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Yoon, H. S.

Publications and source records attributed to Yoon, H. S..

9 recordsLinked to original sources

Bridging Ecological Inference and Decision Optimization for Conservation Using Artificial Intelligence

The ability to model the complex and uncertain population dynamics of endangered species has improved dramatically in recent decades. However, approaches to identify optimal decisions often require a simplified representation of population dynamics. This leads to a conundrum where managers may be unsure about the output of dynamic decision models because they rely on simplified assumptions of the underlying population dynamics. Here, by pairing integrated population models (IPM) that synthesize diverse ecological data with deep reinforcement learning (DRL) capable of optimizing decisions with high-dimensional uncertainty, we introduce a framework that delivers data-driven and ecologically detailed adaptive management strategies. We demonstrate its utility through application to the supplementation program for the endangered Rio Grande silvery minnow. Using our IPM-DRL framework, we developed an adaptive decision model that selects production and distribution decisions of the supplementation program in response to the observed demographic, hydrological, and genetic environment. The decision model outperformed all heuristic approaches in the simulation across management objectives that weighed persistence and effective population size-related genetic impact differently. For example, the currently deployed supplementation strategy performed 5.3% worse than the decision model under the persistence-focused objective scoring and 185% worse under the genetics-focused one. Analysis of the models decisions in relation to demographic and environmental covariates revealed that minimum sub-population size and total population size were primary drivers of the models decisions. The results demonstrate that the IPM-DRL framework offers a high-performing and interpretable decision-support tool for managing endangered species. SignificanceConservation problems, like imperiled species management, are often challenging because the system dynamics are complex and uncertain. We demonstrate how combining an integrated population model that infers key demographic processes from noisy ecological data with a deep reinforcement learning framework that optimizes management actions addresses these challenges by generating high-performing supplementation strategies for a conservation-dependent species. Our approach embeds two decades of monitoring data within a multi-objective decision-making environment that accounts for ecological uncertainty. The result is a generalizable framework that links ecological inference directly to actionable policy outcomes, enabling scientists and managers to move beyond describing system states and processes toward identifying optimal management actions.

ecology↗

Evolution of multicellularity and reproductive strategies in yellow-green algae (Xanthophyceae, Heterokontophyta)

The evolution of multicellularity has long been linked to reproductive strategies. A long-standing debate concerns whether multicellular organisms are primarily stabilized by small single-cell propagules that minimize genetic heterogeneity or by larger multicellular and multinucleate propagules that may improve developmental success and survival of individuals. the Xanthophyceae provides an excellent model for investigating these questions, exhibiting transitions between unicellular to multicellular filamentous and coenocytic forms together with diverse reproductive modes, including single-cell zoospores and autospores, and multinucleate monospores and akinetes. However, a robust phylogenetic framework and systematic analyses of character evolution have remained lacking in this lineage. Here, we present a phylogenomic framework based on a nuclear dataset of 680 genes from 18 species, including 17 newly generated transcriptomes. Nuclear phylogenies robustly resolve all sampled inter-ordinal and inter-familial relationships with full concordance between concatenation and coalescent analyses, while plastid (141 genes) and mitochondrial (31 genes) datasets from 33 species recover identical topologies. Based on these results, we establish one new order (Pseudopleurochloridales), emend one order (Heterococcales), and propose five new families. Ancestral character reconstruction indicates at least four independent transitions from unicellular ancestors to simple multicellularity. Bayesian analyses of multicellularity and reproductive characters show that these transitions were consistently accompanied by shifts from multiple autospore-type propagules toward single monospore- and akinete-type propagules, whereas reversions to unicellularity were associated with the reappearance of autospore-based reproduction. These results provide a phylogenomic framework for understanding multicellular evolution in Xanthophyceae and shed light on the relationship between reproductive modes and the emergence of simple multicellularity.

evolutionary biology↗

The genomic basis of evolutionary stasis in the 500-million-year-old red seaweed genus Ahnfeltia

The red seaweed genus Ahnfeltia is an ancient lineage that has persisted for over 500 million years with remarkably limited diversification despite a global distribution in cold-temperate intertidal habitats. Compared to the highly diverse sister lineage, Rhodymeniophycidae, Ahnfeltia provides a unique system for investigating long-term evolutionary persistence in marine macroalgae. Here, we generated chromosome-scale genomes from five populations across three species and combined population genomics with paleogeographic niche modelling. Our results reveal remarkable genomic conservation, strong geographic isolation with limited gene flow, high homozygosity, and evidence of purifying selection. Niche projections indicate long-term stability and spatial connectivity of suitable cold-temperate habitats. These findings suggest that Ahnfeltias persistence and limited diversification are linked to genomic constraints and stable ecological niches over geological timescales. This study provides new insights into the genomic basis of evolutionary stasis in ancient marine lineages and highlights potential vulnerability to ongoing climate change affecting cold-water coastal ecosystems.

evolutionary biology↗

Who Formed All That Iron?: A Novel Antarctic Chemolithotroph Drives Iron Biomineralization

Iron mineralization has profoundly influenced Earths biogeochemical history1,2, yet the specific mechanisms underlying banded iron formation (BIF) remain unresolved3-5. Here we profile the microbiomes of Holocene sediments beneath the Larsen C Ice Shelf (LCIS), Antarctica6-8, through stratigraphic analysis of sedimentary ancient DNA combined with metagenomics. Distinct microbial phases aligned with glacial facies boundaries, with sub-ice shelf communities dominated by chemolithoautotrophs including an uncultured Thermodesulfovibrionia. This bacterium, visualized by fluorescence in situ hybridization and designated Candidatus Mariimomonas ferrooxydans (phylum Nitrospirota), emerged as a keystone taxon with high network centrality. Its genome encodes Cyc2, a fused porin-cytochrome outer membrane protein implicated in Fe(II) oxidation. Heterologous expression of Cyc2 in Escherichia coli confirmed its ability to catalyze iron oxidation, supporting iron precipitation under dark, anoxic conditions. These pristine LCIS sediments, unaltered since the last glacial maximum, provide a modern analogue for synglacial BIFs deposited during Neoproterozoic Snowball Earth events. Our findings deliver direct genomic and functional evidence for chemolithotrophic iron oxidation, challenge phototroph-centric models of BIF genesis, and highlight microbial iron cycling as a recurring force in Earths geochemical evolution. Beyond Earth, these insights inform interpretations of iron deposits on other planetary bodies.

microbiology↗

Community-wide interactions sustain life in geothermal spring habitats

We investigated an alga-dominated geothermal spring community in Yellowstone National Park, USA. Our goal was to determine how cells cope with abiotic stressors during diurnal sampling that spanned over two orders of magnitude in solar irradiance. We report a community level response to toxic metal resistance and energy cycling that spans the three domains of life. Arsenic detoxification is accomplished via complementary gene expression by different lineages. Photosynthesis is dominated by Cyanidioschyzon, with the mixotroph, Galdieria, relegated to nighttime heterotrophy. Many key functions, including the cell cycle, are strongly regulated by diurnal light fluctuations. These results demonstrate that biotic interactions are highly structured in extreme habitats. We suggest this was also the case on the early Earth when geothermal springs were cradles of microbial life, prior to the origin of eukaryotes.

evolutionary biology↗

Paulinella micropora KR01 holobiont genome assembly for studying primary plastid evolution

The widespread algal and plant (Archaeplastida) plastid originated >1 billion years ago, therefore relatively little can be learned about plastid integration during the initial stages of primary endosymbiosis by studying these highly derived species. Here we focused on a unique model for endosymbiosis research, the photosynthetic amoeba Paulinella micropora KR01 (Rhizaria) that underwent a more recent independent primary endosymbiosis about 124 Mya. A total of 149 Gbp of PacBio and 19 Gbp of Illumina data were used to generate the draft assembly that comprises 7,048 contigs with N50=143,028 bp and a total length of 707 Mbp. Genome GC-content was 44% with 76% repetitive sequences. We predicted 32,358 genes that contain 73% of the complete, conserved genes in the BUSCO database. The mean intron length was 882 bp, which is significantly greater than in other Rhizaria (86[~]184 bp). Symbiotic bacteria from the culture were isolated and completed genomes were generated from three species (Mesorhizobium amorphae Pch-S, Methylibium petroeiphilum Pch-M, Polaromonas sp. Pch-P) with one draft genome (Pimelobacter simplex Pch-N). Our holobiont data establish P. micropora KR01 as a model for studying plastid integration and the role of bacterial symbionts in Paulinella biology.

evolutionary biology↗

The genome of Ectocarpus subulatus highlights unique mechanisms for stress tolerance in brown algae

Brown algae are multicellular photosynthetic stramenopiles that colonize marine rocky shores worldwide. Ectocarpus sp. Ec32 has been established as a genomic model for brown algae. Here we present the genome and metabolic network of the closely related species, Ectocarpus subulatus Kutzing, which is characterized by high abiotic stress tolerance. Since their separation, both strains show new traces of viral sequences and the activity of large retrotransposons, which may also be related to the expansion of a family of chlorophyll-binding proteins. Further features suspected to contribute to stress tolerance include an expanded family of heat shock proteins, the reduction of genes involved in the production of halogenated defence compounds, and the presence of fewer cell wall polysaccharide-modifying enzymes. Overall, E. subulatus has mainly lost members of gene families down-regulated in low salinities, and conserved those that were up-regulated in the same condition. However, 96% of genes that differed between the two examined Ectocarpus species, as well as all genes under positive selection, were found to encode proteins of unknown function. This underlines the uniqueness of brown algal stress tolerance mechanisms as well as the significance of establishing E. subulatus as a comparative model for future functional studies.

genomics↗

Modeling Epidemics: A Primer and Numerus Software Implementation

Epidemiological models are dominated by SEIR (Susceptible, Exposed, Infected and Removed) dynamical systems formulations and their elaborations. These formulations can be continuous or discrete, deterministic or stochastic, or spatially homogeneous or heterogeneous, the latter often embracing a network formulation. Here we review the continuous and discrete deterministic and discrete stochastic formulations of the SEIR dynamical systems models, and we outline how they can be easily and rapidly constructed using the Numerus Model Builder, a graphically-driven coding platform. We also demonstrate how to extend these models to a metapopulation setting using both the Numerus Model Builder network and geographical mapping tools.

epidemiology↗

The Parasite Extinction Assessment & Red List: an open-source, online biodiversity database for neglected symbionts

Parasite conservation is a rapidly growing field at the intersection of ecology, epidemiology, parasitology, and public health. The overwhelming diversity of parasitic life on earth, and recent work showing that parasites and other symbionts face severe extinction risk, necessitates infrastructure for parasite conservation assessments. Here, we describe the release of the Parasite Extinction Assessment & Red List (PEARL) version 1.0, an open-access database of conservation assessments and distributional data for almost 500 macroparasitic invertebrates. The current approach to vulnerability assessment is based on range shifts and loss from climate change, and will be expanded as additional data (e.g., host-parasite associations and coextinction risk) is consolidated in PEARL. The web architecture is also open-source, scalable, and extensible, making PEARL a template for more eZcient red listing for other high-diversity, data-de1cient groups. Future iterations will also include new functionality, including a user-friendly open data pository and automated assessment and re-listing.

ecology↗