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Species distribution models (SDMs) are widely applied to understand the processes governing spatial and temporal variation in species abundance and distribution but often do not account for measurement errors such as false negatives and false positives. We describe unmarked, a package for the freely available and open‐source R software that provides a complete workflow for modelling species distribution and abundance while explicitly accounting for measurement errors. Here we focus on recent advances in unmarked functionality to support multi‐species, multi‐state, and multi‐season data, as well as support for fitting models with random effects. For illustration, we present an analysis of Acadian Flycatcher Empidonax virescens abundance on Roanoke River National Wildlife Refuge, North Carolina, USA, over 18 years. We found that Acadian Flycatcher abundance was initially greater in hardwood plantation habitat relative to bottomland hardwood forest along river levees but that abundance declined over time in both habitats. We plan for unmarked development to keep pace with advances in hierarchical modelling in ecology, including better handling of continuous‐time data from camera trap and automated recording units and integrated models for multiple data streams.

The decline of neotropical migratory birds in North America is closely tied to habitat loss, including the degradation of bottomland hardwood and riparian forests, which provide essential habitats for numerous species. To address this, the U.S. Fish and Wildlife Service conducts bird surveys to monitor restoration efforts and evaluate conservation outcomes. This study assessed avian surveys from three National Wildlife Refuges in Texas and Oklahoma, using simulations, field data, and literature to evaluate current sampling protocols. Our findings revealed that achieving acceptable precision in bird density estimates (coefficient of variation: 0.15, 0.25) often requires more than 200 bird point counts, depending on the species and study area. While data aggregation across sites and years improved precision, it masked local trends critical for refuge-specific management. Imprecise results, particularly for rare species, underscored the need for improved protocols, such as repeat visits within a year, targeted sampling for priority species, and adaptive designs incorporating forest composition and structure data. These adjustments would enhance the precision of multispecies surveys, making them more effective for detecting changes in habitat quality. This study provides actionable recommendations to support service-wide efforts in strategic, data-driven monitoring and long-term conservation planning for neotropical migratory birds.

Context Flood protection zones in the Lower Mississippi Alluvial Valley, the often-inundated unprotected side or “batture” and the intermittently flooded protected side, are a juxtaposition of sharply different landscapes and ecological conditions. Swamp rabbits ( Sylvilagus aquaticus ), an indicator species for bottomland hardwood forests, inhabit both zones in the southeastern USA. Though the batture side of the levee offers more habitat and better-connected patches, increased flood severity (frequency and duration) due to climate change or other factors may displace swamp rabbits and other terrestrial vertebrates potentially making the area less habitable. Objectives We used a habitat model to delineate swamp rabbit habitat patches in the flood zones and conducted occupancy surveys of the patches to determine whether swamp rabbits benefited from conditions on the batture side, despite the flood risk. Methods The presence of swamp rabbits in habitat patches of southeastern Missouri, USA was ascertained through the observation of latrine logs. Swamp rabbit habitat patches were identified using species distribution modeling and a subset were further characterized using Q1 LiDAR. We evaluated detection and occupancy models which included patch and detection covariates to determine differences across flood risk zones. Results Patch occupancy was high and similar across zones but detection probability was much higher on the batture side. Habitat patches on the protected side levee were generally smaller with thicker canopy and less understory than those on the batture side of the levee. Conclusions Since visual obstruction was not an obvious factor, the higher detection rate on the unprotected side may have resulted from greater abundance driven by lower patch isolation. Levees that disconnect rivers from the floodplains have a profound effect on landscapes. Swamp rabbits can thrive in the landscape and habitat of the unprotected floodplain, despite their increased exposure to frequent flooding.

Climate changes in temperate regions are expected to result in warmer, shorter winters in temperate latitudes. These changes may have consequences for germination of plant species that require a period of physiological dormancy. The effect of cold duration on seed germination has been investigated in a number of plant taxa, but has not been well studied in wetland and bottomland forest tree species, an ecosystem that is threatened by habitat homogenization. Our work sought to test the role of changing winter temperatures on seed germination in specialist ( Nyssa aquatica and Taxodium distichum ) and generalist ( Acer rubrum and Liquidambar styraciflua ) tree species within forested wetlands throughout the eastern U.S. The experiment was conducted in an environmental chamber in Norfolk, VA, USA. Seeds of T. distichum, N. aquatica, A. rubrum, and L. styraciflua were exposed to each of seven pre-germination cold exposure durations (0, 15, 30, 45, 60, 75, and 90 days) and observed for germination for 30 days. Cold stratification duration positively impacted total percent germination in N. aquatica ( p  < 0.0001) as well as A. rubrum (p = 0.0008) and T. distichum ( p  = 0.05). Liquidambar styraciflua seeds exhibited more rapid rates of germination with increasing cold exposure duration and greater percent germination compared to the others regardless of cold stratification duration. Our results provide insight into how community dynamics and biodiversity of wetland and bottomland trees may shift with a changing climate. Further, this work emphasizes the importance of understanding the role of plant functional traits in early life stages in community dynamics and has implications for management practices.

Bottomland hardwoods are floodplain forests along rivers and streams throughout the southeastern United States. The interrelations among hydrology, soils, geomorphic landforms, and tree species composition are the foundation of forest management in bottomland hardwoods, and historically their correspondence has allowed for somewhat predictable forest responses based upon the hydrogeomorphic setting. However, extensive hydrologic and geomorphic modifications in floodplains have disrupted these interrelations and, on many sites, have created novel disturbance regimes resulting in unpredictable forest responses. Reduced or altered timing of surface flooding and groundwater declines are common in the region and have favored increases in stem densities, particularly of species less tolerant of flooding and more tolerant of shade. In these highly modified systems, more process-level understanding of floodplain hydrology, soil moisture dynamics, interspecific tree competition, and regeneration is needed to develop more effective management prescriptions and for forestry to be represented in integrated water-resource management decisions.

We examine the efficiency with which a suite of ecosystem services can be restored by different reforestation configurations. We use a spatial analysis to quantify the ecosystem service trade-offs and synergies of five equal-area, large-scale bottomland hardwood reforestation scenarios for a study area in the Mississippi Alluvial Valley. Each reforestation configuration is designed to achieve a different environmental objective: nutrient retention, intact riparian and floodplain areas, forest breeding bird habitat, and black bear habitat connectivity. A random reforestation of the same area is also created to represent an opportunistically driven scenario. The opportunistic reforestation delivered services between 85% and 94% less efficiently than targeted reforestation. We also find a distinct service trade-off between reforestation to address water quality and reforestation to provide habitat for large vertebrates. This analysis underscores the importance of spatially quantifying ecosystem services and their trade-offs when seeking to optimize the ecosystem service benefits of restoration.

Key messageWhereas Shumard oak seedlings are intolerant of dormant season flood, Nuttall oak seedlings are tolerant. Flooding more than 1–2 months beyond budbreak may have persistent negative impacts on Nuttall oaks.Since flooding in winter and spring is an integral part of bottomland hardwood ecosystems in the southeastern United States, moderately flood-tolerant oaks, like Nuttall oak (Quercus texana), should be well adapted to flooding during these seasons. To quantify the potential for injury from different lengths of winter flooding, we flooded seedlings of Nuttall oak and moderately flood intolerant Shumard oak (Q. shumardii) for 0, 1, 2, and 3 months, with the first month of flooding occurring during the dormant season. Flooding during dormancy had no effect on Nuttall oak, but Shumard oak seedlings had reduced growth in the spring. Flooding that extended beyond budbreak resulted in reduced leaf area and root biomass accumulation in spring for both species, while Shumard oaks also experienced high mortality. At the end of the growing season, Nuttall oaks that had been flooded accumulated tissue biomasses similar to non-flooded seedlings, except taproot biomass, which was reduced 40% by 3 months of flooding. It appears that Nuttall oak delayed fully investing in spring growth until after flooding subsided, and then was largely able to compensate following flooding that extended one month beyond budbreak. However, flooded Shumard oaks did not show similar signs of recovery. Thus, sites that flood at any time of year would not be suitable for Shumard oak. Our results suggest that natural or human-imposed flooding can extend several weeks beyond budbreak without harming Nuttall oaks, but inundation prolonged several months beyond budbreak could weaken the ability to respond to subsequent stresses.

Planting hardwood trees on retired marginal agricultural land is one of the main strategies used to restore forested wetlands. Evaluating effectiveness of wetland restoration requires efficient monitoring to evaluate recovery trajectories and desired conditions. Recent advancements in unmanned aerial system (UAS) technologies have prompted wide-scale adoption of UAS platforms in providing a range of ecological data. In this study, we examined the use of UAS Structure from Motion (SfM) derived point clouds in estimating tree density, canopy height, and percent canopy cover for bottomland hardwood plantations within four wetland reserve easements. Using a local maxima approach for individual tree detection produced plantation level estimates with mean absolute errors of 150 trees per hectare, 0.5 m, and 18.4% for tree density, canopy height, and percent canopy cover, respectively. At the plot level, UAS-derived tree counts ( r  = 0.53, p  < 0.01) and canopy height ( r  = 0.57, p  < 0.01) were significantly correlated with ground-based estimates. We demonstrate that UAS-SfM is a viable method of assessing bottomland hardwood plantations for applications that require precision levels congruent with the mean absolute errors reported here. The accuracy of tree density estimates was reliant upon specific local maxima window parameters relative to stand conditions. Therefore, acquisition of leaf-off and leaf-on imagery may allow for better individual tree detection and subsequently more accurate tree density and other structural attributes.

Thirty-five years post-harvest, effects of harvest disturbances upon tree composition and aboveground biomass were evaluated in a water-tupelo (Nyssa aquatica) - baldcypress ( Taxodium distichum ) bottomland. The forested wetland, along the Tensaw River, is within the Mobile-Tensaw River Delta in southwest Alabama. Nine replications of four disturbances were evaluated: no harvest reference (REF), clearcutting with helicopter removal (HELI), HELI combined with skidder extraction simulation (SKID), and HELI combined with broadcast herbicide application (glyphosate) to sprouts and seedlings for two years (GLYPH). Thirty-five years post-treatment, species, diameter at breast height (DBH; 1.37 m or above swell) and tree height were measured within treatments and converted to aboveground dry weight biomass. Clip plots were installed for herbaceous and woody stems < 1.37 m. Density and biomass results indicate HELI and SKID are on a trajectory to produce species, densities and biomass similar to REF. GLYPH coppice and seedlings were removed, so GLYPH regenerated from seedbanks and flood disseminated seed. GLYPH has transitioned from an herbaceous freshwater marsh to an open woodland/savanna community. GLYPH exemplifies advantages of coppice for rapid tree regeneration and growth on sites with long hydroperiods. This research demonstrates the capacity for long-term recovery of forested wetland ecosystems following harvest where multiple site/stand factors favored recovery. Adequate stocking of flood tolerant species capable of stump sprouting favored survival of original species. Floods provided annual sediment deposits to offset rutting. Compaction was additionally ameliorated by shrink-swell clays. Finally, nearby forests provided seed sources for areas. Collectively, these factors favored rapid recovery from disturbances.

Abstract The objective of this study was to examine the relation of dormancy break requirements to winter submergence effects on germination and viability in cherrybark, willow, and Nuttall oak acorns. Acorns were submerged in a greentree reservoir and received 0, 21, 42, 63, or 84 days of winter submergence, followed by 8 weeks of incubation in four temperature regimes (15/6°, 20/10°, 25/15°, and 30/20° C). Winter submergence substituted for cold stratification requirements of cherrybark oak acorns, and dormancy break was achieved with 63 days of submergence. Although winter submergence exerted a positive effect on germination in Nuttall and willow oak acorns, dormancy break was not achieved in acorns of either species. Germination percentages were highest in the 30/20° C incubation temperature—cherrybark oak acorns (75–83 percent), followed by Nuttall oak (33–55 percent) and willow oak (14–52 percent). Among treatment combinations, all willow oak nongerminants were viable. Viability loss in cherrybark and Nuttall oak acorns was greatest in the 63- and 84-day treatments. The dynamics of acorn germination in response to winter hydrologic regime is influenced by submergence duration that may, or may not, satisfy dormancy break requirements in acorns of these red oak species.