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1,140 results for “Colony”
EvolvingSTEM Bioinformatics mutant colony sequencing
<p>Mutant colony sequencing for EvolvingSTEM Bioinformatics</p>
Data for Publication "Comparing individuals buried in flexed and extended positions at the Greek colony of Chersonesos (Crimea) using cranial metric, dental metric, and dental nonmetric traits"
<p>Data for Publication: H. Rathmann, R. Stoyanov, and R. Posamentir, Comparing individuals buried in flexed and extended positions at the Greek colony of Chersonesos (Crimea) using cranial metric, dental metric, and dental nonmetric traits.</p>
Experimental treatments and survival of transplanted harvester ant colonies
<p>In sessile organisms such as plants and benthic invertebrates, founding propagules typically suffer extremely high rates of mortality due to both extrinsic and intrinsic factors. Many social insect species share similarities with these groups, but factors influencing early colony survival are relatively unstudied. </p> <p>We used a field experiment to measure the importance of environmental quality relative to intrinsic colony properties in the harvester ant, Pogonomyrmex occidentalis, by monitoring the survival of 584 experimental colonies. Colony survival was primarily determined by intrinsic factors. Multiple mating by the queen and larger colony size at the time of transplant increased survival, but queen size, maternal lineage and the composition of plant species in the vicinity of the colony did not. Food supplementation increased survival significantly when natural food was scarce, but was not consistently beneficial, in contrast to predictions. </p> <p>Our results emphasize the general importance of rapid growth and early attainment of large size in the survival of sessile species. However, attributes specific to ants, their sociality and mating system, also strongly affected survival. Colonies with multiply-mated queens were more likely to survive over a wide range of circumstances, highlighting the importance of this trait even at the early stages of colony life.</p> <p>These are data to support the paper "The benefits of being big and diverse: early colony survival in harvester ants." The data are the experimental traits of the colonies used for transplantation (size and lineage of the queen, size of the colony, mating status, food treatment, local vegetation), the characteristics of the transplant itself (year of transplant and the transplant set) as well as the experimental results (the duration of survival and whether the colony survived until the end of the experiment).</p>
Data from: Evaluating the strength of western honey bees (Apis mellifera L.) colonies fed pollen subsitutes over winter
<p>We fed managed honey bee colonies one of two commercially available pollen substitutes (MegaBee, AP23) or no diet over late fall and winter in Florida, U.S.A. We measured the change in mass of adult bees, brood, and full colonies after nine weeks of feeding. We also measured the average mass per pupa, amount of pollen substitute patty consumed, the average total mass of natural pollen collected, and the proportion of pollen foragers.</p>
The multidimensional nutritional niche of fungus-cultivar provisioning in free-ranging colonies of a neotropical leafcutter ant
<p>Foraging trails of leafcutter colonies are iconic scenes in the Neotropics, with ants collecting freshly-cut plant fragments to provision a fungal food crop. We hypothesized that the fungus-cultivar's requirements for macronutrients and minerals govern the foraging niche breadth of <i>Atta colombica </i>leafcutter ants. Analyses of plant fragments carried by foragers showed how nutrients from fruits, flowers, and leaves combine to maximize cultivar performance. While the most commonly foraged leaves delivered excess protein relative to the cultivar's needs, <i>in vitro </i>experiments showed that the minerals P, Al, and Fe may expand the leafcutter foraging niche by enhancing the cultivar's tolerance to protein-biased substrates. A suite of other minerals reduces cultivar performance in ways that may render plant fragments with optimal macronutrient blends unsuitable for provisioning. Our approach highlights how the nutritional challenges of provisioning a mutualist can govern the multidimensional realized niche available to a generalist insect herbivore. </p>
Perl et al 2022 Substantial variability in morphological scaling among bumblebee colonies
<p>Data and R code for the submitted manuscript Perl et al 2021 Substantial variability in morphological scaling among bumblebee colonies</p>
Colony fitness increases in the honey bee at queen mating frequencies higher than genetic diversity asymptote
Abstract Across the eusocial Hymenoptera, a queen's mating frequency is positively associated with her workers' genetic diversity and colony's fitness. Over 90% of a colony's diversity potential is achieved by its mother's tenth effective mating (me); however, many females mate at levels of me > 10, a zone we here call hyperpolyandry. We compared honey bee colony fitness at mating levels near and above this genetic diversity asymptote. We were interested in how hyperpolyandry affects colony phenotypes arising from both common tasks (brood care) and rare specialized tasks (parasite resistance). We used an unselected wild line of bees and a Varroa Sensitive Hygiene (VSH) line selected to resist the parasite Varroa destructor. Virgin queens were instrumentally inseminated to replicate the following queen/colony conditions: (1) VSH semen/low polyandry (observed mating number = mo = 9), (2) VSH semen/high polyandry (mo = 54), (3) wild type semen/low polyandry, or (4) wild semen/high polyandry. There was a positive effect of polyandry on brood survival, an outcome of common tasks, with highest values at mo = 54. There was an interaction between polyandry and genetics such that differences between genetic lines expressed only at mo = 54, with fewer mites in VSH colonies. These results are consistent with two hypotheses for the evolution of mating levels in excess of the genetic diversity asymptote: hyperpolyandry improves colony fitness by (1) optimizing genotype compositions for common tasks and (2) by capturing rare specialist allele combinations, resisting cliff-edge ecological catastrophes. Significance statement Polyandry is a female's practice of mating with several males, storing their sperm, and using it to produce one or more clutches of genetically diverse offspring. In the social Hymenoptera, polyandry increases the genetic diversity and task efficiency of workers, leading to improved colony fitness. Over 90% of the increase in a colony's diversity potential is achieved by its mother's tenth mating; however, many females practice hyperpolyandry, a term we reserve here for mating levels above this genetic diversity asymptote. We show that a token of colony fitness arising from common tasks, brood survival, improves universally as one moves from sub- to hyperpolyandrous mating levels. However, a colony phenotype arising from a rare parasite resistance task is only expressed in the presence of the controlling alleles and under conditions of hyperpolyandry. These results suggest adaptive mechanisms by which hyperpolyandry could evolve.
Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies
<p>Infections early in life can have enduring effects on an organism's development and immunity. In this study, we show that this equally applies to developing "superorganisms" – incipient social insect colonies. When we exposed newly mated <i>Lasius niger</i> ant queens to a low pathogen dose, their colonies grew more slowly than controls before winter, but reached similar sizes afterwards. Independent of exposure, queen hibernation survival improved when the ratio of pupae to workers was small. Queens that reared fewer pupae before worker emergence exhibited lower pathogen levels, indicating that high brood rearing efforts interfere with the ability of the queen's immune system to suppress pathogen proliferation. Early-life queen pathogen-exposure also improved the immunocompetence of her worker offspring, as demonstrated by challenging the workers to the same pathogen a year later. Transgenerational transfer of the queen's pathogen experience to her workforce can hence durably reduce the disease susceptibility of the whole superorganism.</p>
Data from: Agroecological measures in meadows promote honey bee colony development and winter survival
<p><span>The homogenization of agricultural landscapes has led to a decrease in pollinator diversity and abundance. In response to this decline, farmers have implemented agroecological measures, which, in meadows, aim at providing more floral resources. These measures are the availability of unmown floral strips, delayed mowing, and discouraging the use of the conditioner, a device known to harm insects. The aim of our study was to investigate the cascade of effects of these agroecological measures on honey bee colony development and winter survival. We (i) determined the effect of these measures on colony size during the nectar and pollen collecting season in spring and summer, (ii) evaluated the effect of spring and summer colony sizes on autumn size, and (iii) described the effect of colony size in autumn on winter mortality. In this study, 300 honey bee colonies were monitored over three years </span><span>in three cantons of Switzerland. Colony size was defined by the number of brood cells and adult workers, Honey bee colony size in summer and autumn were improved by agroecological measures on meadows and likely contributed to the increased overwintering success.</span> <span>This study is a first step towards the targeted identification of viable agroecological measures on temporary meadows that can be implemented to promote honey bee colonies' health in the agricultural landscape.</span></p>
Datasets for: Colony-nesting gulls restrict activity levels of native top carnivore during the breeding season
<p>Although nesting in colonies can offer substantial reproductive benefits for many seabird species, increased visibility to predators remains a significant disadvantage for most colony-breeders. To counteract this, some seabird species have evolved aggressive nest defense strategies to protect vulnerable eggs and chicks. Here we used an experimental approach to test whether colony inhabitance by breeding gulls (<em>Larus</em> spp.) in western Norway impacts visitation rates of a native, mammalian predator, the Eurasian otter (<em>Lutra</em> <em>lutra</em>) during the breeding season. Camera traps were placed inside of and on the periphery of seabird colonies prior to the breeding season and left to run for one continuous year. Sighting frequency of otters on these cameras was compared to a control region free of gull nesting. We found that otter activity was significantly reduced on the colonies when gulls were incubating and rearing chicks, compared to time periods when gulls were building nests and absent from the colonies. Rhythmic activity patterns did not seem to be significantly impacted by the presence of gulls. This study provides clear evidence that certain colony-nesting species can have a direct, negative impact on visitation rates of a native carnivore. Seasonal carnivore activity patterns are likely to be highly dependent on differing nesting strategies and level of nest defense by seabirds.</p>
Wolbachia-infected pharaoh ant colonies have higher egg production, metabolic rate, and worker survival
<p><span><em>Wolbachia</em> is a widespread endosymbiotic bacteria with diverse phenotypic effects on its insect hosts, ranging from parasitic to mutualistic. <em>Wolbachia</em> also commonly infects social insects, where it faces unique challenges associated with its hosts' caste-based reproductive division of labor and colony living. Here we dissect the benefits and costs of <em>Wolbachia</em> infection on life-history traits of the invasive pharaoh ant, <em>Monomorium</em> <em>pharaonis</em>. Pharaoh ants are relatively short-lived and show natural variation in <em>Wolbachia</em> infection between colonies, thereby making them an ideal model system for this study. We quantified effects on the lifespan of queen and worker castes, the egg-laying rate of queens across queen lifespan, and the metabolic rates of whole colonies and colony members. Newly-infected queens laid more eggs than uninfected queens but had similar metabolic rates and lifespans. Surprisingly, infected workers outlived uninfected workers. At the colony level, infected colonies were more productive due to increased queen egg-laying rates and worker longevity, and infected colonies had higher metabolic rates during peak colony productivity. While some effects of infection, such as elevated colony-level metabolic rates may be detrimental in more stressful natural conditions, we did not find any costs of infection under relatively benign laboratory conditions. Overall, our study emphasizes the beneficial effects of <em>Wolbachia</em> on colony-level growth and metabolism in this species.</span></p>
The impact of dietary breadth on bumblebee colony fitness
<p>The current decline of pollinators may disrupt ecosystems and ecosystem services with potentially harmful effects on nature and human society. While the importance of habitat loss and fragmentation, pollution and increased disease risk in driving pollinator decline has been clearly demonstrated, the impact of resource diversity is less well understood. In this study, we investigated the effect of pollen diversity and composition on reproductive success and fitness of <em>Bombus terrestris</em> colonies. We asked the question whether a higher plant diversity results in a more diverse diet, lower pathogen incidence and a higher colony fitness. To answer these questions, colonies of lab-reared bumblebees were placed in species-poor heathland and species-rich semi-natural grasslands that strongly differed in plant community composition and diversity. We examined pollen loads on the bodies of foragers and identified the plant taxa present in the realized diet via DNA metabarcoding of the ITS2 marker. Liquid chromatography-mass spectrometry (LC-MS) was used to compare peptide composition of pollen samples from both habitats. Colony fitness was assessed by counting the number of sexuals produced by the colony at the end of its cycle. At the same time, colonies were examined for parasite incidence. Pollen composition and diversity on pollinators' bodies differed significantly between bees foraging in grasslands and heathlands. Concomitantly, peptide composition differed significantly between pollen samples from grasslands and heathlands. Colonies developed significantly better in heathland sites than in grasslands. In addition, colony fitness was only weakly related to pollen diversity and effects in some cases depended on the habitat where the bees were foraging. Pathogen incidence was very low and not affected by habitat. Overall, our results indicate that plant diversity is not necessarily a good predictor of colony fitness, and that vegetation composition and associated differences in both the quantity and quality of pollen are more important than pollen diversity per se.</p>
Data for Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in the antibiotic response
<p>Data from simulations used to generate the figures in the paper <em>Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in the antibiotic response</em>.</p> <p>To reproduce analyses, extract <em>colony_data.zip</em> in the <em>data</em> folder after cloning the <em>vivarium-ecoli</em> repository.</p> <p>The extracted folder contains the following items:</p> <ul> <li><em>sim_dfs</em>: a folder containing the CSV files that represent a subset of the raw simulation data used for downstream analyses.</li> <li><em>glc_10000_fluxome.csv</em>: Each row represents a reaction in central carbon metabolism (in same order as listed in <em>validation/ecoli/flat/toya_2010_central_carbon_fluxes.tsv</em>). Each column represents a single time point for a single cell in a baseline glucose simulation (seed 10000). Each value is a flux (mmol/L/hr). Provided as input to <em>ecoli/analysis/centralCarbonMetabolism.py </em>script to reproduce fluxome validation plot.</li> <li><em>glc_10000_proteome_avgs.csv</em>: Each row represents a protein monomer (in same order as <em>sim_data.translation.monomer_data["id"]</em> where <em>sim_data</em> is <em>reconstruction/sim_data/kb/validationData.cPickle</em>). Each column represents a cell in a baseline glucose simulation (seed 10000). Each row represents a protein monomer. Each value represents the average count of a given protein monomer for a given cell. Provided as input to <em>ecoli/analysis/proteinCountsValidation.py</em> script to reproduce proteome validation plot.</li> <li><em>glc_10000_expressome.csv</em>: Each column represents a gene (with the exception of the final two metadata columns: "Time" and "Agent ID"). Each row represents a specific cell (agent) at a specific time in a baseline glucose simulation (seed 10000). Each value represents the number of new RNA transcripts for a given gene in a given cell at a given time. Provided as input to <em>ecoli/analysis/antibiotics_colony/subgen_gene_plots/count_subgen.py</em> script to calculate number of sub-generational genes among all genes and antibiotic response genes.</li> <li><em>glc_10000_total_mrna.json</em>: Mapping of agent IDs for all cells in a baseline glucose simulation (seed 10000) to their average total mRNA count. Used by <em>ecoli/analysis/antibiotics_colony/plot.py </em>to generate Fig. 2C,D.</li> <li><em>jenner_2013.csv</em>: Data extracted from Fig. 2C of <a href="https://doi.org/10.1073/pnas.1216691110">10.1073/pnas.1216691110</a>. Used by <em>ecoli/analysis/antibiotics_colony/plot.py </em>to generate Fig. S6A.</li> <li><em>olson_2006.csv</em>: Data extracted from Fig. 2D of <a href="https://doi.org/10.1128%2FAAC.01499-05">10.1128/AAC.01499-05</a>. Used by <em>ecoli/analysis/antibiotics_colony/plot.py </em>to generate Fig. S6A.</li> <li><em>lysis_ratios.csv</em>: Data extracted from Fig. 2 of <a href="https://doi.org/10.1099/00221287-31-3-339">10.1099/00221287-31-3-339</a>. Used by <em>ecoli/analysis/antibiotics_colony/plot.py </em>to generate Fig. 4N.</li> </ul>
Eusocial evolution without a nest: kin structure of social aphids forming open colonies on bamboo
<p><span>Living in nests is an almost universal feature of eusocial animals. In some aphids, however, sterile soldier castes have evolved in open colonies without a nest. To clarify the factors promoting the evolution of eusociality in these colonies, we used newly developed microsatellite markers to compare the kin structure of the open colonies of two aphid species on bamboo: the non-eusocial colonies of <em>Astegopteryx bambucifoliae</em> and the eusocial colonies of <em>Pseudoregma alexanderi</em>on <em>Dendrocalamus latiflorus</em>. </span><br><br><span>Our samples, from over 1,000 hectares, contained 99 clones of <em>A. bambucifoliae</em> and 19 of <em>P. alexanderi</em>. Clonal mixing occurred in both species: average pairwise relatedness within a colony was 0.54 in <em>A. bambucifoliae</em> and 0.71 in <em>P. alexanderi</em>. Each clone of <em>A. bambucifoliae</em> occurred in a unique location, whereas those of <em>P. alexander</em>i occurred in multiple locations and more than 90% of individuals came from just four clones. There was significant genetic variation among different colonies in the same clu</span><span>mp (stem-cluster)</span><span> in <em>A. bambucifoliae</em> but not in <em>P. alexanderi</em>, indicating that <em>P. alexanderi</em> colonies in a</span><span> single</span><span> clump are genetically homogenized, functioning as a large colony. In <em>P. alexanderi</em>, the proportion of sterile soldiers to normal first-instar nymphs was significantly different across the four clones. </span><br><br><span>Our results indicate that the lack of input of migrants from the primary host and feeding on a large, stable host plant are important ecological factors that might favour the evolution of eusociality, enabling the production of genetically homogenised, large, and long-lived colonies. After eusociality evolves on the secondary host, the optimal strategy of soldier production might vary between different clones.</span></p>
Colonial coral resilience by decreasing size: reaction to increased detrital influx during onset of the late Palaeozoic Ice Age
<p><span>Modern coral reefs and associated biodiversity are severely threatened by increasing terrestrial runoff. Similar scenarios could be suspected for geological times, but reef coral resilience is still an enigma. In late Visean</span><span>-</span><span>Serpukhovian (Mississippian foraminiferal zones/MFZ 14-16) times, a major glaciation phase of the late Palaeozoic Ice Age (LPIA) associated with enhanced terrestrial weathering and runoff coincides with a biodiversity crisis and coral reef decline. In this study, the impact of enhanced terrestrial runoff is tested on size variations of colonial corals <em>Aulina rotiformis</em> and <em>Lithostrotion decipiens</em> along a gradient of contemporaneous (Serpukhovian) open marine carbonate to nearshore siliciclastic facies in South China. Along this gradient, their sizes decrease from carbonate, through intermediate carbonate-siliciclastic, to siliciclastic facies. This is consistent with increasing abundance of terrestrial materials of high silicon, aluminium, and phosphorus values. On a larger million</span><span>-</span><span>year</span><span>-</span><span>long interval (MFZ14-16) and for several palaeocontinents, size data of <em>Lithostrotion decipiens</em> and <em>Siphonodendron pauciradiale</em> show a distinct decline in late Visean, when enhanced terrestrial weathering occurred commonly with palaeosols developed during regression. This suggests that terrestrial sediment and nutrient input may have mainly controlled phenotypic plasticity in Mississippian reef corals, with a decrease in size as a component of resilience across the LPIA onset.</span></p>
Data from: Drought-induced relocation of ant colonies and its consequences for the long-term spatial ecology of a population under stress
<ol> <li>Maintaining a central refuge such as a nest or burrow can offer protection against environmental stressors but comes at the expense of the capacity to disperse to new locations. This trade-off with mobility can be detrimental when environmental conditions become adverse for extended periods, necessitating animals to relocate in order to track shifting niche envelopes.</li> <li>Long-lived ant colonies that invest in the construction of large nests are especially susceptible to changing environmental conditions. The Australian meat ant, <em>Iridomyrmex</em> <em>purpureus</em>, build large terrestrial nests at sites that balance shade and solar exposure.</li> <li>Long-term study of a population of meat ants showed low nest turnover and a stable spatial distribution of nests across typical rainfall years. With the onset of drought, a dramatic surge in the production of new nests occurred through a process of budding that far exceeded historic trends. This appears to have allowed colonies to relocate nests into areas with more favourable microclimate conditions in a strategy reminiscent of the production of runners in stressed plants. The consequence has also been the packing of nests into a narrow habitable zone that has resulted in an apparent increase in competition among large rival colonies. Following the break in drought and the thinning of some nests through abandonment, competition has progressively eased in later years.</li> <li>The surge in nest budding triggered by acute environmental stress in this population offers a possible strategy for long-lived colonies to effectively migrate across the landscape. With changes in environmental conditions becoming more frequent and severe with the climate crisis, any strategy available to central place foragers to track windows of preferred conditions are likely to become increasingly important.</li> </ol>
Colony-level coral demographic data from Japan & Australia (2016-2019)
<p>The persistent exposure of coral communities to more variable abiotic regimes is assumed to augment their resilience to future climatic variability. Yet, while the determinants of coral population resilience across species remain unknown, we are unable to predict the winners and losers across reef ecosystems exposed to increasingly variable conditions. Using annual surveys of 3171 coral individuals across Australia and Japan (2016-2019), we explored spatial variation across the short- and long-term dynamics of competitive, stress-tolerant, and weedy assemblages to evaluate how thermal variability mediates the structural composition of coral communities. Here this dataset contains the raw colony-level data collected during these annual surveys, detailing the size, survival, and recruitment of coral colonies within a series of permenant plots arranged throughout the reef communities of Okinawa, Kochi (both Japan), the Solitary Islands Marine Park, and Heron Island (both Australia). This data set facilitates the comparison of coral population dynamics between tropical and subtropical ecoregions and between different taxonomic and morpho-functional groups.</p>
Reduced parasite burden in feral honeybee colonies
<p>Bee parasites are the main threat to apiculture and since many parasite taxa can spill over from honeybees (Apis mellifera) to other bee species, honeybee disease management is important for pollinator conservation in general. It is unknown whether honeybees that escaped from apiaries (i.e. feral colonies) benefit from natural parasite‐reducing mechanisms like swarming or suffer from high parasite pressure due to the lack of medical treatment. In the latter case, they could function as parasite reservoirs and pose a risk to the health of managed honeybees (spillback) and wild bees (spillover). We compared the occurrence of 18 microparasites among managed (N = 74) and feral (N = 64) honeybee colony samples from four regions in Germany using qPCR. We distinguished five colony types representing differences in colony age and management histories, two variables potentially modulating parasite prevalence. Besides strong regional variation in parasite communities, parasite burden was consistently lower in feral than in managed colonies. The overall number of detected parasite taxa per colony was 15% lower and Trypanosomatidae, chronic bee paralysis virus, and deformed wing viruses A and B were less prevalent and abundant in feral colonies than in managed colonies. Parasite burden was lowest in newly founded feral colonies, intermediate in overwintered feral colonies and managed nucleus colonies, and highest in overwintered managed colonies and hived swarms. Our study confirms the hypothesis that the natural mode of colony reproduction and dispersal by swarming temporally reduces parasite pressure in honeybees. We conclude that feral colonies are unlikely to contribute significantly to the spread of bee diseases. There is no conflict between the conservation of wild‐living honeybees and the management of diseases in apiculture.</p>
Data from: Parasites, depredators, and limited resources as potential drivers of winter mortality of feral honeybee colonies in German forests
<p>Wild honeybees (<em>Apis mellifera</em>) are considered extinct in most parts of Europe. The likely causes of their decline include increased parasite burden, lack of high-quality nesting sites and associated depredation pressure, and food scarcity. In Germany, feral honeybees still colonize managed forests, but their survival rate is too low to maintain viable populations. Based on colony observations collected during a monitoring study, data on parasite prevalence, experiments on nest depredation, and analyses of land cover maps, we explored whether parasite pressure, depredation or expected landscape-level food availability explain feral colony winter mortality. Considering the colony-level occurrence of 18 microparasites in the previous summer, colonies that died did not have a higher parasite burden than colonies that survived. Camera traps installed at cavity trees revealed that four woodpecker species, great tits, and pine martens act as nest depredators. In a depredator exclusion experiment, the winter survival rate of colonies in cavities with protected entrances was 50% higher than that of colonies with unmanipulated entrances. Landscapes surrounding surviving colonies contained on average 6.4 percentage points more cropland than landscapes surrounding dying colonies, with cropland being known to disproportionately provide forage for bees in our study system. We conclude that the lack of spacious but well-protected nesting cavities and the shortage of food are currently more important than parasites in limiting populations of wild-living honeybees in German forests. Increasing the density and diversity of large tree cavities and promoting bee forage plants in forests will probably promote wild-living honeybees despite parasite pressure.</p>
Limited outbreak of highly pathogenic influenza A(H5N1) virus in a Herring Gull colony, Canada, 2022
<p class="MsoNormal">In summer 2022, highly pathogenic influenza A(H5N1) virus reached the Herring Gull (<em>Larus argentatus</em>) breeding colony on Kent Island, New Brunswick, Canada. Real-time monitoring revealed a self-limiting outbreak with low mortality. Proactive seabird surveillance is crucial for monitoring such limited outbreaks, protecting vulnerable seabirds, and tracing potential zoonotic transmission routes.</p>
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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