cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.40qp5
title: Data from: Interactions between genetic and ecological effects on the evolution of life cycles

description: Sexual reproduction leads to an alternation between haploid and diploid
 phases, whose relative length varies widely across taxa. Previous
 genetical models showed that diploid or haploid life cycles may be
 favored, depending on dominance interactions and on effective
 recombination rates. By contrast, niche differentiation between haploids
 and diploids may favor biphasic life cycles, in which development occurs
 in both phases. In this paper, we explore the interplay between genetical
 and ecological factors, assuming that deleterious mutations affect the
 competitivity of individuals within their ecological niche, and allowing
 different effects of mutations in haploids and diploids (including
 antagonistic selection). We show that selection on a modifier gene
 affecting the relative length of both phases can be decomposed into a
 direct selection term favoring the phase with the highest mean fitness
 (either due to ecological differences or to differential effects of
 mutations), and an indirect selection term favoring the phase in which
 selection is more efficient. When deleterious alleles occur at many loci
 and in the presence of ecological differentiation between haploids and
 diploids, evolutionary branching often occurs and leads to the stable
 coexistence of alleles coding for haploid and diploid cycles, while
 temporal variations in niche sizes may stabilize biphasic cycles.
description: C++ code for simulations
 of the evolution of life cycles.The program simulates a
 haploid-diploid population under density-dependent control (logarithmic
 growth)life_cycles_eco_genet.zip
DOI: 10.5061/dryad.2b222
title: Data from: Escherichia coli populations adapt to complex, unpredictable fluctuations by minimizing trade-offs across environments

description: In nature, organisms are simultaneously exposed to multiple stresses (i.e.
 complex environments) that often fluctuate unpredictably. Although both
 these factors have been studied in isolation, the interaction of the two
 remains poorly explored. To address this issue, we selected laboratory
 populations of Escherichia coli under complex (i.e. stressful combinations
 of pH, H2O2 and NaCl) unpredictably fluctuating environments for ~900
 generations. We compared the growth rates and the corresponding trade-off
 patterns of these populations to those that were selected under constant
 values of the component stresses (i.e. pH, H2O2 and NaCl) for the same
 duration. The fluctuation-selected populations had greater mean growth
 rate and lower variation for growth rate over all the selection
 environments experienced. However, whereas the populations selected under
 constant stresses experienced trade-offs in the environments other than
 those in which they were selected, the fluctuation-selected populations
 could bypass the across-environment trade-offs almost entirely.
 Interestingly, trade-offs were found between growth rates and carrying
 capacities. The results suggest that complexity and fluctuations can
 strongly affect the underlying trade-off structure in evolving
 populations.
description: Fitness values for
 selected and control populationsThis .xlsx file contains
 the fitness values for six selection regimes (20 replicate populations in
 each), assayed in 5 assay environments. Fitness is measured in two
 different ways, namely maximum growth rate and maximum density. Each
 selection X assay X replicate has two independent measurements. We also
 assayed the ancestors in all the assay environments,Data for
 Dryad.xlsx
DOI: 10.5061/dryad.6h68k
title: Data from: Effects of small-scale, shading-induced seagrass loss on blue carbon storage: Implications for management of degraded seagrass ecosystems

description: 1. Seagrass meadows are important global ‘blue carbon’ sinks. Despite a
 30% loss of seagrasses globally during the last century, there is limited
 empirical research investigating the effects of disturbance and loss of
 seagrass on blue carbon stocks. 2. In this study, we hypothesised that
 seagrass loss would reduce blue carbon stocks. Using shading cloth, we
 simulated small-scale die-offs of two subtropical seagrass species,
 Halodule wrightii and Thalassia testudinum, in a dynamic northern Gulf of
 Mexico lagoon. The change in quantity and quality of sediment organic
 matter and organic carbon were compared among kill, control and bare plots
 before the kill treatment, shortly after the kill treatment and 11 months
 after the kill treatment. 210 Pb age dating was performed on bare and
 Thalassia plots at 11 months to evaluate the impact of sediment erosion in
 the absence of vegetation. 3. The small-scale die-off led to a 50-65%
 organic matter (OM) loss in the sediment in the top 8 cm of Halodule
 plots. Thalassia plots lost significant portions OM (50%) and organic
 carbon (C; 21-47%) in only the top 1 cm of sediment. The 210 Pb profiles
 indicated Thalassia die-off reduced the C sequestration rate by 10%, in
 addition to a loss of ~1 years’ worth of C stocks (~22 g m-2&lt;).
 Furthermore, analyses on O Morg quality indicated a loss of labile OM/C
 and enhanced remineralisation by microbes. 4. Synthesis and applications:
 This study provides empirical evidence that small-scale shading-induced
 seagrass die-offs can reduce seagrass carbon sequestration capacity and
 trigger losses of blue carbon stocks. While the losses recorded here are
 modest, these losses in blue carbon storage capacity are notable due to
 the proximity of shading structures (for example, boat docks) to seagrass
 habitats. Thus, policies to avoid or protect seagrass habitats from common
 small-scale, shading disturbances are important for optimising both carbon
 sequestration capacity and coastline development and
 management.17-Nov-2017
description: Trevathan-Tackett_etal_JAE_rawdataAll data is included in one file and includes, sampling descriptions, GPS points, organic matter data, elemental and isotope data, thermogravimetric analysis data, and age-dating data.
DOI: 10.5061/dryad.8gg68
title: Data from: Relative importance of abiotic, biotic, and disturbance drivers of plant community structure in the sagebrush steppe

description: Abiotic conditions, biotic factors, and disturbances can act as filters
 that control community structure and composition. Understanding the
 relative importance of these drivers would allow us to understand and
 predict the causes and consequences of changes in community structure. We
 used long-term data (1989-2002) from the sagebrush steppe in Washington
 state, USA, to ask three questions: 1) What are the key drivers of
 community-level metrics of community structure? 2) Do community-level
 metrics and functional groups differ in magnitude or direction of response
 to drivers of community structure? 3) What is the relative importance of
 drivers of community structure? The vegetation in 2002 was expressed as
 seven response variables: three community-level metrics (species richness,
 total cover, compositional change from 1989 to 2002) and the relative
 abundances of four functional groups. We used a multi-model inference
 framework to identify a set of top models for each response metric
 beginning from a global model that included two abiotic drivers, six
 disturbances, a biotic driver (initial plant community), and interactions
 between the disturbance and biotic drivers. We also used a permutational
 relative variable importance (pRVI) metric to rank the influence of
 drivers. Moisture availability was the most important driver of species
 richness and of native forb cover. Fire was the most important driver of
 shrub cover and training area usage was important for compositional
 change, but disturbances, including grazing, were of secondary importance
 for most other variables. Biotic drivers, as represented by the initial
 plant communities, were the most important driver for total cover and for
 the relative covers of exotics and native grasses. Our results indicate
 that the relative importance of drivers is dependent on the choice of
 metric, and that drivers such as disturbance and initial plant community
 can interact.
description: Total Model
 DataThis csv file contains
 all of the data needed to run scripts provided with this manuscript.
 Contains plot, environmental, and vegetation data.Mitchell.data.160923.csvMitchell_EcolApp_Script_160923Scripts for running all analyses in manuscript using Total Model Data file.
DOI: 10.5061/dryad.9r4v1
title: Data from: Exposure to dairy manure leads to greater antibiotic resistance and increased mass-specific respiration in soil microbial communities

description: Intensifying livestock production to meet the demands of a growing global
 population coincides with increases in both the administration of
 veterinary antibiotics and manure inputs to soils. These trends have the
 potential to increase antibiotic resistance in soil microbial communities.
 The effect of maintaining increased antibiotic resistance on soil
 microbial communities and the ecosystem processes they regulate is
 unknown. We compare soil microbial communities from paired reference and
 dairy manure-exposed sites across the USA. Given that manure exposure has
 been shown to elicit increased antibiotic resistance in soil microbial
 communities, we expect that manure-exposed sites will exhibit (i)
 compositionally different soil microbial communities, with shifts toward
 taxa known to exhibit resistance; (ii) greater abundance of antibiotic
 resistance genes; and (iii) corresponding maintenance of antibiotic
 resistance would lead to decreased microbial efficiency. We found that
 bacterial and fungal communities differed between reference and
 manure-exposed sites. Additionally, the β-lactam resistance gene ampC was
 5.2-fold greater under manure exposure, potentially due to the use of
 cephalosporin antibiotics in dairy herds. Finally, ampC abundance was
 positively correlated with indicators of microbial stress, and microbial
 mass-specific respiration, which increased 2.1-fold under manure exposure.
 These findings demonstrate that the maintenance of antibiotic resistance
 associated with manure inputs alters soil microbial communities and
 ecosystem function.
description: Edaphic and microbial
 data from paired manure-exposed and reference soils across the United
 StatesThis is an excel file
 containing edaphic and microbial data describing soils from dairy
 operations across the United States. Sites are organized by state postal
 code, with a numerical qualifier for the instance of multiple field sites
 within Georgia. Relevant abbreviations: SIR, substrate induced
 respiration; C-min, carbon mineralization; qCO2, microbial metabolic
 quotient; DOC, dissolved organic carbon; POM, particulate organic
 matter.Wepking et al.
 2017.xlsx
DOI: 10.5061/dryad.kp98j
title: Data from: Population structure of mountain pine beetle symbiont Leptographium longiclavatum and the implication on the multipartite beetle-fungi relationships

description: Over 18 million ha of forests have been destroyed in the past decade in
 Canada by the mountain pine beetle (MPB) and its fungal symbionts.
 Understanding their population dynamics is critical to improving modeling
 of beetle epidemics and providing potential clues to predict population
 expansion. Leptographium longiclavatum and Grosmannia clavigera are fungal
 symbionts of MPB that aid the beetle to colonize and kill their pine
 hosts. We investigated the genetic structure and demographic expansion of
 L. longiclavatum in populations established within the historic
 distribution range and in the newly colonized regions. We identified three
 genetic clusters/populations that coincide with independent geographic
 locations. The genetic profiles of the recently established populations in
 northern British Columbia (BC) and Alberta suggest that they originated
 from central and southern BC. Approximate Bayesian Computation supports
 the scenario that this recent expansion represents an admixture of
 individuals originating from BC and the Rocky Mountains. Highly
 significant correlations were found among genetic distance matrices of L.
 longiclavatum, G. clavigera, and MPB. This highlights the concordance of
 demographic processes in these interacting organisms sharing a highly
 specialized niche and supports the hypothesis of long-term multipartite
 beetle-fungus co-evolutionary history and mutualistic relationships.
description: LL_suppTable1Microsatellite profiles of 10 loci for 241 Leptographium longiclavatum isolates (isolates in grey are clones). First column is the name of the isolates, and the second represents the location.
DOI: 10.5061/dryad.dv415
title: Data from: Shared evolutionary origin of MHC polymorphism in sympatric lemurs

description: Genes of the Major Histocompatibility Complex (MHC) play a central role in
 adaptive immune responses of vertebrates. They exhibit remarkable
 polymorphism, often crossing species boundaries with similar alleles or
 allelic motifs shared across species. This pattern may reflect parallel
 parasite-mediated selective pressures, either favouring the long
 maintenance of ancestral MHC allelic lineages across successive speciation
 events by balancing selection (‘trans-species polymorphism’), or
 alternatively favouring the independent emergence of functionally similar
 alleles post-speciation via convergent evolution. Here we investigate the
 origins of MHC similarity across several species of dwarf and mouse lemurs
 (Cheirogaleidae). We examined MHC class II variation in two highly
 polymorphic loci (DRB, DQB) and evaluated the overlap of gut-parasite
 communities in four sympatric lemurs. We tested for parasite-MHC
 associations across species to determine whether similar parasite
 pressures may select for similar MHC alleles in different species. Next,
 we integrated our MHC data with those previously obtained from other
 Cheirogaleidae to investigate the relative contribution of convergent
 evolution and co-ancestry to shared MHC polymorphism by contrasting
 patterns of codon usage at functional versus neutral sites. Our results
 indicate that parasites shared across species may select for functionally
 similar MHC alleles, implying that the dynamics of MHC-parasite
 co-evolution should be envisaged at the community level. We further show
 that balancing selection maintaining trans-species polymorphism, rather
 than convergent evolution, is the primary mechanism explaining shared MHC
 sequence motifs between species that diverged up to 30 million years ago.
description: MHC_parasite data
 lemurs_Kaesler et al.
DOI: 10.5281/zenodo.15870002
title: SNAC-DB: Structural NANOBODY® (VHH) and Antibody (VH-VL) Complex Database

description: Welcome to the SNAC-DB — a comprehensive and curated resource of antibody and NANOBODY® VHH structures designed to support computational modeling, machine learning, structural biology research, and available in ML-ready formats. This release includes dataset curated by using the SNAC-DB pipeline (https://github.com/Sanofi-Public/SNAC-DB) on protein structures sourced from the RCSB PDB (https://www.rcsb.org/), as well as a benchmarking dataset for evaluation.

At the moment, we have processed all PDBs released up until 31 December, 2025. 

Paper: https://www.researchgate.net/publication/393900649_SNAC-DB_The_Hitchhiker's_Guide_to_Building_Better_Predictive_Models_of_Antibody_NANOBODY_R_VHH-Antigen_Complexes
DOI: 10.5281/zenodo.15870003
title: SNAC-DB: Structural NANOBODY® (VHH) and Antibody (VH-VL) Complex Database

description: ***Please use the latest version. Access to earlier version can be requested directly from the authors.***

Welcome to the SNAC-DB — a comprehensive and curated resource of antibody and NANOBODY® VHH structures designed to support computational modeling, machine learning, structural biology research, and available in ML-ready formats. This release includes dataset curated by using the SNAC-DB pipeline (https://github.com/Sanofi-Public/SNAC-DB) on protein structures sourced from the RCSB PDB (https://www.rcsb.org/), as well as a benchmarking dataset for evaluation.

At the moment, we have processed all PDBs deposited up until 31 March, 2025.
DOI: 10.5061/dryad.3dt11m7
title: Data from: Collective behavior and colony persistence of social spiders depends on their physical environment

description: The physical environment occupied by group-living animals can profoundly
 affect their cooperative social interactions and therefore their
 collective behavior and success. These effects can be especially apparent
 in human-modified habitats, which often harbor substantial variation in
 the physical environments available within them. For nest-building animal
 societies, this influence of the physical environment on collective
 behavior can be mediated by the construction of nests—nests could either
 buffer animal behavior from changes in the physical environment or
 facilitate shifts in behavior through changes in nest structure. We test
 these alternative hypotheses by examining the differences in collective
 prey-attacking behavior and colony persistence between fence-dwelling and
 tree-dwelling colonies of Stegodyphus dumicola social spiders. Fences and
 trees represent substantially different physical environments: fences are
 two-dimensional and relatively homogenous environments whereas tree
 branches are three-dimensional and relatively heterogeneous. We found that
 fence-dwelling colonies attack prey more quickly and with more attackers
 than tree-dwelling colonies in both field and controlled settings.
 Moreover, in the field, fence-dwelling colonies captured more prey, were
 more likely to persist, and had a greater number of individuals remaining
 at the end of the experiment than tree-dwelling colonies. Intriguingly, we
 also observed a greater propensity for colony fragmentation in
 tree-dwelling colonies than fence-dwelling colonies. Our results
 demonstrate that the physical environment is an important influence on the
 collective behavior and persistence of colonies of social spiders, and
 suggest multiple possible proximate and ultimate mechanisms—including
 variation in web complexity, dispersal behavior, and bet-hedging—by which
 this influence may be realized.
description: fielddatadata collected on the collective prey attacking behavior of experimental colonies of Stegodyphus dumicola social spiders deployed on fences and trees in the field, near Upington, South Africa.labdataData collected on the collective prey attacking behavior of experimental colonies of Stegodyphus dumicola social spiders deployed on fences and trees in the greenhouse.colonymetricsData collected on prey presence, persistence, and other ecologial variables in experimental colonies of Stegodyphus dumicola social spiders deployed on fences and trees in the field, near Upington, South Africa.
DOI: 10.5061/dryad.j87b5b8
title: Data from: Livestock grazing regulates ecosystem multifunctionality in semi‐arid grassland

description: 1. Ecological theories and experimental evidence indicate that human
 activity induced losses in biodiversity can have substantial impacts on
 multiple ecosystem functions. It remains unclear, however, how grazing
 affects grassland biodiversity and ecosystem multifunctionallity (EMF). 2.
 Here, we assessed the grazing effects on different dimensions of
 biodiversity (i.e. plants and soil microbes) and EMF based on a 11-year
 field experiment in a semi-arid grassland. 3. We found that soil organic
 C, available nitrogen, and plant functional diversity all decreased even
 at low grazing intensity while aboveground primary production and
 bacterial abundance decreased only at high levels of grazing intensity.
 Grazing pressure effects on EMF can be well predicted by changes in plant
 functional diversity. 4. Structural equation models reveal that EMF was
 dominated by grazing pressure and was not directly affected by plant or
 microbial composition. 5. Synthesis. Our results showed that ecosystem
 functions differ in their sensitivity to grazing intensity, limiting the
 effectiveness of a target grazing level to achieve multiple goals in the
 Eurasian steppe. These findings suggest that grazing-induced alterations
 in interactions among plants, microbes and environmental factors
 critically affect the grazing threshold and deserve some major attention
 in decision-making for grazing.
description: soil and plant
 dataNew
 Dataset 01.09.18.xlsx
DOI: 10.5061/dryad.h6k0q
title: Data from: Voluntary locomotor activity mitigates oxidative damage associated with isolation stress in the prairie vole (Microtus ochrogaster)

description: Organismal performance directly depends on an individual's ability to
 cope with a wide array of physiological challenges. For social animals,
 social isolation is a stressor that has been shown to increase oxidative
 stress. Another physiological challenge, routine locomotor activity, has
 been found to decrease oxidative stress levels. Because we currently do
 not have a good understanding of how diverse physiological systems like
 stress and locomotion interact to affect oxidative balance, we studied
 this interaction in the prairie vole (Microtus ochrogaster). Voles were
 either pair housed or isolated and within the isolation group, voles
 either had access to a moving wheel or a stationary wheel. We found that
 chronic periodic isolation caused increased levels of oxidative stress.
 However, within the vole group that was able to run voluntarily, longer
 durations of locomotor activity were associated with less oxidative
 stress. Our work suggests that individuals who demonstrate increased
 locomotor activity may be better able to cope with the social stressor of
 isolation.
description: Vole exercise oxidative
 stress dataThis file includes all
 data for the study (vole IDs, exercise distance, and oxidative stress
 markers).VExOx complete
 data.xlsx