of light acclimation in the conservation and restoration of coral reefs.

ecology↗

bioRxiv2024

Genomic divergence of sympatric lineages within Stichopus cf. horrens (Echinodermata: Stichopodidae): Insights on reproductive isolation inferred from SNP markers

How reproductive barriers arise in early stages of divergence among broadcast spawning organisms that exist in sympatry remains poorly understood. Reproductively isolated lineages (Clade A and B) of Stichopus cf. horrens were previously reported across the western Pacific, with an additional putative cryptic species detected within Clade B lineage warranting further examination. The present study further examines the hypothesis that the two mitochondrial lineages (Clade A and Clade B) of Stichopus cf. horrens represent putative cryptic species and whether another cryptic species within the Clade B lineage exists using a reduced representation genomic approach. Using double-digest RAD (ddRAD) sequencing, a total of 9,788 single nucleotide polymorphism (SNP) markers were used to examine divergence among Stichopus cf. horrens lineages (n = 82). Individuals grouped into three SNP genotype clusters, broadly concordant with their mitochondrial lineages and microsatellite genotype clusters, with limited gene flow inferred among clusters. Outlier analysis recovered highly divergent SNP loci with significant homology to proteins related to rhodopsin and tachykinin receptor signaling, sperm motility, transmembrane transport and hormone response. This study confirms the existence of three reproductively isolated genotype clusters within Stichopus cf. horrens and highlights gene regions related to reproduction that may contribute to establishing reproductive barriers between broadcast spawning species at an early stage of divergence.

evolutionary biology↗

bioRxiv2024

assessPool: a fexible pipeline for population genomic analyses of pooled sequencing data

Despite the dramatic decrease in high-throughput sequencing costs over time, sequencing the ideal number of individuals for population genetic inference remains prohibitively expensive. When research questions require only population-level resolution, pooling individual samples before sequencing (pool-seq) can substantially reduce costs while still providing allele frequencies of Single Nucleotide Polymorphisms (SNPs). However, analyzing pooled data is comparatively difficult and less standardized than individual-based analyses. Although several programs have been developed to handle pool-seq data, most require extensive formatting or programming skills to operate. Here we introduce assessPool, an open-source R and Bash pipeline for pool- seq analyses with a focus on population structure. AssessPool accepts a Variant-Call Format (VCF) file and a FASTA-formatted reference, providing a straightforward transition from commonly used pipelines such as Stacks or dDocent. AssessPool handles varying numbers of pools and utilizes PoPoolation2 to generate locus-by-locus pairwise FST values and associated Fisher T-test values as measures of population structure. Starting with a VCF file containing all identified SNPs, assessPool facilitates several key functionalities for population genetic analyses: i) filtering SNPs based on adjustable criteria with parameter suggestions for pool-seq data, ii) organizing data structures for analysis based on input pools, iii) creating customizable run scripts for FST calculations using PoPoolation2 and/or the {poolfstat} R package, for all pairwise comparisons, iv) calculating locus-specific FST values using PoPoolation2 and/or {poolfstat}, v) importing FST output into a format compatible with R, vi) producing population genomic summary statistics, and vii) generating interactive plots to visualize and explore data. A pooled dataset generated from wild populations is used here to showcase the features of the assessPool pipeline for population genomic analyses.

bioinformatics↗

bioRxiv2024

Coral microbiomes from the Atlantic and Indo-Pacific oceans have the same alpha diversity but different composition

Corals are early-branching animals highly reliant on diverse symbionts for growth and reproduction. Most coral groups, including stony corals and hydrocorals, exhibit deep genetic divergence between the Atlantic (ATO) and Indo-Pacific (IPO) oceans, hampering their direct comparison. Although sibling zoanthid species (Hexacorallia: Zoantharia) deviate from this pattern, their symbioses have so far only been studied on local scales. Here, we examined the microbiomes of Palythoa caribaeorum from the ATO and P. tuberculosa from the IPO. Our extensive geographical sampling and metabarcoding revealed that Palythoa microbiomes have similar alpha diversity in both oceans. The primary exceptions are the symbiodiniacean Cladocopium and Chlamydiae bacteria, which mirror the global diversity patterns of corals. Despite distinct overall microbial compositions between oceans, some regions shared remarkably similar communities, hinting at the importance of both symbiont phylogeny and function. Finally, we explore the shift from commensal/mutualistic microbes to opportunistic pathogens, crucial amid the ongoing environmental changes.

microbiology↗

bioRxiv2023

Genomic DNA extraction optimization and validation for genome sequencing using the marine gastropod Kellet's whelk

Next-generation sequencing technologies, such as Nanopore MinION, Illumina Hiseq and Novaseq, and PacBio Sequel II, hold immense potential for advancing genomic research on non-model organisms, including the vast majority of marine species. However, application of these technologies to marine invertebrate species is often impeded by challenges in extracting and purifying their genomic DNA due to high polysaccharide content and other secondary metabolites. In this study, we help resolve this issue by developing and testing DNA extraction protocols for Kellets whelk (Kelletia kelletii), a subtidal gastropod with ecological and commercial importance, by comparing four DNA extraction methods commonly used in marine invertebrate studies. We identified an optimized protocol that balances efficiency, cost, and DNA extraction quality; the Salting out protocol. We validated the protocol using an independent set of tissue samples, then applied it to extract high-molecular-weight (HMW) DNA from over three thousand Kellets whelk tissue samples. The protocol demonstrated scalability and, with added clean-up, suitability for RAD-seq, GT-seq, as well as whole genome sequencing using both long read (ONT MinION) and short read (Illumina Novaseq) sequencing platforms. Our findings offer a robust and versatile DNA extraction and clean-up protocol for supporting genomic research efforts on non-model marine organisms, to help mediate the under-representation of invertebrates in genomic studies.

genomics↗

bioRxiv2022

Metadata preservation and stewardship for genomic data is possible, but must happen now

Genetic diversity within species represents a fundamental yet underappreciated level of biodiversity. Because genetic diversity can indicate species and population resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies of evolutionary biology, molecular ecology and conservation genetics produce large amounts of genome-scale genetic diversity data for wild populations. While open data policies have ensured an abundance of freely available genomic data stored in the databases of the International Nucleotide Sequence Database Collaboration (INSDC), only about 13% of current accessions have the associated spatial and temporal metadata in INSDC necessary to be reused in monitoring programs, macrogenetic studies, or for acknowledging the sovereignty of nations or Indigenous Peoples. We undertook a "distributed datathon" to quantify the availability of these missing metadata in sources external to the INSDC and to test the hypothesis that these metadata decay with time. We also worked to remediate these missing metadata by extracting them, when present, from associated published papers, online repositories, and/or from direct communication with authors. Starting with 848 programmatically identified candidate datasets (INSDC BioProjects), we manually determined that 561 contained samples from wild populations. We successfully restored spatiotemporal metadata (locality name and/or geospatial coordinates and collection year) for 78% of these 561 datasets (N = 440 BioProjects comprising 45,105 individuals or BioSamples from 762 species in 17 phyla). We also quantified the availability of 33 additional categories of metadata in sources external to the INSDC. Information about associated publications and the type of habitat from which the samples were taken was the most easily found; information about sampling permits was the most challenging to locate. Looking at papers and online repositories was much more fruitful than contacting authors, who only replied to our email requests 45% of the time. Overall, 23% of our email queries to authors discovered useful metadata. Importantly, we found that the probability of retrieving spatiotemporal metadata declines significantly with the age of the dataset, with a 13.5% yearly decrease for metadata located in published papers or online repositories and up to a 22% yearly decrease for metadata that were only available from authors. This observable metadata decay, mirrored in studies of other types of biological data, should motivate swift updates to data sharing policies and researcher practices to ensure that the valuable context provided by metadata is not lost forever.

bioinformatics↗

bioRxiv2022

Coral environmental history is primary driver of algal symbiont composition, despite a mass bleaching event

Coral reefs are iconic examples of climate change impacts because climate-induced heat stress causes the breakdown of the coral-algal symbiosis leading to a spectacular loss of color, termed coral bleaching. To examine the fine-scale dynamics of this process, we re-sampled 600 individually marked Montipora capitata colonies from across K[a]ne ohe Bay, Hawaii and compared the algal symbiont composition before and after the 2019 bleaching event. The relative proportion of the heat-tolerant symbiont Durusdinium in corals increased in most parts of the bay following the bleaching event. Despite this widespread increase in abundance of Durusdinium, the overall algal symbiont community composition was largely unchanged, and hydrodynamically defined regions of the bay retained their distinct pre-bleaching compositions. Furthermore, depth and temperature variability were the most significant drivers of Symbiodiniaceae community composition by site regardless of bleaching intensity or change in relative proportion of Durusdinium. Our results suggest that the plasticity of symbiont composition in corals may be constrained to adaptively match the long-term environmental conditions surrounding the holobiont, independent of an individual corals stress and bleaching response.

ecology↗

bioRxiv2021

Community composition of coral associated Symbiodiniaceae is driven by fine scale environmental gradients

The survival of reef-building corals is dependent upon a symbiosis between the coral and the community of Symbiodiniaceae. Montipora capitata, one of the main reef building coral species in Hawaii, is known to host a diversity of symbionts, but it remains unclear how they change spatially and whether environmental factors drive those changes. Here, we surveyed the Symbiodiniaceae community in 600 M. capitata colonies from 30 sites across K[a]neohe Bay and tested for host specificity and environmental gradients driving spatial patterns of algal symbiont distribution. We found that the Symbiodiniaceae community differed markedly across sites, with M. capitata in the most open-ocean (northern) site hosting few or none of the genus Durusdinium, whereas individuals at other sites had a mix of Durusdinium and Cladocopium. Our study shows that the algal symbiont community composition responds to fine-scale differences in environmental gradients; depth and temperature variability were the most significant predictor of Symbiodiniaceae community, although environmental factors measured in the study explained only about 20% of observed variation. Identifying and mapping Symbiodiniaceae community distribution at multiple scales is an important step in advancing our understanding of algal symbiont diversity, distribution and evolution, and the potential responses of corals to future environmental change.

ecology↗

bioRxiv2020

Genomic divergence and differential gene expression between crustacean ecotypes across a marine thermal gradient

Environmental gradients between marine biogeographical provinces separate distinct faunal communities; in the absence of absolute dispersal barriers numerous species nonetheless occur on either side of such boundaries. While the regional populations of such widespread species tend to be morphologically indistinguishable from each other, genetic evidence suggests that they represent unique ecotypes, and likely even cryptic species, that may be uniquely adapted to their local environment. Here, we explored genomic divergence in four sympatric southern African decapod crustaceans whose ranges span the boundary between the cool-temperate west coast (south-eastern Atlantic) and the warm-temperate south coast (south-western Indian Ocean) near the southern tip of the African continent. Using genome-wide data, we found that all four species comprise distinct west- and south coast ecotypes, with molecular dating suggesting divergence during the Pleistocene. Using transcriptomic data from one of the decapod crustaceans, we further found a clear difference in gene expression profiles between the west- and south coast ecotypes. This was particularly clear in the individual from the south coast, which experienced a transcriptomic shock at low temperatures that are more typical of the west coast and may explain their absence from that coastline. Our results shed new light on the processes involved in driving genomic divergence and incipient speciation.

genomics↗

bioRxiv2019

Genetic structure is stronger across human-impacted habitats than among islands in the coral Porites lobata

We examined genetic structure in the lobe coral Porites lobata among pairs of highly variable and high-stress nearshore sites and adjacent less variable and less impacted offshore sites on the islands of Oahu and Maui, Hawai i. Using an analysis of molecular variance framework, we tested whether populations were more structured by geographic distance or environmental extremes. The genetic patterns we observed followed isolation by environment, where nearshore and adjacent offshore populations showed significant genetic structure at both locations (AMOVA FST = 0.04 [~] 0.19, P < 0.001), but no significant isolation by distance between islands. In contrast, a third site with a less impacted nearshore site showed no significant structure. Strikingly, corals from the two impacted nearshore sites on different islands over 100km apart with similar environmentally stressful conditions were genetically closer (FST[~] 0, P = 0.733) than those within a single location less than 2 km apart (FST= 0.041[~]0.079, P < 0.01). Our results suggest that ecological boundaries appear to play a strong role in forming genetic structure in the coastal environment, and that genetic divergence in the absence of geographical barriers to gene flow may be explained by disruptive selection across contrasting habitats.

genetics↗

bioRxiv2018

High-frequency temperature variability mirrors fixed differences in thermal limits of the massive coral Porites lobata (Dana, 1846)

Spatial heterogeneity in environmental characteristics can drive adaptive differentiation when contrasting environments exert divergent selection pressures. This environmental and genetic heterogeneity can substantially influence population and community resilience to disturbance events. Here, we investigated corals from the highly variable back reef habitats of Ofu Island in American Samoa that thrive in thermal conditions known to elicit widespread bleaching and mortality elsewhere. To investigate the hypothesis that thermal variability is the driving force shaping previously observed differences in coral tolerance limits in Ofu, specimens of the common Indo-Pacific coral Porites lobata (Dana, 1846) from locations with differing levels of thermal variability were acclimated to low and high thermal variation in controlled common garden experimental aquaria. Overall, there was minimal effect of the acclimation exposure. Corals native to the site with the highest level of daily variability grew fastest, regardless of acclimation treatment. When exposed to lethal thermal stress, corals native to both variable sites contained elevated levels of heat shock proteins and maintained photosynthetic performance for 1-2 days longer than corals from the stable environment. Despite being separated by < 5 km, there was significant genetic differentiation among coral colonies (FST = 0.206, p < 0.0001; nuclear ribosomal DNA), while Symbiodinium phylotypes were all ITS2-type C15. Our study demonstrates consistent signatures of adaptation in growth and stress resistance in corals from naturally thermally variable habitats, emphasizing that existing genetic diversity of corals is an important asset in strategies to protect and manage coral reef ecosystems in the face of global change.\n\nSummary StatementCorals native to highly variable habitats demonstrate greater thermal tolerance than corals from less variable habitats after 36-days of acclimation to thermally stable or variable common garden treatments.

evolutionary biology↗

bioRxiv2017

Divergence times in demosponges (Porifera): firstinsights from new mitogenomes and the inclusion offossils in a birth-death clock model

Approximately 80% of all recent sponge species belong to the class Demospongiae. Yet, despite their diversity and importance, accurate divergence times are still unknown for most demosponge clades. The estimation of demosponge divergence time is key to answering fundamental questions like e.g. the origin of Demospongiae, their diversification and historical biogeography. Molecular sequence data alone is not informative on an absolute time scale, and therefore needs to be \"calibrated\" with additional data such as fossils. Here, we apply the fossilized birth-death model (FBD), which has the advantage, compared to strict node dating with the oldest fossil occurrences, that it allows for the inclusion of young and old fossils in the analysis of divergence time. We use desma-bearing sponges, a diverse group of demosponges that form rigid skeletons and have a rich and continuous fossil record dating back to the Cambrian ([~]500 Ma), aiming to date the demosponge radiation and constrain the timing of key evolutionary events, like the transition from marine to freshwater habitats. To do so, we assembled mitochondrial genomes of six desma-bearing demosponges from size-selected reduced-representation genomic libraries and apply a fossilized birth-death model including 30 fossils and 33 complete demosponge mitochondrial genomes to infer a dated phylogeny of Demospongiae. Our study supports a Neoproterozoic origin of Demospongiae. Novel age estimates for the split of freshwater and marine sponges dating back to the Carboniferous and the previously assumed Recent ([~]18 Ma) diversification of freshwater sponges is supported. Moreover, we provide detailed age estimates for a possible diversification of Tetractinellidae ([~]315 Ma), the Astrophorina ([~]240 Ma), the Spirophorina ([~]120 Ma) and the family Corallistidae ([~]188 Ma) all of which are considered as key groups for dating the Demospongiae, due to their extraordinary rich and continuous fossil history.

evolutionary biology↗