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opencc-by-4.0May 2020View details →

Data from: Spatio-temporal trends in richness and persistence of bacterial communities in decline-phase water vole populations

ABSTRACT Understanding the driving forces that control vole population dynamics requires identifying bacterial parasites hosted by the voles and describing their dynamics at the community level. To this end, we used high-throughput DNA sequencing to identify bacterial parasites in cyclic populations of montane water voles that exhibited a population outbreak and decline in 2014-2018. An unexpectedly large number of 155 Operational Taxonomic Units (OTUs) representing at least 13 genera in 11 families was detected. Individual bacterial richness was higher during declines, and vole body condition was lower. Richness as estimated by Chao2 at the local population scale did not exhibit clear seasonal or cycle phase-related patterns, but at the vole meta-population scale, exhibited seasonal and phase-related patterns. Moreover, bacterial OTUs that were detected in the low density phase were geographically widespread and detected earlier in the outbreak; some were associated with each other. Our results demonstrate the complexity of bacterial community patterns with regard to host density variations, and indicate that investigations about how parasites interact with host populations must be conducted at several temporal and spatial scales: multiple times per year over multiple years, and at both local and long-distance dispersal scales for the host(s) under consideration. FILE DESCRIPTION: Trapping, physical, and demographic data for the 1376 Arvicola terrestris included in sequencing runs 1 to 8 This XLSX file contains the following information concerning the 1376 animals included in the eight sequencing runs: location, session numbering, animal_id,         trap_name, capture_date, species, sex (1=male, 2=female), weight (g), length_body (mm),  length_tail (mm, testes (0=abdominal, 1=scrotal), testes_length (mm), testes_width (mm), nipples (0=small, 1=lactating), vagina (0=not perforate, 1=perforate), pub_symph (0=closed, 1=open), uterus_scars (#), embryos(#), lens_weight (g), lens_weight2 (g) and sequencing labels File name: Animal_details.xlsx   Information concerning the Arvicola terrestris samples and the positive and negative controls multiplexed in the 16Sv4 MiSeq sequencing runs 1 to 8 This XLSX file contains the Run IDs, Sample IDs, Sample types, Dates & Site names, DNA extraction kit, PCR IDs, PCR replicate numbers, numbers of reads before and after filtering and the fastq file names for the 6615 PCR products multiplexed in the eight different Illumina MiSeq runs. File name: Sample_and_sequencing_informations.xlsx   MiSeq raw sequences of the 16Sv4 rRNA gene from Arvicola terrestris samples (Run1) This ZIP file contains the Run1 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each Arvicola terrestris sample using the MiSeq platform. The 1570 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx. File name: MiSeq_Reads_16S_Arvicola_terrestris_Run1.zip   MiSeq raw sequences of the 16Sv4 rRNA gene from Arvicola terrestris samples (Run2) This ZIP file contains the Run2 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each Arvicola terrestris sample using the MiSeq platform. The 1668 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx. File name: MiSeq_Reads_16S_Arvicola_terrestris_Run2.zip   MiSeq raw sequences of the 16Sv4 rRNA gene from Arvicola terrestris samples (Run3) This ZIP file contains the Run3 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each Arvicola terrestris sample using the MiSeq platform. The 1646 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx. File name: MiSeq_Reads_16S_Arvicola_terrestris_Run3.zip   MiSeq raw sequences of the 16Sv4 rRNA gene from Arvicola terrestris samples (Run4) This ZIP file contains the Run4 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each Arvicola terrestris sample using the MiSeq platform. The 1712 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx. File name: MiSeq_Reads_16S_Arvicola_terrestris_Run4.zip   MiSeq raw sequences of the 16Sv4 rRNA gene from Arvicola terrestris samples (Run5) This ZIP file contains the Run5 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each Arvicola terrestris sample using the MiSeq platform. The 1680 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx. File name: MiSeq_Reads_16S_Arvicola_terrestris_Run5.zip   MiSeq raw sequences of the 16Sv4 rRNA gene from Arvicola terrestris samples (Run6) This ZIP file contains the Run6 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each Arvicola terrestris sample using the MiSeq platform. The 1704 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx. File name: MiSeq_Reads_16S_Arvicola_terrestris_Run6.zip   MiSeq raw sequences of the 16Sv4 rRNA gene from Arvicola terrestris samples (Run7) This ZIP file contains the Run7 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each Arvicola terrestris sample using the MiSeq platform. The 1620 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx. File name: MiSeq_Reads_16S_Arvicola_terrestris_Run7.zip   MiSeq raw sequences of the 16Sv4 rRNA gene from Arvicola terrestris samples (Run8) This ZIP file contains the Run8 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each Arvicola terrestris sample using the MiSeq platform. The 1630 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx. File name: MiSeq_Reads_16S_Arvicola_terrestris_Run8.zip   Raw abundance table of the 16v4 rRNA gene from Arvicola terrestris samples before data filtering (Run1 to 8) This CSV file contains the number of reads for each distinct variant (OTU) and each of the 6615 PCR products, including the Arvicola terrestris samples and the controls, sequenced in the MiSeq runs 1 to 8 before the data filtering. File name: Read_abundance_table_before_filtering.csv   Abundance table of the 16v4 rRNA gene from Arvicola terrestris samples after data filtering (Run1 to 8) This CSV file contains the number of reads for each distinct variant (OTU) and each Arvicola terrestris sample sequenced in the MiSeq runs 1 to 8 after the data filtering. File name: Read_abundance_table_after_filtering.csv

opencc-by-4.0May 2020View details →

Data from: Genome-wide Screens Implicate Loss of Cullin Ring Ligase 3 in Persistent Proliferation and Genome Instability in TP53-Deficient Cells

CSV files of whole-Genome Knockout Screens for Proliferation and Tumorigenic Growth. The data is retrieved from: Title: "Genome-wide Screens Implicate Loss of Cullin Ring Ligase 3 in Persistent Proliferation and Genome Instability in TP53-Deficient Cells" DOI: https://doi.org/10.1016/j.celrep.2020.03.029 The excel sheet with data shown in figure 1B is converted to CSV files.

opencc-zeroJul 2020View details →

Data from: Genotypic variation in the induction and persistence of transgenerational responses to seasonal cues

Phenotypes respond to environments experienced directly by an individual, via phenotypic plasticity, or to the environment experienced by ancestors, via transgenerational environmental effects. The adaptive value of environmental effects depends not only on the strength and direction of the induced response, but also on how long the response persists within and across generations, and how stably it is expressed across environments that are encountered subsequently. Little is known about the genetic basis of those distinct components, or even whether they exhibit genetic variation. We tested for genetic differences in the inducibility, temporal persistence, and environmental stability of transgenerational environmental effects in Arabidopsis thaliana. Genetic variation existed in the inducibility of transgenerational effects on traits expressed across the life cycle. Surprisingly, the persistence of transgenerational effects into the third generation was uncorrelated with their induction in the second generation. While environmental effects for some traits in some genotypes weakened over successive generations, others were stronger or even in the opposite direction in more distant generations. Therefore, transgenerational effects in more distant generations are not merely caused by the retention or dissipation of those expressed in prior generations, but they may be genetically independent traits with the potential to evolve independently.

opencc-zeroDec 2020View details →

Data from: Risk of short-term biodiversity loss under more persistent precipitation regimes

Recent findings indicate that atmospheric warming increases the persistence of weather patterns in the mid-latitudes, resulting in sequences of longer dry and wet periods compared to historic averages. The alternation of progressively longer dry and wet extremes could increasingly select for species with a broad environmental tolerance. As a consequence, biodiversity may decline. Here, we explore the relationship between the persistence of summer precipitation regimes and plant diversity by subjecting experimental grassland mesocosms to a gradient of dry-wet alternation frequencies whilst keeping the total precipitation constant. The gradient varied the duration of consecutive wet and dry periods, from 1 up to 60 days with or without precipitation, over a total of 120 days. An alternation of longer dry and wet spells led to a severe loss of species richness (up to –75% relative to the current rainfall pattern in W-Europe) and functional diversity (enhanced dominance of grasses relative to nitrogen (N)-fixers and non-N-fixing forbs). Loss of N-fixers and non-N-fixing forbs in severe treatments was linked to lower baseline competitive success and higher physiological sensitivity to changes in soil moisture compared to grasses. The extent of diversity losses also strongly depended on the timing of the dry and wet periods. Regimes in which long droughts (≥ 20 days) coincided with above-average temperatures showed significantly more physiological plant stress over the experimental period, greater plant mortality, and impoverished communities by the end of the season. Across all regimes, the duration of the longest period below permanent wilting point was an accurate predictor of mortality across the communities, indicating that increasingly persistent precipitation regimes may reduce opportunities for drought stress alleviation. We conclude that without recruitment, which was precluded in this experiment, summer precipitation regimes with longer dry and wet spells will likely diminish plant diversity, at least in the short term.

opencc-zeroDec 2017View details →

Data from: Experimental warming in the field delays phenology and reduces body mass and survival: implications for the persistence of a pollinator under climate change

1. Climate change is rapidly altering thermal environments across the globe. The effects of increased temperatures in already warm environments may be particularly strong because organisms are likely to be near their thermal safety margins, with limited tolerance to additional heat stress. 2. We conduct an in situ field experiment over two years to investigate the direct effects of temperature on an early-season solitary bee in a warm, arid region of the Southwestern USA. Our field experiment manipulates the thermal environment of Osmia ribifloris (Megachilidae) from larval development through adult emergence, simulating both previous cooler (ca. 1950; nest boxes painted white), and future warmer (2040–2099; nest boxes painted black) climate conditions. In each year we measure adult emergence phenology, linear body size, body mass, fat content, and survival. 3. Bees in the warming treatment exhibit delayed emergence and a substantial increase in phenological variance. Increases in temperature also lead to reductions in body mass and fat content. Whereas bees in the cooling and control treatments experience negligible amounts of mortality, bees in the warming treatment experience 30–75% mortality. 4. Our findings indicate that temperature changes that have occurred since ca. 1950 have likely had relatively weak and non-negative effects, but predicted warmer temperatures create a high stress thermal environment for O. ribifloris. Later and more variable emergence dates under warming likely compromise phenological synchrony with floral resources and the ability of individuals to find mates. The consequences of phenological asynchrony, combined with reductions in body mass and fat content, will likely impose fitness reductions in surviving bees. Combined with high rates of mortality, our results suggest that O. ribifloris may face local extirpation in the warmer parts of its range within the century. 5. Temperature increases in already warm ecosystems can have substantial consequences for key components of life history, physiology, and survival. Our study suggests that the response of ectothermic insects to temperature increases in already warm environments may be insufficient to mitigate the negative consequences of future warming.

opencc-zeroDec 2017View details →

Data from: Field-scale experiments reveal persistent yield gaps in low-input and organic cropping systems

Knowledge of production-system performance is largely based on observations at the experimental plot scale. Although yield gaps between plot-scale and field-scale research are widely acknowledged, their extent and persistence have not been experimentally examined in a systematic manner. At a site in southwest Michigan, we conducted a 6-y experiment to test the accuracy with which plot-scale crop-yield results can inform field-scale conclusions. We compared conventional versus alternative, that is, reduced-input and biologically based–organic, management practices for a corn–soybean–wheat rotation in a randomized complete block-design experiment, using 27 commercial-size agricultural fields. Nearby plot-scale experiments (0.02-ha to 1.0-ha plots) provided a comparison of plot versus field performance. We found that plot-scale yields well matched field-scale yields for conventional management but not for alternative systems. For all three crops, at the plot scale, reduced-input and conventional managements produced similar yields; at the field scale, reduced-input yields were lower than conventional. For soybeans at the plot scale, biological and conventional managements produced similar yields; at the field scale, biological yielded less than conventional. For corn, biological management produced lower yields than conventional in both plot- and field-scale experiments. Wheat yields appeared to be less affected by the experimental scale than corn and soybean. Conventional management was more resilient to field-scale challenges than alternative practices, which were more dependent on timely management interventions; in particular, mechanical weed control. Results underscore the need for much wider adoption of field-scale experimentation when assessing new technologies and production-system performance, especially as related to closing yield gaps in organic farming and in low-resourced systems typical of much of the developing world.

opencc-zeroDec 2018View details →

Data from: Soil microbiomes underlie population persistence of an endangered plant species

Microbiomes can dramatically alter individual plant performance, yet how these effects influence higher order processes is not well resolved. In particular, little is known about how microbiome effects on individual plants alter plant population dynamics, a question critical to imperiled species conservation. Here, we integrate bioassays, multidecadal demographic data, and integral projection modeling to determine how the presence of the natural soil microbiome underlies plant population dynamics. Simulations indicated that the presence of soil microbiomes boosted population growth rates (λ) of the endangered Hypericum cumulicola by 13% on average, the difference between population growth versus decline in 76% of patches. The greatest benefit (47% increase in λ) occurred in low nutrient, high elevation habitats, suggesting that the soil microbiome may help expand H. cumulicola's distribution to include these stressful habitats. Our results demonstrate that soil microbiomes can significantly affect plant population growth and persistence, and support the incorporation of soil microbiomes into conservation planning. plant population growth and persistence, and support the incorporation of soil microbiomes into conservation planning.

Data from: Detecting signals of chronic shedding to explain pathogen persistence: Leptospira interrogans in California sea lions

Identifying mechanisms driving pathogen persistence is a vital component of wildlife disease ecology and control. Asymptomatic, chronically infected individuals are an oft-cited potential reservoir of infection but demonstrations of the importance of chronic shedding to pathogen persistence at the population level remain scarce. Studying chronic shedding using commonly collected disease data is hampered by numerous challenges, including short-term surveillance that focuses on single epidemics and acutely ill individuals, the subtle dynamical influence of chronic shedding relative to more obvious epidemic drivers, and poor ability to differentiate between the effects of population prevalence of chronic shedding versus intensity and duration of chronic shedding in individuals. We use chronic shedding of Leptospira interrogans serovar Pomona in California sea lions (Zalophus californianus) as a case study to illustrate how these challenges can be addressed. Using leptospirosis-induced strands as a measure of disease incidence, we fit models with and without chronic shedding, and with different seasonal drivers, to determine the timescale over which chronic shedding is detectable and the interactions between chronic shedding and seasonal drivers needed to explain persistence and outbreak patterns. Chronic shedding can enable persistence of L. interrogans within the sea lion population. However, the importance of chronic shedding was only apparent when surveillance data included at least two outbreaks and the intervening inter-epidemic trough during which fadeout of transmission was most likely. Seasonal transmission, as opposed to seasonal recruitment of susceptibles, was the dominant driver of seasonality in this system, and both seasonal factors had limited impact on long-term pathogen persistence. We show that the temporal extent of surveillance data can have a dramatic impact on inferences about population processes, where the failure to identify both short- and long-term ecological drivers can have cascading impacts on understanding higher-order ecological phenomena, such as pathogen persistence.

Data from: A persistent lack of international representation on editorial boards in environmental biology

The scholars comprising journal editorial boards play a critical role in defining the trajectory of knowledge in their field. Nevertheless, studies of editorial board composition remain rare, especially those focusing on journals publishing research in the increasingly globalized fields of science, technology, engineering, and math (STEM). Using metrics for quantifying the diversity of ecological communities, we quantified international representation on the 1985–2014 editorial boards of 24 environmental biology journals. Over the course of 3 decades, there were 3,827 unique scientists based in 70 countries who served as editors. The size of the editorial community increased over time—the number of editors serving in 2014 was 4-fold greater than in 1985—as did the number of countries in which editors were based. Nevertheless, editors based outside the "Global North" (the group of economically developed countries with high per capita gross domestic product [GDP] that collectively concentrate most global wealth) were extremely rare. Furthermore, 67.18% of all editors were based in either the United States or the United Kingdom. Consequently, geographic diversity—already low in 1985—remained unchanged through 2014. We argue that this limited geographic diversity can detrimentally affect the creativity of scholarship published in journals, the progress and direction of research, the composition of the STEM workforce, and the development of science in Latin America, Africa, the Middle East, and much of Asia (i.e., the "Global South").

opencc-zeroDec 2017View details →

Data from: Response to persistent er stress in plants: a multiphasic process that transitions cells from prosurvival activities to cell death

The unfolded protein response (UPR) is a highly conserved response that protects plants from adverse environmental conditions. The UPR is elicited by endoplasmic reticulum (ER) stress, in which unfolded and misfolded proteins accumulate within the ER. Here, we induced the UPR in maize (Zea mays) seedlings to characterize the molecular events that occur over time during persistent ER stress. We found that a multiphasic program of gene expression was interwoven among other cellular events, including the induction of autophagy. One of the earliest phases involved the degradation by regulated IRE1-dependent RNA degradation (RIDD) of RNA transcripts derived from a family of peroxidase genes. RIDD resulted from the activation of ZmIRE1 for promiscuous ribonuclease activity that attacks the mRNAs of secreted proteins. This was followed by an upsurge in expression of the canonical UPR genes indirectly driven by ZmIRE1 due to its splicing of Zmbzip60 to make an active transcription factor that directly upregulates many of the UPR genes. At the peak of UPR gene expression, a global wave of alternative RNA processing led to the production of many aberrant UPR gene transcripts, likely tempering the ER stress response. During later stages of ER stress, ZmIRE1's activity declined as did the expression of survival modulating genes, Bax inhibitor1 and Bcl-2-associated athanogene7, amidst a rising tide of cell death. Thus, in response to persistent ER stress, maize seedlings embark on a course of gene expression and cellular events progressing from adaptive responses to cell death.

Data from: Differential persistence favors habitat preferences that determine the distribution of a reef fish

A central focus of population ecology is understanding what factors explain the distribution and abundance of organisms within their range. This is a key issue in marine systems, where many organisms produce dispersive larvae that develop offshore before returning to settle on benthic habitat. We investigated the distribution of the neon goby, Elacatinus lori, on sponge habitat and evaluated whether variation in the persistence of recently settled individuals (i.e., settlers) among different sponge types can result in habitat preferences and establish their observed distribution. We found that E. lori settlers were more likely to occur on large yellow tube sponges (Aplysina fistularis) than on small yellow sponges or brown tube sponges (Agelas conifera). An experiment seeding settlers onto multiple species and sizes of sponge habitat revealed that settlers persist longer on large yellow sponges than on small yellow sponges or brown sponges. Habitat preference experiments also indicated that settlers prefer large yellow sponges over small yellow sponges or brown sponges. Settlers achieved these preference behaviors using visual, but not chemical, cues. Finally, new settlers arriving from the water column were more likely to occur on large yellow sponges than on small yellow sponges or brown sponges, indicating that the observed habitat preferences existed independent of prior experience. These results support the hypothesis that E. lori have evolved behavioral preferences for sponge habitats that will maximize their post-settlement persistence, and that decisions at settlement will shape the population level pattern of settler distribution on coral reefs.

Data from: Long-term in situ persistence of biodiversity in tropical sky-islands revealed by landscape genomics

Tropical mountains are areas of high species richness and endemism. Two historical phenomena may have contributed to this: (1) fragmentation and isolation of habitats may have promoted the genetic differentiation of populations and increased the possibility of allopatric divergence and speciation, and; (2) the mountain areas may have allowed long-term population persistence during global climate fluctuations. These two phenomena have been studied using either species occurrence data or estimating species divergence times. However, only few studies have used intraspecific genetic data to analyse the mechanisms by which endemism may emerge at the microevolutionary scale. Here, we use landscape analysis of genomic SNP data sampled from two high-elevation plant species from an archipelago of tropical sky-islands (the Transmexican Volcanic Belt) to test for population genetic differentiation, synchronous demographic changes and habitat persistence. We show that genetic differentiation can be explained by the degree of glacial habitat connectivity among mountains, and that mountains have facilitated the persistence of populations throughout glacial/interglacial cycles. Our results support the ongoing role of tropical mountains as cradles for biodiversity by uncovering cryptic differentiation and limits to gene flow.

opencc-zeroDec 2015View details →

Data from: Resistance in persisting bat populations after white-nose syndrome invasion

Increases in anthropogenic movement have led to a rise in pathogen introductions and the emergence of infectious diseases in naive host communities worldwide. We combined empirical data and mathematical models to examine changes in disease dynamics in little brown bat (Myotis lucifugus) populations following the introduction of the emerging fungal pathogen Pseudogymnoascus destructans, which causes the disease white-nose syndrome. We found that infection intensity was much lower in persisting populations than in declining populations where the fungus has recently invaded. Fitted models indicate that this is most consistent with a reduction in the growth rate of the pathogen when fungal loads become high. The data are inconsistent with the evolution of tolerance or an overall reduced pathogen growth rate that might be caused by environmental factors. The existence of resistance in some persisting populations of little brown bats offers a glimmer of hope that a precipitously declining species will persist in the face of this deadly pathogen. This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'.

Data from: Priority effects can persist across floral generations in nectar microbial metacommunities

The order of species arrival can influence how species interact with one another and, consequently, which species may coexist in local communities. This phenomenon, called priority effects, has been observed in various types of communities, but it remains unclear whether priority effects persist over the long term spanning multiple generations of local communities in metacommunities. Focusing on bacteria and yeasts that colonize floral nectar of the sticky monkey flower, Mimulus aurantiacus, via hummingbirds and other flower-visiting animals, we experimentally manipulated initial microbial dominance on plants (regarded as metacommunities) to examine whether its effects persisted across multiple generations of flowers (regarded as local microbial habitats). The experimental introduction of Neokomagataea (= Gluconobacter) bacteria and Metschnikowia yeasts into wild flowers showed that the effects of initial dominance were observable across multiple floral generations. Three weeks after introduction, corresponding approximately to three floral generations, Neokomagataea introduction led to exclusion of yeasts, whereas Metschnikowia introduction did not result in the exclusion of Neokomagataea. Our results suggest that, even when local habitats are ephemeral, priority effects may influence multiple generations of local communities within metacommunities.

opencc-by-4.0Jul 2023View details →

Data for The Persistence of Memory in Ionic Conduction Probed by Nonlinear Optics

Experimental and computational data and analysis workflows for the manuscript "The Persistence of Memory in Ionic Conduction Probed by Nonlinear Optics" (doi:10.1038/s41586-023-06827-6). Python scripts:<ol><li>paper_tke_plots_pub.py is for experimental TKE plots</li><li>analysis_pumping_pub.py is for computational TKE plots</li></ol>Python requirements for the work-up of experimental data are the typical scientific python stack: numpy, matplotlib, scipy, pandas, sympy. Computational counterpart of the TKE experiment uses essentially the same hopping analysis as our computational study https://www.nature.com/articles/s41563-022-01316-z with its scripting available at https://github.com/apoletayev/anomalous_ion_conduction/ . The python package requirements are, in addition to above, networkx, freud, deepgraph, fastparquet, pyarrow. All python scripts work best when run in a notebook-like fashion cell by cell (e.g. with spyder). Experimental data: TKE, OKE, THz transmission. Computational data: example simulations of Na beta-alumina, K beta-alumina, K beta"-alumina. The files include tracking the simulation temperatures, centers of mass of the mobile ions, and hopping.  Basic usage: download and unzip data. Install python dependencies (e.g. using conda or pip). Run python from the same directory in which the data folders are located. All paths in the scripts are relative.

opencc-zeroOct 2023View details →

Data from: Increases in understory plant cover and richness persist following restoration treatments in Pinus ponderosa forests

A combination of forest thinning followed by prescribed burning is widely applied in the western US to increase ecosystem resistance and resilience to disturbances. Understory plant community responses may be driven both by management treatments and climatic factors. Thus, responses to treatments during a 20-year megadrought have implications for the role of management in fostering adaptive capacity to climate change. We used a network of five sites (600 plots) spanning an environmental gradient in ponderosa pine (Pinus ponderosa) forests of the American Southwest, an ecosystem that is broadly distributed and actively managed throughout the western US. We used repeated long-term monitoring data to quantify plant community responses to treatment 1-5, 6-10, and >10 years post-implementation. Specifically, we focused on the effects of treatment and abiotic conditions on native and nonnative plant cover and species richness, and on the proportion of native species with northern (cool-mesic) biogeographic affinities. Overall, thinning and prescribed burning nearly doubled native cover and increased native species richness by about 50% relative to untreated controls. These effects persisted for over a decade after treatment, even under the influence of significant and persistent drought. Cover and richness were also greater on intermediate to wet sites. Finally, native species with northern biogeographic affinities were reduced for up to five years after treatment relative to those with southern (warm-xeric) affinities, and in dry years, indicating that both management and interannual climate variability may foster shifts in plant communities that are more resilient to a warming climate. Synthesis and applications: In ponderosa pine forests of the American Southwest, tree thinning followed by prescribed burning will generally promote restoration goals of increasing resilience to climate change by enhancing the diversity and abundance of native understory plant species, even during a persistent 20-year megadrought.

opencc-by-4.0Aug 2023View details →

Data from: Prioritizing global land protection for population persistence can double the efficiency of habitat protection for reducing mammal extinction risk

Halting the alarming rate of species extinction, driven primarily by habitat destruction, motivated the international community to adopt (2022) the Global Biodiversity Framework and it’s 23 targets aimed at reversing habitat and species loss. Due to urgency and resource constraints, a key challenge is meeting targets effectively and efficiently. Here we conduct a global prioritization linking 70,492 unique population maps and life history characteristics for 861 threatened terrestrial mammal species. Incorporating individual population data boosted viability for 84% more populations compared to using a more typical approach that uses species distributions alone, nearly doubling the security of long-term species persistence. We map and rank global mammal persistence priority areas and assess how well the current protected areas (PA) system captures these important regions. Our results will provide conservation actors a more direct and quantifiable linkage between conservation action and extinction risk than has previously been possible at a global scale.

opencc-by-4.0Dec 2022View details →

Data from: Direct and higher-order interactions in plant communities under increasing weather persistence

ABSTRACT: Climate change is increasing the weather persistence in the midlatitudes, prolonging both dry and wet spells compared to historic averages. These newly emerging environmental conditions destabilize plant communities, but the role of species interactions in this process is unknown. Here, we tested how direct and higher-order interactions (HOIs) between species may change in synthesized grassland communities along an experimental gradient of increasing persistence in precipitation regimes. Our results indicate that species interactions (including HOIs) are an important determinant of plant performance under increasing weather persistence. Out of the 12 most parsimonious models predicting species productivity, 75 % contained significant direct interactions and 92 % significant HOIs. Inclusion of direct interactions or HOIs respectively tripled or quadrupled the explained variance of target species biomass compared to null models only including the precipitation treatment. Drought dominated the plant responses, with longer droughts increasing direct competition but also HOI-driven facilitation. Despite these counteracting changes, drought intensified net competition. Grasses were generally more involved in competitive interactions whereas legumes had a stronger affinity for facilitative interactions. Under longer drought, species affinity for nutrient rich or wet environments resulted in more negative direct interactions or HOIs, respectively. We conclude that higher-order interactions, crucially depending on species identity, only partially stabilize community dynamics under increasing weather persistence

opencc-by-4.0Nov 2023View details →

Supporting data for von Fromm et al. (2023) Controls on timescales of soil organic carbon persistence across sub-Saharan Africa

This file contains the supporting data for von Fromm et al. (2024) Controls on timescales of soil organic carbon persistence across sub-Saharan Africa, Global Change Biology, <a href="https://doi.org/10.1111/gcb.17089">https://doi.org/10.1111/gcb.17089</a> We used wet soil chemistry data from Vågen et al., 2021 (<a href="https://doi.org/10.34725/DVN/66BFOB">https://doi.org/10.34725/DVN/66BFOB</a>). In addition, we added newly measured radiocarbon data, extracted global climate data, gross primary productivity and quantified soil mineralogy based on X-ray powder diffraction data. Turnover time for carbon (mean C age) was calculated from Δ14C (&permil;) values by using an one-pool model. For more details about the sampling, calculations, and units see the associated publication. To reproduce all analysis, including calculating the mean C age, please visit the author's github page: <a href="https://github.com/SophievF/AfSIS_14C">https://github.com/SophievF/AfSIS_14C</a>.  The dataset is also part of the International Soil Radiocarbon Database (<a href="https://soilradiocarbon.org/">https://soilradiocarbon.org/</a>).