cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.n5tb2rbrv
title: Sex-independent senescence in a cooperatively breeding mammal

description: 1. Researchers studying mammals have frequently interpreted earlier or
 faster rates of ageing in males as resulting from polygyny and the
 associated higher costs of reproductive competition. 2. Yet few studies
 conducted on wild populations have compared sex-specific senescence
 trajectories outside of polygynous species, making it difficult to make
 generalised inferences on the role of reproductive competition in driving
 senescence, particularly when other differences between males and females
 might also contribute to sex-specific changes in performance across
 lifespan. 3. Here, we examine age-related variation in body mass,
 reproductive output and survival in dominant male and female meerkats,
 Suricata suricatta. Meerkats are socially monogamous cooperative breeders
 where a single dominant pair virtually monopolize reproduction in each
 group and subordinate group members help to rear offspring produced by
 breeders. 4. In contrast to many polygynous societies, we find that
 neither the onset nor the rate of senescence in body mass or reproductive
 output show clear differences between males and females. Both sexes also
 display similar patterns of age-related survival across lifespan, but
 unlike most wild vertebrates, survival senescence (increases in annual
 mortality with rising age) was absent in dominants of both sexes, and as a
 result, the fitness costs of senescence were entirely attributable to
 declines in reproductive output from mid- to late-life. 5. We suggest that
 the potential for intrasexual competition to increase rates of senescence
 in females – who are hormonally masculinised and frequently aggressive –
 is offset by their ability to maintain longer tenures of dominance than
 males, and that these processes combined lead to similar patterns of
 senescence in both sexes. 6. Our results stress the need to consider the
 form and intensity of sexual competition as well as other sex-specific
 features of life history when investigating the operation of senescence in
 wild populations.
description: Data was collected using standard observational methods employed
 at the Kalahari Meerkat Project since 1992. All details are provided in
 the main paper.
description: The data is given as entered into the models, so no further
 information is needed to reproduce our models given the informationin the
 methods.
DOI: 10.5281/zenodo.18394509
title: HydraNet Academic: Interactive Platform with Automatic Interpretation for the Analysis and Learning of Hydraulic Networks in Civil Engineering HydraNet Academic: Plataforma Interactiva con Interpretación Automática para el Análisis y Aprendizaje de Redes Hidráulicas en Ingeniería Civil E. O. Ladino-Moreno   E-mail: eoladinom@udistrital.edu.co

description: HydraNet Academic: Interactive Platform with Automatic Interpretation for the Analysis and Learning of Hydraulic Networks in Civil Engineering

HydraNet Academic: Plataforma Interactiva con Interpretación Automática para el Análisis y Aprendizaje de Redes Hidráulicas en Ingeniería Civil

E. O. Ladino-Moreno 

E-mail: eoladinom@udistrital.edu.co
DOI: 10.5281/zenodo.18394510
title: HydraNet Academic: Interactive Platform with Automatic Interpretation for the Analysis and Learning of Hydraulic Networks in Civil Engineering HydraNet Academic: Plataforma Interactiva con Interpretación Automática para el Análisis y Aprendizaje de Redes Hidráulicas en Ingeniería Civil E. O. Ladino-Moreno   E-mail: eoladinom@udistrital.edu.co

description: HydraNet Academic: Interactive Platform with Automatic Interpretation for the Analysis and Learning of Hydraulic Networks in Civil Engineering

HydraNet Academic: Plataforma Interactiva con Interpretación Automática para el Análisis y Aprendizaje de Redes Hidráulicas en Ingeniería Civil

E. O. Ladino-Moreno 

E-mail: eoladinom@udistrital.edu.co
DOI: 10.5061/dryad.0vt4b8gv9
title: Species differences in phenology shape coexistence

description: Ecological theory produces opposing predictions about whether differences
 in the timing of life history transitions, or ‘phenology’, promote or
 limit coexistence. Phenological separation is predicted to create temporal
 niche differences, increasing coexistence, yet phenological separation
 could also competitively favour one species, increasing fitness
 differences and hindering coexistence. We experimentally manipulated
 relative germination timing, a critical phenological event, of two annual
 grass species, Vulpia microstachys and V. octoflora, to test these
 contrasting predictions. We parameterized a competition model to estimate
 within-season niche differences, fitness differences, and coexistence, and
 to estimate coexistence when year-to-year fluctuations of germination
 timing occur. Increasing germination separation caused parallel changes in
 niche and fitness differences, with the net effect of weakening
 within-year coexistence. Both species experienced a competitive advantage
 by germinating earlier and a four-day head start allowed the generally
 inferior competitor to exclude the otherwise superior competitor. The
 overall consequence of germination separation was to limit coexistence
 within a given year, although year-to-year variation in relative timing of
 germination was sufficient to support long-term coexistence. Our results
 clarify how phenological differences structure competitive interactions
 and highlight the need to quantify year-to-year variation in these
 differences to better understand species coexistence.
DOI: 10.5061/dryad.fn2z34tq5
title: Urbanization and translocation disrupt the relationship between host density and parasite abundance

description: 1.) The species interactions that structure natural communities are
 increasingly disrupted by radical habitat change resulting from the
 widespread processes of urbanization and species translocations. Although
 many species are disadvantaged by these changes, others thrive in these
 new environments, achieving densities exceeding those found in natural
 habitats. Often the same species that benefit from urbanization are
 successful invaders in introduced habitats, suggesting that similar
 processes promote these species in both environments. 2.) Both processes
 may especially benefit certain species by modifying their interactions
 with harmful parasites (“enemy release”). To detect such modifications, we
 first need to identify the mechanisms underlying host-parasite
 associations in natural populations, then test whether they are disrupted
 in cities and introduced habitats. 3.) We studied the interaction between
 the cane toad (Rhinella marina), a globally invasive species native to
 South America, and its Amblyomma ticks. Our field study of 642 cane toads
 across 46 sites within their native range in French Guiana revealed that
 56% of toads carried ticks, and that toads with ticks were in poor body
 condition relative to uninfected conspecifics. Across natural and
 disturbed habitats, tick prevalence and abundance increased with toad
 density, but this association was disrupted in the urban environment,
 where tick abundance remained low even where toad densities were high, and
 prevalence decreased with density. 4.) Reductions in the abundance of
 ticks in urban habitats may be attributable to pesticides (which are
 sprayed for mosquito control, but are also lethal to ticks), and our
 literature review shows that tick abundance is generally lower in cane
 toads from urban habitats across South America. In the invasive range,
 ticks were either absent (in 1,960 toads from Puerto Rico, Hawai’i, Japan,
 and Australia) or less abundant (in Florida and the Caribbean; literature
 review). 5.) The positive relationship between host density and parasite
 abundance is thought to be a key mechanism through which parasites
 regulate host populations; anthropogenic processes that disrupt this
 relationship may allow populations in urban and introduced habitats to
 persist at densities that would otherwise lead to severe impacts from
 parasites.
DOI: 10.5061/dryad.w3r2280m5
title: Assisted migration across fixed seed zones detects adaptation lags in two major North American tree species

description: Boreal forests are experiencing dramatic climate change, having warmed
 1-1.9°C over the last century. Yet forest regeneration practices are often
 still dictated by a fixed seed zone framework, in which seeds are both
 harvested from and planted into predefined areas. Our goal was to
 determine whether seedlings sourced from southern seed zones in Minnesota
 USA are already better adapted to northerly seed zones because of climate
 change. Bur oak (Quercus macrocarpa) and northern red oak (Quercus rubra)
 seedlings from two seed zones (i.e. tree ecotypes) were planted into 16
 sites in two northern seed zones and measured for three years. Our
 hypotheses were threefold: 1) tree species with more southern geographic
 distributions would thrive in northern forests where climate has already
 warmed substantially, 2) southern ecotypes of these species would have
 higher survival and growth than the northern ecotype in northern
 environments, and 3) natural selection would favor seedlings that
 expressed phenotypic and phenological traits characteristic of trees
 sourced from the more southern seed zone. For both species, survival was
 high (&gt;93%), and southern ecotypes expressed traits consistent with
 our climate adaptation hypotheses. Ecotypic differences were especially
 evident for red oak; the southern ecotype had had higher survival, lower
 SLA, faster height and diameter growth, and extended leaf phenology
 relative to the northern ecotype. Bur oak results were weaker, but the
 southern ecotype also had earlier budburst and lower SLA than the northern
 ecotype. Models based on the fixed seed zones failed to explain seedling
 performance as well as those with continuous predictors (e.g. climate and
 geographical position), suggesting that plant adaptations within current
 seed zone delineations do align with changing climate conditions. Adding
 support for this conclusion, natural selection favored traits expressed by
 the more southern tree ecotypes. Collectively, these results suggest that
 state seed sourcing guidelines should be reexamined to permit plantings
 across seed zones, a form of assisted migration. More extensive
 experiments (i.e. provenance trails) are necessary to make
 species-specific seed transfer guidelines that account for climate trends
 while also considering the precise geographic origin of seed sources.
DOI: 10.15468/dl.56bcfa
title: Occurrence Download

description: A dataset containing 25820 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ochotona"
 ]
}

 The dataset includes 25820 records from 151 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002115-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ywhrss
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Xerosicyos pubescens",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002116-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.3j9kd51d9
title: Enhancing crop domestication through genomic selection, a case study of intermediate wheatgrass

description: Perennial grains could simultaneously provide food for humans and a host
 of ecosystem services, including reduced erosion, minimized nitrate
 leaching, and increased carbon capture. Yet most of the world’s food and
 feed is supplied by annual grains. Efforts to domesticate intermediate
 wheatgrass (Thinopyrumn intermedium, IWG) as a perennial grain crop have
 been ongoing since the 1980’s. Currently, there are several breeding
 programs within North America and Europe working toward developing IWG
 into a viable crop. As new breeding efforts are established to provide a
 widely adapted crop, questions of how genomic and phenotypic data can be
 used among sites and breeding programs have emerged. Utilizing five cycles
 of breeding data that span eight years and two breeding programs,
 University of Minnesota, St. Paul, MN, and The Land Institute, Salina, KS,
 we developed genomic selection (GS) models to predict IWG traits. Seven
 traits were evaluated with free-threshing seed, seed mass, and
 non-shattering being considered domestication traits while agronomic
 traits included spike yield, spikelets per inflorescence, plant height,
 and spike length. We used 6,199 genets - unique, heterozygous, individual
 plants - that had been profiled with genotyping-by-sequencing, resulting
 in 23,495 SNP markers to develop GS models. Within cycles, the predictive
 ability of GS was high, ranging from 0.11 to 0.97. Across-cycle
 predictions were generally much lower, ranging from -0.22 to 0.76. The
 prediction ability for domestication traits was higher than agronomic
 traits, with non-shattering and free threshing prediction abilities
 ranging from 0.27 to 0.75 whereas spike yield had prediction abilities
 ranging from -0.22 to 0.26. These results suggest that progress to reduce
 shattering and increase the percent free-threshing grain can be made
 irrespective of the location and breeding program. While site-specific
 programs may be required for agronomic traits, synergies can be achieved
 in rapidly improving key domestication traits for IWG. As other species
 are targeted for domestication, these results will aid in rapidly
 domesticating new crops.
description: Data set was collected over eight years 2011-2019 from two
 different intermediate wheatgrass (IWG, <em>Thinopyrum
 intermedium</em>) breeding programs at The Land Institute, Salina
 KS, and the University of Minnesota, St. Paul, MN. 
 Genotyping-by-sequencing was used for genomic profiling. 
description: Readme file indicates data scripts and file structures in the
 zipped data file.
DOI: 10.5281/zenodo.18394496
title: anteaeolidiella_chromosoma_decontaminated_FSCR.fasta.gz
DOI: 10.5281/zenodo.18394495
title: anteaeolidiella_chromosoma_decontaminated_FSCR.fasta.gz
DOI: 10.25338/b8532t
title: Exploring the role of attitude in the acceptance of self-driving shuttles

description: Self-driving vehicles, as a revolution in mobility, are emerging and
 developing rapidly. However, public attitudes toward this new unproven
 technology are still uncertain. Given the significant influence of
 attitude toward a new technology on the intention to use it, the question
 arises as to why some people are in favor of this technology whereas
 others are not. Additionally, questions about the key attitudes
 influencing self-driving technology acceptance, where these attitudes come
 from, and how they interact with each other have not yet been addressed.
 This study aims to explore these research questions based on data
 collected from people who live or work in the West Village (WV) area of
 the University of California, Davis (UCD) campus after a self-driving
 electric shuttle was piloted in this area. Structural Equation Modeling
 (SEM) was employed to explore interactions between attitude elements. The
 results show that affect, the core of the concept of attitude, strongly
 explains the acceptance of self-driving technology. A higher level of
 affect could be formed by strengthening an individual’s trust.
 Additionally, trust works as an important mediator between perceived risk,
 usefulness, and ease of use on both affect and intention to ride
 self-driving vehicles. Perceived risk captured more security and
 functional concerns, reflecting uncertainty around current self-driving
 technology. The model identified important bi-directional influences
 between trust and affect. Significant effects of mental and physical
 intangibility were also shown, but each works differently on cognitive
 beliefs. Individuals’ socio-demographic, lifestyle, and mobility
 characteristics also exert influences on attitude and self-driving
 technology acceptance.
DOI: 10.5061/dryad.h18931zgh
title: Regional replication of landscape genetics analyses of the Mississippi slimy salamander, Plethodon mississippi

description: Context Landscape genetics can identify habitat features that facilitate
 or resist gene flow, providing a framework for anticipating the impacts of
 land use changes on dispersal of individuals. To inform management, a
 better understanding of how inferences derived from one study region are
 applicable to other regions is needed. Objectives We investigated the
 manner in which five landscape variables correlated with gene flow
 among Plethodon mississippi populations in two study
 regions. We compared order of importance, direction (facilitation vs.
 resistance of gene flow) and scale of effect, and functional relationships
 of variables within each study area. Methods In forests in Mississippi and
 Alabama, USA, we tested individual-based genetic distances derived from
 microsatellite genotypes against effective distances caused by
 agriculture, hardwoods, pine, manmade structures, and wetlands that were
 optimized for both scale and transformation using maximum likelihood
 population effects modeling. Results Of the landscape variables,
 agriculture and wetlands ranked at the top of both study areas’ models. In
 both forest regions, agriculture was consistently associated with
 resistance, whereas pine was inferred to facilitate gene flow. However, we
 found region-specific differences in effects of wetlands, hardwoods, and
 manmade structures. Configuration of the latter landscape variables
 differed between forest regions, which may explain the contrasting
 outcomes. Conclusions Our results underscore the value of metareplication
 in revealing which components of landscape genetics models may be
 consistent across different portions of a species’ range, and those that
 have context-dependent impacts on gene flow. We also highlight the need to
 consider habitat configuration when interpreting the results of landscape
 genetics analyses.
DOI: 10.5061/dryad.xwdbrv19c
title: Identifying drivers of forest resilience in long-term records from the Neotropics

description: Here we use 30 long-term, high-resolution palaeoecological records from
 Mexico, Central and South America to address two hypotheses regarding
 possible drivers of resilience in tropical forests as measured in terms of
 recovery rates from previous disturbances. First, we hypothesise that
 faster recovery rates are associated with regions of higher biodiversity,
 as suggested by the insurance hypothesis. And second, that resilience is
 due to intrinsic abiotic factors that are location specific, thus regions
 presently displaying resilience in terms of persistence to current
 climatic disturbances should also show higher recovery rates in the past.
 To test these hypotheses, we applied a threshold approach to identify past
 disturbances to forests within each sequence. We then compared the
 recovery rates to these events with pollen richness before the event. We
 also compared recovery rates of each site with a measure of present
 resilience in the region as demonstrated by measuring global vegetation
 persistence to climatic perturbations using satellite imagery. Preliminary
 results indeed show a positive relationship between pre-disturbance
 taxonomic diversity and faster recovery rates. However, there is less
 evidence to support the concept that resilience is intrinsic to a region;
 patterns of resilience apparent in ecosystems presently are not
 necessarily conservative through time.
description: Here you can find csv files with pollen counts from 15 sites of
 the neotropics. The additional datasets used in the manuscript were
 downloaded from the Neotoma Paleoecology Database (https://www.neotomadb.org/) and can be downloaded from there or by using the Neotoma R package (https://cran.r-project.org/web/packages/neotoma/neotoma.pdf). Details of these datasets can be found in the electronic supplementary material file. To use the R scripts found in this depository on the data from the Neotoma Paleoecology Database, the first three rows of the datasets must be 1. the header row with "name", "group", "element", etc rows. 2. The "Depth" row. 3. The "Sample ID" row. After these three rows, the pollen taxa rows should follow. Any other rows (e.g. "Thickness", "AnalysisUnitName", "Sample Name", and rows referring to ages of samples should be removed prior to running the R scripts.  You can also find the R codes to retrieve disturbances from these datasets (*dataset*_mean_sd), diversity calculations (adapted from Dr. Daniele Colombaroli's diversity scripts, *dataset*_formatting_div) and the R script for the statistical modelling of the hypoteses to be tested in the paper (RecoveryR_Richness_Statistics_Script_12Nov19). Additionally, the data for the statistical analyses can be found in the .csv filest "RecoveryRates_BiolLetters_rich.csv" (for the first hypothesis) and "RecoveryRates_BiolLetters_vsi.csv" (for the second hypothesis).
DOI: 10.5061/dryad.k0p2ngf4m
title: Biogeographic barriers, Pleistocene refugia, and climatic gradients in the southeastern Nearctic drive diversification in corn snakes (Pantherophis guttatus complex)

description: The southeastern Nearctic is a biodiversity hotspot that is also rich in
 cryptic species. This richness can be explained by numerous hypotheses
 affecting divergence, which include biogeographic barriers, adaptation to
 climatic gradients across this region, and Pleistocene speciation in
 glacial refugia. However, previous phylogeographic studies have both
 supported and refuted these hypotheses. Therefore, while one or more of
 these hypotheses may explain diversification, it is likely that taxa are
 forming within this region in species-specific ways. Here we generate a
 genomic dataset for the cornsnakes (P. guttatus complex), which are
 widespread across this region, spanning both biogeographic barriers and
 climatic gradients. We use phylogeographic model selection combined with
 hindcast ecological niche models to determine regions of habitat stability
 through time. This combined approach suggests that numerous hypotheses are
 required to explain the current diversity of this group of snakes. The
 Mississippi River caused initial speciation in this species complex, with
 more recent divergence events linked to adaptations to ecological
 heterogeneity and allopatric Pleistocene refugia. Lastly, we discuss the
 taxonomy of this group and suggest there may be additional cryptic species
 in need of formal recognition.
description: Included in the 'Assembled_rad_data' directory are
 assembled rad seq data from ipyrad in .loci, .phy, .ustr (unlinked
 structure input), and vcf formats, as well as a converted and subsampled
 nexus file for BFD* species delimitation with SNAPP. In
 the 'ENM_locality_info' directory are the localities and museum
 species numbers of georeferenced specimens downloaded from VertNet and
 used for ENMs. In the 'ENM_output_ascii'
 directory are the ENM ascii files from ENMs under different model
 parameters. Lastly, in the
 'fastsimcoal2_models' are all inputs for the two, four
 population models and all six, two population demographic models tested
 for the P. guttatus complex.
description: If the methods are followed from this paper these data set should
 allow users to reproduce our results and figures in this manuscript.
 Please feel free to contact the corresponding author with any
 questions.