Archbold Biological Station

Abstract The Wetland Reserve Easement (WRE/WRP) programs, administered by the United States Department of Agriculture, restore freshwater wetlands in agricultural areas to reestablish critical ecosystem functions. While these wetlands provide valuable services such as wildlife habitat and carbon sequestration, the potential loss of carbon through greenhouse gas emissions—specifically carbon dioxide (CO₂) and methane (CH₄)—has not been thoroughly evaluated. This study examined carbon cycling across ten seasonal wetland sites located on the Archbold Reserve and Buck Island Ranch, an operating cattle ranch in south-central Florida, both managed by the Archbold Biological Station. Sites had one of three treatment types: grazed-restored, ungrazed-restored, and grazed-unrestored (control). Over the course of the study, CO₂ and CH₄ fluxes were measured every two to three months using a LI-7810 LI-COR CO₂/CH₄/H₂O trace gas analyzer. Groundwater and surface water levels were monitored, and soil and plant samples were analyzed for total carbon, nitrogen, and phosphorus to assess nutrient storage. Results indicate that hydrology, water residence time, and grazing are key determinants of carbon storage and greenhouse gas emissions. Well-drained ephemeral wetlands primarily lost carbon through CO₂ emissions, while more poorly drained wetlands supported CH₄ production due to lower oxygen concentrations. Grazing was found to further increase soil methane emissions. Although wetlands remain effective carbon sinks overall, restoration and management strategies that consider hydrologic regime and inundation duration could enhance carbon capture and minimize seasonal greenhouse gas losses.

Abstract Plant species distributions are shaped by interactions with the abiotic and biotic environment. Despite the known importance of soil microbiomes in shaping plant diversity and function, no study has explicitly determined the ability of the soil microbiome to predict plant species distributions at large scales. We employed paired above- and belowground surveys of plant occurrence and soil microbial taxa and functions across habitat patches (n = 676), applying machine-learning-based distribution modeling to identify the relative influence of the soil microbiome and environmental attributes in predicting plant species (n = 50) distributions across the landscape. We discovered that while abiotic gradients of known importance in this ecosystem were the strongest predictors of many plant species’ distributions, microbial predictors could have similar or greater influence. Microbiome predictors were collectively more important than abiotic environmental variables for 38% of plant species in this study and explained >70% of the predicted distribution for one species. We identified four microbiome attributes of landscape-scale importance for predicting plant species distributions including prokaryotic richness, fungal richness, the abundance of fungal pathogens, and the abundance of prokaryotic phosphate transport genes in soil. Our findings reveal a previously underappreciated role of the soil microbiome in shaping plant species distributions at a landscape scale, with implications for plant community structure in the context of both ecosystem restoration and future global change.

Across agroecosystems, water is a key driver of primary production, and the relationship between precipitation and production (i.e., water-use efficiency; WUE) provides an important indicator for evaluating agroecosystem resilience to changes in water availability. While this relationship has been well-characterized in relatively unmanaged, native ecosystems, cross-site syntheses spanning diverse agroecosystems and climate gradients are lacking. We leveraged the USDA's Long-Term Agroecosystem Research (LTAR) network to assess the relationship between annual precipitation and aboveground net primary production (ANPP) across an extensive set of climate conditions and agroecosystems, representing native rangelands, croplands, and pasturelands and various management intensities. We utilized long-term ANPP data (mean=17years) from fifteen sites spanning a large precipitation gradient (265 to 1347mmyr-1). We observed a positive relationship between annual precipitation and productivity across precipitation gradients; however, this nonlinear pattern differed from native ecosystems and varied by agroecosystem type. Rangeland ANPP was strongly coupled to annual precipitation, increasing nearly 20% for every 100mm of precipitation. Croplands and pasturelands showed significantly decreased sensitivity, although grouping crops by photosynthetic pathway and crop type revealed some significant patterns. Underlying these patterns in sensitivity were large differences in overall ANPP among agroecosystems; cropland ANPP was up to 6.7-fold greater than rangelands and 2.6-fold greater than pasturelands, despite overlapping precipitation gradients. While agroecosystem type captured much of the variability in the precipitation-production relationship at the continental scale, understanding the more subtle differences in precipitation sensitivities will be fundamental for identifying production vulnerabilities and adapting to changing water resources.

Abstract India has a rich history of ornithology, and bird research in this field has expanded considerably in recent decades, spurred by a growing number of birdwatchers and ornithologists. Despite this progress, critical gaps remain. This paper highlights key areas where further research is needed and identifies pressing questions that will shape Indian ornithology in the coming years. Drawing from diverse inputs, we present a curated list of 101 research questions spanning across the various disciplines in ornithology – Natural History, Physiology and Disease Ecology, Behaviour, Population and Community Ecology, Habitat Ecology, Macroecology and Biogeography, Population Genetics and Evolution, Applied/Economic Ornithology and Conservation. The list was compiled through a multi-stage process, starting with a public open call for questions, followed by review and curation by a smaller panel of subject specialists. Each question was independently scored by a panel of experts based on three criteria: generality, novelty, and relevance. To account for variation in scoring styles, scores were normalised using Z-scores. The top 101 research questions were then selected based on these standardised scores. Each question is accompanied by an annotation that describes the significance of the question, and highlights opportunities to address it. While our list of research questions highlights significant research priorities, it is not intended to be exhaustive. Rather, it reflects the perspectives of those involved in its curation, who deemed these questions particularly relevant and impactful towards advancing Indian ornithology. We expect these questions to spark new project ideas among students, researchers, and citizen scientists, while guiding funders, managers, and policymakers toward priority research areas.

Cooperatively breeding species frequently live in family groups of related individuals, with helpers delaying their own reproduction and participating in alloparental care, predator vigilance, and territory defense. It remains challenging to disentangle the roles of the indirect fitness benefits of helping kin and the potential direct fitness benefits helpers receive in the evolution of cooperative breeding. While many studies test for associations between helper relatedness and helping effort, few estimate the realized fitness consequences of helping in relation to these factors. Understanding these fitness outcomes elucidates the selective forces that maintain helping behavior, whether through inclusive fitness gains by helping related individuals or as a means of gaining access to later direct fitness benefits. Using 29 years of extensive demographic data from a closely monitored population of Florida scrub-jays ( Aphelocoma coerulescens ), we quantified the effect of helpers on breeder survival, offspring survival, and nestling production and how these effects depend on relatedness and sex of helpers. We found that female breeder survival was significantly greater when more helpers were present and that offspring survival was greater when more male helpers were present on small territories. Neither effect of helpers depended on the relatedness between helpers and the individuals they helped. Our results suggest that helping behavior is highly context-dependent and varies based on the potential impact of helping and the direct fitness benefits helpers receive.

Wildfire is a dynamic event that rapidly alters habitats on an asynchronous timeframe. The occurrence of wildfire, or its suppression, can be stressful to organisms that rely on fire-regulated habitats. Epigenetic mechanisms are induced by the environment and can facilitate organismal response to stress by regulating gene expression. Here, we screened DNA methylation in the federally threatened Florida Sand Skink ( Plestiodon reynoldsi ) from 13 sites at Archbold Biological Station spanning three categories of time since last fire (TSF): recent (3–6 y), intermediate (7–17 y), and long unburned (18–39 y). We detected thousands of differentially methylated regions in the genome of the Florida Sand Skink among and within TSF categories. We detected a negative relationship between DNA methylation and TSF in this species. Further, we detected an increase in variance of DNA methylation among individuals in recently burned areas, which suggests the Florida Sand Skink uses epigenetic buffering as a response to wildfire stress. The variation in DNA methylation detected among sites within TSF categories indicates that the Florida Sand Skink uses DNA methylation to respond to local conditions, unmeasured in this study, beyond wildfire. Our results indicate that the Florida Sand Skink alters its DNA methylation patterns in response to wildfire and suggest that the changes in DNA methylation facilitate their resilience to wildfire.

BackgroundTorque teno sus virus 1 (TTSuV1), a member of the Anelloviridae family, is highly prevalent in swine populations and exhibits substantial genetic diversity. Despite its ubiquity, TTSuV1 remains understudied, particularly regarding its genetic diversity, host-specific differentiation, and intra-host variation. These characteristics are critical for understanding its evolution, transmission dynamics, and potential applications in biosecurity monitoring.MethodsField and laboratory protocols included capturing wild pigs, collecting whole blood samples, and screening for TTSuV1-positive samples through PCR. TOPO TA cloning was used to amplify individual viral variants within hosts, and whole genome sequencing (WGS) was performed on selected clones. A dated phylogenetic tree was reconstructed using TTSuV1 whole genome sequences obtained from wild pig samples in this study and all available sequences from NCBI. To evaluate genetic differentiation between wild and domestic pigs, partial viral sequences (~700 bp) were analyzed using phylogenetic D statistic and analysis of molecular variance (AMOVA). Intra-host variation was assessed by calculating pairwise identity percentages among viral clones from individual hosts and constructing haplotype networks.ResultsPhylogenetic analysis of whole genome sequences grouped TTSuV1 into four clades, with sequences from wild pigs distributed across all clades. Known subtypes 1a, 1b, and 1c were localized within Clades 3 and 4, leaving sequences in Clades 1 and 2 with unidentified subtypes. Partial sequence analysis revealed significant host-specific genetic differentiation: the D statistic confirmed a non-random association between host type (wild vs. domestic) and phylogeny, and AMOVA further showed contributions of both host type and geography to overall variation. Intra-host variation analysis provided evidence for multiple sources of genetic diversity within individual hosts. Pairwise identity percentages among viral clones ranged from 63.6% to 100%, with lower identity values indicating co-infection with distinct viral variants. Haplotype network analysis revealed mutational steps between haplotypes from the same host, suggesting that intra-host evolution also contributes to within-host genetic variation.ConclusionsThis study highlights the significant genetic diversity and host-specific differentiation of TTSuV1, with wild pigs playing a key role in its evolution. Both intra-host evolution and co-infection contribute to its diversity, underscoring its potential as a tool for monitoring biosecurity risks and cross-transmission between wild and domestic pigs.

Un estudio histórico, de 4 años de duración, iniciado en 1977 en Nueva York (EE.UU.), descubrió que Ammospiza caudacuta anidaron sintópicamente con A. maritima, ambas en cierta abundancia, en un hábitat atípico, natural (joven), de marisma mareal baja. Ammospiza caudacuta ocuparon especialmente una extensa zona de Spartina alterniflora de altura intermedia, que cubría el 89% de la zona de estudio con vegetación y albergó alrededor del 97% de los nidos. Realizamos un análisis retrospectivo del destino de los nidos, la altura de los nidos y la supervivencia comparativa de los nidos utilizando herramientas analíticas actuales para averiguar el éxito de los nidos de A. caudacuta en relación con los nidos de A. maritima en el mismo hábitat, que era el hábitat típico de esta última especie. Fue similar el destino de los nidos de A. caudacuta y de A. maritima en este hábitat de marisma baja; las causas más importantes del fracaso de los nidos fueron la depredación (38%, 37%) y la inundación (18%, 14%). Ammospiza caudacuta colocó sus nidos a mayor altura sobre la superficie del barro en la marisma baja (7,4 ± 0,4 cm) que en su hábitat típico de marisma alta (4,8 ± 0,6). La tasa media global de supervivencia diaria (TSD) de los nidos (n = 231) de A. caudacuta fue de 0,974 ± 0,0017 y la probabilidad de sobrevivir los 25 días de nidificación fue de 0,52 ± 0,02, tan alta como la alcanzada por A. maritima (n = 319; TSD = 0,970 ± 0,0021), y tan alta como los niveles más altos de supervivencia media diaria de los nidos en otros estudios de A. caudacuta. La TSD disminuyó con la edad del nido, pero sólo para A. maritima, y la TSD fue baja para ambas especies en 1980 en comparación con los demás años. La creación de nuevos hábitats de marismas bajas puede ofrecer la posibilidad de realizar esfuerzos innovadores de conservación para evitar la extinción amenazada, a mediados de siglo, de A. caudacuta. PALABRAS CLAVEconservación; plasticidad del hábitat; destino de los nidos; supervivencia de los nidos; análisis retrospectivo; Spartina alterniflora; Ammospiza de marisma mareal

\papertype Original Article The pace of global change presents challenges for adequately assessing outcomes of agricultural management, hindering decision-making by producers, researchers, and consumers. The Long-Term Agroecosystem Research Network (

Long-term research is essential for guiding the development of agroecosystems to meet escalating production demands in a manner that is environmentally sound and socially acceptable. Research must integrate biophysical and socioeconomic factors to provide geographically scalable knowledge that involves stakeholders across the research-education-extension-policy spectrum. In response to this need, the Long-Term Agroecosystem Research (LTAR) network developed a "Common Experiment," which seeks to develop and disseminate multi-region, science-based information to enable implementation of visionary agricultural innovations while simultaneously promoting food security, well-being, environmental quality, and climate adaptation and mitigation. The core design of the Common Experiment contrasts prevailing and alternative/aspirational production systems, with the latter including novel innovations hypothesized to advance sustainable intensification in locally appropriate ways. Treatments in the Common Experiment represent a diversity of production systems under cropland, grazing land, and integrated crop/grazing land management. Where possible, treatments are evaluated at multiple spatial scales (e.g., from plot to enterprise) and are designed to evolve over the course of the experiment with stakeholder input. A common assessment framework guides data collection for the experiment and is complemented by metric-specific protocols and an emerging data management infrastructure. Currently, there are large differences among sites in the application of the experimental framework and degree of stakeholder engagement; differences largely grounded in pragmatic issues related to land access, site expertise, and resource availability. The full potential of the LTAR Common Experiment may be realized with strategic investments in network capacity.