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Results for “Marine Ornithology: Journal of Seabird Research and Conservation”

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USGS2026

Nonstationary demographic state-space models using unreplicated counts for species undergoing environmental stressors

A fundamental task in ecological statistics is to estimate abundance and growth rate distributions from wildlife monitoring data to inform conservation management. Modeling time series of wildlife populations presents a number of challenges from both statistical and ecological perspectives, including discreteness; lack of replication; nonstationarity; and observation, demographic, and other phenomenological processes. Nonstationary dynamics are often exhibited by populations undergoing environmental stressors. Models must account for these characteristics to produce reliable estimates of abundance and trends, yet estimation can be challenging with unreplicated data. We propose nonstationary demographic state-space models using unreplicated counts for populations undergoing environmental stressors. A reduced growth rate model matches the complexity of the unreplicated count data, and a fecundity bound on growth rate distributions allows the separation of processes affecting growth rates like environmental stressors from those affecting abundance external to growth rates like migration. NDSSMs allow for the embedding of nonstationary model components, and we explore the use of changepoints, volatility clustering, and migration processes. We apply the proposed nonstationary models in case studies of herons affected by predator/competitor reestablishment and three bat species affected by a fungal pathogen causing white-nose syndrome. Nonstationary models outperform stationary models and generalized linear mixed effects models according to model scoring and visual inspection of predictions, and provide estimates more consistent with published values. Incorporating migration improves model fit universally, even with approximate one-way immigration, most likely because populations are extirpated, recolonized, and increase multiple-fold over the upper bound set by species fecundity. In addition, estimates of the timing and severity of the environmental stressor differed for models with migration. Including nonstationary and demographic components in a fecundity-bounded growth rate model improves inference and benefits interpretability of hyperparameters. In turn, this adjusts uncertainties in predictions of abundance and growth rates over time, providing the ingredients needed for informed conservation analysis and for directing future monitoring of at-risk species.

Journal of Agricultural, Biological and Environmen↗
USGS2026

A Lake Charr pangenome reveals highly conserved Ohnologs as drivers of phenotypic diversity

Whole-genome duplication (WGD) is hypothesized to spur evolutionary diversification by producing genome-wide duplicate gene sets (Ohnologs) that are initially functionally redundant but can diverge markedly as the effects of relaxed selection accumulate over time. However, the underlying mechanisms remain unclear, in part because genomic studies often reconstruct Ohnolog evolution over millions of years, during which subsequent mutations can obscure deep-time signals. Investigating the relationship between Ohnolog evolution and diversification on a contemporary timescale offers clearer insights. We explore this relationship in Lake Charr ( Salvelinus namaycush ), where ∼10% of genes are retained highly conserved polyploid duplicates following the Salmonid-Specific Fourth Round WGD. Using 31 chromosome-level assemblies of Lake Charr from morphologically and ecologically diverse populations, joined into a pangenome graph, we characterized 189,555 structural variants (SVs) that were significantly less likely to affect genes retained as sequence-conserved Ohnolog pairs, nuancing the hypothesis that gene redundancy, relaxed selection, and functional diversification are intertwined. However, we found that SVs affecting such conserved Ohnologs may be potent drivers of adaptive evolution. Notably, we identified a putative 938-Kb interchromosomal translocation containing 25 genes with highly conserved Ohnologs in a paralogous (but untranslocated) genomic block. This putative translocation appears to have facilitated Ohnolog divergence in ankrd11 and hp , genes putatively linked to craniofacial and lipid metabolic diversity in sympatric Lake Superior morphs. This research reveals that conserved Ohnologs previously presumed to be redundant remain a reservoir for adaptive change.

BioRxiv↗
USGS2025

Scientific opportunities in the National Landscape Conservation System

The National Landscape Conservation System consists of unique and beautiful places across America’s landscapes where identified resources and values are protected and science is highlighted. The mission of the National Landscape Conservation System (NLCS), which is managed by the Bureau of Land Management and is often referred to as the agency’s National Conservation Lands, is to conserve, protect, and restore nationally significant landscapes for their cultural, ecological, and scientific values. This clear inclusion of science in the NLCS mission sets the stage for individual units to serve as places of learning, teaching, discovery, and innovation. Science is an integral part of managing the National Conservation Lands, and science conducted within and across the more than 900 units that make up the NLCS can inform and influence conservation and public land management well beyond its boundaries. Here, we highlight seven core aspects of National Conservation Lands that present valuable science opportunities: (1) the scientific values for which individual units are designated; (2) the many other resources, objects, and values within units; (3) the value of units as “control” sites for understanding the effects of activities such as mineral extraction that commonly occur elsewhere on multiple-use public lands but are often prohibited within National Conservation Lands; (4) the value of units for studying the effects of activities such as recreation that regularly occur and may be intensified on National Conservation Lands; (5) the high visibility of units, which draws strong interest and engagement from scientists, partners, and the public; (6) the functioning of the units as a network managed for a common purpose, which provides an opportunity to explore cross-cutting science questions across widely varying contexts and geographies; and (7) the opportunities units provide to promote and apply Indigenous Knowledge to scientific research to manage natural and cultural resources. Because of all of these characteristics, National Conservation Lands can serve as hubs for basic and applied science that can inform management of all public lands and resources into the future. We highlight these science opportunities through examples from existing units and suggest two actions that could help further science activities and impact on National Conservation Lands.

Parks Stewardship Forum↗
USGS2026

Keeping pace: Migrating sea lampreys adjust swim speed in response to shifting water velocity to maintain a constant ground speed

Upstream migrating fish must balance energetic costs with environmental and ecological constraints. Theoretical models predict that fish can conserve energy by adjusting swim speed in response to changing water velocity, but detailed field tests of these predictions remain rare. We used fine-scale acoustic telemetry and hydrodynamic modeling to track adult sea lamprey (Petromyzon marinus) migrating through a river and evaluated how movement speeds varied with environmental conditions and individual traits. Swim speed increased with faster water velocities, while ground speed remained constant, supporting the hypothesis that lampreys regulate swim effort to maintain a fixed migration pace. The average ground speed aligned with a predicted optimum of ∼1 body length per second. Both swim and ground speeds declined slightly in deeper water, suggesting a trade-off between movement efficiency and predator avoidance. These findings provide field-based support for a theoretical model of energy optimization and underscore how migratory fish adaptively adjust behavior to local hydrodynamic conditions. Our results highlight the value of using high-resolution tracking and environmental modeling to reveal behavioral tactics that underlie efficient migration strategies.

Michigan↗
USGS2026

Effects of a low-lipid diet on the gut microbiome and head kidney transcriptome of juvenile Chinook Salmon

Objective Pacific salmon Oncorhynchus spp. reared in production hatcheries are typically fed high-lipid, energy-dense diets to achieve large size and high body condition prior to release. In contrast, juveniles in natural environments tend to consume low-lipid, high-protein diets, and fish reared for research or conservation purposes are sometimes fed diets that are formulated to mimic natural diets and promote wild-like phenotypes. Understanding how these alternative diets affect fish health beyond growth and body condition could ultimately contribute to improving hatchery fish fitness. Methods In this work, we evaluated changes in the fecal microbiome and gene expression of juvenile Chinook Salmon O. tshawytscha on a standard high-lipid hatchery diet versus a low-lipid diet formulated to mimic the nutrition profile of natural-origin fish. To evaluate the time scale at which diet alters the fecal microbiome, we collected longitudinal samples over a 12-week period and switched the diets of a subset of fish twice during the experiment. We used 16S ribosomal RNA gene amplicon sequencing to characterize fecal microbiome differences between fish on the two diets as well as hatchery-reared fish at a production hatchery, hatchery fish that had been captured after release into a stream, and natural-origin, stream-reared fish of similar ages. Additionally, we conducted RNA sequencing on head kidney samples from laboratory-reared fish to evaluate changes in gene expression in this important immune organ. Results We found that the low-lipid diet and the hatchery diet resulted in microbiomes that differed from the microbiome of natural-origin fish and from each other and that diet-driven changes to the microbiome could occur in under 14 d. The low-lipid diet did not result in a microbiome that resembled the microbiome of naturally produced fish. Instead, the low-lipid diet resulted in a microbiome community that was distinct from those of fish reared on the hatchery diet and fish sampled from the wild. The RNA sequencing results indicated differential enrichment of pathways related to immunity, metabolism, and hormone synthesis between fish that were fed the two experimental diets. Conclusions The results suggest that additional environmental factors influence the microbiome more strongly than diet formulation or that the low-lipid diet has a smaller effect on the microbiome than a natural, ­invertebrate-based diet. Given that the gut microbiome and systemic immune function contribute significantly to disease resistance, our findings highlight the importance of understanding how diets fed to fish in captivity may affect fish health beyond growth and body condition metrics.

Journal of Aquatic Animal Health↗
USGS2025

Multi-scale predictors of Northern Long-eared Bat (Myotis septentrionalis) occupancy in the United States

Historically, Myotis septentrionalis (Northern Long eared Bat) was among the most common forest-interior species in North America. Largely due to high mortality from white-nose syndrome, this species has experienced severe population declines across its range. To create an updated species distribution map representing summer occupancy probabilities from 2017 to 2022, we integrated stationary acoustic data with live-capture data from the database of the North American Bat Monitoring Program into a multi-scale, multi-method occupancy modeling framework. Our results provide data-driven predictions with quantified uncertainty for summer occupancy probabilities for Northern Long-eared Bats at 2 spatial scales across the range of the species, while also accounting for inherent observation biases (e.g., imperfect detection).

Journal of North American Bat Research↗
USGS2025

Fossil diatoms in Arctic marine surface sediments

Diatoms are one of the main constituents of marine phytoplankton in the Arctic, and thanks to their siliceous skeletons, diatom fossils are relatively well preserved in sediments. Due to their species-specific sensitivity to different ocean conditions, their abundance and assemblages in sediments are routinely used by paleoceanographers to reconstruct the state of the surface ocean in the past (Koç 2007). By using statistical methods, we can obtain valuable knowledge about their ecological preferences (Oksman et al. 2019) and generate quantitative reconstructions of various parameters, such as sea-surface temperature and sea-ice concentration through time (Krawczyk et al. 2021; Sha et al. 2014). The Marine Arctic Diatoms (MARDI) working group (WG) ( pastglobalchanges.org/mardi ) aims to advance knowledge on marine-diatom ecology and diatom-based reconstructions by compiling and harmonizing data from surface-sediment samples across the Arctic.

Pages Magazine↗
USGS2026

Synthesizing a twelve-year sediment trap time series of planktic foraminiferal flux in the Gulf of America (Mexico)

Sediment trap time series provide powerful frameworks for testing hypotheses about planktic foraminiferal assemblage composition, seasonality, and geochemical responses to environmental variability, all of which are central to improving paleoceanographic reconstructions. We present high resolution foraminiferal assemblage data from a long-running sediment trap (2008–2020) in the northern Gulf of America (Mexico). This study summarizes the species composition, seasonality, and size distribution of the fifteen most abundant species of planktic foraminifera, which account for 98% of total flux. Foraminiferal flux peaks in winter and reaches a minimum in summer, following the seasonal pattern of primary production in the northern Gulf. Winter assemblages are dominated by non-spinose taxa, whereas spinose taxa prevail during summer. Across nearly all species, average monthly test size covaries with temperature, independent of seasonal flux trends. Notably, Trilobatus sacculifer and Neogloboquadrina dutertrei show a significant decline in relative abundance and flux during 2017–2020, nearly disappearing from the assemblage.

Journal of Foraminiferal Research↗
USGS2026

Decadal-scale characteristics of natural and anthropogenic dune morphology along North Carolina Barrier Islands (SE Atlantic Coast)

Dunes offer protection to coastal communities from storms, yet quantitative research characterizing human influences on dune systems across decades and 10–100 km spatial scales constitutes a known data gap. This study analyzed a multidecadal archive of dune crest elevations and positions to map mesoscale spatiotemporal trends in foredune morphology across the barrier island coastline of North Carolina, SE Atlantic coast. Results are summarized within four categories of coastline representing a range of coastal management intensities, integrating beach width and dune lateral accommodation space to assess the comparative influence of differing intensities of anthropogenic intervention on dune morphology. These categories account for the presence of structures, roads, and alongshore connectivity to anthropogenic sediment sources (beach nourishment). These categories show distinct dune and beach system characteristics. Dunes are largest in the areas with the longest legacy of coastal management. As categories decrease in development intensity, dune and beach system characteristics generally depart from the large, static dunes and narrow beaches consistent with hold-the-line management. Where small or transgressive dunes exist on heavily developed coasts, they coincide with relatively strong hydrodynamic forcing or sediment-limiting geology. There is evidence of indirect coastal management influence on undeveloped barrier islands with alongshore connectivity to developed barriers. While this analysis was conducted at the mesoscale, the results provide researchers with the framework to make insights at smaller scales than those demonstrated in this study.

North Carolina↗
USGS2024

Integrating Sr isotopes, microchemistry, and genetics to reconstruct Salmonidae species and life history

Recent approaches to fisheries research emphasize the importance of the coproduction of knowledge in building resilient and culturally mindful fisheries management frameworks. Despite widespread recognition of the need for Indigenous knowledge and historical reference points as baseline data, archaeological data are rarely included in conservation biology research designs. Here we propose a novel multiproxy method to learn from former fisheries stewards by generating archaeological data on past salmonid population parameters. We used a newly developed, high throughput qPCR (HT-qPCR) chip, originally designed for environmental DNA (eDNA), for species identification of archaeological salmonid vertebrae. We combine this with the laser ablation split-stream (LASS) approach to identify ocean-migration versus freshwater residency. We test this multidisciplinary approach using both contemporary and archaeological salmonid samples and new radiocarbon dates from the Tronsdal Site on the Skagit River, Washington State, USA. This is a useful approach for extracting information about Salmonidae species and life history diversity from archaeological remains to reconstruct historic baselines for several population parameters in anadromous species with long periods of freshwater residency. The approach outlined in this paper may be particularly useful for research investigating past fisheries dynamics, offering hundreds to thousands of years of temporal depth for modern fisheries management, harvest policies, restoration ecology, and conservation biology.

Idaho, Oregon, Washington↗
USGS2025

3D viscoelastic models of slip-deficit rate along the Cascadia subduction zone

Interseismic deformation in the Pacific Northwest is constrained by the horizontal crustal velocity field derived from the Global Positioning System (GPS) in addition to vertical rates derived from GPS, leveling, and tide gauge measurements. Such measurements were folded in to deformation models of fault slip rates as part of the 2023 National Seismic Hazard Model (NSHM) update. Here I build upon one of the contributing models, the viscoelastic earthquake-cycle model of Pollitz [2022]. This model permits inclusion of effects of time-dependent viscoelastic relaxation within earthquake cycles (i.e., ‘ghost transients’) and laterally variable elastic and/or ductile material properties. I lever-age these capabilities to incorporate the Cascadia megathrust into Western U.S.-wide deformation models in which crustal fault slip rates are estimated simultaneously with slip deficit rates along the interplate boundary between the descending Juan de Fuca plate and North American plate. This effort includes construction of a margin-wide model of viscoelastic structure founded on the Slab 2.0 model and probes different models of the ductile properties of the surrounding oceanic asthenosphere, continental lower crust, and mantle asthenosphere. This results in new estimates of the distribution of slip deficit rate along the ∼ 1000 km long margin, highlights the importance of correcting for glacial-isostatic adjustment effects, and permits assessment of sensitivity of results to assumed ductile properties.

California, Oregon, Washington↗
USGS2026

Regional variations in sea ice and primary productivity in the Bering Sea during Marine Isotope Stage 11

Marine Isotope Stage (MIS) 11 (424-374 ka) has long been an analog for Holocene climate, because it is the most recent interglacial period with similar orbital conditions. However, there is significant global and regional variability in the climate response to MIS 11 warmth. Here, we review sediment core records from across the Bering Sea to investigate changes in paleoceanographic conditions during Marine Isotope Stages 12-10. Sea ice was present over much of the Bering Sea during MIS 11, but today, none of the sites investigated are ever ice-covered. This suggests that sea ice regimes in the Bering Sea during MIS 11 were different to those of the Holocene. There are also regional differences in the response of sea ice to MIS 11 warming. At the Umnak Plateau, Southeastern Bering Sea, sea ice concentrations decline during deglaciation, but they remain high at the slope sites until Peak MIS 11. Sea ice re-advances over the Umnak Plateau during peak interglacial warmth, at the same time that it declines over the slope sites. Late MIS 11 is characterized by high concentrations of seasonal sea ice at the Umnak Plateau, whilst sea ice at the slope sites fluctuates between consolidated and unconsolidated ice cover. This east-west dichotomy may be explained by changes in the behavior of the Aleutian Low. Productivity increases dramatically during deglaciation due to increased upwelling and sea level rise bringing fresh nutrients into the oceans. This is characterized by increased diatom productivity, increased terrestrial carbon deposition, and laminations at all sites.

Alaska↗
USGS2000

Storm impact scale for barrier islands

A new scale is proposed that categorizes impacts to natural barrier islands resulting from tropical and extra-tropical storms. The proposed scale is fundamentally different than existing storm-related scales in that the coupling between forcing processes and the geometry of the coast is explicitly included. Four regimes, representing different levels of impact, are defined. Within each regime, patterns and relative magnitudes of net erosion and accretion are argued to be unique. The borders between regimes represent thresholds defining where processes and magnitudes of impacts change dramatically. Impact level 1 is the 'swash' regime describing a storm where runup is confined to the foreshore. The foreshore typically erodes during the storm and recovers following the storm; hence, there is no net change. Impact level 2 is the 'collision' regime describing a storm where the wave runup exceeds the threshold of the base of the foredune ridge. Swash impacts the dune forcing net erosion. Impact level 3 is the 'overwash' regime describing a storm where wave runup overtops the berm or, if present, the foredune ridge. The associated net landward sand transport contributes to net migration of the barrier landward. Impact level 4 is the 'inundation' regime describing a storm where the storm surge is sufficient to completely and continuously submerge the barrier island. Sand undergoes net landward transport over the barrier island; limited evidence suggests the quantities and distance of transport are much greater than what occurs during the 'overwash' regime.

Journal of Coastal Research↗
USGS2025

Confocal laser-scanning microscopy (CLSM)-based thermal maturity of Tasmanites and progress in standardization of fluorescence microspectrometry

Evaluation of thermal maturity in vitrinite-free or vitrinite-deficient sediments via fluorescence microspectrometry can provide relevant information related to petroleum exploration and thermal history assessment. However, variation in spectral fluorescence properties of alginite macerals with increasing thermal maturity is largely underexplored. Here, authors of this study have applied confocal laser-scanning microscopy (CLSM) in conjunction with fluorescence microspectrometry to a maturity series of marine Upper Devonian Tasmanites algae from the Ohio Shale (Huron Member) and a single sample from the Marcellus Formation of the Appalachian Basin. Spectral fluorescence properties of Tasmanites were evaluated in relation to orientation, measurement location, and the number of measurements per sample, and were compared to published literature. Emission spectra of Tasmanites from continuous wave laser excitation (405 nm) were acquired from sections perpendicular and parallel to bedding and at different positions within individual Tasmanites bodies. The results showed a progressive red-shift in emission maxima (λ max ) in a large sample sized maturity series ( N = 19), e.g., 493 to 578 nm for the perpendicular section at middle position. Further, blue-shifted apex and mineral-adjacent positions within sections perpendicular to bedding were observed, with the latter being reported here for the first time. While blue-shift at apex positions can be attributed to mechanical deformation-induced reorientation of photoselected fluorophores, the blue-shifted mineral-adjacent positions could result from strain loading and development of a plastic deformation region at the mineral contact zone with Tasmanites . A decrease in standard deviation with increasing number of measured emission maxima is well-observed, and 15 to 20 individual measurements per sample appears sufficient for low standard deviation and coefficient of variance. CLSM-derived thermal maturity parameters indicated that a moderate positive correlation of red/green quotient (Q 650/500 ; R 2 = 0.67) with solid bitumen reflectance (BR o in %) exists. For reproducible results, the determination of λ max and Q 650/500 should be conducted exclusively in the middle position at perpendicular and parallel sections of the polished whole-rock pellets, where the lowest standard deviation in measurement was observed. These results strengthen the suitability and relevance of the CLSM technique in thermal maturity studies of dispersed organic matter (DOM) and contribute to the standardization of fluorescence microspectrometry methods in organic petrology investigation.

Kentucky, Ohio, Virginia, West Virginia↗
USGS2025

Bølling-Allerød productivity in the subarctic Pacific driven by seasonal upwelling

The Bølling-Allerød deglacial event is marked by high diatom productivity and opal deposition throughout the subarctic Pacific. This opal could either constitute a strengthened biological pump and thus carbon sequestration, or a weakened biological pump and release of marine-sequestered CO 2 to the atmosphere. We quantify silicic acid supply at IODP Site U1340 in the Bering Sea using biogenic opal and δ 30 Si of Coscinodiscus , a diatom genus. These records, along with diatom environmental indicators, suggest the Bølling-Allerød had high silicic acid availability related to a shift from stratification to seasonal upwelling dynamics. We thus propose the primary cause of the high productivity event was increased macronutrient supply from vertical exchange that injected old, nutrient-rich, CO 2 -rich waters into the surface. Enhanced CO 2 release from the subarctic Pacific may help explain critical intervals of CO 2 rise that occur at the onsets of the Bølling-Allerød and PreBoreal.

Geophysical Research Letters↗
USGS2024

RegionGrow3D: A deterministic analysis for characterizing discrete three-dimensional landslide source areas on a regional scale

Regional-scale characterization of shallow landslide hazards is important for reducing their destructive impact on society. These hazards are commonly characterized by (a) their location and likelihood using susceptibility maps, (b) landslide size and frequency using geomorphic scaling laws, and (c) the magnitude of disturbance required to cause landslides using initiation thresholds. Typically, this is accomplished through the use of inventories documenting the locations and triggering conditions of previous landslides. In the absence of comprehensive landslide inventories, physics-based slope stability models can be used to estimate landslide initiation potential and provide plausible distributions of landslide characteristics for a range of environmental and forcing conditions. However, these models are sometimes limited in their ability to capture key mechanisms tied to discrete three-dimensional (3D) landslide mechanics while possessing the computational efficiency required for broad-scale application. In this study, the RegionGrow3D (RG3D) model is developed to broadly simulate the area, volume, and location of landslides on a regional scale (≥1,000 km 2 ) using 3D, limit-equilibrium (LE)-based slope stability modeling. Furthermore, RG3D is incorporated into a susceptibility framework that quantifies landsliding uncertainty using a distribution of soil shear strengths and their associated probabilities, back-calculated from inventoried landslides using 3D LE-based landslide forensics. This framework is used to evaluate the influence of uncertainty tied to shear strength, rainfall scenarios, and antecedent soil moisture on potential landsliding and rainfall thresholds over a large region of the Oregon Coast Range, USA.

Journal of Geophysical Research: Earth Surface↗