cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.80725jn
title: Data from: Testing eco-evolutionary predictions using fossil data: Phyletic evolution following ecological opportunity

description: Fossil sequences provide observations of phenotypes within a lineage over
 time and represent essential data for increasing our understanding of
 phyletic evolution beyond microevolutionary timescales. I investigate if
 fossil times-series of the diatom Stephanodiscus niagarae/yellowstonensis
 follow evolutionary dynamics compatible with hypotheses for how the
 adaptive landscape changes when a population enters a new environment. The
 lineage – which has a remarkably detailed stratigraphic record – invaded
 Yellowstone Lake immediately after recession of ice from the basin 14,000
 years ago. Several phyletic models portraying different types of
 evolutionary dynamics – both compatible and not compatible with changes in
 the adaptive landscape following ecological opportunity – were fitted to
 the fossil times-series of S. niagarae/yellowstonensis. Different models
 best describe the three analyzed traits. Two of the models (a new model of
 decelerated evolution and an Ornstein-Uhlenbeck model) capture trait
 dynamics compatible with an event of ecological opportunity, while the
 third model (random walk) does not. Entering a new environment may
 accordingly affect trait dynamics for thousands of years, but the effects
 can vary across phenotypes. However, tests of model adequacy reveal
 shortcomings in all three models explaining the trait dynamics, suggesting
 model development is needed to more fully understand the phyletic
 evolution in Stephanodiscus niagarae/yellowstonensis.
description: R scripts and
 dataThe zip-file contains
 data files and r code to reproduce all analyses. The data were originally
 published in Theriot, E. C., S. C. Fritz, C. Whitlock, and D. J. Conley.
 2006. Late Quaternary rapid morphological evolution of an endemic diatom
 in Yellowstone Lake, Wyoming. Paleobiology 32:38–54.R files and
 data.zip
DOI: 10.5061/dryad.t8sm4m6
title: Data from: Loss of olfaction in sea snakes provides new perspectives on the aquatic adaptation of amniotes

description: Marine amniotes, a polyphyletic group, provide an excellent opportunity
 for studying convergent evolution. Their sense of smell tends to
 degenerate, but this process has not been explored by comparing
 fully-aquatic species with their amphibious relatives in an evolutionary
 context. Here, we sequenced the genomes of fully-aquatic and amphibious
 sea snakes, and identified repertoires of chemosensory receptor genes
 involved in olfaction. Snakes possess large numbers of the olfactory
 receptor (OR) genes and the type-2 vomeronasal receptor (V2R) genes, and
 expression profiling in the olfactory tissues suggests that snakes use the
 ORs in the main olfactory system (MOS) and the V2Rs in the vomeronasal
 system (VNS). The number of OR genes has decreased in sea snakes, and
 fully-aquatic species lost the MOS which is responsible for detecting
 airborne odors. In contrast, sea snakes including fully-aquatic species
 retain a number of V2R genes and a well-developed VNS for smelling
 underwater. This study suggests that the sense of smell also degenerated
 in sea snakes, particularly in fully-aquatic species, but their residual
 olfactory capability is distinct from that of other fully-aquatic
 amniotes. Amphibious species show an intermediate status between
 terrestrial and fully-aquatic snakes, implying their importance in
 understanding the process of aquatic adaptation.
description: Supplemental Data
 S1Deduced amino acid
 sequences of the intact GPCR genes identified in this
 study.Supplemental_Data_S1.txtSupplemental Table S6Locus of each gene of Hydrophis melanocephalus identified in this study.Supplemental_Table_S6.xlsxSupplemental Table S7Locus of each gene of Emydocephalus ijimae identified in this study.Supplemental_Table_S7.xlsxSupplemental Table S8Locus of each gene of Laticauda laticaudata identified in this study.Supplemental_Table_S8.xlsxSupplemental Table S9Locus of each gene of Laticauda colubrina identified in this study.Supplemental_Table_S9.xlsxSupplemental Table S10Locus of each gene of a king cobra (OphHan 1.0, GenBank accession GCA_000516915.1) identified in this study.Supplemental_Table_S10.xlsxSupplemental Table S11Locus of each gene of a garter snake (Thamnophis_sirtalis-6.0, GenBank accession GCA_001077635.2) identified in this study.Supplemental_Table_S11.xlsxSupplemental Table S12Locus of each gene of a common viper (Vber1.0, GenBank accession GCA_000800605.1) identified in this study.Supplemental_Table_S12.xlsxSupplemental Table S13Locus of each gene of a green anole (AnoCar2.0, GenBank accession GCA_000090745.2) identified in this study.Supplemental_Table_S13.xlsx
DOI: 10.5061/dryad.4871d7b
title: Data from: Optimizing the genetic composition of a translocation population: incorporating constraints and conflicting objectives

description: Translocations of threatened species can reduce the risk of extinction
 from a catastrophic event. For plants, translocation consists of moving
 individuals, seeds, or cuttings from a native (source) population to a new
 site. Ideally a translocation population would be genetically diverse and
 consist of fit founding individuals. In practice, there are challenges to
 designing such a population, including constraints on the availability of
 material, and tradeoffs between different goals. We present an approach
 for designing a translocation population that identifies sets of founders
 that are optimized according to multiple criteria (e.g., genetic
 diversity), while also conforming to constraints on the representation of
 different founders (e.g., propagation success). It uses flexible inputs,
 including SNP genotypes, matrices of similarity between individuals, and
 vectors of phenotype data. We apply the approach to a critically
 endangered plant, Hibbertia puberula subsp. glabrescens (Dilleniaceae),
 which was genotyped at thousands of SNP loci. The goals of minimizing
 genetic similarity among the founding individuals and maximizing genetic
 diversity were largely complementary – populations optimized for one of
 these criteria were near-optimal for the other. We also performed analyses
 in which we minimized genetic similarity among founding individuals while
 imposing selection (against hypothetical deleterious alleles, and against
 undesirable phenotypes, respectively), and here characterized sharp
 tradeoffs. This is useful in allowing the benefits of selection to be
 weighed against ‘costs’ in terms of genetic similarity. In sum, we present
 an approach for designing a translocation population that allows flexible
 inputs, the imposition of realistic constraints, and examination of
 conflicting goals.
description: Archive of data and
 codeAn archive containing
 data and code for the paper: "Optimizing the genetic composition of a
 translocation population: incorporating constraints and conflicting
 objectives," by Jason Bragg, Peter Cuneo, Ahamad Sherieff and
 Maurizio Rossetto.archive.zip
DOI: 10.6073/pasta/14b84c73a06a728345f88c37657bb011
title: Spartina alterniflora marsh vegetation data along the Georgia coast used in the Belowground Ecosystem Resiliency Model version 2.0

description: Study plots (1-m2) were established in eight Spartina alterniflora-dominated marshes (7 on Sapelo Island, Georgia, and 1 on Skidaway Island, Georgia). At three sites, plots were sampled once each during May, July, August, September, and October of 2016. At all sites, plots were sampled once each during June, August, and November of 2021, February, May, August, and November of 2022, and February of 2023. One long-term (quarterly 2013 to 2023) GCE LTER sampling site is also included. Nine replicate plots were placed in vegetated marsh along transects that spanned 3 Landsat-8 and -9 pixel footprints, with 3 plots per pixel footprint. In each plot, measurements included plant biomass, plant species, stem density, and height. Aboveground biomass was calculated using allometric relationships between plant height and mass from plant clipping studies. During these surveys, destructive core sampling was also performed in the proximity of the plots (n = 1 per plot) to measure above and below ground biomass. Chlorophyll, foliar N, and Leaf Area Index measurements were taken in the proximity of the plots.

This dataset reflects an update to the "PLT-GCED-2106" dataset (doi: 10.6073/pasta/03f4f78c6498aecca34faf4339591129). This project also utilized data from the "PLT-GCEM-1610" dataset doi: 10.6073/pasta/9746c71b35e9f8c544ea12c601c33949). Those data utilized in this project are duplicated here for completeness.
DOI: 10.5061/dryad.2q1301v
title: Data from: Sex-specific transcriptomic responses to changes in the nutritional environment

description: Males and females typically pursue divergent reproductive strategies and
 accordingly require different dietary compositions to maximise their
 fitness. Here we move from identifying sex-specific optimal diets to
 understanding the molecular mechanisms that underlie male and female
 responses to dietary variation in Drosophila melanogaster. We examine male
 and female gene expression on male-optimal (carbohydrate-rich) and
 female-optimal (protein-rich) diets. We find that the sexes share a large
 core of metabolic genes that are concordantly regulated in response to
 dietary composition. However, we also observe smaller sets of genes with
 divergent and opposing regulation, most notably in reproductive genes
 which are over-expressed on each sex's optimal diet. Our results
 suggest that nutrient sensing output emanating from a shared metabolic
 machinery are reversed in males and females, leading to opposing
 diet-dependent regulation of reproduction in males and females. Furt her
 analysis and experiments suggest that this reverse regulation occurs via
 the Tor pathway.
description: rapamycin (experiment
 3)Here we looked at
 sex-specific fitness under two diets and four rapamycin
 concentrations.Male fitness was measured as competitive fertility and
 female fitness was measured as fecundity.rapamycin.xls
DOI: 10.5061/dryad.c856930
title: Data from: Host genetic diversity limits parasite success beyond agricultural systems: a meta-analysis

description: There is evidence that human activities are reducing the population
 genetic diversity of species worldwide. Given the prediction that
 parasites better exploit genetically homogeneous host populations, many
 species could be vulnerable to disease outbreaks. Whilst agricultural
 studies have shown the devastating effects of infectious disease in crop
 monocultures, the widespread nature of this diversity-disease relationship
 remains unclear in natural systems. Here, we provide broad support that
 high population genetic diversity can protect against infectious disease
 by conducting a meta-analysis of 23 studies, with a total of 67 effect
 sizes. We found that parasite functional group (micro- or macroparasite)
 affects the presence of the effect and study setting (field or lab-based
 environment) influences the magnitude. Our study also suggests that host
 genetic diversity is overall a robust defence against infection regardless
 of host reproduction, parasite’s host range, parasite diversity,
 virulence, and the method by which parasite success was recorded.
 Combined, these results highlight the importance of monitoring declines of
 host population genetic diversity as shifts in parasite distributions
 could have devastating effects on at-risk populations in nature.
description: Meta-analysis
 datasetMeta.dataset.csvMeta-analysis R codeSupplementary R Code.txt
DOI: 10.5061/dryad.2m0sr43
title: Data from: Multidimensional stable isotope analysis illuminates resource partitioning in a sub-Antarctic island bird community

description: 1. A central theme in community ecology is understanding how similar
 species co-exist and how their interactions may evolve in the context of
 climate change. Most studies of resource partitioning among central place
 foragers, particularly birds, focus on the offspring-rearing period, when
 they are accessible, but breeding success may be determined earlier and
 little is known about how such species partition resources at the onset of
 breeding. 2. We used a non-invasive approach to evaluate resource
 partitioning in co-existing females at a sub-Antarctic island during their
 pre-laying periods. 3. Three hypotheses were tested using carbon, nitrogen
 and oxygen stable isotope ratios measured in shells and membranes of
 hatched eggs as ecological tracers: 1) resource partitioning by geographic
 location and trophic level will exist among the 12 bird species and will
 be enhanced within taxonomic groups; 2) given the absence of strong oxygen
 gradients in the Southern Ocean we will not detect spatial structuring
 based on oxygen isotopes, but differences will exist between resident and
 oceanic species as the former may use meteoric water; 3) capital and
 income breeder strategies can be differentiated using stable isotopes of
 egg remains. 4. Two and three dimensional isotopic data showed resource
 partitioning among species. As predicted, segregation was evident within
 the four main taxonomic groups: penguins, albatrosses, burrowing petrels
 and giant petrels. Unexpectedly, oxygen isotopes revealed widespread use
 of meteoric water among a suite of sub-Antarctic birds. Stable isotopes
 allowed us to identify females of most species as income breeders at the
 onset of breeding, with the exception of the two crested penguin females
 exhibiting a mix of income and capital resources use. 5. Multidimensional
 isotopic analyses revealed that resource partitioning exists at multiple
 stages of the annual cycle in ways likely to be important under global
 change, exhibiting wide potential for ecosystem analysis.
description: Connan et al_Ecography
 2019_Stable isotopes dataDetailed stable isotope
 data of egg shells and egg membranes for 12 bird species breeding at
 Marion Island (Southern Ocean).dryad data_Connan et
 al_Ecography_2019.xlsx
DOI: 10.5061/dryad.2j6t1mb
title: Data from: The many faced symbiotic snakelocks anemone (Anemonia viridis, Anthozoa): host and symbiont genetic differentiation among colour morphs

description: How can we explain morphological variations in a holobiont? The genetic
 determinism of phenotypes is not always obvious and could be
 circumstantial in complex organisms. In symbiotic cnidarians, it is known
 that morphology or colour can misrepresent a complex genetic and symbiotic
 diversity. Anemonia viridis is a symbiotic sea anemone from temperate
 seas. This species displays different colour morphs based on pigment
 content and lives in a wide geographical range. Here, we investigated
 whether colour morph differentiation correlated with host genetic
 diversity or associated symbiotic genetic diversity by using
 RAD-sequencing and symbiotic dinoflagellate typing of 140 sea anemones
 from the English Channel and the Mediterranean Sea. We did not observe
 genetic differentiation among colour morphs of A. viridis at the animal
 host or symbiont level, rejecting the hypothesis that A. viridis colour
 morphs correspond to species level differences. Interestingly, we however
 identified at least four independent animal host genetic lineages in A.
 viridis that differed in their associated symbiont populations. In
 conclusion, although the functional role of the different morphotypes of
 A. viridis remains to be determined, our approach provides new insights on
 the existence of cryptic species within A. viridis.
description: Host SNPs and symbiont
 ITS2 rDNA sequencesPORROetal_Heredity2019.zip
DOI: 10.5281/zenodo.18392903
title: A dataset of formal proofs in lean from the 1000 theorems project, for integration into the MaRDI knowledge graph.

description: The dataset was created by the following python code in the context of https://github.com/MaRDI4NFDI/MaRDIRoadmap/issues/65:

 



import yamlimport pandas as pd#obtained from https://github.com/leanprover-community/mathlib4/blob/master/docs/1000.yamlwith open("~/1000.yaml",encoding='utf-8') as stream:    theorems_dict = yaml.safe_load(stream)theorems_project_df = pd.DataFrame(theorems_dict).transpose()theorems_project_df.index.name = 'wikidata_qid'sparql_query = 'https://w.wiki/HcXE'#theorems from wikidata with english-language wikipedia article. obtained from wikidata via query https://w.wiki/HcXEnamed_theorems_json = '~/Downloads/named_theorems.json'with open(named_theorems_json, encoding='utf-8') as named_theorems_fh:    named_theorems = json.load(named_theorems_fh)theorems_df = pd.read_json(named_theorems_json)theorems_df['wikidata_qid'] = theorems_df.cid.apply(lambda x:x.split('/')[-1])theorems_df = theorems_df.join(theorems_project_df,how='outer',on='wikidata_qid')theorems_df['P31'] = 'Q6480412'theorems_df['P37']='Q6480413'theorems_df['P1603']=theorems_df.apply(lambda x:x['decl'] if x['decl'] else x['url'],axis=1)theorems_df['P1460'] = 'Q6534201'theorems_df['P12'] = theorems_df['wikidata_qid']theorems_df = theorems_df.rename({'date':'P140','comment':'Den','title':'Len'})theorems_df['P205'] = theorems_df.apply(lambda x:"https://leanprover-community.github.io/1000.html#"+x['P12'] if x['decl'] or x['url'] else '')theorems_df['P1648'] = 'Q27041'formal_proofs_df = theorems_df.drop(columns=['P1460','P37','P31','P1603','cid','label','article','decl','authors','url','statement'])formal_proofs_df = formal_proofs_df.dropna(columns=['P205'])formal_proofs_df.fillna('').to_csv('~/formal_proofs_mardi.csv',index=False)
DOI: 10.5061/dryad.pv5kh6p
title: Data from: Direct and indirect effects of invasive species: biodiversity loss is a major mechanism by which an invasive tree affects ecosystem functioning

description: 1.Global change, such as exotic invasions, dramatically affects ecosystem
 functioning. However, the mechanisms behind the impacts are often unclear
 and despite extensive experimental work, we know little about the
 importance of biodiversity loss as a component of global change effects in
 real‐world ecosystems. 2.We disentangled several mechanisms by which an
 exotic invader affected ecosystem functioning in East African drylands in
 Kenya and Ethiopia. We used structural equation modelling to separate
 direct effects of a woody invader (Prosopis juliflora) on a range of
 ecosystem functions from indirect effects mediated through changes in
 biodiversity (plant species richness) and ecosystem functioning
 (herbaceous biomass). We analysed effects on ecosystem functions linked to
 soil biogeochemical cycling and transfer of energy between trophic levels.
 3.We found that the mean size of individual indirect effects mediated by
 biodiversity and herbaceous biomass was about twice as large as the mean
 size of individual direct effects of Prosopis on ecosystem functions,
 showing that indirect effects are an important component of the
 invader's overall environmental impacts. Changes in both herbaceous
 biomass and biodiversity were approximately equally important as drivers
 of indirect effects, indicating that we need to expand our view of
 indirect effects to consider a wider range of mechanisms. Simple
 univariate models failed to capture some Prosopis invader effects because
 positive direct effects on soil stability and predatory invertebrates were
 counteracted by negative indirect effects on biodiversity or biomass loss.
 The majority of effects were similar in both study systems. Suggestions
 that woody invaders are able to increase certain ecosystem functions may
 therefore have arisen because these negative indirect effects were not
 considered. 4.Synthesis Our study indicates that successful management of
 exotic invasions is likely to require not only control of the invader but
 also restoration of diverse and productive herbaceous communities as they
 are important for many ecosystem functions. This highlights the importance
 of biodiversity as a driver of ecosystem functioning also in real‐world
 systems.
description: Data for lme and sem
 analysesThis file contains all
 data used as input for the analysis, both the mixed effect models and the
 structural equation modelling, in the first sheet. The second sheet,
 Explanation of columns, provides a description and the units used for each
 variable.RawEcologicalDataForAnalysis.xlsx
DOI: 10.5061/dryad.5nj70ks
title: Data from: A trait-based framework for understanding predator-prey relationships: trait matching between a specialist snake and its insect prey

description: 1. High-quality information on predator-prey relationships is fundamental
 in understanding food webs, community assembly and ecosystem functioning.
 Recent analytical advances have made it possible to develop new
 trait-based approaches to study trophic relationships and evaluate
 trait-matching between predators and prey. 2. Here we develop a novel
 analytical approach based on generalized linear mixed-effects models
 (GLMM) to test the importance of prey availability and to identify the set
 of prey traits that best explain the occurrence and number of prey in the
 predator’s diet. 3. We demonstrate the approach by using an extensive
 dataset on prey availability, prey traits, and gut content collected in
 all known populations of Vipera graeca, a little-known, endangered snake
 of alpine grasslands in the Pindos Mountains of the Balkan Peninsula.4. We
 show that V. graeca is a unique, venomous snake specialised on
 bush-crickets and grasshoppers (Orthoptera). Prey selection GLMMs showed
 that the ideal prey of V. graeca is abundant, large-bodied, has poor
 escape abilities (flightless, slow-moving, bad jumper) and prefers loose
 grasslands (as opposed to bare ground/rock or closed sward). Vipers
 restrict their feeding to periods of high Orthoptera abundance in the late
 summer and need to reach a certain body size to become able to catch
 large-sized prey. 5. Our analytical approach provides a framework for
 trait matching between predators and prey and unprecedented fine-scale
 information on the importance of prey traits in prey selection by a
 specialist predator. The narrow trophic niche of V. graeca likely
 increases the vulnerability of this cold-adapted snake to extinction.
description: gmv_diet_dfThis data file contains the locality, abundance and dietary data of the Vipera graeca. Moreover, you can find here the trait data of the orthoptera species what we found in the stomach of the snakes.
DOI: 10.15482/usda.adc/25464097
title: Central Grasslands Research Extension Center (North Dakota) patch-burning and grazing management

description: These data are the result of a four-year (2017-2020) study comparing rangeland forage and cattle responses across three grazing management practices in central North Dakota. In each season, cow-calf pairs grazed on n = 4 pastures for each grazing management practice: <i>Patch burned</i>, in which a 40-ac patch of 160-ac pastures were burned with prescribed fire each spring with no internal fences; <i>Continuous</i>, in which neither prescribed fire nor internal fences were used; and <i>Rotational</i>, in which 40-ac pastures were sub-divided into 4 paddocks each with no prescribed fire. The data were primarily managed by Megan Wanchuk in support of her Master's thesis: Wanchuk, MR. 2022. <i>Patch-Burning Improves Forage Nutritive Value and Livestock Performance over Rotational and Continuous Grazing Strategies</i> (Master's Thesis, North Dakota State University, Fargo, North Dakota).