cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3n5tb2rm3
title: Data for: Stronger niche than dispersal effects on α- and β-diversity of stream algae, insects, and fish across latitudes in the US

description: Aim: Niche and dispersal processes influence biodiversity, but their
 relative importance along latitude is unclear. We predicted that: i) niche
 processes would dominate at high latitudes due to increased climatic
 stress, consistent with the physiological tolerance hypothesis and the
 Dobzhansky-MacArthur hypothesis and ii) dispersal limitation would prevail
 at low latitudes due to narrower niches and smaller range sizes, as
 postulated by the dispersal-ecological specialization tradeoff hypothesis,
 the latitude-niche breadth hypothesis, and Rapoport’s rule. 
 Location: Central United States Time Period: 1993-2019 Major taxa studied:
 Stream algae, insects, and fish Methods: We examined the relative effects
 of environment (climate and physicochemistry) vs. space on stream
 biodiversity in seven latitudinal zones, spanning 19 latitudinal degrees.
 In each zone, species richness (α-diversity) was analyzed with multiple
 regression and variance partitioning. Compositional dissimilarity
 (β-diversity) within zones was assessed with distance-based RDA and
 variance partitioning. Results: For α-diversity, latitudinal variability
 of niche and dispersal processes conformed to our predictions in all three
 groups, except for dispersal processes in insects. However, the drivers of
 β-diversity did not follow our predictions. The latitude-niche breadth
 hypothesis and Rapoport’s rule were weakly supported only in fish. Main
 Conclusions: The importance of niche and dispersal processes varied
 predictably along the latitudinal gradient only for α-diversity. However,
 the niche effects were driven mostly by physicochemistry, and the
 dispersal effects were not always linked with ecological specialization
 and range size. This suggests that climate-based biodiversity theories do
 not have particular relevance for the streams in our study. Niche
 processes had a greater impact than dispersal processes across species
 groups and diversity metrics, emphasizing the primary role of the
 environment.
description: Datasets containing 2687 algal sites, 3809 insect sites, and 2753
 fish sites from streams in the conterminous United States were used to
 measure species range size and niche breadth. Smaller subsets from the
 middle United States (349 algal, and 350 insect and fish sites) were used
 to determine the relative importance of niche and dispersal processes on
 α- and β-diversity along a latitudinal gradient, comprising seven
 latitudinal zones. 
description: Files can be accessed using Microsoft Excel and R.
DOI: 10.5061/dryad.jsxksn0d2
title: Data from: Interactive effects of wildfires, season, and predator activity shape mule deer movements

description: Wildfires are increasing in size, frequency, and severity due to climate
 change and fire suppression, but the direct and indirect effects on
 wildlife remain largely unresolved. Fire removes forest canopy, which can
 improve forage for ungulates but also reduce snow interception, leading to
 a deeper snowpack and potentially increased vulnerability to predation in
 winter. If ungulates exhibit predator-mediated foraging, burns should
 generally be selected for in summer to access high-quality forage and
 avoided in winter to reduce predation risk in deep snow. Fires also
 typically increase the amount of deadfall and initiate growth of dense
 understory vegetation, creating obstacles that may confer a hunting
 advantage to stalking predators and a disadvantage to coursing predators.
 To minimize risk, ungulates may therefore avoid burns when and where
 stalking predators are most active, and use burns when and where coursing
 predators are most active. We used telemetry data from GPS-collared mule
 deer (Odocoileus hemionus), cougars (Puma concolor), and wolves (Canis
 lupus) to develop step selection functions to examine how mule deer
 navigated species-specific predation risk across a landscape in northern
 Washington, USA that has experienced substantial wildfire activity during
 the past several decades. We considered a diverse array of wildfire
 impacts, accounting for both the severity of the fire and time since the
 burn (1 to 35 years) in our analyses. We observed support for the predator
 mediating foraging hypothesis: mule deer generally selected for burned
 areas in summer and avoided burns in winter. In addition, deer increased
 use of burned areas when and where wolf activity was high and avoided
 burns when and where cougar use was high in winter, suggesting the hunting
 mode of resident predators mediated the seasonal response of deer to
 burns. Deer were not more likely to die by predation in burned than in
 unburned areas, indicating that they adequately manage fire-induced
 changes to predation risk. As fire activity increases with climate change,
 our findings indicate the impact on ungulates will depend on tradeoffs
 between enhanced summer forage and functionally reduced winter range,
 mediated by characteristics of the predator community.
description: Data were collected by GPS collars affixed to mule deer
 (Odocoileus hemionus) in northern Washington, USA. The first three weeks
 of locations post-capture, and migratory movements, were removed. Data was
 additionally filtered to June 15-Septemeber 30 for the summer locations
 and December 1 - March 15 for winter locations. Five random locations were
 generated to pair with each used location based on the step length of and
 turning angle of deer movement in each season. We extracted covariates for
 each random and used location. Due to the sensitive nature of the data,
 and as per the Washington Department of Fish and Wildlife Policy, the
 coordinates of the used and random locations have been removed.
DOI: 10.5061/dryad.wdbrv15rx
title: Dietary data of an anuran assemblage from Yasuní National Park

description: This dataset describes the diet of a highly diverse tropical anuran
 assemblage. We report the diet composition of 35 species collected at
 Yasuní National Park, based on the examination of the gastrointestinal
 contents of 396 frog specimens available in the Museo de Zoología (QCAZ)
 of Pontificia Universidad Católica del Ecuador. Anuran species belong to
 six families: Aromobatidae, Bufonidae, Dendrobatidae, Hylidae,
 Leptodactylidae, and Strabomantidae. We were able to identify 4,085 prey
 items that were classified into 71 categories. We present information on
 anuran-prey interactions, prey-items volume, and anuran specimens'
 associated data. This data set contributes to understanding the trophic
 ecology of anuran species and their role in tropical ecosystems.
description: We
 extracted the gastrointestinal contents of 396 adult frogs. Using a
 stereoscopic microscope, we identified prey items to the lowest taxonomic
 level possible and estimated their volume (mm<sup>3</sup>)
 based on the length and width of intact prey items. The number of
 specimens examined per species varied according to their availability at
 the museum collection.
description: No special programs or software are required to open the data
 flies.
DOI: 10.25338/b84d17
title: Data for: Accuracy of genomic selection and long‐term genetic gain for resistance to Verticillium wilt in strawberry

description: Verticillium wilt, a soil-borne disease caused by the fungal
 pathogen Verticillium dahliae, threatens strawberry
 (Fragaria × ananassa) production worldwide. The
 development of resistant cultivars has been a persistent challenge, in
 part because the genetics of resistance is complex. The heritability of
 resistance and genetic gains in breeding for resistance to this pathogen
 have not been well documented. To elucidate the genetics, assess long-term
 genetic gains, and estimate the accuracy of genomic selection for
 resistance to Verticillium wilt, we analyzed a genetically diverse
 population of elite and exotic germplasm accessions (n = 984),
 including 245 cultivars developed since 1854. We observed a full range of
 phenotypes, from highly susceptible to highly resistant:
 &lt; 3% were classified as highly resistant,
 whereas &gt; 50% were classified as moderately to
 highly susceptible. Broad-sense heritability estimates ranged from
 0.70–0.76, whereas narrow-sense genomic heritability estimates ranged from
 0.33–0.45. We found that genetic gains in breeding for resistance to
 Verticillium wilt have been negative over the last 165 years (mean
 resistance has decreased over time). We identified several highly
 resistant accessions that might harbor favorable alleles that are either
 rare or non-existent in modern populations. We did not observe the
 segregation of large-effect loci. The accuracy of genomic predictions
 ranged from 0.38–0.53 among years and whole-genome regression methods. We
 show that genomic selection has promise for increasing genetic gains and
 accelerating the development of resistant cultivars in strawberry by
 shortening selection cycles and enabling selection in early developmental
 stages without phenotyping.
description: This DRYAD & ZENODO repository are data repositories
 containing copies of the supplemental material associated with the The
 Plant Genome manuscript "Accuracy of genomic selection and long-term
 genetic gain for resistance to Verticillium wilt in strawberry"
 (https://doi.org/10.1002/tpg2.20054). The DRYAD hosts the data files
 originally submitted as Supplemental Material alongside the manuscript.
 The ZENODO hosts the figures originally submitted as Supplemental Material
 alongside the manuscript.
DOI: 10.15468/dl.8yagu3
title: Occurrence Download

description: A dataset containing 271 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dussia tessmannii",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 271 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003256-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jadbq6
title: Occurrence Download

description: A dataset containing 2128 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Universitat de València, Colecciones de Criptógamas: VAL_Algae"
 ]
}

 The dataset includes 2128 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003258-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8sf7m0cs2
title: How the Easter Egg Weevils got their spots: Phylogenomics reveals Müllerian mimicry in Pachyrhynchus (Coleoptera, Curculionidae)

description: The evolutionary origins of mimicry in the Easter Egg weevil,
 Pachyrhynchus, have fascinated researchers since first noted more than a
 century ago by Alfred Russel Wallace. Müllerian mimicry, or mimicry in
 which two or more distasteful species look similar, is widespread
 throughout the animal kingdom. Given the varied but discrete color
 patterns in Pachyrhynchus, this genus presents one of the best
 opportunities to study the evolution of both perfect and imperfect
 mimicry. We analyzed more than 10,000 UCE loci using a novel partitioning
 strategy to resolve the relationships of closely related species in the
 genus. Our results indicate that many of the mimetic color patterns
 observed in sympatric species are due to convergent evolution. We suggest
 that this convergence is driven by positive frequency-dependent selection.
description: <em>Divergence Dating Biogeography</em>
 We used MCMCTREE (Yang 2007) to perform our divergence dating
 analyses. We used the topology from our ASTRAL analyses as the starting
 topology for the MCMCTREE. No fossils exist for our ingroup or near
 relatives, so we used a geological calibration for the maximum age of the
 Philippine Islands. We used 25–30 Ma as the root node of the
 Pachyrhynchini, an approximate date for the emergence of the Philippine
 proto-islands proposed by Hall (2002). We used MCMCtreeR (Puttick 2019) to
 estimate a normal distribution around the maximum age of our calibration
 point as well as to format the tree file for MCMCTREE. Next, we used the
 aforementioned tree to obtain a rough estimate of the substitution rate
 using basml (Dos Reis and Yang 2013). To help accomplish this, we randomly
 selected 300 loci, using many more will prevent the analysis from
 completing, as well as using more data is not necessary to approximate the
 uncertainty of the divergence dates (Dos Reis and Yang 2013; Zhu et al.
 2015). Finally, we estimated the gradient and Hessian of the branch
 lengths (Dos Reis and Yang 2011) to assist in the final estimation of our
 divergence dates.
DOI: 10.5061/dryad.mcvdnck43
title: Data from: Grazing by non-native ungulates negatively impacts vegetation important to a native species of concern

description: Non-native grazers compete with native species across the globe. In the
 northwestern Great Basin of the western United States competition among
 livestock, feral horses, and Greater Sage-grouse has been the subject of
 numerous legal actions and management policies, yet spatially explicit
 temporal data documenting the details of this competition are lacking. We
 present a novel approach to studying the composition of the herbaceous
 understory across three study areas within the Great Basin with different
 historic and contemporary grazing regimes.  We surveyed the
 landscape using distance sampling for livestock and horse feces as an
 index of use. In addition, we surveyed the herbaceous understory of random
 sites as well as sites chosen by female Greater Sage-grouse to nest and
 brood their chicks. We used a novel Bayesian hierarchical modeling
 framework to link vegetation metrics with the spatial-temporal
 distribution of horses and livestock while accounting for observation
 error. When livestock and feral horses were not present, we found that
 Greater Sage-grouse chose sites with higher percentages of perennial
 grasses and forbs to build their nests and brood their chicks compared to
 what was available to them. As livestock increased, we found evidence for
 decreases in the percentage of perennial grasses, forbs, cheatgrass
 (Bromus tectorum), and increases in the amount of bare ground. These
 effects were consistent at available sites and brood sites, however, we
 found less evidence for an impact of livestock at nest sites. As feral
 horses increased, we observed similar results at available sites, but at
 sites chosen by females to nest and brood their chicks, we observed
 increases in the amount of invasive cheatgrass as feral horses increased,
 which could reflect attempts by Greater Sage-grouse to compensate for
 reductions in protective cover.  We present a noninvasive
 approach to assess space use that can be applied to other species. More
 importantly, we document that grazing by non-native ungulates impacts
 components of the plant community important to Greater Sage-grouse
 reproduction. We provide spatial-temporal maps of livestock and feral
 horse use to aid managers attempting to balance the needs of livestock
 producers, feral horses, Greater Sage-grouse, and ecosystem function.
DOI: 10.5061/dryad.s7h44j19h
title: Know what you don't know: Embracing state uncertainty in disease-structured multistate models

description: Hidden Markov models (HMMs) are broadly applicable hierarchical models
 that derive their utility from separating state processes from observation
 processes yielding the data. Multistate models such as mark-recapture and
 dynamic multistate occupancy models are examples of HMMs that are
 frequently used in ecology. In their early formulations, states, such as
 pathogen infection status, were assumed to be perfectly observed without
 ambiguity in state assignment. However, state uncertainty is a pervasive
 feature of many ecological systems, and multievent models were developed
 to explicitly account for it. We developed a novel extended multievent
 mark-recapture model that incorporates state uncertainty at multiple
 levels of detection. Using a disease-structured example, both
 false-negative and false-positive state assignment errors are modeled at
 two levels of state assignment---the pathogen sampling process and the
 diagnostic process that samples are subjected to. We additionally describe
 methods to jointly model infection intensity to integrate heterogeneity in
 ecological parameters, such as survival, and the pathogen detection
 processes. We provide code to simulate and analyze datasets with various
 underlying ecological processes and fit our model to a mark-recapture
 dataset of Mixophyes fleayi (Fleay's barred frog) infected with the
 amphibian chytrid fungus (Batrachochytrium dendrobatidis, Bd). In our case
 study, we found evidence for various state assignment errors: the sampling
 protocol performed poorly in detecting Bd, pathogen detection was highly
 dependent on infection intensity, and false-positives were non-negligible.
 Incorporating state uncertainty yielded significantly higher estimates of
 infection prevalence and 4--5 times lower rates of infection state
 transitions compared to those obtained from a traditional multistate
 model. Our results highlight that incorporating state assignment errors
 improves inference on the ecological state process, especially when
 sensitivity and specificity of the state assignment processes are low. The
 general model structure can be applied to other HMMs, providing a
 foundation for modeling state uncertainty in a range of related models. --
description: Weekly surveys for juvenile Fleay's barred frog
 (<em>Mixophyes</em> <em>fleayi</em>) were
 conducted over a 3.5-month period at Brindle Creek, Border Ranges National
 Park, New South Wales, Australia. There were two missing surveys (so with
 a biweekly interval instead of a weekly interval) which were padded with
 NAs in the capture history. Recaptured individuals were swabbed
 for <em>Bd</em>, DNA was extracted using Prepman Ultra, and
 DNA was amplified and quantified using qPCR and GeneBlocks synthetic gene
 fragments. See the README for more details on the data.
 Data were analysed with the novel multievent model and a
 traditional Arnason-Schwarz model (see manuscript and code) using NIMBLE
 0.12.2 in R 4.2.1.
DOI: 10.15468/dl.whbxsb
title: Occurrence Download

description: A dataset containing 1816 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Material sample, Specimen, Occurrence evidence)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Hypoponera eduardi",
 "Year 1000-2025"
 ]
}

 The dataset includes 1816 records from 69 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003257-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.mw6m9060f
title: Physiological roles of peptidoglycan carboxypeptidases DacC and DacA in Escherichia coli

description: Peptidoglycan (PG) is an essential bacterial architecture pivotal for
 shape maintenance and adaptation to osmotic stress. Although PG synthesis
 and modification are tightly regulated under harsh environmental stresses,
 few related mechanisms have been investigated. In this study, we aimed to
 investigate the coordinated and distinct roles of the PG carboxypeptidases
 DacC and DacA, in adaptation to alkaline and salt stresses and shape
 maintenance in Escherichia coli. We found that DacC is an alkaline PG
 carboxypeptidase, whose enzyme activity and protein stability are
 significantly enhanced under alkaline stress. Both DacC and DacA were
 required for bacterial growth under alkaline stress, whereas only DacA was
 required for the adaptation to salt stress. Under normal growth
 conditions, only DacA was necessary for cell shape maintenance, while
 under alkaline stress conditions, both DacA and DacC were necessary for
 cell shape maintenance, but their roles were distinct. Notably, all these
 roles of DacC and DacA were independent of ld-transpeptidases, which are
 necessary for the formation of PG 3-3 crosslinks and covalent bonds
 between PG and the outer membrane lipoprotein Lpp. Instead, DacC and DacA
 interacted with penicillin-binding proteins (PBPs), dd-transpeptidases,
 mostly in a C-terminal domain-dependent manner, and these interactions
 were necessary for most of their roles. Collectively, our results
 demonstrate the coordinated and distinct novel roles of PG
 carboxypeptidases in stress adaptation and shape maintenance and provide
 novel insights into the cellular functions of PG carboxypeptidases
 associated with PBPs.
DOI: 10.5061/dryad.8w9ghx3qj
title: Alignments of PSGs along with the crucial primate nodes

description: Comparative analysis of primate genomes within a phylogenetic context is
 crucial for understanding the evolution of human genetic architecture and
 the diversity of primates. Here, we present a phylogenomic study
 of 50 primate species spanning 38 genera and 14 families,
 including 27 new genomes first reported in this study with many from
 previously less represented groups, the New World monkeys and
 Strepsirrhini. Our analyses reveal heterogeneous rates of genomic
 rearrangement and gene evolution across primate lineages. Thousands of
 genes were under positive selection in different lineages that have roles
 in the nervous, skeletal and digestive systems and may have contributed to
 primate innovations and adaptations. Our study reveals many key genomic
 innovations occurred in the Simiiformes ancestral node that may have
 profound impacts on the radiation of Simiiformes and human evolution.