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openbsd-3-clauseJul 2023View details →

SCEC Community Stress Model (CSM)

<a href="https://www.scec.org/science/csm" target="_blank" rel="noopener">The SCEC Community Stress Model (CSM)</a> is a group of models of stress and stressing rate within the California crust and lithosphere, compiled by the CSM Working Group of the <a href="https://www.scec.org">Statewide California Earthquake Center (SCEC)</a>. “Stress” models are models of the 3-D symmetric stress tensor (6 components), describing the forces present within a continuous volume. “Stressing rate” models are models of how the 3-D stress tensor changes over time, for example due to stress accumulating along a tectonic plate boundary. The CSM is one of several <a href="https://www.scec.org/science/cem">SCEC Community Earth Models</a>, but unlike some, it does not attempt to provide a single consensus model of stress or stressing rate. Instead, the intention is to compile a set of models of stress and stressing rate. The current version of the CSM includes 22 distinct models: 14 of stress, and 8 of stressing rate. The model techniques, assumptions, and input datasets vary, so no two models provide the exact same result. In some cases, the contributed models have been published in a peer reviewed journal. In other cases, the methods or datasets were previously published in a peer reviewed journal, but the exact contributed model is not published. For the fourteen stress models, the orientation of the stress tensor is mostly derived from the inversion of earthquake focal mechanisms. Eleven of the models are based solely on earthquake focal mechanisms, and thus do not provide information on stress magnitude. One model provides an estimate of the deviatoric stress required to support existing topography. Two models provide an estimate of the full absolute stress tensor, based on forward physics-based modeling of the tectonic loading of the southern California fault system. Note that even when sampled “on” a major fault surface, these model values should be regarded as estimates of stress in the adjacent continuum rather than estimates from “within” fault gouge zones. The eight stressing rate models are based either on geodetic data or on kinematic or mechanical models constrained by such data. Some are based on estimates of velocity field or strain rate that are then translated into stressing rate. Others involve forward physics-based modeling of tectonic loading of the fault system, but focus on deriving stressing rate rather than the absolute stress tensor. Each of the models was contributed by an author or group of authors, the earliest in 2012, the most recent in 2024, and some models were taken directly from the literature. Values in the crust (≤ 25 km depth) are reported for a uniform grid of latitude and longitude points, covering all of California at a resolution of ~2 km (0.0180º latitude, 0.0217º longitude), for a total of 160,663 unique points. Values in the deeper lithosphere (≥ 50 km) are reported for a uniform grid with a resolution of ~5 km (0.0450º latitude, 0.0543º longitude), for a total of 25,666 unique points. Depths are reported every 2 km from 1 km to 25 km depth, and then every 25 km to 100 km depth, for a total of 16 unique depths. Points that lie outside the defined volume for a particular model, given its assumptions and available data, are omitted from that model’s file. The model contributions include the 6-component cartesian stress tensor (in East, North, Up, tension positive) at each grid point, and then several values calculated from the tensor components that describe different aspects of the orientation or magnitude of the 3-D tensor. For visualization of these models, see the CSM web explorer on the SCEC CSM homepage, <a href="https://www.scec.org/science/csm">https://www.scec.org/science/csm</a>. Between 2012 and 2016, the CSM working group undertook a series of comparison exercises to assess consistency among southern California stress and stressing rate models that were available at that time. Broadly, the stress models tended to agree on stress axis orientations but not on magnitudes. Stressing rate models tend to agree along major fault segments, but disagree in secondary fault or off-fault areas. For details see the archived homepage for SCEC CSM v2023, <a href="https://southern.scec.org/research/csm">https://southern.scec.org/research/csm</a>. KEY TECHNICAL DEVELOPMENTS In 2024, as SCEC transitioned to a focus on California statewide, we compiled existing estimates of stress orientation from published literature for regions outside the original Southern California focus area. We also developed new statewide stressing rate models, based on recent estimates of strain rate across the western United States. These resulted in 11 additional contributions to the CSM.

opencc-by-4.0Aug 2021View details →

Plankton community composition and productivity near the Subantarctic Prince Edward Islands archipelago in autumn

This data set, shows hydrographic (CTD) and biogeochemical (Chl-a, nitrate+nitrite, nitrite, ammonium and silicic acid concentrations) parameters, nitrate uptake rates and net primary production, egg production rates (Calanus simillimus), Pheophytin-a concentrations in zooplankton guts, and phytoplankton and zooplankton abundances and biomass from the Prince Edward Islands archipelago in the Indian Sector of the Subantarctic Ocean, during April-May 2017.

opencc-by-4.0Nov 2021View details →

Fish community data in the Shubuto River system, Japan

Summary This dataset contains fish community data collected in the Shubuto River basin, Japan. Sampling protocols are described in Terui and Miyazaki (2016) and Miyazaki and Terui (2016) Colum specification <ul> <li>Year: sampling year</li> <li>StCode: site code</li> <li>VisitCode: visit code</li> <li>Genus: genus of the species</li> <li>LatinName: scientific name of the species</li> <li>Species_ja: Japanese name of the species</li> <li>Abundance: number of individuals collected</li> <li>Sample_area: area sampled (unit: square meter)</li> <li>Lat: latitude (WGS84)</li> <li>Lon: longitude (WGS84)</li> </ul> References Miyazaki Y, Terui A (2016) Temporal dynamics of fluvial fish community caused by marine amphidromous species in the Shubuto River, southwestern Hokkaido, Japan. Ichthyological Research 63: 173-179. <a href="https://doi.org/10.1007/s10228-015-0474-7">https://doi.org/10.1007/s10228-015-0474-7</a> Terui A, Miyazaki Y (2016) Three ecological factors influencing riverine fish diversity in the Shubuto River system, Japan: habitat capacity, habitat heterogeneity and immigration. Limnology 17: 143-149. <a href="https://doi.org/10.1007/s10201-015-0472-5">https://doi.org/10.1007/s10201-015-0472-5</a>

openother-openJun 2020View details →

When female leaders believe that men make better leaders: Empowerment in community-based water management in rural Namibia

The code in this repository can be used to reproduce the figures and regression analysis in Stata (some packages need to be installed via SSC) but the data file can of course be used with other programs like R or SPSS. <ul> <li>"female_leaders.do" includes the Stata code</li> <li>"female_leaders.dta" includes the data from the behavioral task and surveys data in Stata format (.dta) & "female_leaders.xlsx" includes these data in Excel format (.xlsx)</li> </ul>

opencc-zeroNov 2021View details →

Siderophores drive invasion dynamics in bacterial communities through their dual role as public good versus public bad

Microbial invasions can compromise ecosystem services and spur dysbiosis and disease in hosts. Nevertheless, the mechanisms determining invasion outcomes often remain unclear. Here, we examine the role of iron-scavenging siderophores in driving invasions of Pseudomonas aeruginosa into resident communities of environmental pseudomonads. Siderophores can be "public goods" by delivering iron to individuals possessing matching receptors; but they can also be "public bads" by withholding iron from competitors lacking these receptors. Accordingly, siderophores should either promote or impede invasion, depending on their effects on invader and resident growth. Using supernatant feeding and invasion assays, we show that invasion success indeed increased when the invader could use its siderophores to inhibit (public bad) rather than stimulate (public good) resident growth. Conversely, invasion success decreased the more the invader was inhibited by the residents' siderophores. Our findings identify siderophores as a major driver of invasion dynamics in bacterial communities under iron-limited conditions.

opencc-by-4.0Nov 2021View details →

Data from: Metacommunity theory review and its application in community assembly of soil animals

We were interested in community assembly of soil animals and performed a literature study to find out what is known about soil metacommunities. We aimed to study keywords co-occurrence relationships of scientific journal articles in the field of "metacommunity" research from 1992-2017 as a whole. We also investigated the co-occurrence of the top 20 most frequent keywords in five 5-year time periods.     In September 2017 we searched the Web of Science with ‘metacommunity’ as the only keyword, and found 1226 English papers published in international journals between January 1992 and September 2017. And we exported these papers from Web of Science as a plain text file (.txt) with the option ‘Full Record and Cited References’, which is archived here. The text file thus contains full records and cited references (in a concise format, so without the titles of the cited papers), and each field is prefaced by a two-character field tag. Afterwards we used the software ‘Citespace’ to create Table 1 and Figure 2 in Guo et al. (2018). We created that Figure 2 using the following settings in Citespace: we choose the “co-occurrence” function and “keyword” as node types, then created keywords co-occurrence relationships (Figure 2). Next, we created lists of the top 20 keywords in different periods, which can reveal the research hotspots (Table 1). The method for extracting the top 20 most frequent keywords was as follows: We use the Web of Science database to retrieve scientific papers from 1992 to 2017, taking into account the relationship between citation and publication time. We calculated the percentage of 200 most cited papers published in each of the 5-year periods. To do so we followed the following steps: Step1: we selected the 200 most cited papers from the entire datset (1226 in the 1992-2017 period). Step 2: we calculated the percentage of those 200 papers published each 5-year period. Step 3: we also calculated an correction coefficient by taking, for each 5-year period, the number of top-200 most cited papers published in that period, and dividing that number by the total number of papers (out of the 1226 selected papers) published in that period. Step 4 Last, we calculate the real keyword frequency by multiplying the keyword frequency in specific 5-year periods with the correction coefficient.

opencc-zeroDec 2020View details →

Functional biogeography of Neotropical moist forests: trait-climate relationships and assembly patterns of tree communities

Aim: Here we examine the functional profile of regional tree species pools across the latitudinal distribution of Neotropical moist forests, and test trait-climate relationships among local communities. We expected opportunistic strategies (acquisitive traits, small seeds) to be overrepresented in species pools further from the equator due to long-term instability, but also in terms of abundance in local communities in currently wetter, warmer and more seasonal climates. Location: Neotropics. Time period: Recent. Major taxa studied: Trees. Methods: We obtained abundance data from 471 plots across nine Neotropical regions, including ~100,000 trees of 3,417 species, in addition to six functional traits. We compared occurrence-based trait distributions among regional species pools, and evaluated single trait-climate relationships across local communities using community abundance-weighted means (CWM). Multivariate trait-climate relationships were assessed by a double-constrained correspondence analysis that tests both how CWMs relate to climate and how species distributions, parameterized by niche centroids in climate space, relate to their traits. Results: Regional species pools were undistinguished in functional terms, but opportunistic strategies dominated local communities further from the equator, particularly in the northern hemisphere. Climate explained up to 57% of the variation in CWM traits, with increasing prevalence of lower-statured, light-wooded and softer-leaved species bearing smaller seeds in more seasonal, wetter and warmer climates. Species distribution were significantly but weakly related to functional traits. Main conclusions: Neotropical moist forest regions share similar sets of functional strategies, from which local assembly processes, driven by current climatic conditions, select for species with different functional strategies. We can thus expect functional responses to climate change driven by changes in relative abundances of species already present regionally. Particularly, equatorial forests holding the most conservative traits and large seeds are likely to experience the most severe changes if climate change triggers the proliferation of opportunistic tree species.

opencc-by-4.0Nov 2021View details →

Geographical variation of floral scents in generalist entomophilous species with variable pollinator communities

This is the dataset used for the article: "Geographical variation of floral scents in generalist entomophilous species with variable pollinator communities" by de Manincor N. et al., 2021 published in Functional Ecology (https://besjournals.onlinelibrary.wiley.com/doi/10.1111/1365-2435.13984) In this study we investigated the floral scent (Volatile Organic Compounds, VOCs) variation of four perennial plant species, with generalist pollination, in two different environments: under natural condition (field) and controlled condition (greenhouse). The focal plant species are: Anthyllis vulneraria (AV), Globularia vulgaris (GV), Pilosella officinarum (PO) and Ranunculus bulbosus (RB). The dataset is composed by different files that have been used to investigate (1) variation of VOCs under natural condition (files "field"), (2) variation of VOCs under controlled condition (files "greenhouse"), (3) the effect of the reared condition and the role of phenotypic plasticity (field vs greenhouse, files "FvsGH") and (4) variation of the pollinator community associated with the four focal species (files "poll_" and (5) whether changes in floral scents in the field were associated to some variation in the pollinator communities (at the species level, using an RDA analysis, files "Pollinators-2017", "VOC-2017"). We also provided two scripts: the script with an example to calculate VOCs variation, and the script for the RDA analysis.

opencc-by-4.0Dec 2014View details →

Fig. 3 in Impact Of Coastal Wetland Restoration Strategies In The Chongming Dongtan Wetlands, China: Waterbird Community Composition As An Indicator

Fig. 3. Densities of Charadriidae (a), Anatidae (b), Ardeidae (c), and Laridae (d) among autumn, winter and spring in four sites. Error bars represent ±1 SE.

Fig. 4 in Microcrustacean (Cladocera, Copepoda) Communities In Artificial Lakes In The Region Of The North Hungarian Mountains, With Special Reference To The Adventive Species

Fig. 4. Occurrences of the non-indigenous microcrustacean species in the investigated artificial lakes of north-eastern Hungary. Abbrev.: Eurytemora velox: +, Daphnia ambigua: ▲, Pleuroxus denticu-

Fig. 1 in Microcrustacean (Cladocera, Copepoda) Communities In Artificial Lakes In The Region Of The North Hungarian Mountains, With Special Reference To The Adventive Species

Fig. 1. Species accumulation curves of the fish ponds for total microcrustaceans (a) and for cladocerans and copepods separately (b)

Fig. 3 in Microcrustacean (Cladocera, Copepoda) Communities In Artificial Lakes In The Region Of The North Hungarian Mountains, With Special Reference To The Adventive Species

Fig. 3. Frequency of occurrence (incl. species occurring in at least 5 fish ponds). Abbrev.: Chy_sph – Chydorus sphaericus, Bos_lon – Bosmina longirostris, Cyc_vic – Cyclops vicinus, Dap_cuc – Daphnia cucullata, Euc_ser – Eucyclops serrulatus, Aca_tra – Acanthocyclops trajani, Eud_gra – Eudiaptomus gracilis, Mac_alb – Macrocyclops albidus, Ple_adu – Pleuroxus aduncus, Sim_vet – Simocephalus vetulus, Mac_lat – Macrothrix laticornis, Euc_spe – Eucyclops speratus, The_oit – Thermocyclops oithonoides, Nit_hib – Nitocra hibernica, Alo_rec – Alona rectangula, Sca_muc – Scaphole-

Fig. 5 in Microcrustacean (Cladocera, Copepoda) Communities In Artificial Lakes In The Region Of The North Hungarian Mountains, With Special Reference To The Adventive Species

Fig. 5. The relative frequencies of Eurytemora velox (white), Eudiaptomus gracilis (black) and all other microcrustacean species (grey) in those fish ponds where the invasive E. velox was present

opencc-by-4.0Dec 2020View details →

Fig. 4 in Helminth communities from amphibians inhabiting agroecosystems in the Pampean Region (Argentina)

Fig. 4. Helminth prevalence (A), abundance (B) and richness (C) at infracommunity level, in relation to land use and host species. B. pulchella (Bp), L. latrans (Ll), R. fernandezae (Rf).

opencc-by-4.0Dec 2017View details →

FIGURE 3 in Species diversity and community structure of fruit-feeding butterflies (Lepidoptera: Nymphalidae) in an eastern amazonian forest

FIGURE 3: Whittaker plot (rank-abundance distribution) for the total sample of fruit-feeding butterflies in an eastern Amazonian forest. The y axis represents species abundance and the x axis ranks each species in order from most to least abundant.

opencc-by-4.0Dec 2017View details →

FIGURE 1 in Species diversity and community structure of fruit-feeding butterflies (Lepidoptera: Nymphalidae) in an eastern amazonian forest

FIGURE 1: Location of Sítio Aguahy, in the eastern Amazon. (A) Maps of Brazil and the state of Maranhão, demonstrating the distribution of the Brazilian Amazon forest. (B) Dense rainforest (C) Secondary forest.

opencc-zeroDec 2021View details →

Rapid ant community re-assembly in a Neotropical forest: recovery dynamics and land-use legacy

Regrowing secondary forests dominate tropical regions today, and a mechanistic understanding of their recovery dynamics provides important insights for conservation. In particular, land-use legacy effects on the fauna have rarely been investigated. One of the most ecologically dominant and functionally important animal groups in tropical forests are ants. Here, we investigated the recovery of ant communities in a forest – agricultural habitat mosaic in the Ecuadorian Chocó region. We used a replicated chronosequence of previously used cacao plantations and pastures with 1 – 34 years of regeneration time to study the recovery dynamics of species communities and functional diversity across the two land use legacies. We compared two independent components of responses on these community properties: resistance, which is measured as the proportion of an initial property that remains following the disturbance; and resilience, which is the rate of recovery relative to its loss. We found that compositional and trait structure similarity to old-growth forest communities increased with regeneration age, whereas ant species richness remained always at a high level along the chronosequence. Land-use legacies influenced species composition, with former cacao plantations showing higher resemblance to old-growth forests than former pastures along the chronosequence. While resistance was low for species composition and high for species richness and traits, all community properties had similarly high resilience. In essence, our results show that ant communities of the Chocó recovery rapidly, with former cacao reaching predicted old-growth forest community levels after 21 years and pastures after 29 years. Recovery in this community was faster than reported from other ecosystems and was likely facilitated by the low-intensity farming in agricultural sites and their proximity to old-growth forest remnants. Our study indicates the great recovery potential for this otherwise highly threatened biodiversity hotspot.

opencc-by-4.0Sep 2021View details →

Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions

Polysaccharide utilization loci (PULs) in the human gut microbiome have critical roles in shaping human health and ecological dynamics. We develop a CRISPR-FnCpf1-RecT genome-editing tool to study 23 PULs in the highly abundant species B. uniformis (BU). We identify the glycan-degrading functions of multiple PULs and elucidate transcriptional coordination between PULs that enables the population to adapt to the loss of PULs. Exploiting a pooled BU mutant barcoding strategy, we demonstrate that the in vitro fitness and the colonization ability of BU in the murine gut is enhanced by deletion of specific PULs and modulated by glycan availability. We show that BU PULs can mediate complex glycan-dependent interactions with butyrate producers that depend on the mechanism of degradation and the butyrate producer glycan utilizing ability. In sum, PULs are major determinants of community dynamics and butyrate production and can provide a selective advantage or disadvantage depending on the nutritional landscape.

opencc-zeroDec 2021View details →

Simulated treatment effects on bird communities inform landscape‐scale dry conifer forest management

Human land use and climate change have increased forest density and wildfire risk in dry conifer forests of western North America, threatening various ecosystem services, including habitat for wildlife. Government policy supports active management to restore historical structure and ecological function. Information on potential contributions of restoration to wildlife habitat can allow assessment of tradeoffs with other ecological benefits when prioritizing treatments. We predicted avian responses to simulated treatments representing alternative scenarios to inform landscape‐scale forest management planning along the Colorado Front Range. We used data from the Integrated Monitoring in Bird Conservation Regions program to inform a hierarchical multispecies occupancy model relating species occupancy and richness with canopy cover at two spatial scales. We then simulated changes in canopy cover (remotely sensed in 2018) under three alternative scenarios, (1) a "fuels reduction" scenario representing landscape‐wide 30% reduction in canopy cover, (2) a "restoration" scenario representing more nuanced, spatially variable treatments targeting historical conditions, and (3) a reference, no‐change scenario. Model predictions showed areas of potential gains and losses for species richness, richness of ponderosa pine forest habitat specialists, and the ratio of specialists to generalists at two (1 km2 and 250 m2) spatial scales. Under both fuels reduction and restoration scenarios, we projected greater gains than losses for species richness. Surprisingly, despite restoration more explicitly targeting ecologically relevant historical conditions, fuels reduction benefited bird species richness over a greater spatial extent than restoration, particularly in the lower montane life zone. These benefits reflected generally positive species associations with moderate canopy cover promoted more consistently under the fuels reduction scenario. In practice, contemporary forest management is likely to lie somewhere between the fuels reduction and restoration scenarios represented here. Therefore, our results inform where and how active forest management can best support avian diversity. Although our study raises questions regarding the value of including landscape‐scale heterogeneity as a management objective, we do not question the value of targeting finer-scale heterogeneity (i.e., stand and treatment level). Rather, our results combined with those from previous work clarify the scale at which targeting structural heterogeneity and historical reference conditions can promote particular ecosystem services.