cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fqz612jxp
title: Simulation code for: Effects of population size change on the genetics of adaptation following an abrupt change in environment

description: Since the rediscovery of Mendelian genetics over a century ago, there has
 been much debate about the evolutionary importance of mutations with large
 phenotypic effects. While population genetic models predict that
 large-effect mutations will typically contribute to adaptation following
 an abrupt change in environment, the prediction applies to populations of
 stable size and overlooks effects of population size change on adaptation
 (e.g., population decline following habitat loss; growth during range
 expansion). We evaluate the phenotypic and fitness effects of mutations
 contributing to adaptation immediately following an abrupt environmental
 shift that alters both selection and population size dynamics. We show
 that large-effect mutations are likely to contribute to adaptation in
 populations declining to a new carrying capacity, somewhat smaller-effect
 mutations contribute to evolutionary rescue, and small-effect mutations
 predominate in growing populations. We also show that the relative
 contributions of positively selected and overdominant mutations to
 adaptation depend on interactions between the phenotypic effect size
 distribution for new mutations and the specific form of population size
 change during adaptation (i.e., growth, decline, or evolutionary rescue).
 Our results illustrate how population size dynamics can shape the genetic
 basis of adaptation, which should motivate empirical comparisons of
 populations adapting in different demographic contexts.
description: This is R simulation code used in the paper.
description: The code will run in R/Rstudio.
DOI: 10.5061/dryad.qv9s4mwkt
title: Data from: How do resource distribution and taxonomy affect the use of dual foraging in seabirds?: A review

description: In many seabird species, parents feeding young switch between short and
 long foraging excursions in a strategy known as “dual foraging”. To
 investigate whether habitat quality near breeding colonies drives the use
 of dual foraging, we conducted a systematic review of the seabird
 literature, compiling the results of 103 studies which identified
 dual-foraging in 50 species across nine families from all six seabird
 orders. We estimated the mean distance from the colony of each
 species' short and long foraging trips and obtained remote-sensed
 data on chlorophyll concentrations within the radius of both short and
 long trips around each colony. We then assessed, for each seabird family,
 the relationship between the use of dual foraging strategies and the
 difference in the quality of foraging locations between short- and
 long-distance foraging trips. We found that the probability of dual
 foraging grew with increasing difference in the quality of foraging
 locations available during short- and long-distance trips. We also found
 that when controlling for differences in habitat quality, albatrosses and
 penguins were less likely to use dual foraging than Procellariidae, which
 in turn were less likely to use dual foraging than Sulids. This study
 helps clarify how environmental conditions and taxon-specific
 characteristics influence seabird foraging behaviour. Keywords: seabirds,
 dual foraging, habitat quality, central-place foraging, interspecific
 differences.
DOI: 10.5061/dryad.rv15dv4d2
title: Programming correlated magnetic states with gate-controlled moiré geometry

description: Understanding quantum many-body systems is at the heart of condensed
 matter physics. The ability to control the underlying lattice geometry of
 a system, and thus its many-body interactions, would enable the
 realization of, and transition between, emergent quantum ground states.
 Here, we report in-situ gate switching between honeycomb and triangular
 lattice geometries of an electron many-body Hamiltonian in R-stacked MoTe2
 moiré bilayers, resulting in switchable magnetic exchange interactions. At
 zero electric field, we observe a correlated ferromagnetic insulator near
 one hole per moiré unit cell (v=-1), i.e., a quarter-filled honeycomb
 lattice, with a widely tunable Curie temperature up to 14K. A fully
 polarizing layer pseudospin via electric field switches the system into a
 half-filled triangular lattice with antiferromagnetic interactions.
 Further doping this layer-polarized superlattice introduces carriers into
 the empty layer, tuning the antiferromagnetic exchange interaction back to
 ferromagnetic. Our work demonstrates R-stacked MoTe2 moirés to be a new
 laboratory for engineering correlated states with nontrivial topology.
DOI: 10.5061/dryad.q2bvq83qt
title: Haemanthus deformis seed dispersal data

description: Most plants with fleshy fruits have seeds that are ingested by animals,
 but a less well-understood mode of seed dispersal involves fleshy fruits
 containing seeds that are discarded by frugivorous animals because they
 are too large or toxic to be ingested. We studied the seed dispersal
 biology of Haemanthus deformis, an amaryllid lily species found in a
 mosaic of bush clumps in a grassland matrix in South Africa. We asked
 whether seed dispersal is directed in and among bush clumps and whether
 germination and survival are greater for seeds dispersed to bush clumps
 than to those dispersed into grassland. Using camera trapping, we found
 that fruits are consumed mainly by birds and rodents. The pulp was removed
 from the seeds which were then discarded without ingestion. Whilst many
 seeds were dispersed close to the parent plant, most (c. 78.5%) were
 dispersed further than one meter away from the parent plant. Longer
 distance dispersal resulted mainly from birds flying off with seeds in
 their bill or from rodents engaging in scatter-hoarding behaviour.
 Seedling survival was most successful within bush clumps as compared to
 grasslands and shade was identified as a primary requirement for seedling
 survival. Seeds from which the fruit pulp had been removed germinated
 faster than those in intact fruits. Haemanthus deformis deploys a system
 of directed seed dispersal, whereby both birds and rodents contribute to
 dispersal of seeds within patchy bush clumps that are favourable for
 seedling survival.
DOI: 10.25574/cdc.461
title: Chandra X-ray Observatory Chandra Data Collection for request #461

description: Chandra Data Collection for request #461
description: DOI updated to include the publication's DOI on 2026-01-28-10:00:00
DOI: 10.5061/dryad.gmsbcc2t7
title: Data for: Colonization persistence trade-offs in natural bacterial communities

description: Fitness equalizing mechanisms, such as trade-offs, are recognized as one
 of the main factors promoting species coexistence in community ecology.
 However, they have rarely been explored in microbial communities. Although
 microbial communities are highly diverse, the coexistence of their
 multiple taxa is largely attributed to niche differences and high
 dispersal rates, following the principle “everything is everywhere, but
 the environment selects”. We use a dynamical stochastic model based on the
 Theory of Island Biogeography to study highly diverse microbial
 communities over time across three different systems (soils, alpine lakes,
 and shallow saline lakes). Assuming fitness equalization mechanisms, here
 we newly analytically derive colonization-persistence trade-offs, and
 report a signal of such trade-offs in natural microbial communities.
 Moreover, we show that different subsets of species in the community drive
 this trade-off. Rare taxa, which are occasional and more likely to follow
 independent colonization/extinction dynamics, drive this trade-off in the
 aquatic communities, while the core sub-community did it in the soils. We
 conclude that equalizing mechanisms may be more important than previously
 recognized in microbial communities. Our work also emphasizes the
 fundamental value of dynamical models for understanding temporal patterns
 and processes in highly diverse communities.
DOI: 10.5061/dryad.0p2ngf25t
title: Data for: Behavioral evidence of olfactory imprinting during embryonic and larval stages in lake sturgeon

description: Many migratory fishes are thought to navigate to natal streams using
 olfactory cues learned during early life stages. However, direct evidence
 for early-life olfactory imprinting is largely limited to Pacific salmon,
 and other species suspected to imprint show life history traits and
 reproductive strategies that raise uncertainty about the generality of the
 salmonid-based conceptual model of olfactory imprinting in fishes. Here,
 we studied early-life olfactory imprinting in lake sturgeon (Acipenser
 fulvescens), which have a life cycle notably different from Pacific
 salmon, but are nonetheless hypothesized to home via similar mechanisms.
 We tested one critical prediction of the hypothesis that early-life
 olfactory imprinting guides natal homing in lake sturgeon: that exposure
 to odorants during early-life stages results in increased
 activity when exposed to those odorants later in life. Lake sturgeon were
 exposed to artificial odorants (phenethyl alcohol and morpholine) during
 specific developmental windows and durations (limited to the egg,
 free-embryo, exogenous feeding larvae, and juvenile stages), and later
 tested as juveniles for behavioral responses to the odorants that were
 demonstrative of olfactory memory. Experiments revealed that lake sturgeon
 reared in stream water mixed with artificial odorants for as little as 7
 days responded to the odorants in behavioral assays over 50 days after the
 initial exposure, specifically implicating the free-embryo and larval
 stages as critical imprinting periods. Our study provides evidence for
 olfactory imprinting in a non-salmonid fish species, and supports further
 consideration of conservation tactics such as stream-side rearing
 facilities that are designed to encourage olfactory imprinting to targeted
 streams during early life stages. Continued research on lake sturgeon can
 contribute to a model of olfactory imprinting that is more generalizable
 across diverse fish species and will inform conservation actions for one
 of the world’s most imperiled fish taxonomic groups.
DOI: 10.5061/dryad.gtht76hrr
title: Data for: Artificial squares, rectangles and Xray images in random rotational orientations, centered and in different sizes

description: SORFAC-CT (Cylindrical-Topology Self-Organizing Reference-Free Alignment
 and Classification; pronounced sôr-fakt or sôr-fak-si-ti) is an efficient
 method of reference-free rotational image alignment. SORFAC-CT
 circumvents the dependence of subjective user- or computer-generated
 external or internal reference images used by other reference-based
 techniques. Alignment is performed using a Kohonen self-organizing map
 (SOM), configured on a cylindrical array of artificial neurons. Although
 alternative alignment protocols often depend on an expert to adjust many
 ad hoc parameters, SORFAC-CT instead achieves the minimization of one
 objectively calculated target function by varying only two free
 parameters. Because SOMs preserve the topological properties of the
 training (dataset) images, the relative in-plane rotational orientations
 of dataset images are obtained directly from the array’s intrinsic
 cylindrical coordinate system by noting each mapped dataset image’s
 respective azimuthal angle coordinate placement around the cylinder.
 Dataset images are not rotated into alignment with internally or
 externally generated reference images. Instead, SORFAC-CT starts with a
 cylindrical array of proto-models consisting of random pixel values. The
 proto-models gradually morph to become the rotational class models by an
 unsupervised process. The dataset images are then mapped to the class
 models according to greatest similarity; the alignment angles directly
 read off the cylinder. This was tested on datasets including square,
 rectangular and hexagonal geometrical shapes in six different sizes, to
 introduce heterogeneity. It was also tested using noisy 2-dimensional
 projections of the AQP-1 x-ray model. The results were near-perfect
 alignments that could be improved by increasing cylinder circumference,
 until the resolution limits of the dataset images are reached.
description: As explained in the Materials and Methods, these datasets were
 generated using IMAGIC software. 
description: SORFAC or SORFAC-CT may be used on these three sets of test
 images. The full-featured software is freely available upon request to the
 author, and the source code is available too.
DOI: 10.25326/b5q7-mx18
title: Atmospheric simulation chamber study: Guaiacol + OH - Gas-phase oxidation - product study - 2023-05-15
DOI: 10.6076/d1rw2g
title: Data from: Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction

description: Phylogenetic trees inferred using commonly-used models of sequence
 evolution are unrooted, but the root position matters both for
 interpretation and downstream applications. This issue has been long
 recognized; however, whether the potential for discordance between the
 species tree and gene trees impacts methods of rooting a phylogenetic tree
 has not been extensively studied. In this paper, we introduce a new method
 of rooting a tree based on its branch length distribution; our method,
 which minimizes the variance of root to tip distances, is inspired by the
 traditional midpoint rerooting and is justified when deviations from the
 strict molecular clock are random. Like midpoint rerooting, the method can
 be implemented in a linear time algorithm. In extensive simulations that
 consider discordance between gene trees and the species tree, we show that
 the new method is more accurate than midpoint rerooting, but its relative
 accuracy compared to using outgroups to root gene trees depends on the
 size of the dataset and levels of deviations from the strict clock. We
 show high levels of error for all methods of rooting estimated gene trees
 due to factors that include effects of gene tree discordance, deviations
 from the clock, and gene tree estimation error. Our simulations, however,
 did not reveal significant differences between two equivalent methods for
 species tree estimation that use rooted and unrooted input, namely, STAR
 and NJst. Nevertheless, our results point to limitations of existing
 scalable rooting methods.
description: All the data sets are the results of simulations generated using
 Simphy. 
 D1—30-taxon heterogeneous dataset: The number of ingroup species
 was fixed to 30. We include 100 replicates, each with 500 gene
 trees.  D2—Large heterogeneous dataset: Has two
 subsets, one with 2000 and another with 5000 taxa, each with 20 replicates
 and 50 gene trees. D3—ASTRAL-II dataset: We reused a
 previously published dataset
 (http://www.ncbi.nlm.nih.gov/pubmed/26072508) with the number of species
 varying: 10, 50, 100, 200, 500, and 1000.
DOI: 10.5061/dryad.tht76hf4f
title: Projected changes in forest biomass to 2100 by county and species for 20 future scenarios

description: Climate change and atmospheric deposition of nitrogen (N) and sulfur (S)
 are important drivers of forest demography. Here we apply
 previously-derived growth and survival responses for 94 tree species,
 representing &gt;90% of the contiguous U.S. forest basal area, to
 project how changes in mean annual temperature, precipitation, and N and S
 deposition from 20 different future scenarios may affect forest
 composition to 2100. We find that under the low climate change scenario
 (RCP 4.5), reductions in aboveground tree biomass from higher temperatures
 are roughly offset by increases in aboveground tree biomass from
 reductions in N and S deposition. However, under the higher climate change
 scenario (RCP 8.5) the decreases from climate change overwhelm increases
 from reductions in N and S deposition. These broad trends underlie wide
 variation among species. We found that averaged across temperature
 scenarios, the relative abundance of 60 species was projected to decrease
 by more than 5%, 20 species were projected to increase by more than 5%,
 and reductions of N and S deposition led to a decrease for 13 species and
 an increase for 40 species. This suggests large shifts in the composition
 of U.S. forests in the future. Negative climate effects were mostly from
 elevated temperature and were not offset by scenarios with wetter
 conditions. We found that by 2100 an estimated 1 billion trees under the
 RCP 4.5 scenario and 20 billion trees under the RCP 8.5 scenario may be
 pushed outside the temperature record upon which these relationships were
 derived. These results may not fully capture future changes in forest
 composition as several other factors were not included. Overall efforts to
 reduce atmospheric deposition of N and S will likely be insufficient to
 overcome climate change impacts on forest demography across much of the
 United States unless we adhere to the low climate change scenario.
DOI: 10.5061/dryad.hdr7sqvnz
title: Data from: Comparative LCA studies of simulated HMF-biorefineries from maize and miscanthus as an example of first- and second-generation biomass as a tool for process development

description: 5-Hydroxymethylfurfural (HMF) is a versatile platform chemical for a
 fossil free, bio-based chemical industry. HMF can be produced by using
 fructose as a feedstock. Using edible, first-generation biomass to produce
 chemicals has been questioned in terms of potential competition with food
 supply. Second-generation biomass like miscanthus could be an alternative.
 However, there is a lack of information if second-generation
 lignocellulosic biomass is a more sustainable feedstock to produce HMF.
 Therefore, a life cycle assessment was performed in this study to
 determine the environmental impacts of HMF production from miscanthus and
 to compare it with HMF from high fructose corn syrup (HFCS). HFCS from
 either Hungary or Baden-Württemberg (Germany) was considered. Compared to
 the HFCS biorefineries the miscanthus concept is producing less emissions
 in all impact categories studied, except land occupation. Overall, the
 production and usage of second-generation biomass could be especially
 beneficial in areas where the use of N-fertilizers is restricted. Besides,
 conclusions for the further development of the on-farm-biorefinery concept
 were elaborated. For this purpose, process simulations from a previous
 study were used. Results of the previous study in terms of TEA and the
 current LCA study in terms of environmental sustainability indicate that
 the lignin depolymerization unit in the miscanthus biorefinery has to be
 improved. The scenario without lignin depolymerization performs better in
 all impact categories. The authors recommend to not further convert the
 lignin to products like phenol and other aromatic compounds. The results
 of the contribution analyses show that the major impact in the HMF
 production is caused by the auxiliary materials in the separation units
 and the required heat. Further technical development should focus on
 efficient heat as well as solvent use and solvent recovery. At this point
 further optimizations will lead to reduced emissions and costs at the same
 time. The presented data set is the used inventory to model the
 environmental impacts. 
description: The data was collected using data from pilot plant campaigns and
 the mass and energy flows of an AspenPlus(C) process simulation.
 Calculations of the environmental impacts were conducted using the LCA
 software Brightway 2.
DOI: 10.5061/dryad.z34tmpgkd
title: Data for: Capturing synchronization with complexity measure of ordinal pattern transition network constructed by Crossplot

description: To evaluate the synchronization of bivariate time series has been a hot
 topic and a number of measures have been proposed. In this work, by
 introducing the ordinal pattern transition network (OPTN) into the
 crossplot, a new method for measuring the synchronisation of bivariate
 time series is proposed. After the crossplot been partitioned and coded,
 the coded partitions are defined as network nodes and a directed weighted
 network is constructed based on the temporal adjacency of the nodes. The
 crossplot transition entropy (CPTE) of the network is proposed as an
 indicator of the synchronization between two time series. To test the
 characteristics and performance of the method, it is used to analyse the
 unidirectional coupled Lorentz model and  compared it with
 existing methods. The results showed the new method had the advantages of
 easy parameter setting, efficiency, robustness, good consistency and
 suitable for short time series. Finally, EEG data from auditory evoked
 potential EEG-Biometric dataset are investigated, and some useful and
 interesting results are obtained.
description: 1. Two Lorenz dynamic models with coupling relationships were
 used. 2. Using sliding window method for
 processing. 3. Add white noise to see the impact on the
 analysis of the proposed method.
description: Application: MATLAB
 version 2012 or above
DOI: 10.5061/dryad.bnzs7h4gn
title: Data from: Egg predators improve the hatching success of salamander eggs

description: A common challenge that oviparous animals face is securing survivorship
 during the vulnerable embryonic stage. One of the parental investment
 strategies to improve survivorship is providing physical structures to
 protect the embryos. In amphibians, there is a notable diversity in
 jelly-layer structures surrounding eggs. Previous studies show that these
 jelly layers provide eggs with protection against egg predators, egg
 pathogens, and desiccation. However, few studies examined the cost–benefit
 relationship of the jelly-layer structures. By using the predator–prey
 interaction between wood frog (Lithobates sylvaticus) tadpoles and spotted
 salamander (Ambystoma maculatum) eggs as a model system, we tested three
 hypotheses: (1) having the outer jelly layers would be costly to the
 embryos, (2) the relative benefit of the structural egg defense would
 become apparent and increase as the intensity of egg predation increases,
 and (3) a certain degree of predation would increase the hatching success
 of salamander embryos by mechanically thinning the thick outer jelly
 layers and increasing oxygen diffusion throughout an egg mass. To test
 these hypotheses, we conducted a factorial experiment in which we crossed
 four egg-predation levels with two jelly-layer conditions, intact or
 removed. We found that the jelly layers were essential in protecting
 spotted salamander embryos from wood frog tadpoles but that the associated
 cost was apparent in no-predation treatments. The differential
 survivorship between intact eggs and eggs without jelly layers showed that
 the fitness advantage of jelly layers increased as the level of predation
 increased. Finally, the hatching success of intact egg masses was highest
 under the high predation conditions. These results imply that the
 evolution of the jelly-layer thickness occurred under constant
 egg-predation pressure. Given this predator–prey coevolution, egg
 predators may play a critical role in improving the hatching success of
 salamander embryos under certain conditions.
description: Embryos of spotted salamanders were monitored, and the number of
 hatchlings were counted each day.
description: R, MS excel etc.
description: # Title of Dataset *** This file contains two data types, hatching success
 and incubation period of spotted salamander embryos monitored in a lab
 setting. ## Description of the data and file structure There are three
 factors, egg (type), Layers, and Predation. All egg types are white eggs.
 Layers consist of Yes (presence of jelly layers surrounding eggs) and No
 (without jelly layers). There are four predation levels, no, low, medium,
 and high depending on the number of egg predators (tadpoles). ##
 Sharing/Access information Links to other publicly accessible locations of
 the data: \*N/A Data was derived from the following sources: \*N/A ##
 Code/Software Please see the corresponding publication