Across much of the semiarid conifer forests of western North America (“dry conifer forests”), the dominant tree species are non-serotinous, lack soil seedbanks, and rarely disperse seeds much farther than 100 m, so tree regeneration in large, high-severity burned patches is expected to be highly seed-limited. Conifer seedlings do, however, sometimes establish at high densities deep within high-severity patches in these forests, implying that seeds can sometimes survive intense wildfire even when all overstory trees die. Does seed survival in the canopies of non-serotinous trees provide an unexpected source of forest resilience? To answer this question, we surveyed tree survival, fire severity, and seedling abundance across two very large wildfires in the first year after fire. Several of the study species had a good seed cone production year at the time of the fires. We stratified many of our plots deep within high-severity patches far from surviving trees, where existing models predict regeneration failure due to a lack of viable seeds. Contrary to such expectations, we found that conifer seedling densities in these areas were generally far greater than needed to replace fire-killed trees and sometimes approached seedling densities observed near surviving trees. Seedling densities in high-severity areas far from surviving trees correlated negatively with local burn intensity (canopy foliage consumption), supporting the local origin of the seeds and highlighting a critical driver of post-fire recovery that is easily missed by traditional surveys conducted > 2 years following fire. Seedling density was also strongly associated with burn date, suggesting that persistence of viable canopy seeds depends on synchrony between wildfire and cone ripening dates. Together, our results demonstrate that under the right conditions, canopy seed survival can lead to dense seedling establishment across large, severely burned areas and may substantially support the resilience of dry conifer forests to the uncharacteristically severe fires that are becoming increasingly prevalent in this system.

This repository contains all code, data, and instructions needed to reproduce the analyses, figures, and tables presented in the manuscript “fastfocal: A Fast, Light, and Sustainable R Package for Focal Raster Operations.” Contents include:R scripts for accuracy tests, runtime benchmarking, and energy measurementSimulated raster data used in benchmarking and accuracy comparisonsOutput tables and figuresThese materials ensure full reproducibility of the study and allow users to replicate or extend the benchmarking experiments on their own systems.

This repository contains all code, data, and instructions needed to reproduce the analyses, figures, and tables presented in the manuscript “fastfocal: A Fast, Light, and Sustainable R Package for Focal Raster Operations.” Contents include:R scripts for accuracy tests, runtime benchmarking, and energy measurementSimulated raster data used in benchmarking and accuracy comparisonsOutput tables and figuresThese materials ensure full reproducibility of the study and allow users to replicate or extend the benchmarking experiments on their own systems.

The primary objective of this study aims to examine and compare the dynamics of phytoplankton blooms at different stages of upwelling. We combined environmental and physiological observations to put together a narrative of phytoplankton community succession. In doing so, we postulate that the four stations sampled represent a mosaic of different stages of relatively early upwelling cycles such that they can be classified as either the initial onset of upwelling (early stage, denoted by E1) in which the subsurface community only recently transitioned to the surface, or the relatively later phases (later stage, denoted by L2, L3, and L4) where the community has just started to build up biomass and is undergoing the "shift-up" response. Four sites experiencing upwelling were sampled off the coast of Northern California on May 30, 2019 (E1 and L2) and June 05, 2019 (L3 and L4). Seawater was collected using a CTD-Rosette sampler, at four depths throughout the euphotic zone at each station corresponding to 50%, 30%, 10%, and 1% incident irradiance. Samples for temperature, salinity, PAR, chlorophyll a, dissolved inorganic nutrients, dissolved metal micronutrients, and physiology were obtained. PUPCYCLE I (Phytoplankton response to the UPwelling CYCLE) took place in summer 2019 onboard the R/V Oceanus (OC 1905b), led by Chief Scientist Adrian Marchetti.

The primary objective of this study was to assess the physiological and molecular response of subsurface phytoplankton communities to a simulation of the Upwelling Conveyor Belt Cycle (UCBC). To capture this phenomenon, we performed on-deck incubation experiments that spanned different time points representing the different stages of growth (initial deep-water community at T0, and stimulated growth phases at T1 and T2). We further subjected the incubations to various Fe-related treatments to test how Fe might play a role in determining their physiological and molecular response to upwelling. The first incubation was conducted from 27 May to 01 June 2019 in a wide continental shelf, and the second incubation was conducted from 02 June to 06 June 2019 in a narrow continental shelf. For each time point, the incubation was harvested and analyzed for chlorophyll, nutrients, particulate organic carbon and nitrogen, and dissolved and particulate Fe and Sc concentrations. 6-hour incubations using trace concentrations of stable isotopes of 13C and 15N were also conducted to assess uptake kinetics of dissolved inorganic carbon (DIC) and nitrate (NO3) in bulk-size fractionated phytoplankton communities. PUPCYCLE I (Phytoplankton response to the UPwelling CYCLE) took place in summer 2019 onboard the R/V Oceanus (OC1905b), led by Chief Scientist Adrian Marchetti.

These data include tree-ring chronologies and stable carbon isotope data for locations in southwestern Alaska that were used in the study Decoupling of temperature and growth of white spruce at western treeline, Alaska is unrelated to intrinsic water stress. The ring-width index (RWI) chronologies were produced by first removing age-related declines in growth by fitting a modified negative exponential curve, or a zero-slope curve if there were no age-related declines, to each ring-width series and then by averaging the individual indices together using a Tukey bi-weight robust mean (Cook and Kairiukstis 1990) using the dplR package (Bunn 2008) in R (R Core Team 2018). RWI is a dimentionless index used for tree ring chronologies. Carbon stable isotope chronologies were produced for a 30-50 year period from each side. Wood was sub-sampled to alpha cellulose using the modified Brendel et al. (2005) method (Gaudinski et al. 2011) and analyzed at the University of Arizona, Environmental Isotope Laboratory. Uncorrected Carbon isotopes (δ13C) are provided with the units in per mil. Analytical error is 0.03 per mil. δ13C was converted to 13C discrimination (Δ13C) to correct for changing atmospheric δ13CO2 since the Industrial Revolution and is also provided in the data set.

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These data are from the research project Drought and Sagebrush: Management Implications, conducted by Kerry Byrne and Kristen Kaczynski from 2016 - 2020. The dataset contains research results related to species composition, forb density, and above and belowground net primary production in response to four years of experimental drought using rainout shelters and control plots. We used rainfall shelters to create a 1-in-100-year drought at each site to understand how chronic (4 year) drought will impact common, but understudied sagebrush steppe plant communities. We conducted our study at two sites approximately 60 m apart within a grazing exclosure established in 1993 in Klamath County, Oregon, USA (42.301111, -121.018056). The two study sites have unique edaphic features that lead to differences in the ecological structure and function of the plant communities. One site (AA site) is dominated by Artemisia arbuscula (low sagebrush) while the other site (AC site) is dominated by A. cana (silver sagebrush). We found that above- and belowground net primary production at both sites were remarkably resistant to drought. Litter increased over time in drought plots at the more productive AC site, and we hypothesize that hydraulic lift and litter interacted to increase shallow soil water content under drought at that site. The AA site, with harsher edaphic features and a soil duripan, experienced fewer changes in plant community composition than the more productive AC site, potentially due to the presence of specialized plant species at the harsher site. Non-native plant cover increased (primarily from Ventenata dubia, an invasive annual grass) and native forb cover and density decreased over time. This suggests that management may be needed to conserve native forb diversity and limit species invasion, especially as climate and fire regimes change.

Sequoia sempervirens (coast redwood) trees were sampled for a dendroseismological investigation along the North Coast Section of the San Andreas Fault, and the data were fully analyzed, interpreted, and discussed in a journal article and supplemental material (Carroll et al., 2025). Here, were provide data associated with this work: 1200 dpi resolution images of tree cores and stumps, raw ring width measurements for living trees and stumps with associated crossdating categories, standard tree and location chronologies with sample depths, and descriptions of tree cores. Please refer to the journal article and supplemental material for full details, supporting material, and context.Tree ring samples were collected at two locations: Fort Ross Historic State Park (Fort Ross) and Gualala Redwood Timber Company (Gualala). Eleven living trees (8 at Fort Ross, 3 at Gualala) were climbed with ropes, and 5-mm-diameter increment cores were collected at various positions on the main and reiterated trunks. Skilled sawyers took plunge cuts from 23 Sequoia stumps at Gualala, sometimes taking multiple pieces from one stump.Ring series were scanned at 1200 dpi. Child folders include scans of living tree and stump samples. Pencil marks guide crossdating, but final dating is expressed in the ring width files with associated crossdating categories. Ring widths were measured to 0.001 mm precision using WinDendro software (v.2009b, Régent Instruments Inc., Québec, Canada). Crossdating proceeded using a multi-pronged approach combining visual assessment of marker years with correlation analysis, fully detailed in the journal article. Due to the complex nature of crossdating Sequoia, every year was assigned a level of crossdating confidence following previously defined protocol (Carroll et al., 2014; Carroll and Sillett, 2023) with categories of high and moderate confidence to distinguish sections with some ambiguity. For example, moderate confidence applied when missing ring(s) were known, but the placement may be in several positions. Undated rings were either 1) bound by dated rings, allowing the number of missing rings and total radial growth to be determined or 2) not bound by dated rings, as may occur for inner rings.File “Tree Ring Widths_Carroll et al 2025.xlsx” lists ring width measurements in microns for 126 series from 11 living Sequoia trees at Fort Ross and Gualala. Crossdating categories are color coded, and these categories must be considered for proper use of the data. Measurements with no highlighting are dated with high confidence, measurements highlighted in orange are dated with moderate confidence, measurements highlighted in red are undated. Undated rings do not correspond with calendar years. Zeros (0s) reflect missing rings. Zeros (0s) in undated (red) sections reflect a known number of missing rings but unknown annual placement. Green highlighting reflects broken or crumbly sections. File "TreeRingWidths.json" provides these same data in a more easily machine-readable format. File “Tree Core Logsheet_Carroll et al 2025.csv” lists descriptions associated with these series.File “Stump Ring Widths_Carroll et al 2025.xlsx” lists ring width measurements in microns for 37 sections from 23 Sequoia stumps at Gualala. Crossdating categories are color coded, and these categories must be considered for proper use of the data. Dated or partially dated paths are listed in columns B to S and correspond with calendar years in the first column. Measurements with no highlighting are dated with high confidence, measurements highlighted in orange are dated with moderate confidence, measurements highlighted in red are undated (and do not correspond with calendar years). Zeros (0s) in undated (red) sections reflect a known number of missing rings but unknown annual placement. Completely undated paths are listed in columns U to AM, do not correspond with calendar years, and are listed in descending order (from outer ring toward center). File "StumpRingWidths.json" provides these same data in a more easily machine-readable format. Descriptions of each stump sample are found in the supplementary material of the journal article.Rings dated with high confidence were used to generate inter-annual reference chronologies for each tree and locations. First, tree-level chronologies were produced using only series dated with high confidence. Series were standardized via ARSTAN software (Cook, 1985) using a cubic smoothing spline with a 50 % frequency cutoff at 32-yr (32-yr spline) to remove geometric growth trends and low-frequency variation. Standard (STD) tree chronologies were then combined into location chronologies with no further detrending using a biweight robust mean (Cook and Kairiukstis, 1990). File “Tree and Location Chronologies_Carroll et al 2025.csv” lists the standardized ring indices for each tree and location with associated sample depths.