Biology subjects

Clark, M.

Publications and source records attributed to Clark, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Unexpected diversity of Isidoides (Anthozoa: Octocorallia: Isidoidae) revealed by morphology and phylogenomics analysis with descriptions of four new species

Isidoidae Heestand Saucier, France & Watling, 2021 is a rare octocoral family currently represented by a single genus and species, Isidoides armata Nutting, 1910 recorded in the western Pacific Ocean. The taxonomic status and diversity of Isidoides is unclear, due to the lack of diagnostic taxonomic features and limited taxon sampling. Based on 23 Isidoides specimens obtained from the northwestern to southwestern Pacific, we carried out morphological and phylogenetic analyses to reveal the taxonomic status of new species and develop reliable features for species identification. The 23 specimens could be classified into four well-supported clades by the phylogenomic analysis of ultraconserved elements (UCEs), four groups by 28S rDNA, and two groups by mtMutS-cox1. Integrating morphology and molecular data, we uncovered unexpected diversity of Isidoides composed of the known species Isidoides armata and three new species, viz., I. elegans sp. nov., I. gracilis sp. nov. and I. pseudarmata sp. nov. The morphological analysis showed high intraspecific morphological variation in colony color and the size, shape and arrangement of polyps. By contrast, sclerite forms with their surface sculpturing are more diagnostic features for species identification. Our phylogenetic and species delimitation analyses indicate that UCEs have higher resolution than the nuclear 28S rDNA and the mitochondrial genes mtMutS and cox1 for species discrimination within Isidoidae. ZooBank: urn:lsid:zoobank.org:pub:392485F5-502E-4383-B153-45B167571190

zoology↗

bioRxiv2025

Breaking Through Biology's Data Wall: Expanding the Known Tree of Life by Over 10x using a Global Biodiscovery Pipeline

Advancements in the life sciences have always been built upon our collective understanding of life on Earth. Now, the rise of generative biology - the use of AI foundation models to design, generate, and annotate proteins, pathways and therapeutics - is creating unprecedented demand for large, diverse biological sequence datasets. While a limited subset of such data can be generated in clinical or laboratory settings, the vast majority of the training data for unsupervised models must be sourced from the natural world - the product of nearly four billion years of evolutionary history. However, the public databases that currently supply this data, while foundational to research, were established to aggregate results from academic experiments, not as training datasets for machine learning. Their human-centric data structure limits model performance due to redundancy, taxonomic and geographic bias, limited biological context, and inconsistent provenance. With 68% of all sequence data in the SRA database coming from just 5 species, this is one of the most severe class imbalance problems ever encountered in AI. Legal and infrastructural constraints further exacerbate this bottleneck. To address these limitations and support scalable model training, we introduce BaseData: the largest and fastest-growing biological sequence database ever built, and the first purpose-built for training foundation models. As of late 2024, BaseData contained 9.8 billion novel genes, representing more than a 10-fold expansion in known protein diversity after accounting for redundancy. BaseData also contains more than 1 million species not represented in other genomic databases. Its partnership-driven data supply chain across 26 countries and autonomous regions enables growth of up to 2 billion novel genes per month, far exceeding public repositories. All data is collected under benefit sharing agreements using standardized protocols and structured using graph-based, ontology-rich metadata that preserves evolutionary context. BaseData represents a new, ethically-grounded infrastructure for training biological foundation models, complementing public efforts and enabling the next era of generative biology. Short AbstractProgress of AI in biology is now being limited by the availability of high-quality biological sequence data from nature. To get past this data wall, we introduce BaseData, a new biological database built on top of a global, scalable biodiscovery pipeline. As of 2024, BaseData had already expanded the known protein universe by over 10x.

genomics↗

bioRxiv2025

A pan-generic marker panel for apples to enable genetic research and breeding across Malus species

AbstractWild Malus species harbor untapped genetic diversity to advance apple breeding, particularly for disease resistance and stress tolerance. However, existing marker panels, developed mainly using Malus domestica accessions, introduce ascertainment bias and limit detecting rare variants in wild species. We developed and validated a medium-density and cost-effective pan-generic 3K apple DArTag panel optimized to capture genome-wide variation across the Malus genus. The panel was constructed using conserved, syntenic, and collinear genomic blocks identified within the core genome of 13 Malus accessions for cross-species transferability. The panel was validated across three bi-parental mapping populations totaling 593 progeny. Across these populations, 2,461-3,234 SNP markers were polymorphic and 1,482-2,620 were informative. Each population contained over 900 multiallelic micro-haplotype loci, with several hundred loci exhibiting three or four distinct haplotypes. Markers were uniformly distributed across all 17 chromosomes, each containing between 60- 230 informative SNPs. The panel was further evaluated on 174 diverse germplasm accessions from 20 Malus species. It exhibited strong cross-species transferability, exceptionally low rates of missing data (<0.5%), and clear genetic differentiation between wild and domesticated accessions. Genome-wide association studies (GWAS) identified a major locus on chromosome 4 significantly linked to fruit length, weight, and width in addition to trait-specific associations on chromosomes 1, 6, 9, and 11. The cost-effectiveness of genotyping per sample (<$15), combined with these results, underscore the panels broad utility for quantitative trait locus (QTL) mapping in bi- parental and diverse populations, marker-assisted selection in the breeding programs, and genetic diversity analysis across the Malus genus.

genetics↗

bioRxiv2025

Efficient CRISPR-Cas9-mediated genome editing of the cane toad (Rhinella marina)

Invasive species inflict major ecological, economic, social, and cultural harm worldwide, highlighting the urgent need for innovative and effective control strategies. Genome editing offers exciting possibilities for creating highly targeted control methods for invasive species. Here, we demonstrate CRISPR-Cas9 genome editing in the cane toad (Rhinella marina), one of Australias most notorious invasive species, by targeting the tyrosinase gene to produce albino phenotypes that provide clear visual markers for assessing editing efficiency. Microinjection of Cas9 protein and guide RNAs into one-cell zygotes resulted in 87.6% of mosaic larvae displaying nearly complete albinism, with 2.3% exhibiting complete albinism. For completely albino individuals, genomic analysis confirmed predominantly frameshift mutations or large deletions at the target site, with no wild-type alleles detected. Germline transmission rates reflected the extent of albinism in the mosaic adult, where we achieved maternal germline transmission rates of almost 100%. This technology, representing the first application of CRISPR-Cas9 in the Bufonidae family, opens possibilities for exploring both basic research questions and strategies for population control.

synthetic biology↗

bioRxiv2025

FGF and MafB regulated cadherin expression drives lamina formation in the auditory hindbrain

The avian auditory brainstem contains specialized nuclei critical for sound localization, including the nucleus laminaris (nL), which forms as a single-cell-thick lamina essential for computing interaural time differences. Despite its functional importance, the molecular mechanisms guiding nL lamina formation have remained poorly understood. Here, we identify a signalling cascade involving FGF8, MafB, and cadherin-22 that orchestrates this morphogenetic process. We show that FGF8 is selectively expressed in the developing auditory hindbrain and correlates spatiotemporally with lamina formation in the nL. Disruption of FGF signalling--either via misexpression of FGF8 or dominant-negative FGFR1--perturbs the formation of the nL and alters cadherin-22 expression. In vitro culture experiments further reveal that nL lamination is sensitive to FGF8 dosage, with an optimal concentration required for both FGF8 and MafB expression and correct structural organization. We demonstrate that FGF8 induces MafB, which in turn regulates cadherin-22 expression. Functional disruption of cadherins impairs lamina formation and leads to reduced FGF8 expression, indicating a feedback loop between adhesion and signalling. Cadherin protein expression appears enriched in the dendrites of nL neurons and computational models--both static and dynamic--show that bipolar, dendrite-localized, adhesion can drive laminar architecture as the maximum adhesion configuration. These findings establish a novel molecular and biophysical mechanism for neuronal lamination in the vertebrate hindbrain, showing how local FGF signalling, transcriptional regulation, and dendritic adhesion converge to shape neural circuitry essential for sound localization.

developmental biology↗

bioRxiv2025

Resolution of in situ inflammation in human lupus nephritis into principal immune cell trajectories

In human lupus nephritis (LuN), tubulointerstitial inflammation (TII) is prognostically more important than glomerular inflammation. However, a comprehensive understanding of both TII complexity and heterogeneity is lacking. Herein, we used high-dimensional confocal microscopy and specialized computer vision techniques to quantify immune cell populations and localize these within normal and diseased renal cortex structures. With these tools, we compared LuN to renal allograft rejection (RAR) and normal kidney. In both LuN and RAR, the 33 characterized immune cell populations formed discrete subgroups whose constituents co-varied in prevalence across biopsies. In both diseases, these co-variant immune cell subgroups organized into the same unique niches. Therefore, inflammation could be resolved into trajectories representing the relative prevalence and density of cardinal immune cell members of each co-variant subgroup. Indeed, in any one biopsy, the inflammatory state could be characterized by quantifying constituent immune cell trajectories. Remarkably, LuN heterogeneity could be captured by quantifying a few myeloid immune cell trajectories while RAR was more complex with additional T cell trajectories. Our studies identify rules governing renal inflammation and thus provide an approach for resolving LuN into discrete mechanistic categories. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=89 SRC="FIGDIR/small/638655v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@109dd33org.highwire.dtl.DTLVardef@995037org.highwire.dtl.DTLVardef@161525dorg.highwire.dtl.DTLVardef@6692d8_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG

immunology↗

bioRxiv2025

Predicting the responses of the world's bird species to increases in agricultural production

The intensification and expansion of croplands are among the greatest threats to biodiversity, but the likely responses to these changes remain unknown for most species. Using data on responses of 862 bird species to changes in yields of arable crops, we extrapolate vulnerability to agriculture for the worlds other terrestrial birds based on their traits and taxonomy. We estimate that 74-78% of terrestrial bird species globally suffer population declines where natural habitats are replaced by croplands, and that over half cannot persist in cropland at even the lowest current yields. Past impacts of agriculture on birds have been greatest in the tropics, particularly in coastal forest regions of Central and South America and West Africa and in southern and South-East Asia. Using these estimates to model the impacts of future scenarios of agricultural change, we find that continuing current rates of cropland expansion and yield increases (i.e., extrapolating business-as-usual trends to 2050) is expected to have more negative impacts on birds (particularly in Central and South America, Eastern Europe, sub-Saharan Africa and South and East Asia) than a potential alternative of a targeted strategy of closing yield gaps while limiting cropland expansion. However, we also identify biodiverse regions of the world where closing yield gaps may have more severe impacts on birds than business-as-usual, such as the Pampas of South America and parts of the Sahel region in West Africa. The strategy of least impact for a particular area can be predicted from the response characteristics of the communities of species present there, offering opportunities to take account of regional context for designing less damaging global food production systems.

ecology↗

bioRxiv2025

Chiari II brain malformation is secondary to open spina bifida

Chiari II brain malformation affects 90% of children with open spina bifida. Hindbrain herniation leads to hydrocephalus, together with higher brain anomalies including cerebral cortical defects implicated in learning disability, which affects 20-25% of children with spina bifida. The causal link between Chiari II and spina bifida has long been debated, and we aimed to determine whether Chiari II arises secondary to spina bifida, rather than as a separate effect of shared genetic or non-genetic factor(s). Pax3 gene function was conditionally deleted by Cdx2cre specifically in the lower body of mice, leaving the head genetically intact. Open spina bifida is seen in all Cdx2cre/+; Pax3fl/flfetuses, together with many features of Chiari II in the wild-type brain and skull. These include: hindbrain herniation, callosal and hippocampal hypogenesis, cortical thinning with neuronal heterotopia, a thickened ventricular zone, and posterior skull defects. Hence, the brain and skull defects of Chiari II arise secondary to open spina bifida, with likely disturbance of neurogenesis and neuronal migration early in gestation. The Cdx2cre/+; Pax3fl/fl mouse provides a model for improved understanding of Chiari II pathogenesis.

developmental biology↗

bioRxiv2024

Behavioral risk models explain locomotor and balance changes when walking at virtual heights

Walking in daily life requires humans to adapt to environments that can influence ones fear of falling and anxiety about a potential fall. In such environments, individuals may adopt compensatory locomotor and balance changes to maintain a constant expected risk function equal to the product of the probability of some event (e.g., a fall) and the cost of that event (e.g., injury or death). Here, we tested whether locomotor behaviors broadly align with this risk model in two experiments with height-related threats in immersive virtual reality. In Experiment 1, we examined how individuals change their locomotor trajectory while walking along a straight high-elevation walkway. In Experiment 2, we examined how individuals change trajectory and balance control during curved walking where the location of high elevation threat varied. Participants adopted two behaviors that decreased their probability of falling off the edge and aligned with the risk-based model: participants altered their proximity to perceived threats that pose high costs (e.g., a high-elevation ledge), and decreased mediolateral center of mass velocity when that was not possible. Taken together, our results suggest that individuals alter locomotor behavior to change the probability of falling based on the perceived cost of that fall.

neuroscience↗

bioRxiv2024

Continuous cell type diversification throughout the embryonic and postnatal mouse visual cortex development

The mammalian cortex is composed of a highly diverse set of cell types and develops through a series of temporally regulated events that build out the cell type and circuit foundation for cortical function. The mechanisms underlying the development of different cell types remain elusive. Single-cell transcriptomics provides the capacity to systematically study cell types across the entire temporal range of cortical development. Here, we present a comprehensive and high-resolution transcriptomic and epigenomic cell type atlas of the developing mouse visual cortex. The atlas was built from a single-cell RNA-sequencing dataset of 568,674 high-quality single-cell transcriptomes and a single-nucleus Multiome dataset of 194,545 high-quality nuclei providing both transcriptomic and chromatin accessibility profiles, densely sampled throughout the embryonic and postnatal developmental stages from E11.5 to P56. We computationally reconstructed a transcriptomic developmental trajectory map of all excitatory, inhibitory, and non-neuronal cell types in the visual cortex, identifying branching points marking the emergence of new cell types at specific developmental ages and defining molecular signatures of cellular diversification. In addition to neurogenesis, gliogenesis and early postmitotic maturation in the embryonic stage which gives rise to all the cell classes and nearly all subclasses, we find that increasingly refined cell types emerge throughout the postnatal differentiation process, including the late emergence of many cell types during the eye-opening stage (P11-P14) and the onset of critical period (P21), suggesting continuous cell type diversification at different stages of cortical development. Throughout development, we find cooperative dynamic changes in gene expression and chromatin accessibility in specific cell types, identifying both chromatin peaks potentially regulating the expression of specific genes and transcription factors potentially regulating specific peaks. Furthermore, a single gene can be regulated by multiple peaks associated with different cell types and/or different developmental stages. Collectively, our study provides the most detailed dynamic molecular map directly associated with individual cell types and specific developmental events that reveals the molecular logic underlying the continuous refinement of cell type identities in the developing visual cortex.

neuroscience↗

bioRxiv2024

Enhancer AAV toolbox for accessing and perturbing striatal cell types and circuits

We present an enhancer AAV toolbox for accessing and perturbing striatal cell types and circuits. Best-in-class vectors were curated for accessing major striatal neuron populations including medium spiny neurons (MSNs), direct and indirect pathway MSNs, as well as Sst-Chodl, Pvalb-Pthlh, and cholinergic interneurons. Specificity was evaluated by multiple modes of molecular validation, three different routes of virus delivery, and with diverse transgene cargos. Importantly, we provide detailed information necessary to achieve reliable cell type specific labeling under different experimental contexts. We demonstrate direct pathway circuit-selective optogenetic perturbation of behavior and multiplex labeling of striatal interneuron types for targeted analysis of cellular features. Lastly, we show conserved in vivo activity for exemplary MSN enhancers in rat and macaque. This collection of striatal enhancer AAVs offers greater versatility compared to available transgenic lines and can readily be applied for cell type and circuit studies in diverse mammalian species beyond the mouse model.

neuroscience↗

bioRxiv2024

Modulating DNA Polα Enhances Cell Reprogramming Across Species

As a fundamental biological process, DNA replication ensures the accurate copying of genetic information. However, the impact of this process on cellular plasticity in multicellular organisms remains elusive. Here, we find that reducing the level or activity of a replication component, DNA Polymerase (Pol), facilitates cell reprogramming in diverse stem cell systems across species. In Drosophila male and female germline stem cell lineages, reducing Pol levels using heterozygotes significantly enhances fertility of both sexes, promoting reproductivity during aging without compromising their longevity. Consistently, in C. elegans the pola heterozygous hermaphrodites exhibit increased fertility without a reduction in lifespan, suggesting that this phenomenon is conserved. Moreover, in male germline and female intestinal stem cell lineages of Drosophila, pol heterozygotes exhibit increased resistance to tissue damage caused by genetic ablation or pathogen infection, leading to enhanced regeneration and improved survival during post-injury recovery, respectively. Additionally, fine tuning of an inhibitor to modulate Pol activity significantly enhances the efficiency of reprogramming human embryonic fibroblasts into induced pluripotent cells. Together, these findings unveil novel roles of a DNA replication component in regulating cellular reprogramming potential, and thus hold promise for promoting tissue health, facilitating post-injury rehabilitation, and enhancing healthspan.

developmental biology↗

bioRxiv2024

Enhancer AAVs for targeting spinal motor neurons and descending motor pathways in rodents and macaque

Experimental access to cell types within the mammalian spinal cord is severely limited by the availability of genetic tools. To enable access to lower motor neurons (LMNs) and LMN subtypes, we generated single cell multiome datasets from mouse and macaque spinal cords and discovered putative enhancers for each neuronal population. We cloned these enhancers into adeno-associated viral vectors (AAVs) driving a reporter fluorophore and functionally screened them in mouse. We extensively characterized the most promising candidate enhancers in rat and macaque and developed an optimized pan LMN enhancer virus. Additionally, we generated derivative viruses expressing iCre297T recombinase or ChR2-EYFP for labeling and functional studies, and we created a single vector with combined enhancer elements to achieve simultaneous labeling of layer 5 extratelencephalic projecting (ET) neurons and LMNs. This unprecedented LMN toolkit will enable future investigations of cell type function across species and potential therapeutic interventions for human neurodegenerative diseases.

neuroscience↗

bioRxiv2024

The transcriptomic and spatial organization of telencephalic GABAergic neuronal types

The telencephalon of the mammalian brain comprises multiple regions and circuit pathways that play adaptive and integrative roles in a variety of brain functions. There is a wide array of GABAergic neurons in the telencephalon; they play a multitude of circuit functions, and dysfunction of these neurons has been implicated in diverse brain disorders. In this study, we conducted a systematic and in-depth analysis of the transcriptomic and spatial organization of GABAergic neuronal types in all regions of the mouse telencephalon and their developmental origins. This was accomplished by utilizing 611,423 single-cell transcriptomes from the comprehensive and high-resolution transcriptomic and spatial cell type atlas for the adult whole mouse brain we have generated, supplemented with an additional single-cell RNA-sequencing dataset containing 99,438 high-quality single-cell transcriptomes collected from the pre- and postnatal developing mouse brain. We present a hierarchically organized adult telencephalic GABAergic neuronal cell type taxonomy of 7 classes, 52 subclasses, 284 supertypes, and 1,051 clusters, as well as a corresponding developmental taxonomy of 450 clusters across different ages. Detailed charting efforts reveal extraordinary complexity where relationships among cell types reflect both spatial locations and developmental origins. Transcriptomically and developmentally related cell types can often be found in distant and diverse brain regions indicating that long-distance migration and dispersion is a common characteristic of nearly all classes of telencephalic GABAergic neurons. Additionally, we find various spatial dimensions of both discrete and continuous variations among related cell types that are correlated with gene expression gradients. Lastly, we find that cortical, striatal and some pallidal GABAergic neurons undergo extensive postnatal diversification, whereas septal and most pallidal GABAergic neuronal types emerge simultaneously during the embryonic stage with limited postnatal diversification. Overall, the telencephalic GABAergic cell type taxonomy can serve as a foundational reference for molecular, structural and functional studies of cell types and circuits by the entire community.

neuroscience↗

bioRxiv2024

Forecasting the adoption and spread of a community-based marine management initiative using agent-based models

While many successful initiatives for conserving nature exist, efforts to take them to scale have been inadequate. Moreover, conservation science currently lacks a systematic methodology for determining if or when interventions will reach effective scales and how programmatic decisions will affect the scaling process. This paper presents a modelling framework that aims to address both issues by operationalizing Diffusion of Innovations theory and local knowledge using agent-based modelling and Bayesian inference. By applying our framework to existing data on the spatiotemporal adoption of a community-based marine management initiative in Fiji, we demonstrate that our approach can identify the mechanisms that govern the observed adoption patterns. In this case, the relative advantage of the intervention, village social networks, and perceived knowledge stand out as important drivers of adoption. Using the identified causal processes, our approach can forecast business-as-usual and counterfactual future scenarios and hence inform conservation policy. Finally, we highlight the importance of spatiotemporal data for making detailed scaling predictions. We structure the paper as a step-by-step guide, highlighting our modelling decisions and possible limitations. Thus, besides presenting a case study, this paper serves as a template for practitioners and researchers to better model the scaling process of other conservation interventions.

ecology↗

bioRxiv2024

Neuron Derived Cytokine Interleukin-34 Controls Developmental Microglia Function

Neuron-microglia interactions dictate the development of neuronal circuits in the brain. However, the factors that regulate these processes across development are largely unknown. Here, we find that IL34, a neuron-derived cytokine, is upregulated in early development and maintains neuroprotective, mature microglia in the anterior cingulate cortex (ACC) of mice. We show that IL34 is upregulated in the second week of postnatal life and is expressed primarily in excitatory neurons. Excitatory-neuron specific knock-out of IL34 reduced microglia number and TMEM119 expression and increased aberrant microglial phagocytosis of excitatory thalamocortical synapses in the ACC. Acute, low dose blocking of IL34 at postnatal day 15 similarly decreased TMEM119 and inappropriately increased microglial phagocytosis of synapses. Viral overexpression of IL34 induced TMEM119 expression and prevented appropriate microglial phagocytosis of synapses. These findings establish IL34 as a key regulator of neuron-microglia crosstalk in postnatal brain development, controlling both microglial maturation and synapse engulfment.

neuroscience↗

bioRxiv2024

Microglial MyD88-dependent pathways are regulated in a sex specific manner in the context of HMGB1-induced anxiety

Chronic stress is a significant risk factor for the development and recurrence of anxiety disorders. Chronic stress impacts the immune system, causing microglial functional alterations in the medial prefrontal cortex (mPFC), a brain region involved in the pathogenesis of anxiety. High mobility group box 1 protein (HMGB1) is an established modulator of neuronal firing and a potent pro-inflammatory stimulus released from neuronal and non-neuronal cells following stress. HMGB1, in the context of stress, acts as a danger-associated molecular pattern (DAMP), instigating robust proinflammatory responses throughout the brain, so much so that localized drug delivery of HMGB1 alters behavior in the absence of any other forms of stress, i.e., social isolation, or behavioral stress models. Few studies have investigated the molecular mechanisms that underlie HMGB1-associated behavioral effects in a cell-specific manner. The aim of this study is to investigate cellular and molecular mechanisms underlying HMGB1-induced behavioral dysfunction with regard to cell-type specificity and potential sex differences. Here, we report that both male and female mice exhibited anxiety-like behavior following increased HMGB1 in the mPFC as well as changes in microglial morphology. Interestingly, our results demonstrate that HMGB1-induced anxiety may be mediated by distinct microglial MyD88-dependent mechanisms in females compared to males. This study supports the hypothesis that MyD88 signaling in microglia may be a crucial mediator of the stress response in adult female mice.

neuroscience↗

bioRxiv2024

Regional Variations in Live Proportions of Southwest Pacific Cold-Water Coral Solenosmilia variabilis Reefs

Reef-building cold-water-corals (CWC) form deep-sea habitats that can create biodiversity hotspots. As live coral and dead intact framework provide disparate ecosystem services and are vulnerable to different anthropogenic stressors, it is important to quantify the proportions of each on CWC reefs. We analysed 1,160 images of Solenosmilia variabilis reefs at four sites off New Zealand (Valerie and Forde Guyots at the Louisville Seamount Chain & Ghoul and Gothic Seamounts at the Graveyard Seamount Complex) to determine the ratio of live coral to the whole reef area (termed live:reef). We found live:reef ratios are significantly different between sites at the offshore Louisville Seamount Chain and onshore Graveyard Seamount Complex. This could be driven by reef position relative to the aragonite saturation horizon (ASH) as corals in the Louisville Seamount Chain live below the ASH in colder and deeper waters than those at the Graveyard Seamount Complex, which live above the ASH. In the southwest Pacific, depth is a driver of live:reef ratios, with a larger proportion of live coral at shallow depths and dead intact framework at deeper depths. The live:reef ratios at Gothic Seamount within the Graveyard Seamount Complex remained stable between 2015 and 2020 despite significant differences in live coral, dead intact framework, and reef structure surface area. Our results indicate live:reef ratios can be used to estimate the amount of dead intact framework threatened by shoaling ASH due to ocean acidification at each site, which can help inform which sites could be protected as possible climate change refugia.

ecology↗