Biology subjects

Okamoto, D. K.

Publications and source records attributed to Okamoto, D. K..

8 recordsLinked to original sources

bioRxiv2026

Environmental variability alters and obscures fisheries-induced evolution

Shifts in predation and human harvest often coincide with changes in life history trait distributions in prey populations. These changes may arise via evolution or plasticity, and extrinsic environmental effects may affect such traits. This complexity prompts questions about how trait distributions are shaped by multiple factors' interactions. We hypothesized that food availability and climate affect both the magnitude, and mechanism (evolution vs. plasticity), by which traits change in response to harvest's intensity and size selectivity. We tested these hypotheses using individual-based bioenergetic population models allowing both plasticity and evolution. We exposed genetically diverse fish populations to gradients of productivity and stochasticity in food availability, crossed with gradients of selective or nonselective fishing mortality. Food availability shaped traits both plastically and evolutionarily, and modulated how harvesting influenced those responses. Food effects can suppress harvest impacts altogether, or obscure evolution's effects on phenotypes. However, when climatic factors shape food-driven changes by affecting both fish and their prey, either synergistic or antagonistic interactions can emerge between food variation and harvest in determining phenotype distributions. Our research suggests that understanding consumer-resource dynamics, and climatic processes shaping them, is essential to interpreting how harvest can shape traits relevant to population viability and fisheries sustainability.

ecology↗

bioRxiv2025

Estimating Historical Food Web Variation in Chesapeake Bay Using Isotope Variation in Museum Fish Specimens

Trophic interactions are hypothesized to change in response to rapid anthropogenic environmental changes. Documenting these trends may aid biological conservation. One tool to measure trophic level is stable isotope analysis. Nitrogen isotope values ({delta}15N) of bulk tissue may be used as indirect indicators of an organisms trophic level and the isotopic composition of its prey. In contrast, compound-specific isotope analysis can estimate trophic level directly. For the fishes of Chesapeake Bay, museum collections provide a unique opportunity to characterize trophic trends collected as early as the 1850s, from an ecosystem that has been overfished and subjected to increasingly high nutrient loading and land use change during the past three centuries. To assess isotope data for evidence of change in predator species trophic level, we analyzed tissue from 183 museum specimens of three predators (Striped Bass, Morone saxatilis; Summer Flounder, Paralichthys dentatus; and Bluefish, Pomatomus saltatrix) and two lower-trophic-level species (Bay Anchovy, Anchoa mitchilli; and Menhaden, Brevoortia tyrannus). Predatory Striped Bass did not show an increase through time in {delta}15N values, despite such a trend in Bay Anchovy, suggesting possible change in trophic level. Analysis of Striped Bass tissue using compound specific analysis indicates their mean trophic level has been stable for decades. These findings imply that Striped Bass are part of a diverse food web within Chesapeake Bay beyond that reflected by our two included prey species and are stable through time in their average size-specific trophic level, a valuable insight into their ecological role.

ecology↗

bioRxiv2025

Nucleosome positioning and sensitivity suggest novel functional organization of the purple sea urchin (Strongylocentrotus purpuratus) genome

The eukaryotic nucleosome is the fundamental subunit of chromatin and plays functional roles in DNA templated processes, including replication and transcription. In eukaryotic promoters, nucleosome organization is highly structured, with nucleosomes occupying canonical positions flanking the transcription start site (TSS), thereby regulating access of the transcriptional machinery to the underlying DNA. We determine whether this canonical distribution is present in the purple sea urchin, Strongylocentrotus purpuratus, a species of ecological importance and a model organism for developmental biology and climate science. We used titrations of micrococcal nuclease to produce high throughput maps of nucleosome distribution and sensitivity to digestion from female urchin gonad tissue. Unlike yeast, flies, zebrafish, maize, mice or humans, urchins have extended nucleosome repeat lengths and lack a nucleosome depleted region over TSSs. Urchin promoters are dominated by strongly positioned and highly occupied +1 and +2 nucleosomes which are most prominent in highly expressed genes. Additionally, urchin promoters exhibit distinct patterns of susceptibility to nuclease digestion, with heightened sensitivity upstream of the TSS and limited resistance to nuclease digestion. Discretely positioned sensitive nucleosomes were enriched in promoters of highly expressed genes, suggesting a relationship between nucleosome sensitivity and transcriptional regulation. Collectively, we present a comprehensive overview of the unique interplay between nucleosome positioning and chromatin sensitivity in sea urchins. Our study not only provides a better understanding of dynamics of gene expression in a key developmental organism, but also reveals potential heterogeneity in a key structural property of chromatin previously thought to be homogeneous in model eukaryotes. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/653534v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@c724dforg.highwire.dtl.DTLVardef@45c163org.highwire.dtl.DTLVardef@19b6043org.highwire.dtl.DTLVardef@1ccf475_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2024

Biomarkers of recovery: characterizing trophic flow following ecological restoration

Coastal kelp forests are important sources of primary productivity and provide essential habitat and ecosystem services. In many areas around the world, the formation and persistence of urchin barrens threatens kelp forest ecosystems. Over the past several decades, restoration efforts have emerged aiming to increase the abundance of foundation species like kelp in such systems. However, we lack a comprehensive understanding of how successful kelp restoration affects the nutritional landscape and the fitness of kelp forest herbivores. We bridge this knowledge gap with a Before-After-Control-Impact Paired Series (BACIPS) focused on kelp forest restoration where reductions of herbivorous sea urchins in Haida Gwaii resulted in substantial increases in kelp abundance in habitat previously characterized as barrens. Specifically, we document body size specific shifts in the fatty acid (FA) profiles of red sea urchins (Mesocentrotus franciscanus) and northern abalone (Haliotis kamtschatkana). FAs associated with bacteria and diatoms were elevated in tissues of urchins and abalone in barrens habitat while kelp biomarkers were elevated in restored kelp forest habitat. For urchins, these shifts tracked the increase in gonad mass following kelp forest recovery. For abalone, these results varied depending on animal body size. Specifically, abalone exhibited a continuous size-specific shift from biofilm-associated markers at small sizes to kelp-associated markers as animals increased in size. For both species, a marked increase in essential fatty acids was observed following kelp restoration. Our results demonstrate kelp restoration via sea urchin reduction enhances not only the quantity but also the quality and diversity of food in previously degraded habitats, and subsequently enhances the amount and nutritional quality of roe (i.e., gonads) in sea urchins therein.

ecology↗

bioRxiv2024

A blueprint for national assessments of the blue carbon capacity of kelp forests applied to Canadas coastline

Kelp forests offer substantial carbon fixation, with the potential to contribute to natural climate solutions (NCS). However, to be included in national NCS inventories, governments must first quantify the kelp-derived carbon stocks and fluxes leading to carbon sequestration. Here, we present a blueprint for assessing the national carbon sequestration capacity of kelp forests in which data synthesis and Bayesian hierarchical modelling enable estimates of kelp forest carbon production, storage, and export capacity from limited data. Applying this blueprint to Canadas extensive coastline, we find kelp forests store an estimated 1.4 Tg C in short-term biomass and produce 3.1 Tg C yr-1 with modest carbon fluxes to the deep ocean. Arctic kelps had the highest carbon stocks and production capacity, while Pacific kelps had greater carbon fluxes overall due to their higher productivity and export rates. Our transparent, reproducible blueprint represents an important step towards accurate carbon accounting for kelp forests.

ecology↗

bioRxiv2019

The impact of Hurricane Michael on longleaf pine habitats in Florida

The longleaf pine (Pinus palustris) ecosystem of the North American Coastal Plain (NACP) is a global biodiversity hotspot. Disturbances such as tropical storms play an integral role in ecosystem maintenance in these systems. However, altered disturbance regimes as a result of climate change may be outside the historical threshold of tolerance. Hurricane Michael impacted the Florida panhandle as a Category 5 storm on October 10th, 2018. In this study, we estimate the extent of Florida longleaf habitat that was directly impacted by Hurricane Michael. We then quantify the impact of Hurricane Michael on tree density and size structure using a Before-After study design at four sites (two wet flatwood and two upland pine communities). Finally, we identify the most common type of tree damage at each site and community type. We found that 39% of the total remaining extent of longleaf pine habitat was affected by the storm in Florida alone. Tree mortality ranged from 1.3% at the site furthest from the storm center to 88.7% at the site closest. Most of this mortality was in mature sized trees (92% mortality), upon which much of the biodiversity in this habitat depends. As the frequency and intensity of extreme events increases, management plans that mitigate for climate change impacts need to account for large-scale stochastic mortality events in order to effectively preserve critical habitats.

ecology↗

bioRxiv2018

Geographically Opposing Responses of Sea Urchin Recruitment to Changes in Ocean Climate

Sea urchins are voracious herbivores that influence the ecological structure and function of nearshore ecosystems throughout the world. Like many species that produce planktonic larvae, their recruitment is thought to be particularly sensitive to climatic fluctuations in temperature that directly or indirectly affect adult reproduction and larval transport and survival. Yet how climate alters sea urchin populations in space and time by modifying larval recruitment and year-class strength on the time-scales that regulate populations remains understudied. Using a, spatially replicated weekly-biweekly dataset spanning 27 years and 1100 km of coastline, we characterized seasonal, interannual, and spatial patterns of larval settlement of the purple sea urchin (Strongylocentrotus purpuratus). We show that large spatial differences in temporal patterns of larval settlement were associated with different responses to fluctuations in ocean temperature and climate. Importantly, we found a strong correlation between larval settlement and regional year class strength suggesting that such temporal and spatial variation in settlement plays an important role in controlling population dynamics. These results provide strong evidence over extensive temporal and spatial domains that climatic fluctuations shape broad-scale patterns of larval settlement and subsequent population structure of an important marine herbivore known to control the productivity, community state and provisioning services of marine ecosystems.

ecology↗

bioRxiv2018

Spatial variation in exploited metapopulations obscures risk of collapse

Unanticipated declines among exploited species have commonly occurred despite harvests that appeared sustainable prior to collapse. This is particularly true in the oceans where spatial scales of management are often mismatched with spatially complex metapopulations. We explore causes, consequences and potential solutions for spatial mismatches in harvested metapopulations in three ways. First, we generate novel theory illustrating when and how harvesting metapopulations increases spatial variability and in turn masks local scale volatility. Second, we illustrate why spatial variability in harvested metapopulations leads to negative consequences using an empirical example of a Pacific herring metapopulation. Finally, we construct a numerical management strategy evaluation model to identify and highlight potential solutions for mismatches in spatial scale and spatial variability. Our results highlight that spatial complexity can promote stability at large scales, however ignoring spatial complexity produces cryptic and negative consequences for people and animals that interact with resources at small scales. Harvesting metapopulations magnifies spatial variability, which creates discrepancies between regional and local trends while increasing risk of local population collapses. Such effects asymmetrically impact locally constrained fishers and predators, which are more exposed to risks of localized collapses. Importantly, we show that dynamically optimizing harvest can minimize local risk without sacrificing yield. Thus, multiple nested scales of management may be necessary to avoid cryptic collapses in metapopulations and the ensuing ecological, social and economic consequences.

ecology↗