Biology subjects

Connolly, R. M.

Publications and source records attributed to Connolly, R. M..

7 recordsLinked to original sources

bioRxiv2025

Shedding light on day-night habitat use of oyster reefs by fish

Oyster reefs provide key ecosystem functions, including the provision of habitat for fish. While their importance in supporting fish assemblages is widely accepted, an assessment of intertidal oyster reefs at night remains a knowledge gap. Documenting habitat use at night could reveal new species reliant on these systems and help uncover diel fish movements among structured and unstructured habitats. We hypothesise that habitat use will interact with time and habitat, whereby differences in fish assemblages between oyster reef and unstructured habitats would be greater during the day. In this study, we used infrared-capable remote underwater video stations (RUVS) to sample paired intertidal oyster reefs and unstructured habitat during day and night. Assemblages using these habitats during the day do not match those at night, consistent with diel shifts observed in similar habitats. Consistent with our hypothesis, during the day oyster reefs had higher diversity and richness than unstructured habitat, whereas both habitats had low diversity and richness at night. The high relative abundance of piscivores in oyster reefs during the day suggests reefs create food webs that extend beyond benthic matter and sustain higher trophic levels. Nighttime abundances and diversity in oyster reefs dropped to levels similar to those of unstructured habitats during the day and night, likely a product of temporal niche partitioning and dynamic predation risks. Nighttime studies were important in documenting a wider suite of species and can thus provide a more complete understanding of fish-habitat interactions. Furthermore, this study used novel methods that enabled depth and size estimation from a single camera unit. While still in its infancy, this can serve as a force multiplier in monitoring intertidal habitats and lead towards a cost-effective method for standardising day/night abundance measurements and obtaining fish size estimates.

ecology↗

bioRxiv2025

Optimizing seagrass planting arrangements for animal benefits in a multi-habitat restoration seascape

Restoring lost and degraded ecosystems to enhance biodiversity and ecosystem services is a global priority, and animal responses to the restoration of habitats are a critical but undervalued component. Identifying the key drivers of animal colonization in restored habitats provides critical insights for restoration practitioners seeking to maximize ecological outcomes. When integrated into predictive frameworks and spatial decision- support tools, this knowledge becomes especially valuable for strategic planning, particularly in complex multi-habitat restoration projects where spatial configuration remains a crucial yet understudied dimension influencing ecosystem recovery trajectories. We collect and analyze animal data from one of the worlds largest multi- habitat coastal restoration systems in Denmark, comprising restored seagrass (Zostera marina), boulder reefs and mussel reefs. Using fine-scale spatial patterns in population abundances, we develop spatially explicit predictions across the seascape for various seagrass restoration scenarios and produce a series of optimizations, showing that it is practical to configure restoration to optimize biodiversity objectives, including those linked with fished species. Species-specific responses translated to variable outcomes across restoration scenarios and optimizations. While the optimal number and arrangement of restored patches varied depending on the target species or species group (e.g., fisheries species or seagrass specialists), one near-ubiquitous arrangement was patchy seagrass planting. This aligns with current practice, maximizes restoration efficiency, and highlights the importance of not homogenizing seascapes for biodiversity. Our approach provides a practical framework for incorporating animal monitoring data into restoration planning, helping practitioners design and optimize spatial planting configurations to achieve specific ecological objectives. Open Research StatementAll data and code/scripts (R language), including a README file, are freely available at: https://github.com/msievers100/DenmarkSpatial

ecology↗

bioRxiv2025

Cancer systems immunology reveals myeloid - T cell interactions and B cell activation mediate response to checkpoint inhibition in metastatic breast cancer

Sensitization of the immune-suppressed tumor microenvironment (TME) of breast cancer by histone deacetylase inhibition shows promise, but the mechanisms of sensitization are unknown. We investigated the TME of breast-to-lung metastases by combining experimental and clinical data with theory. Knowledge-guided subclustering of single-cell RNA-sequencing data and cell circuits analysis identified 39 cell states and salient interactions, of which myeloid, T cell and B cell subpopulations were most affected by treatment. Using functional immunologic assays, we verified that inhibition of the ICAM pathway partially recapitulated treatment effects. Mathematical modeling of tumor-immune dynamics confirmed that tumor reduction required simultaneous modulation of multiple TME interactions. We found evidence that treatment affected anti-tumor antibody production. Analysis of patient biopsies via spatial proteomics corroborated preclinical findings: in responders we observed increased B cell activation, mature tertiary lymphoid structures, and increased CD8+ T cell--macrophage distances with treatment. Overall, this study provides a framework for the discovery of cell-cell interactions that govern responses in complex TMEs. Statement of significanceThis study provides a framework for the discovery of cell-cell interactions that control responses in complex TMEs. We not only identify impactful tumor immunologic interactions that facilitate sensitization of the metastatic TME but also demonstrate how interdisciplinary data integration fuels cancer systems immunology to accelerate discovery of mechanisms of successful immunotherapeutic response in breast cancers and other previously unresponsive solid tumor types.

cancer biology↗

bioRxiv2024

The global fish and invertebrate abundance value of mangroves

Mangroves are a critical coastal habitat that provides a suite of ecosystem services and supports livelihoods. We undertake the first global analysis to estimate density and abundance of 37 commercially important fish and invertebrates that are known to extensively use mangroves. Geomorphic mangrove type, sea surface salinity and temperature, and length of mangrove forest edge were important in predicting the density of commercial fish and invertebrates, with deltaic systems supporting the highest densities. The model predicted high densities throughout parts of southeast Asia, the northern coast of South America, the Red Sea, and the Caribbean and Central America. Application of our model onto the global mangrove extent, estimates that mangroves support the annual abundance of nearly 800 billion young-of-year fish and invertebrates contained in our model. Our results confirm the critical role of mangroves globally in supporting fish and fisheries, and further builds the case for their conservation and restoration.

ecology↗

bioRxiv2021

Phenotypic shifts of tumor associated macrophages and STAT3 mediated suppression of myeloid derived suppressor cells drive sensitization of HER2+ tumor immunity.

Understanding how novel therapeutic combinations alter solid tumor microenvironments (TME) in immunosuppressive tumors such as breast cancer is essential to improve their responses to immune checkpoint inhibitors (ICIs). Entinostat, an oral histone deacetylase inhibitor (HDACi), has been shown to improve responses to ICIs in various tumor models with immunosuppressive TMEs, but the precise alterations induced by entinostat and mechanisms of synergy with ICIs remain unknown. Here, we employ single-cell RNA-sequencing on HER2 overexpressing breast tumors from mice treated with entinostat + ICIs to characterize these changes across cell types in the TME. This analysis demonstrates that treatment with entinostat induces a shift from a pro-tumor to an anti-tumor TME signature characterized predominantly by changes in the myeloid cells. Notably, myeloid-derived suppressor cells (MDSCs) are shifted toward the less suppressive granulocytic phenotype in association with reduced signaling through the STAT3 pathway. In addition, tumor-associated macrophages are shifted toward an anti-tumor M1 phenotype by epigenetic reprogramming. Overall, these entinostat-induced TME changes reduce immunosuppression and increase mechanisms of tumor cell killing to improve ICI responses and broaden the population of patients who could potentially benefit from immunotherapy.

immunology↗

bioRxiv2020

Future carbon emissions from global mangrove forest loss

Mangroves have among the highest carbon densities of any tropical forest. These "blue carbon" ecosystems can store large amounts of carbon for long periods, and their protection reduces greenhouse gas emissions and supports climate change mitigation. The incorporation of mangroves into Nationally Determined Contributions to the Paris Agreement and their valuation on carbon markets requires predicting how the management of different land-uses can prevent future greenhouse gas emissions and increase CO2 sequestration. Management actions can reduce CO2 emissions and enhance sequestration, but should be guided by predictions of future emissions, not just carbon storage. We project emissions and forgone soil carbon sequestration potential caused by mangrove loss with comprehensive global datasets for carbon stocks, mangrove distribution, deforestation rates, and drivers of land-use change. Emissions from mangrove loss could reach 2,397 Tg CO2eq by the end of the century, or 3,401 Tg CO2eq when considering forgone carbon sequestration. The highest emissions were predicted in southeast and south Asia (West Coral Triangle, Sunda Shelf, and the Bay of Bengal) due to conversion to aquaculture or agriculture, followed by the Caribbean (Tropical Northwest Atlantic) due to clearing and erosion, and the Andaman coast (West Myanmar) and north Brazil due to erosion. Together, these six regions accounted for 90% of the total potential CO2eq future emissions. We highlight hotspots for future emissions and the land-use specfic management actions that could avoid them with appropriate policies and regulation.

biochemistry↗

bioRxiv2017

The assessment of fishery status depends on the condition of fish habitats

At the crux of the debate over the global sustainability of fisheries is what society must do prevent overexploitation of fisheries and aid recovery of fisheries that have historically been overexploited. The focus of debates has been on controlling fishing pressure and assessments have not considered that stock production may be affected by changes in fish habitat. Fish habitats are being modified by climate change, built infrastructure, destructive fishing practices and pollution. We conceptualise how the classification of stock status can be biased by habitat change. Habitat loss can result in either overly optimistic or overly conservative assessment of stock status. The classification of stock status depends on how habitat affects fish demography and what reference points management uses to assess status. Nearly half of the 418 stocks in a global stock assessment database use seagrass, mangroves, coral reefs and macroalgae, habitats that have well documented trends. There is also considerable circumstantial evidence that habitat change has contributed to overexploitation or enhanced production of data-poor fisheries, like inland and subsistence fisheries. Globally many habitats are in decline, so the role of habitat should be considered when assessing the global status of fisheries. New methods and global databases of habitat trends, and use of habitats by fishery species are required to properly attribute the causes of decline in fisheries, and are likely to raise the profile of habitat protection as an important complementary aim for fisheries management.

ecology↗