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opencc-zeroDec 2018View details →

Data from: Functional diversity promotes phytoplankton resource use efficiency

1.Understanding the relationship between biodiversity and ecosystem functioning (BEF) is a central topic in ecology. Multi‐traits based functional diversity has been proposed to improve mechanistic understanding of the BEF relationship; however, how trait‐based functional diversity affects ecosystem functioning and processes has rarely been addressed in aquatic ecosystems. 2.Here, we examined the causal relationships between three phytoplankton functional diversity indices (FAD2, FDc, FRic) and Shannon diversity index versus resource use efficiency for nitrogen (RUEN), phosphorus (RUEP), and silicate (RUESi), with monthly long‐term datasets from the marine (Western English Channel, 2000 ‐ 2014) and freshwater (Lake Kasumigaura, 1984 ‐ 2012) ecosystems. 3.We employed Convergent Cross Mapping (CCM), a novel method developed for identifying causality for nonlinear dynamical systems; this is in contrast to linear approaches that cannot distinguish causality from correlation. CCM found that FDc is the most robust functional diversity index among the selected functional diversity indices (FAD2, FDc, FRic) in predicting phytoplankton resource use efficiency and exhibited a much stronger causal effect than the Shannon index. 4.Furthermore, scenario exploration analysis indicates that most causal effects from phytoplankton diversity indices on resource use efficiency (RUEN, RUEP, and RUESi) are on average positive, and FDc exhibited the most consistent positive causal effects on phytoplankton resource efficiency in both marine and freshwater ecosystems. Thus, increasing FDc can enhance phytoplankton resource use efficiency in aquatic ecosystems. 5.Synthesis. Our results show significant causal effects of functional diversity on phytoplankton resource use efficiency in both marine and freshwater ecosystems. Among all selected functional diversity indices, FDc is the most robust functional diversity index in promoting phytoplankton resource efficiency. Our study provides empirical evidences in natural aquatic systems that trait‐based functional diversity represents better species niche partitioning than the Shannon index and thereafter enhances resource use efficiency. This finding can improve our understanding on trophic transfer and nutrient cycling in aquatic ecosystems.

opencc-zeroDec 2016View details →

Data from: How a generalist bee achieves high efficiency of pollen collection on diverse floral resources

Bees foraging for floral rewards are one of our most thoroughly studied examples of generalist foraging ecology. Generalist bees rely considerably on instrumental (associative) learning to acquire routines that allow them to collect nectar efficiently from diverse plant species. Although such bees must also collect pollen from diverse species, few studies have examined if and how high efficiency is achieved. We characterized how generalist bumble bees (Bombus impatiens) foraged effectively for pollen from diverse floral resources, by manipulating the presence of pollen and anther cues, in a series of experiments using pollen-bearing live flowers, flowers of a sterile pollenless horticultural hybrid, and artificial flowers. We show that generalist bumble bees exhibit flexible and effective pollen collection by switching between 2 routines: "scrabbling" when pollen is abundant and "sonicating" when pollen is scarce. Efficient switching between these behaviors is regulated by the interplay of 2 ubiquitous floral cues: chemical anther cues stimulating pollen collection behavior and mechanical pollen cues suppressing sonication (and eliciting scrabbling). Flexible pollen collection behavior is functional: When pollen on anthers was scarce, bees collected it at a greater rate by sonicating than scrabbling. This mechanism of behavioral flexibility likely allows generalist bees to handle diverse anther morphologies efficiently and may have facilitated the recurrent evolution of plant species that conceal pollen rewards via pored floral morphology. Whereas effective nectar foraging relies heavily on associative learning of unique routines for each flower type, a weighing of 2 types of cues regulates the flexible pollen collection mechanism we describe.

opencc-zeroDec 2016View details →

Data from: Resource competition promotes tumour expansion in experimentally evolved cancer

Tumour progression involves a series of phenotypic changes to cancer cells, each of which presents therapeutic targets. Here, using techniques adapted from microbial experimental evolution, we investigate the evolution of tumour spreading - a precursor for metastasis and tissue invasion - in environments with varied resource supply. Evolutionary theory predicts that competition for resources within a population will select for individuals to move away from a natal site (i.e. disperse), facilitating the colonisation of unexploited resources and decreasing competition between kin. After approximately 100 generations in environments with low resource supply, we find that MCF7 breast cancer spheroids (small in vitro tumours) show increased spreading. Conversely, spreading slows compared to the ancestor where resource supply is high. Common garden experiments confirm that the evolutionary responses differ between selection lines; with lines evolved under low resource supply showing a plastic spreading phenotype. These differences in spreading behaviour between selection lines are heritable (stable across multiple generations), and show that the divergently evolved lines differ in their response to resource supply. It is possible that prolonged resource limitation itself causes a stable switch toward dispersal-like behaviour and an increased sensitivity to resource availability without the need for genetic change. Different clinical strategies may be needed depending on whether tumour progression is due to stable or plastic effects. This study highlights the effectiveness of experimental evolution approaches in cancer cell populations and demonstrates how simple model systems might enable us to observe and measure key selective drivers of clinically important traits.

opencc-zeroJun 2021View details →

Data from: Resource preferences and the emergence of individual niche specialization within populations

Growing evidence that individuals of many generalist animals behave as resource specialists has attracted substantial research interest for its ecological and evolutionary implications. Variation in resource preferences is considered to be critical for developing a general theory of individual specialization. However, it remains to be shown whether diverging preferences can arise among individuals sharing a similar environment, and whether these preferences are sufficiently stable over time to be ecologically relevant. We addressed these issues by means of common garden experiments in feral pigeons (Columba livia), a species known to exhibit among-individual resource specialization in the wild. Food-choice experiments on wild-caught pigeons and their captive-bred cross-fostered descendants showed that short-term variation in food preferences can easily arise within a population, and that this variation may represent a substantial fraction of the population foraging niche. However, the experiments also showed that, rather than being limited by genetic or vertical cultural inheritance, food preferences exhibited high plasticity and tended to converge in the long-term. Although our results challenge the notion that variation in food preferences is a major driver of resource specialization, early differences in preferences could pave the way to specializations when combined with neophobic responses and/or positive feedbacks that reinforce niche conservation.

opennotspecifiedMar 2021View details →

Figure 2 in Patterns of resource use by Asiatic black bear Ursus thibetanus during pre-hibernation in Kashmir Himalaya, India

Figure 2. Boxplots showing variation of black bear scat encounter rates with respect to different habitats, percent vegetation cover and distance classes.

opennotspecifiedMar 2021View details →

Figure 1 in Patterns of resource use by Asiatic black bear Ursus thibetanus during pre-hibernation in Kashmir Himalaya, India

Figure 1. Location of Dachigam National Park in Jammu & Kashmir, India, and the location of sampling trails within the national park.

opennotspecifiedMar 2021View details →

Figure 3 in Patterns of resource use by Asiatic black bear Ursus thibetanus during pre-hibernation in Kashmir Himalaya, India

Figure 3. Boxplot showing the frequency of occurrence of different food types recorded in the scats of Asiatic black bear in Dachigam National Park.

opencc-zeroDec 2016View details →

Data from: Keystone individuals alter ecological and evolutionary consumer-resource dynamics

Intraspecific variation is central to our understanding of evolution and ecology, but these fields generally consider either the mean trait value or its variance. Alternatively, the keystone individual concept from behavioral ecology posits that a single individual with an extreme phenotype can have disproportionate and irreplaceable effects on group dynamics. Here, I generalize this concept to include non-behavioral traits and broader ecological and evolutionary dynamics. I test for the effects of individuals with extreme phenotypes on the ecology and evolution or a gall-forming fly and its natural enemies that select for opposite gall sizes. Specifically I introduce a putatively keystone predator-attracting individual gall-maker, hypothesizing that the presence of such an individual should (i) increase gall-maker population-level mortality, (ii) cause consumer communities to be dominated by species that are most attracted to the keystone individual, (iii) increase selection for traits conferring defense against the most common consumer, and (iv) weaken patterns of stabilizing selection. I find support for both the ecological and evolutionary consequences of single individuals with extreme phenotypes, suggesting that they can be considered keystone individuals. I discuss the generality of the keystone individual concept, suggesting likely consequences for ecology and evolution.

opencc-by-nc-4.0Jul 2021View details →

CURSUS An Online Resource of Medieval Liturgical Texts -- project data files and website

This is a legacy deposit of the data and website of the CURUS Project. An Online Resource of Medieval Liturgical Texts funded by the AHRB from 2000-2003.  This file was uploaded to ZENODO on 2021-07-11 by Dr James Cummings to ensure that there are lots of copies of the CURSUS materials around for the future. A copy is also available at https://github.com/jamescummings/cursus and will be deposited in FigShare as well. Original Creators: Dr James Cummings, Professor David Chadd, Dr Richard Lewis License: Creative Commons, Attribution, Non-Commericial 4.0 International   It includes the TEI P4 XML based markup (with significant project additions documented in the DTD), transformations XSLT 1.0 Stylesheets and an HTML scrape of the website as of 2020-07-11. It includes additional material to the 12 manuscript editions such as a corpus of antiphons/responds/prayers of the Corpus Antiphonalium Officii, and a vulgate bible. The website stopped having new additions in 2009 at the time of Professor David Chadd's sad death.

opencc-by-nc-4.0Jul 2021View details →

Audiovisual providers and resources in Greece

This dataset presents audiovisual providers in Greece and also their resources. Both providers and resources have been reviewed and evaluated with certain selection criteria. The dataset was created to support the Open AudioVisual Archives project, an aggregation service for open access audiovisual material in Greece.

opennotspecifiedJan 2001View details →

FIG. 3 in Resource defence mating system in two ¯ies from Sulawesi: Gymnonerius fuscus Wiedemann and Telostylinus sp. near duplicatus Wiedemann (Diptera: Neriidae)

FIG. 3. Male`A' of G. fuscus is mating with a female on the left beside the active beetleboring that he guarded daily. The small male`C' is ignored while mating with a female on the right. Male`A' subsequently prevented this female from laying any eggs in his prime site.

opennotspecifiedJan 2001View details →

FIG. 2 in Resource defence mating system in two ¯ies from Sulawesi: Gymnonerius fuscus Wiedemann and Telostylinus sp. near duplicatus Wiedemann (Diptera: Neriidae)

FIG. 2. Male`A' of G. fuscus was easily recognized because he had a front leg missing. While copulating with a female he turns at 90ss to face the approaching male`B'.

Figure 7 in Recycling resources: silica of diatom frustules as a source for spicule building in Antarctic siliceous demosponges

Figure 7. Silicon isotope data of sponge spicules, free-swimming diatoms and seawater. A. Silicon isotope (δ30Si) composition for sponges, diatoms and seawater of Deception Island. B. Comparison of our data for δ30Si/ δ29Si in sponges, diatoms and seawater from Deception Island, with values reported in previous datasets of sponges, diatoms and seawater (Hendry et al., 2010; Wille et al., 2010).

Figure 5. Vesicles with silica-like granules within sponge cells. A in Recycling resources: silica of diatom frustules as a source for spicule building in Antarctic siliceous demosponges

Figure 5. Vesicles with silica-like granules within sponge cells. A, an amoeboid sponge cell (spc) in P. areolatus showing a cytoplasm packed with vesicles and an ingested diatom (di) within a large digestive vesicle. Note that three different granule types were identified by microanalysis in the section of this species: silica granules (si), and lead granules (Pb). B–C, highly vesiculated, amoeboid sponge cell in He. pilosus. Note the silica-like granules (si) first present within vesicles and later incorporated within the cytoplasm. D, amoeboid sponge cell in P. areolatus showing an ingested diatom (di) and silica-like granules (si).

Figure 6 in Recycling resources: silica of diatom frustules as a source for spicule building in Antarctic siliceous demosponges

Figure 6. Microanalysis of the content of silica-like vesicles, sponge spicules and diatoms within the sponge tissues. A, sponge cell, probably an amoebocyte (c), of P. areolatus showing accumulation of silica-like granules in the cytoplasm (SiV). B, sclerocyte-like cell (c) of M. tridens showing accumulation of silica-granules in vesicles (SiV). C, diatom (di) engulfed by a sponge cell in M. tridens. D, sclerocyte (sc) of P. areolatus making spicules (sp). E, elemental profile of Figure 6A. F, elemental profile of Figure 6B. G, elemental profile of Figure 6C. H, elemental profile of Figure 6D. Note that the EDX probe measurements were taken on the white circles marked in the images.

Figure 4 in Recycling resources: silica of diatom frustules as a source for spicule building in Antarctic siliceous demosponges

Figure 4. Diatoms (di) ingested by amoeboid sponge cells (spc). A–D, sponge cells (spc) digesting diatoms (di) in P. areolatus. Note the large lipid (li) droplets present within diatoms (di) and later accumulated in the cytoplasm of sponge cells (spc). E–F, sponge cells (spc) digesting diatoms (di) in K. variolosa. Note the silica-like (si) granules being dissolved from the diatom frustule and the well-developed Golgi apparatus (g).

opencc-zeroAug 2021View details →

Data underlying RSOS-210474: Mitochondrial DNA sequencing of a wet-collection syntype demonstrates the importance of type material as genetic resource for Lantern Shark taxonomy (Chondrichthyes: Etmopteridae)

After initial detection of target archival DNA of a 116 year old syntype specimen of the Smooth Lanternshark, Etmopterus pusillus in a single stranded DNA library, we shotgun-sequenced additional 9 million reads from this same DNA library. Sequencing reads were used for extracting mitochondrial sequence information for analyses of mitochondrial DNA characteristics and reconstruction of the mitochondrial genome. The archival DNA is highly fragmented. A total of 4,599 mitochondrial reads were available for the genome reconstruction using an iterative mapping approach. The resulting genome sequence has a 12 times coverage and a length of 16,741 basepairs. All 37 vertebrate mitochondrial loci plus the control region were identified and annotated. The mitochondrial NADH2 gene was subsequently used to place the syntype haplotype in a network comprising multiple E. pusillus samples from various distant localities as well as sequences from a morphological similar species, the Shortfin Smooth Lantern Shark Etmopterus joungi. Results confirm the almost global distribution of E. pusillus and suggest E. joungi to be a junior synonym of E. pusillus. As mitochondrial DNA often represents the only available reference information in non-model organisms, this study illustrates the importance of mitochondrial DNA from an aged, wet-collection type specimen for taxonomy.

opencc-zeroSep 2021View details →

Magnitude and timing of resource pulses interact to affect plant invasion

Human activities can cause resource fluctuations through reducing uptake by the resident vegetation (e.g., disturbance) or through changing external resource supply (e.g., fertilization). Resource fluctuations often occur as pulses which are low frequency, large magnitude and short duration, and now are recognized as an important driver of plant invasions. However, resource pulses often vary dramatically in a number of attributes, yet how these attributes mediate the impacts of resource pulses on plant invasions remains unclear. Erigeron canadensis is a serious invader of disturbed habitats and agricultural fields in China. Thus, it experiences nutrient pulses with different magnitudes and timings. Here, we grew E. canadensis and six co-occurring native plant species with three different magnitudes of nutrient enrichment (low, medium or high). For each magnitude, we added equivalent amounts of nutrients with a constant supply as a control or one of three pulses with different timings (early, middle or late stages). We found that pulse magnitude, timing and their interaction significantly affected E. canadensis growth (biomass production) and invasion (proportion of biomass in a pot). For each timing, E. candensis growth and invasion increased with nutrient magnitude. At low magnitude, middle and late pulses promoted E. canadensis growth and invasion. At medium magnitude, late pulses suppressed E. canadensis growth, but did not affect its invasion. At high magnitude, early and middle pulses strongly suppressed E. canadensis growth and invasion. In contrast, natives generally exhibited different responses to nutrient pulses. Our study shows that plant responses are not just dependent on the presence of a resource pulse but also on its attributes. In contrast to theory and many empirical studies, our results show that resource fluctuation does not always promote plant invasion. We highlight that the attributes of resource pulses are key to understanding the impact of resource fluctuations on plant invasion.

opencc-zeroSep 2021View details →

High resource overlap and small dietary differences are widespread in food-limited warbler communities

Although both interspecific competition and coexistence mechanisms are central to ecological and evolutionary theory, past empirical studies have generally focused on simple (two-species) communities over short time periods. Experimental tests of these species interactions are challenging in complex study systems. Moreover, a number of studies of 'imperfect generalists', consistent with Liem's Paradox, raise questions about the ability of evolved species differences to effectively partition niche space when resources vary considerably across the annual cycle. Here we used a recently developed theoretical framework to combine past research on population-level processes with observational data on resource use to test for ongoing interspecific competition and understand the nature of resource overlap. We compared species diet overlaps and differences in several distinctive communities centred on a focal species, the American Redstart Setophaga ruticilla replicated both spatially and seasonally, in combination with documentation of population regulation to assess the ability of similar species to partition dietary niche space and limit interspecific competition. Our results document high dietary overlap in most of the communities studied, with only subtle differentiation consistent with known species-differences in foraging behaviour and morphology. These findings are largely consistent with species foraging as imperfect generalists. However, in contrast to past studies, the high diet overlaps observed here during times of inferred resource scarcity were driven by low value prey taxa (e.g. small ants) and did not involve truly 'private' resources. All of these factors increase the potential negative impacts of interspecific competition and limit the ability of these birds to avoid competition if conditions further deteriorate, either seasonally or at longer intervals.