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opencc-zeroMay 2022View details →

Concordant patterns of morphological, stable isotope, and genetic variation in a recent ecological radiation (Salmonidae:Coregonus spp.)

Groups of sympatric taxa with low inter-specific genetic differentiation, but considerable ecological differences, offer great opportunities to study the dynamics of divergence and speciation. This is the case of ciscoes (Coregonus spp.) in the Laurentian Great Lakes, which are characterized by a complex evolutionary history and are commonly described as having undergone an adaptive radiation. In this study, morphometrics, stable isotopes and transcriptome sequencing were used to study the relationships within the Coregonus artedi complex in western Lake Superior. We observed general concordance for morphological, ecological and genomic variation, but the latter was more taxonomically informative as it showed less overlap among species in multivariate space. Low levels of genetic differentiation were observed between individuals morphologically identified as C. hoyi and C. zenithicus, which could be evidence of incomplete lineage sorting or recent hybridization between the two groups. Transcriptome-based single nucleotide polymorphisms exhibited significant divergence for genes associated with vision, development, metabolism and immunity among species that occupy different habitats. This study highlights the importance of using an integrative approach when studying groups of taxa with a complex evolutionary history, as individual-level analyses of multiple independent datasets can provide a clearer picture of the patterns and processes associated with the origins of biodiversity.

opencc-zeroMay 2022View details →

A gas-only bioreactor system maintains stable culture environments and reveals that moderate pH deviations trigger transcriptome-wide responses in human cells cultured in physioxia and physiological buffers

Although pH instability is emerging as a potential driver of changes in cell physiology, pH is still poorly controlled during cell culture and in vitro experiments. Standard procedures include the use of chemicals usually not present in the primary physiological buffering system (CO2/HCO3-), such as acids and bases, to manipulate pH levels. This, however, leads to artifacts that potentially affect scientists' findings. Here, we propose a novel method for controlling pH levels by relying only on the physiological buffering system. pH was manipulated in a repurposed commercial bioreactor set-up, using a two-sided control loop of CO2 and N2 gas in NaHCO3--buffered medium. This method produces optimal and stable dO2 profiles and tightly maintains pH levels. With this procedure, we analyzed the effects of different pH levels (6.8, 7.0, 7.2, and 7.4) on the performance and transcriptome of the human GM12878 cell line over a 72-hours experiment. Our results showed that inflammation and negative cellular proliferation are among the signatures activated at low pH. This further highlights the importance of a thorough pH control during cell culture.

opencc-by-4.0May 2022View details →

Dataset: Substantial organic and particulate nitrogen and phosphorus export from geomorphologically stable African tropical forest landscapes

Raw chemical and stream data from the publication 'Substantial organic and particulate nitrogen and phosphorus export from geomophologically stable African tropical forest landscapes'.  Data shows dissolved and particulate nitrogen and phosphorus concentrations of stream waters of two forested first order streams withing the Congo Basin.

opencc-zeroJun 2022View details →

Stable dingo population structure and purity over 11 years of lethal management

Interactions between predators and humans are a key driver of human-wildlife conflicts and can underpin the management of predator populations. Management of the impacts of dingoes (Canis familiaris) on livestock and native species is a prime example of a persistent and contentious predator management issue with potential impacts on the integrity of dingo populations. To manage the potential impacts of dingoes and their control, it is imperative to understand the effects of control approaches on their populations in the short and long term. Hybridisation of dingoes with domestic dogs (C. familiaris) threatens the genetic integrity of pure dingoes. It has been hypothesised that lethal control of dingoes can facilitate hybridisation by disrupting pack social structures leading to increased dingo-domestic dog interactions. Here we use dingo genetic samples from three distinct sampling periods: 2009, 2014, and 2020, within the Murchison Regional Vermin Cell (MRVC) area in Western Australia (WA). At the time of the study, the MRVC was a large, partially-fenced area in which dingo control has been performed for many decades. We assess dingo purity, population clustering, gene flow, and individual relatedness in the context of ongoing control. We identified three genetically distinct populations in the study area, consistent with previous genetic studies of WA, but did not find any evidence of change in dingo purity or population characteristics, however barrier fencing may be influencing recent gene flow. Policy implications: The metapopulation of dingoes in the southern rangelands of WA appears to be stable over the 11 years assessed here and there is no evidence that lethal control to reduce losses to livestock production and for conservation of native wildlife is putting dingo purity at risk. Fencing appears to be an effective management tool as there is some evidence it is separating dingo populations in areas where the fences are well maintained.

opencc-zeroJun 2022View details →

Trophic structure and origin of resources of soil macrofauna in the salt marsh of the Wadden Sea: a stable isotope (15N,13C) study

Salt marshes exist along the gradient of the marine mudflat to the terrestrial dunes, with a gradient of shore height and associated plant zonation. The lower salt marsh (LSM) extends from the mean high tidal level to 35 cm above that level and is followed by the upper salt marsh (USM). Despite changes in the amount of allochthonous marine input and in abiotic conditions, little is known about changes in the trophic structure and used of basal resources by the soil macrofauna along marine – terrestrial boundaries. Natural variations in carbon stable isotope ratios (δ¹³C signatures) allow insight into basal resources of consumers such as marine algae, terrestrial C3 and C4 photosynthesising plants. Furthermore, variations in nitrogen stable isotope ratios (δ¹5N signatures) allow insight into the trophic position of consumers. We investigated spatial and temporal changes in stable isotope signatures in salt marsh soil macrofauna of the island of Spiekeroog, German Wadden Sea. The range of δ¹⁵N signatures indicated no changes in food chain length across salt marsh zones with consumers in both zones comprising primary decomposer, secondary decomposer and first order predators. However, the trophic position of individual species changed between zones, but in particular with season. Contrasting δ¹⁵N signatures, the range in δ¹³C signatures in the LSM was twice that in the USM indicating a wider range of resources consumed. Bayesian mixing models indicated predominant autochthonous resource use in both the LSM and USM, with the use of marine allochthonous resources never exceeding 29.6%. However, the models also indicate an increase in the use of marine resources in certain species in the LSM with no use in the USM. Overall, the results indicate that the resource use of salt marsh macrofauna varies more in space than in time, with the food web being generally based on autochthonous rather than allochthonous resources. However, there also is trophic plasticity in certain species across both temporal and spatial scales including variations in the use of allochthonous resources. Generally, however, marine input contributes little to the nutrition of salt marsh soil macroinvertebrates.

Data from: Stable isotopes in the different trophic levels reveal regional divergence in dietary habits among Tibetan pastoralists

Understanding geographical variation and driving mechanisms of the dietary habits of Tibetan pastoralists is a key to improving their health status under climate change and globalization. Characterization of diet via isotopic signatures along the length of the local food chain could provide this information. We analyzed δ13C and δ15N of soil, plants, animals and pastoralists at different geographical sites ranging in a gradient of easily accessible to remote areas. The high δ15N values in soil and plants were not recovered in animals and pastoralists, indicating use of external feed and food resources respectively. The mean δ13C (-22.0‰) and δ15N values (6.9‰) of pastoralists indicated diets consisting mainly of native C3 plants and animal products. Pastoralists living in the remotest areas maintained more traditional dietary habits based on native animal products. However, dietary changes of pastoralists were triggered by external food resources and alterations in ecological chain of easily accessible areas.

Diet analysis of David's deer (Elaphurus davidianus) based on stable isotope technology

Faecal stable isotopic analysis is now commonly used to investigate diets of mammal herbivores as samples are easy to obtain and reveal short-term dietary trends. In the Jiangsu Dafeng David's Deer National Nature Reserve, supplemental feed has been provided year round for free-ranging deer (Elaphurus davidianus) to survive from food shortages. Plant species are isotopically distinct in the free-ranging area. We assessed the plant species utilization by deer under supplemental feed condition. Diet-faeces trophic shift of deer was obtained in the semi-captive area. Faeces in both areas were collected and faecal δ13C values revealed more variable diets of free-ranging deer than semi-captive deer in different months. Mixing model showed that C4 plants were important food source for free-ranging deer when supplemental feed was provided. We suggest that efficiency and impacts of long-term supplemental feed should be considered for degraded habitat restoration.

Tracking Global Invasion Pathways of the Spongy Moth (Lepidoptera: Erebidae) to the U.S. using Stable Isotopes as Endogenous Biomarkers

The spread of invasive insect species causes enormous ecological damage and economic losses worldwide. A reliable method that tracks back an invaded insect's origin would be of great use to entomologists, phytopathologists and pest managers. The spongy moth (Lymantria dispar (L.d.), Linnaeus 1758) is a persistent invasive pest in the north-eastern United States (U.S.) and periodically causes major defoliations in temperate forests. We analysed field-captured (Europe, Asia, U.S.) and lab-reared L.d. specimens for their natal isotopic hydrogen and nitrogen signatures imprinted in their biological tissues (δ2H and δ15N) and compared these values to the long-term mean δ2H of regional precipitation (Global Network of Isotopes in Precipitation) and δ15N of regional plants at the capture site. We established the percentage of hydrogen-deuterium exchange for L.d. tissue (Pex=8.2%) using the comparative equilibration method and two-source-mixing-models, which allowed the extraction of the moth's natal δ2H value. We confirmed that the natal δ2H and δ15N values of our specimens are related to the environmental signatures at their geographic origins. With our regression models, we were able to isolate potentially invasive individuals and give estimations of their geographic origin. To enable the application of these methods on eggs, we established an egg-to-adult fraction factor for L.d. (Δegg-adult = 16.3‰ ± 4.3‰). Our models suggested that around 25% of the field-captured spongy moths worldwide were not native in the investigated capture sites. East Asia was the most frequently identified location of probable origin. Furthermore, our data suggested that eggs found on cargo ships in U.S. harbors in Alaska, California and Louisiana most probably originated from Asian L.d. in East Russia. These findings show that stable isotope biomarkers give a unique insight into invasive insect species pathways and thus, can be an effective tool to monitor the spread of insect pest epidemics.

Washington harbor seal stable isotope data

Understanding the response of predators to ecological change at multiple temporal scales can elucidate critical predator-prey dynamics that would otherwise go unrecognized. We performed compound-specific nitrogen stable isotope analysis (CSIA) of amino acids on 153 harbor seal museum skull specimens to determine how trophic position of this marine predator has responded to ecosystem change over the past century. The relationships between harbor seal trophic position, ocean condition, and prey abundance, were analyzed using hierarchical modelling of a multi-amino acid framework and applying 1-, 2-, and 3- year temporal lags. We identified delayed responses of harbor seal trophic position to both physical ocean conditions (upwelling, sea surface temperature, freshwater discharge) and prey availability (Pacific hake, Pacific herring and Chinook salmon). However, the magnitude and direction of the trophic position response to ecological changes depended on the temporal delay. For example, harbor seal trophic position was negatively associated with summer upwelling, but had a 1- year delayed response to summer sea surface temperature, indicating some predator responses to ecosystem change are not immediately observable. These results highlight the importance of considering dynamic responses of predators to their environment as multiple ecological factors are often changing simultaneously and can take years to propagate up the food web.

Stable-isotopes (δ2H, δ13C) within feathers from harvested American black ducks (2017-2020)

Stable isotope data from American Black Duck feathers (n = 665) and associated harvest data. The first primary feather (P1) was collected from wings submitted to the Species Composition Survey in Canada and Parts Collection Survey in the United States. From available feathers, we selected individuals for stable-isotope analysis stratified by black duck conservation region, sex, age, and date of harvest, where possible. These data are those that were selected for stable-hydrogen isotope analysis. See Kusack et al. (in press) - 'Origins of harvested American black ducks: stable isotopes support the flyover hypothesis' for additional information on our use of this data.

opencc-by-4.0Aug 2022View details →

Stable Isotope Hydrology Data from Gnamma Systems in the Colorado Front Range

This dataset accompanies a submission to Geophysical Research Letters titled "Stable Isotopes Constrain Water Seepage from Gnammas into Bare Granitic Bedrock".

opencc-by-4.0Aug 2022View details →

Environmental Reconstructions Based on Aquatic and Terrestrial Snails Originating from the Early Bronze Age and the Late Islamic Period– A Stable Isotope Case Study from the Al-Khashbah Archaeological Site, Sultanate of Oman

Supplementary data for the article: "Environmental Reconstructions Based on Aquatic and Terrestrial Snails Originating from the Early Bronze Age and the Late Islamic Period– A Stable Isotope Case Study from the Al-Khashbah Archaeological Site, Sultanate of Oman"

opencc-zeroAug 2022View details →

Baltic Sea stable isotope ecology meta-data collection

Stable isotope analysis (SIA) has become a pivotal method in food web and ecological research, leading to the establishment of the research field "stable isotope ecology". We conducted the first systematic review of stable isotope studies in this field in the Baltic Sea macro-region (Eglite et al. 2022). The meta-data collection provided here includes the information extracted from all 164 studies identified in the systematic review across various dimensions (topic, space, time, taxonomic, and technical focus), but not primary stable isotope data. The first published version of this meta-data collection represents the status as of July 10, 2021, and was used to filter and extract meta-data to produce the figures and tables in the review by Eglite et al. (2022). The meta-data collection is a resource for both experienced isotope ecologists and newcomers to grasp and access all published Baltic Sea SIA work on any fundamental or applied research topic, sub-region, taxon, or trophic group of interest. It also represents an ideal foundation for an envisioned "Baltic Isobank" database of primary stable isotope data, following the vision outlined in Eglite et al. (2022). We will provide regular updates of the meta-data collection in the Dryad repository, based on new runs of the systematic review query and including any additions of research papers and corrections received from the stable isotope ecology community. For this purpose, we encourage researchers to inform us about newly published research papers employing stable isotopes in the Baltic Sea ecology field by sending an e-mail with the publication reference to baltic-isobank@geomar.de.

opencc-by-4.0Aug 2022View details →

Table 1 for Radiocarbon and Stable Carbon Isotope Constraints on the Propagation of Vent CO2 to Fluid in the Acidic Kueishantao Shallow Water Hydrothermal System

This table contains radiocarbon (14C) and stable carbon isotope (13C) compositions of CO2 in vent gas, dissolved inorganic carbon and particulates of hydrothermal fluid from Kueishantao shallow water hydrothermal system, offshore northeastern Taiwan.

opencc-by-4.0Sep 2022View details →

Code and experimental images - Stable and unstable capillary fingering in porous media with a gradient in grain size

Matlab script. Invasion Percolation code in graded matrices and gravity. Pictures: experimental invasion of air at constant flow rate in a 3D-printed graded porous medium wet by glycerol/water. Originally designed for the following article: https://arxiv.org/abs/2203.15524. Accepted in Communications Physics (2022). Can easily be tweaked for other problems

opencc-zeroSep 2022View details →

Data from: New perspectives on soil animal trophic ecology through the lens of C and N stable isotope ratios of oribatid mites

Knowledge of the trophic ecology of soil animals is important for understanding their high alpha diversity as well as their functional role in soil food webs and systems. In the last 20 years, the analysis of natural variations in stable isotope ratios (15N/14N, 13C/12C) has revolutionized our view on soil animal trophic ecology. Here, we review the state of the art of the trophic ecology of a highly abundant and diverse soil animal taxon, oribatid mites (Oribatida), investigated by stable isotope analyses. The review is based on 25 papers reporting stable isotope data of 292 oribatid mite taxa from 30 different sites. Four main findings emerged. (1) Oribatid mites cluster into six trophic groups, i.e. moss feeders, lichen feeders, primary decomposers, fungal feeders/secondary decomposers, predators/scavengers and marine algal feeders, plus one additional group, which incorporates CaCO3 in their cuticle for defence but still belongs to the fungal feeders/secondary decomposers group. (2) Of the 292 species studied 43.7% were classified as fungal feeders/secondary decomposers, 27.0% as primary decomposers and 15.7% as predators/scavengers, only few species include CaCO3 into their skeleton (6.1%), feed on lichens (4.9%), mosses (2.1%) or marine algae (0.7%). (3) In about one-third of the species studied the trophic niche was constant or varied little between sites or habitats, but in two-thirds of the species, their trophic niche varied between habitats, with some species even shifting trophic levels, indicating trophic plasticity. (4) When aggregated at higher taxonomic level oribatid mite species clustered in only three instead of six trophic groups. This indicates that species within the same high-level taxon often belong to different trophic groups, for example, because feeding habits evolved convergently. Therefore, to accurately reflect the trophic ecology of oribatid mites their stable isotope signatures need to be analysed at the species level. However, stable isotope analyses also have limitations, e.g. feeding on bacteria and fungi cannot be separated, and the same is true for feeding on ectomycorrhizal and arbuscular mycorrhizal fungi. Other methods such as fatty acid, amino acid and molecular gut content analyses as well as microbiome analyses may complement stable isotope studies and resolve oribatid mite trophic niche differentiation at a higher resolution. This will contribute to a better understanding of the local coexistence of large numbers of species in soil. Finally, we provide perspectives on how to integrate microarthropods into soil food webs using stable isotope and other methods allowing deeper insight into their trophic structure.

opencc-zeroSep 2022View details →

Data for: Two is better than one: Coupling DNA metabarcoding and stable isotope analysis improves dietary characterizations for a riparian-obligate, migratory songbird

While an increasing number of studies are adopting molecular and chemical methods for dietary characterization, these studies often employ only one of these laboratory-based techniques; an approach which may yield an incomplete, or even biased, understanding of diet due to each method's inherent limitations. To explore the utility of coupling molecular and chemical techniques for dietary characterizations, we applied DNA metabarcoding alongside stable isotope analysis to characterize the dietary niche of breeding Louisiana waterthrush (Parkesia motacilla), a migratory songbird hypothesized to preferentially provision their offspring with pollution-intolerant, aquatic arthropod prey. While DNA metabarcoding was unable to determine if waterthrush provision aquatic and terrestrial prey in different abundances, we found that specific aquatic taxa were more likely to be detected in successive seasons than their terrestrial counterparts, thus supporting the aquatic specialization hypothesis. Our isotopic analysis added greater context to this hypothesis by concluding that breeding waterthrush provisioned Ephemeroptera and Plecoptera, two pollution-intolerant, aquatic orders, in higher quantities than other prey groups, and expanded their functional trophic niche when such prey were not abundantly provisioned. Finally, we found that the dietary characterizations from each approach were often uncorrelated, indicating that the results gleaned from a diet study can be particularly sensitive to the applied methodologies. Our findings contribute to a growing body of work indicating the importance of high-quality, aquatic habitats for both consumers and their pollution-intolerant prey, while also demonstrating how the application of multiple, laboratory-based techniques can provide insights not offered by either technique alone.

opencc-by-4.0Sep 2022View details →

Seismicity modulation due to hydrological loading in a stable continental region: a case study from the Jektvik swarm sequence in Northern Norway

This folder contains earthquake catalog used in "Seismicity modulation due to hydrological loading in a stable continental region: a case study from the Jektvik swarm sequence in Northern Norway" by Shiddiqi et al. (2022) submitted to Geophysical Journal International. note: unrelocated earthquakes are marked with 999 in location errors.

opencc-by-4.0Sep 2022View details →

Earthquake catalog for "Seismicity modulation due to hydrological loading in a stable continental region: a case study from the Jektvik swarm sequence in Northern Norway"