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Commit ed4328f5 authored by Adam Reichold's avatar Adam Reichold
Browse files

Update references and dependencies.

parent 9d38408d
Pipeline #43928 passed with stage
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......@@ -62,9 +62,9 @@ version = "0.1.0"
[[package]]
name = "libc"
version = "0.2.101"
version = "0.2.103"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "3cb00336871be5ed2c8ed44b60ae9959dc5b9f08539422ed43f09e34ecaeba21"
checksum = "dd8f7255a17a627354f321ef0055d63b898c6fb27eff628af4d1b66b7331edf6"
[[package]]
name = "libm"
......@@ -84,9 +84,9 @@ dependencies = [
[[package]]
name = "memmap2"
version = "0.3.1"
version = "0.5.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "00b6c2ebff6180198788f5db08d7ce3bc1d0b617176678831a7510825973e357"
checksum = "4647a11b578fead29cdbb34d4adef8dd3dc35b876c9c6d5240d83f205abfe96e"
dependencies = [
"libc",
]
......@@ -119,9 +119,9 @@ dependencies = [
[[package]]
name = "pkg-config"
version = "0.3.19"
version = "0.3.20"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "3831453b3449ceb48b6d9c7ad7c96d5ea673e9b470a1dc578c2ce6521230884c"
checksum = "7c9b1041b4387893b91ee6746cddfc28516aff326a3519fb2adf820932c5e6cb"
[[package]]
name = "ppv-lite86"
......@@ -173,9 +173,9 @@ dependencies = [
[[package]]
name = "rand_distr"
version = "0.4.1"
version = "0.4.2"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "051b398806e42b9cd04ad9ec8f81e355d0a382c543ac6672c62f5a5b452ef142"
checksum = "964d548f8e7d12e102ef183a0de7e98180c9f8729f555897a857b96e48122d2f"
dependencies = [
"num-traits",
"rand",
......
......@@ -15,6 +15,6 @@ ENV RUSTUP_HOME=/usr/local/rustup \
RUN curl --output rustup-init --location https://static.rust-lang.org/rustup/dist/x86_64-unknown-linux-gnu/rustup-init && \
chmod +x rustup-init && \
./rustup-init -y --no-modify-path --profile minimal --default-toolchain nightly-2021-09-06 --component clippy rustfmt --target x86_64-pc-windows-gnu && \
./rustup-init -y --no-modify-path --profile minimal --default-toolchain nightly-2021-09-30 --component clippy rustfmt --target x86_64-pc-windows-gnu && \
rm rustup-init && \
cargo install cargo-sweep
......@@ -88,9 +88,9 @@ checksum = "e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646"
[[package]]
name = "libc"
version = "0.2.101"
version = "0.2.103"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "3cb00336871be5ed2c8ed44b60ae9959dc5b9f08539422ed43f09e34ecaeba21"
checksum = "dd8f7255a17a627354f321ef0055d63b898c6fb27eff628af4d1b66b7331edf6"
[[package]]
name = "memoffset"
......
......@@ -58,6 +58,20 @@
doi = {10.1371/journal.pone.0007741}
}
@article{flowers_as_dirty_doorknobs,
author = {Burnham, Phillip Alexander and Alger, Samantha A. and Case, Brendan and Boncristiani, Humberto and Hébert-Dufresne, Laurent and Brody, Alison K.},
title = {Flowers as dirty doorknobs: Deformed wing virus transmitted between Apis mellifera and Bombus impatiens through shared flowers},
journal = {Journal of Applied Ecology},
volume = {n/a},
number = {n/a},
pages = {},
keywords = {bumblebees, deformed wing virus, disease ecology, disease transmission, honeybees health, mathematical disease model, RNA virus, virus spillover},
doi = {https://doi.org/10.1111/1365-2664.13962},
url = {https://besjournals.onlinelibrary.wiley.com/doi/abs/10.1111/1365-2664.13962},
eprint = {https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/1365-2664.13962},
abstract = {Abstract In light of bee declines, the importance of pollination services from managed and native bees to our agriculture and economy is of great political, scientific and public interest. Viruses, first observed in honeybees, have been documented in bumblebees and the prevalence and load of some RNA viruses have been associated with managed honeybees. Shared flowers may be the bridge across which viruses pass between bees but no study has yet demonstrated that bumblebees can pick up viruses while foraging on contaminated flowers. Here, through a series of mechanistic laboratory experiments and mathematical modelling, we ask whether viruses can be transmitted between bee genera on shared flowers and how transmission can be effectively mitigated. We demonstrated that deformed wing virus (DWV) can be transmitted from infected honeybees to bumblebees through the use of shared red clover. We were also able to show that the route may work in reverse and bumblebees could contribute to the spread as well. Our model showed that reducing vector-mediated transmission in honeybee colonies could potentially lead to a far greater reduction in bumblebee infection than simply reducing the number of honeybees. Additionally, we identified a dilution effect, whereby increasing floral abundance reduced transmission. Synthesis and applications. In this study, we showed that DWV may be spread between bee genera through the shared use of flowers. Through mathematical simulation, we identified two practical management options for reducing spread. The combination of treating honeybees effectively for the Varroa mite, a known vector of DWV, and increasing floral abundance where honeybees and native pollinators share the landscape were shown to reduce the spread of DWV within bee communities in simulations.}
}
@article{landscape_simplification_shapes_pathogen_prevalence,
author = {Figueroa, Laura L. and Grab, Heather and Ng, Wee Hao and Myers, Christopher R. and Graystock, Peter and McFrederick, Quinn S. and McArt, Scott H.},
title = {Landscape simplification shapes pathogen prevalence in plant-pollinator networks},
......@@ -73,6 +87,21 @@
year = {2020}
}
@article{big_bees_spread_disease,
author = {Van Wyk, Jennifer I. and Amponsah, Eugene R. and Ng, Wee Hao and Adler, Lynn S.},
title = {Big bees spread disease: body size mediates transmission of a bumble bee pathogen},
journal = {Ecology},
volume = {102},
number = {8},
pages = {e03429},
keywords = {body size, Bombus impatiens, bumble bee, Crithidia bombi, disease dynamics, pathogen transmission, pollinator decline, trait-based transmission, trypanosomatid},
doi = {https://doi.org/10.1002/ecy.3429},
url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1002/ecy.3429},
eprint = {https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1002/ecy.3429},
abstract = {Abstract Trait variation can have important consequences for the outcomes of species interactions. Even though some traits vary as much within species as across related species, models and empirical studies typically do not consider the role of intraspecific trait variation for processes such as disease transmission. For example, many pollinator species are in decline because of a variety of stressors including pathogens, but the role of intraspecific trait variation in mediating disease dynamics is rarely considered. For example, pollinator body size could affect pathogen transmission via differences in resistance, foraging behavior and physiology. We tested effects of body size on pollinator pathogen transmission using the common eastern bumble bee Bombus impatiens in field tents, introducing an infected “donor” microcolony of large or small workers with an uninfected average-sized “recipient” microcolony and allowing bees to forage for 9–16 d. Small donor bees had nearly 50\% higher infection intensity (cells/0.02  μL) than large donor bees, but large donor bees were twice as likely to transmit Crithidia bombi to recipient bees. Both behavioral and physiological mechanisms may underlie this apparent paradox. Compared to small bees, large bees foraged more and produced more feces; simulations showed that foraging and defecation rates together had stronger effects on transmission than did donor infection intensity. Thus, effects of bee size on contact rates and pathogen supply may play significant roles in disease transmission, demonstrating the multifaceted impacts of traits on transmission dynamics.},
year = {2021}
}
@article{bee_pathogen_transmission_dynamics,
author = {Figueroa, Laura L. and Blinder, Malcolm and Grincavitch, Cali and Jelinek, Angus and Mann, Emilia K. and Merva, Liam A. and Metz, Lucy E. and Zhao, Amy Y. and Irwin, Rebecca E. and McArt, Scott H. and Adler, Lynn S. },
title = {Bee pathogen transmission dynamics: deposition, persistence and acquisition on flowers},
......@@ -101,6 +130,22 @@
abstract={Parasites are important actors within ecosystems. However, a key aspect to unraveling parasite epidemiology is understanding transmission. The bee pollinator community harbors several multihost parasites, which have been shown to be able to spread between species via flowers. Hence the plant–pollinator network can provide valuable information on the transmission of these parasites between species. Although several controlled experiments have shown that flowers function as a transmission hub for parasites, the link with the plant–pollinator network has rarely been addressed in the field. Here, one can hypothesize that the most central flowers in the network are more likely to enable parasite transmission between species. In this study, we test this hypothesis in three local plant–pollinator networks and show that the centrality of a plant in a weighted plant–pollinator network is a good predictor of the presence of multihost pollinator parasites on the plant’s flowers.}
}
@article{functional_traits_linked_to_pathogen_prevalence,
author="Figueroa, Laura L. and Compton, Sally and Grab, Heather and McArt, Scott H.",
title="Functional traits linked to pathogen prevalence in wild bee communities",
journal="Scientific Reports",
year="2021",
month="Apr",
day="06",
volume="11",
number="1",
pages="7529",
abstract="Reports of pollinator declines have prompted efforts to understand contributing factors and protect vulnerable species. While pathogens can be widespread in bee communities, less is known about factors shaping pathogen prevalence among species. Functional traits are often used to predict susceptibility to stressors, including pathogens, in other species-rich communities. Here, we evaluated the relationship between bee functional traits (body size, phenology, nesting location, sociality, and foraging choice) and prevalence of trypanosomes, neogregarines, and the microsporidian Nosema ceranae in wild bee communities. For the most abundant bee species in our system, Bombus impatiens, we also evaluated the relationship between intra-specific size variation and pathogen prevalence. A trait-based model fit the neogregarine prevalence data better than a taxa-based model, while the taxonomic model provided a better model fit for N. ceranae prevalence, and there was no marked difference between the models for trypanosome prevalence. We found that Augochlorella aurata was more likely to harbor trypanosomes than many other bee taxa. Similarly, we found that bigger bees and those with peak activity later in the season were less likely to harbor trypanosomes, though the effect of size was largely driven by A. aurata. We found no clear intra-specific size patterns for pathogen prevalence in B. impatiens. These results indicate that functional traits are not always better than taxonomic affinity in predicting pathogen prevalence, but can help to explain prevalence depending on the pathogen in species-rich bee communities.",
issn="2045-2322",
doi="10.1038/s41598-021-87103-3",
url="https://doi.org/10.1038/s41598-021-87103-3"
}
@article{trait_based_modeling_of_multihost_pathogen_transmission,
author = {Truitt, Lauren L. and McArt, Scott H. and Vaughn, Andrew H. and Ellner, Stephen P.},
title = {Trait-Based Modeling of Multihost Pathogen Transmission: Plant-Pollinator Networks},
......@@ -307,6 +352,21 @@
year = {1994}
}
@article{nesting_biology_and_flower_preferences_of_megachile_zaptlana,
author = {Adauto Alex dos Santos and Daniele Parizotto and Clemens Schlindwein and Celso Feitosa Martins},
title = {Nesting biology and flower preferences of Megachile (Sayapis) zaptlana},
journal = {Journal of Apicultural Research},
volume = {59},
number = {4},
pages = {609-625},
year = {2020},
publisher = {Taylor & Francis},
doi = {10.1080/00218839.2019.1703084},
URL = {https://doi.org/10.1080/00218839.2019.1703084},
eprint = {https://doi.org/10.1080/00218839.2019.1703084},
abstract = {Megachile zaptlana is a solitary cavity-nesting leafcutter bee widely distributed in Brazil. Using two models of trap nests in sugarcane monoculture and agroecosystem environments in Pernambuco, northeastern Brazil, we studied the nesting biology of this species. We obtained 193 nests, 39.4\% in the monoculture and 60.6\% in the polyculture site. The nests consisted of a linear series of brood cells coated with a mixture of chewed leaves with sand, often followed by a long empty vestibular cell and an operculum at the entrance. A nest contained on average 2.4 (± 1.3) brood cells. Emergence patterns indicate that the species has a multivoltine life cycle without diapause and a peak emergence in the drier months from October to December. The sex ratio females: males, was 1:0.43. Females founded their nests in holes with diameters of 5–10 mm, with a preference for 6 mm (68\%). Pollen analysis of larval diet showed that the species is polylectic, and brood cells contained pollen from 19 plant species, especially from the families Asteraceae, Rubiaceae, Plantaginaceae, and Fabaceae. In the studied agroecosystems, ruderal plants were the most important nectar and pollen sources for Megachile zaptlana. Given that Megachile zaptlana is polylectic and multivoltine, it might be a good candidate for future use as a managed pollinator.}
}
@article{quantitative_pollen_requirements_of_solitary_bees,
abstract = {Knowledge about the quantitative pollen requirements of solitary bees is crucial for the preservation of endangered bee species and the understanding of the evolution of bee–flower relationships. We estimate the number of flowers required to rear a single larva for 41 European bee species (i) by comparing the pollen content of brood cells with the pollen quantity contained in the flowers of the bees' host plants and (ii) by deducing the pollen requirements from a regression model describing the relationship between the average bee dry body mass and the average brood cell pollen content. The flower requirements of the bee species examined vary by three orders of magnitude. Depending on both bee species and host plant, from seven to 1100 flowers or from 0.9 to 4.5 flower heads are needed to rear a single larva. As only about 40\% of the pollen contained in a flower was found to be available to a single female bee, these minimal figures have to be multiplied by a factor of approximately 2.5 to obtain a realistic estimate of bee flower requirements. The amount of pollen lost from flowers for bee nutrition is surprisingly high. We hypothesize that the recent decline of many bee species may have its main cause in a food shortage provoked by a decrease in flower diversity and quantity following habitat destruction and modern agricultural practices. The substantial pollen losses to bees as documented in this study support earlier findings on floral adaptations against excessive pollen harvesting by bees.},
author = {Müller, Andreas and Diener, Stefan and Schnyder, Simone and Stutz, Katharina and Sedivy, Claudio and Dorn, Silvia},
......@@ -352,6 +412,22 @@
doi = {10.1371/journal.pone.0158117}
}
@article{collection_of_pollen_by_bees,
author="Thorp, R. W.",
title="The collection of pollen by bees",
journal="Plant Systematics and Evolution",
year="2000",
month="Mar",
day="01",
volume="222",
number="1",
pages="211--223",
abstract="Bees require pollen for their reproduction and pollen comprises the basic larval food for bees. Most bees acquire pollen passively during flower visitation, but female bees may also collect pollen actively with the aid of various structural and behavioral adaptations. Most bees have evolved adaptations to concentrate pollen into discrete loads and transport pollen back to their nests. The various structural and behavioral adaptations of female bees for acquiring and transporting pollen are the basis of this review.",
issn="1615-6110",
doi="10.1007/BF00984103",
url="https://doi.org/10.1007/BF00984103"
}
@online{agriland_nectar,
title = {Nectar sugar values of common British plant species [AgriLand]},
author = {University of Leeds; Université d'Orléans; University of Bristol;},
......
......@@ -9,6 +9,6 @@ ENV RUSTUP_HOME=/usr/local/rustup \
RUN curl --output rustup-init --location https://static.rust-lang.org/rustup/dist/x86_64-unknown-linux-gnu/rustup-init && \
chmod +x rustup-init && \
./rustup-init -y --no-modify-path --profile minimal --default-toolchain nightly-2021-09-06 && \
./rustup-init -y --no-modify-path --profile minimal --default-toolchain nightly-2021-09-30 && \
rm rustup-init && \
cargo install cargo-sweep
......@@ -6,4 +6,4 @@ license = "GPL-3.0"
edition = "2018"
[dependencies]
memmap2 = "0.3"
memmap2 = "0.5"
......@@ -8,5 +8,5 @@ edition = "2018"
[dependencies]
access = { path = "../libraries/access" }
dump = { path = "../libraries/dump" }
memmap2 = "0.3"
memmap2 = "0.5"
model = { path = ".." }
\subsection{Flower patch}
\label{flower-patch-submodel}
Flower patches \marginpar{rationale} are the source of nectar and pollen for the insects which need nectar to sustain their flight and the protein-rich pollen to fuel their reproductive activities. Only the availability of nectar is modelled explicitly as flowers seem to actively regulate the amount of available nectar. Presumbly this mechanism evolved to force pollinators to visit multiple plants whereas pollen is produced in large quantities to ensure a high probability of pollination for every visitation. \autocite{food_for_pollinators}
Flower patches \marginpar{rationale} are the source of nectar and pollen for the insects which need nectar to sustain their flight and the protein-rich pollen to fuel their reproductive activities. Only the availability of nectar is modelled explicitly as flowers seem to actively regulate the amount of available nectar. Presumbly this mechanism evolved to force pollinators to visit multiple plants whereas pollen is produced in large quantities to ensure a high probability of pollination for every visitation. \autocite{collection_of_pollen_by_bees} \autocite{food_for_pollinators}
Considering the typical oral-fecal infection routes of bee pathogens, the individual flowers are the preferred unit of epidemiological contacts. But resource collection rates for seldomly studied species of wild pollinators are available only on the aggregate level of at least a single foraging bout. Additionally, the computational cost associated with tracking the relevant state variables for each flower as a separate entity has proven untenable. Therefore, the available floral resources are tracked on the aggregate flower patch level and this bulk flow of nutrients is used to drive the exploration of the landscape by the insects.
......
......@@ -232,9 +232,9 @@ dependencies = [
[[package]]
name = "instant"
version = "0.1.10"
version = "0.1.11"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "bee0328b1209d157ef001c94dd85b4f8f64139adb0eac2659f4b08382b2f474d"
checksum = "716d3d89f35ac6a34fd0eed635395f4c3b76fa889338a4632e5231a8684216bd"
dependencies = [
"cfg-if",
]
......@@ -263,9 +263,9 @@ checksum = "830d08ce1d1d941e6b30645f1a0eb5643013d835ce3779a5fc208261dbe10f55"
[[package]]
name = "libc"
version = "0.2.101"
version = "0.2.103"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "3cb00336871be5ed2c8ed44b60ae9959dc5b9f08539422ed43f09e34ecaeba21"
checksum = "dd8f7255a17a627354f321ef0055d63b898c6fb27eff628af4d1b66b7331edf6"
[[package]]
name = "libloading"
......@@ -300,9 +300,9 @@ checksum = "308cc39be01b73d0d18f82a0e7b2a3df85245f84af96fdddc5d202d27e47b86a"
[[package]]
name = "memmap2"
version = "0.3.1"
version = "0.5.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "00b6c2ebff6180198788f5db08d7ce3bc1d0b617176678831a7510825973e357"
checksum = "4647a11b578fead29cdbb34d4adef8dd3dc35b876c9c6d5240d83f205abfe96e"
dependencies = [
"libc",
]
......@@ -466,9 +466,9 @@ dependencies = [
[[package]]
name = "rand_distr"
version = "0.4.1"
version = "0.4.2"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "051b398806e42b9cd04ad9ec8f81e355d0a382c543ac6672c62f5a5b452ef142"
checksum = "964d548f8e7d12e102ef183a0de7e98180c9f8729f555897a857b96e48122d2f"
dependencies = [
"num-traits",
"rand",
......@@ -549,15 +549,15 @@ checksum = "7fdf1b9db47230893d76faad238fd6097fd6d6a9245cd7a4d90dbd639536bbd2"
[[package]]
name = "smallvec"
version = "1.6.1"
version = "1.7.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "fe0f37c9e8f3c5a4a66ad655a93c74daac4ad00c441533bf5c6e7990bb42604e"
checksum = "1ecab6c735a6bb4139c0caafd0cc3635748bbb3acf4550e8138122099251f309"
[[package]]
name = "syn"
version = "1.0.76"
version = "1.0.77"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "c6f107db402c2c2055242dbf4d2af0e69197202e9faacbef9571bbe47f5a1b84"
checksum = "5239bc68e0fef57495900cfea4e8dc75596d9a319d7e16b1e0a440d24e6fe0a0"
dependencies = [
"proc-macro2",
"quote",
......
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