cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tqjq2bw43
title: Stronger effect of individual species’ traits than shading on aquatic plant community productivity and interspecific competition

description: Competition is one of the major factors structuring plant communities.
 Species with similar traits generally compete more intensely and have more
 similar yield than functionally dissimilar species, which often respond
 differently to environmental change. Little is known about how the
 interacting species’ traits influence the effect of environmental
 change on interspecific competition. However, theory predicts that
 environmental change should lead to more asymmetric competition, by
 favouring the species best adapted to the particular environmental change.
 Here we used a mesocosm experiment with three common aquatic plant species
 from the Baltic Sea (Northern Europe), to test how community productivity
 and competition asymmetry were affected by functional dissimilarity,
 individual species’ traits, and a common stressor: shading. Competition
 asymmetry was defined as the absolute difference in reductions in yield
 relative to monocultures of two interacting species. Community
 productivity decreased and competition asymmetry increased with functional
 dissimilarity of the interacting species, possibly explained by the traits
 of the superior species, which had higher specific leaf area, maximum
 canopy height, and primary production rate than the subordinate species.
 Community productivity was not affected by shading, contrary to our
 expectation, while competition asymmetry was higher in shaded than ambient
 conditions. Individual species yield depended on species identity and
 species combination. Only the shortest species was negatively affected by
 shading. Thus, by favouring tall-growing species, shading can alter
 interspecific competition. Together, these findings suggest that
 non-random species loss following environmental change can be caused by
 competitive exclusion, in addition to a direct effect of abiotic
 filtering.
DOI: 10.5061/dryad.k6djh9wbp
title: Data for: Drought impairs herbivore-induced volatiles, but not through constraints on newly assimilated carbon

description: Volatile terpenes serve multiple biological roles including tree
 resistance against herbivores. The increased frequency and severity of
 drought stress observed in forests across the globe may hinder trees from
 producing defense-related volatiles in response to biotic stress. To
 assess how drought-induced physiological stress alters volatile emissions
 alone and in combination with a biotic challenge, we monitored pre-dawn
 water potential, gas exchange, needle terpene concentrations, and terpene
 volatile emissions of ponderosa pine (Pinus ponderosa) saplings during
 three periods of drought and in response to simulated herbivory via methyl
 jasmonate application. Although three-, six-, and seven-week drought
 treatments reduced net photosynthetic rates by 20%, 89%, and 105%,
 respectively, the magnitude of volatile fluxes remained generally
 resistant to drought. Herbivore-induced emissions, however, exhibited
 threshold-like behavior; saplings were unable to induce emissions above
 constitutive levels when pre-dawn water potentials were below the
 approximate zero-assimilation point. By comparing compositional shifts in
 emissions to needle terpene concentrations, we found evidence that drought
 effects on constitutive and herbivore-induced volatile flux and
 composition are primarily via constraints on the de
 novo fraction, suggesting that reduced photosynthesis during
 drought limits the carbon substrate available for de
 novo volatile synthesis. However, results from a
 subsequent 13CO2 pulse-chase labeling experiment then
 confirmed that both constitutive (&lt;3% labeled) and
 herbivore-induced (&lt;8% labeled) de novo emissions
 from ponderosa pine are synthesized predominantly from older carbon
 sources with little contribution from new photosynthates. Taken together,
 we provide evidence that in ponderosa pine, drought does not constrain
 herbivore-induced de novo emissions through substrate
 limitation via reduced photosynthesis, but rather, through more
 sophisticated molecular and/or biophysical mechanisms that manifest as
 saplings reach the zero-assimilation point. These results highlight the
 importance of considering drought severity when assessing impacts on the
 herbivore-induced response and suggest that drought-altered volatile
 metabolism constrains induced emissions once a physiological threshold is
 surpassed.
description: Please see methods section of the manuscript for information on
 how the data were collected, processed, and analyzed.
description: All data were organized in Microsoft Excel and processed in R
 with the packages cited in the manuscript.
DOI: 10.7291/d1bt34
title: Extensive introgression among strongylocentrotid sea urchins revealed by phylogenomics

description: Gametic isolation is thought to play an important role in the evolution of
 reproductive isolation in broadcast-spawning marine invertebrates.
 However, it’s unclear whether gametic isolation commonly develops early in
 the speciation process or only accumulates after other reproductive
 barriers are already in place. It is also unknown whether gametic
 isolation is an effective barrier to introgression following speciation.
 Here, we used whole-genome sequencing data and multiple complementary
 phylogenomic approaches to test whether the well-documented gametic
 incompatibilities among the strongylocentrotid sea urchins have limited
 introgression. We quantified phylogenetic discordance, inferred reticulate
 phylogenetic networks, and applied the Δ statistic using gene tree
 topologies reconstructed from multiple sequence alignments of
 protein-coding single-copy orthologs. In addition, we conducted ABBA-BABA
 tests on genome-wide single nucleotide variants and reconstructed a
 phylogeny of mitochondrial genomes. Our results revealed strong
 mito-nuclear discordance and considerable nonrandom gene tree discordance
 that cannot be explained by incomplete lineage sorting alone. Eight of the
 nine species examined demonstrated a history of introgression with at
 least one other species or ancestral lineage, indicating that
 introgression was common during the diversification of the
 strongylocentrotid urchins. There was strong support for introgression
 between four extant species pairs (Strongylocentrotus pallidus ↔ S.
 droebachiensis, S. intermedius ↔ S. pallidus, S. purpuratus ↔ S.
 fragilis, and Mesocentrotus franciscanus ↔ Pseudocentrotus depressus) and
 additional evidence for introgression on internal branches of the
 phylogeny. Our results suggest that the existing gametic incompatibilities
 among the strongylocentrotid urchin species have not been a complete
 barrier to hybridization and introgression following speciation. Their
 continued divergence in the face of widespread introgression indicates
 that other reproductive isolating barriers likely exist and may have been
 more critical in establishing reproductive isolation early in speciation.
description: The genomes of all strongylocentrotid sea urchin species were
 sequenced at high coverage depth with the Illumina HiSeq 2500. The raw
 sequencing reads were deposited in the NCBI Sequence Read Archive under
 BioProject PRJNA391452.
description: This directory contains all of the code and data used in Glasenapp and
 Pogson (2023). The scripts/ directory contains the bash, python, and R
 scripts used to generate the results. The data/ directory contains the
 input and output data associated with the scripts. There are individual
 README files for each nested folder. The raw sequencing reads used to
 produce all results were deposited in the NCBI Sequence Read Archive under
 BioProject PRJNA391452. The hard-filtered genotype calls for all nine
 strongylocentrotid species are included in the file
 filtered_genotype_calls_pf.g.vcf.gz
DOI: 10.5061/dryad.j9kd51ch9
title: Repository for: Genetic footprints of a rapid and large-scale range expansion: The case of cyclic common vole in Spain

description: Te repository contains the neccesary genetic data (microsatellite allele
 frequencies and GenBank accesion numbers for cytb haplotypes) to be able
 to replicate the analyses performed in the manuscript.
description: All the methodological aspects are extensively described in the
 manuscript.
DOI: 10.5061/dryad.rxwdbrvdh
title: Life history traits of Potamopyrgus antipodarum in variable salinity and temperature

description: Organisms exposed to major environmental change face atypical and
 stressful conditions across multiple environmental variables, yet studies
 of phenotypically plastic responses historically focus on one
 environmental variable at a time. Evaluating multivariate plasticity of
 traits across different, simultaneously varying environmental variables
 provides new insights into the fate of populations amidst environmental
 changes. We aimed to investigate plasticity in multivariate environments
 by 1) examining the individual and joint effects of two environmental
 variables and 2) calculating genotype-by-environment interactions and
 genetic correlations of character states to investigate potential
 evolutionary constraints. We performed a lab controlled-environment
 experiment under a full factorial design of low and high temperatures and
 salinities with multiple maternal lineages of a parthenogenetic freshwater
 snail, Potamopyrgus antipodarum. Our results revealed that predictions of
 plastic trait responses among multivariate environments may be unexpected
 due to non-additive effects of environmental variables and varying
 magnitudes and orientations of genetic correlations among fitness-related
 traits. Considering multivariate environments provides deeper insight and
 advancement of understanding trait evolution by revealing trait patterns
 that would otherwise be missed in univariate studies.
DOI: 10.5061/dryad.jm63xsjg5
title: Asymmetric evolution of protein domains in the leucine-rich repeat receptor-like kinase (LRR-RLK) family of plant developmental coordinators

description: The coding sequences of developmental genes are expected to be conserved
 over deep time, with cis-regulatory change driving the modulation of gene
 function. In contrast, proteins with roles in defense are expected to
 evolve rapidly, in molecular arms races with pathogens. However, some gene
 families include both developmental and defense genes. In these families,
 do the tempo and mode of evolution differ between developmental and
 defense genes, despite shared ancestry and structure? The leucine-rich
 repeat receptor-like kinase (LRR-RLKs) protein family includes many
 members with roles in plant development and defense, thus providing an
 ideal system for answering this question. LRR-RLKs are receptors that
 traverse plasma membranes. LRR domains bind extracellular ligands, RLK
 domains initiate intracellular signaling cascades in response to ligand
 binding. In LRR-RLKs with roles in defense, LRR domains evolve faster than
 RLK domains. To determine whether this asymmetry extends to developmental
 LRR-RLKs, we assessed evolutionary rates and tested for selection acting
 on eleven clades of LRR-RLK proteins, using deeply sampled protein trees.
 To assess functional evolution, we performed heterologous complementation
 assays using Arabidopsis thaliana (arabidopsis) LRR-RLK mutants. We found
 that the LRR domains of developmental LRR-RLK proteins evolved faster than
 their cognate RLK domains. LRR-RLKs with roles in development and defense
 had strikingly similar patterns of molecular evolution. Heterologous
 transformation experiments revealed that the evolution of developmental
 LRR-RLKs likely involves multiple mechanisms, including changes to
 cis-regulation, coding sequence evolution, and escape from adaptive
 conflict. Our results indicate similar evolutionary pressures acting on
 developmental and defense signaling proteins, despite divergent organismal
 functions. In addition, deep understanding of the molecular evolution of
 developmental receptors can help guide targeted genome engineering in
 agriculture.
DOI: 10.6076/d1sw2s
title: Wirewalker data collected during the 2020 Southern California red tide

description: Harmful algal blooms (HABs) are globally increasing economic, health, and
 ecosystem threats. In spite of the relatively frequent occurrence of HABs,
 the mechanisms responsible for their initiation and exceptional abundance
 remain imperfectly understood. A 50-year-old hypothesis posits that dense
 dinoflagellate blooms derive from motility: swimming upward during the day
 to photosynthesize and downward at night to access the deep nutrient pool.
 This allows dinoflagellates to outgrow their nonmotile competitors. We
 tested this hypothesis using in situ data from an autonomous,
 ocean-wave-powered vertical profiling system. We showed that the
 dinoflagellate Lingulodinium polyedra’s vertical migration led to
 depletion of the deep nitrate pool during a 2020 red tide HAB event.
 Downward migration began at dusk, with the maximum migration depth
 determined by local nitrate concentrations. Losses of nitrate at depth
 were balanced by proportional increases in phytoplankton chlorophyll
 concentrations and suspended particle load, conclusively linking vertical
 migration to the access and assimilation of deep nitrate in the ocean
 environment. Vertical migration during the red tide created distinctly
 anomalous biogeochemical conditions compared to 70 years of climatological
 data, demonstrating the capacity of these events to temporarily reshape
 the coastal ocean’s ecosystem and biogeochemistry. Advances in the
 understanding of the physiological, behavioral, and metabolic dynamics of
 HAB-forming organisms from cutting-edge observational techniques will
 improve our ability to forecast HABs and mitigate their consequences in
 the future.
description: This dataset was acquired by a moored ocean-wave-powered
 Wirewalker (WW) profiler. The WW was equipped with a
 conductivity-temperature-depth (CTD) sensor (RBR Concerto), nitrate sensor
 (SUNA V2), Chl-a fluorescence and optical backscatter sensor (SBE
 ECOPuck), and irradiance sensor (SBE OCR-504). Over the three-week period
 from April 29, 2020 to May 21, 2020, The final gridded WW data had 1 m
 vertical resolution and ~15 min temporal resolution. Detailed data
 processing steps can be found in Zheng et al., <em>PNAS,
 </em>2023<em>.</em>
description: Matlab is suggested to open the data file.
DOI: 10.5517/ccdc.csd.cc2hwy9n
title: CCDC 2320762: Experimental Crystal Structure Determination

description: Related Article: Wenbo Zhu, Zilin He, Zhizhong Zhang|2024|Chem.Eng.Journal|493|152443|doi:10.1016/j.cej.2024.152443
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5061/dryad.7wm37pvz0
title: Mesopredator predation risk limits northern bobwhite nesting habitat

description: Predators can significantly limit the amount of available habitat for
 vulnerable prey. Encouraging spatial segregation of predators and prey
 through habitat management prescriptions may be a useful tool to increase
 productivity and abundances of prey species of conservation concern. We
 estimated the total area of low-risk nesting habitat by interacting
 predator habitat selection models with northern bobwhite (Colinus
 virginianus) nest-site selection models. We used trail cameras, transect
 sampling, spotlighting transects, and incidental tracking to survey and
 map occurrences of mesopredators at a site in western Oklahoma, USA. We
 created broad-scale resource selection function models for bobwhite
 nest-site and mesopredator habitat selection using generalized linear
 models to create maps of occurrence probability in ArcGIS. Bobwhite nests
 were more likely to be depredated in areas of high selection by coyotes
 (Canis latrans) and striped skunk (Mephitis mephitis) compared to areas
 with low mesopredator selection. Approximately 392 ha of bobwhite nesting
 habitat (17%) had low probabilities of selection by both coyotes and
 striped skunks. Our results demonstrate the need for incorporating
 species’ interactions into estimations of available habitat. Based on the
 total area of highly selected cover by northern bobwhite, approximately
 29% of the study area would have been deemed suitable for nesting.
 However, only 5% of that area is predicted to have low predation risk.
description: Species occurrence data were collected at Packsaddle Wildlife
 Mangement Area in western Oklahoma using a variety of survey methods:
 scent stations, camera traps, transects for sign, and spotlighting
 surveys. Cover type proportions were extracted on ArcGIS at multiple
 spatial scales, labeled as the radius of buffers in kilometers.
DOI: 10.5517/ccdc.csd.cc2hwybp
title: CCDC 2320763: Experimental Crystal Structure Determination

description: Related Article: Wenbo Zhu, Zilin He, Zhizhong Zhang|2024|Chem.Eng.Journal|493|152443|doi:10.1016/j.cej.2024.152443
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2j9d08
title: CCDC 2332719: Experimental Crystal Structure Determination

description: Related Article: Jonathan Pfeiffer, Clemens Trost, Frank Tambornino|2024|J.Mol.Struct.|1308|138079|doi:10.1016/j.molstruc.2024.138079
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2j9d5f
title: CCDC 2332724: Experimental Crystal Structure Determination

description: Related Article: Jonathan Pfeiffer, Clemens Trost, Frank Tambornino|2024|J.Mol.Struct.|1308|138079|doi:10.1016/j.molstruc.2024.138079
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2j9gz9
title: CCDC 2332811: Experimental Crystal Structure Determination

description: Related Article: Jonathan Pfeiffer, Clemens Trost, Frank Tambornino|2024|J.Mol.Struct.|1308|138079|doi:10.1016/j.molstruc.2024.138079
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2j9cw3
title: CCDC 2332715: Experimental Crystal Structure Determination

description: Related Article: Jonathan Pfeiffer, Clemens Trost, Frank Tambornino|2024|J.Mol.Struct.|1308|138079|doi:10.1016/j.molstruc.2024.138079
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2j9h0c
title: CCDC 2332812: Experimental Crystal Structure Determination

description: Related Article: Jonathan Pfeiffer, Clemens Trost, Frank Tambornino|2024|J.Mol.Struct.|1308|138079|doi:10.1016/j.molstruc.2024.138079
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2j9cx4
title: CCDC 2332716: Experimental Crystal Structure Determination

description: Related Article: Jonathan Pfeiffer, Clemens Trost, Frank Tambornino|2024|J.Mol.Struct.|1308|138079|doi:10.1016/j.molstruc.2024.138079
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2j9cy5
title: CCDC 2332717: Experimental Crystal Structure Determination

description: Related Article: Jonathan Pfeiffer, Clemens Trost, Frank Tambornino|2024|J.Mol.Struct.|1308|138079|doi:10.1016/j.molstruc.2024.138079
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.16081129
title: MAPPING THE PRENATAL GROWTH OF THE MANDIBLE

description: This repository contains all geometrical data and metadata belonging to the paper MAPPING THE PRENATAL GROWTH OF THE MANDIBLE by the MAGIC Amsterdam research consortium. NaN values are used throughout when values were unknown or unavailable. The following contents are uploaded:

fetal_coordinates.csv | 14 x 126 matrix containing the 3-dimensional coordinates of the annotated landmarks of the 42 samples, where the rows are landmarks and the columns are x-, y-, and z-coordinates of the 42 samples formatted [x1, y1, z1, x2, y2, z2, ..., x42, y42, z42]. The order of the landmarks is:1 right coronoid2 right condyle, buccal point3 right condyle, cranial point4 right condyle, lingual point5 right condyle, posterior point6 right gonion7 right menton8 left coronoid9 left condyle, buccal point10 left condyle, cranial point11 left condyle, lingual point12 left condyle, posterior point13 left gonion14 left menton

fetal_measurements.csv | 42 x 11 matrix where rows are samples and columns are measurements. The order of the measurements is:1 body length, right2 body length, left3 ramus height, right4 ramus height, left5 gonial angle, right6 gonial angle, left7 bigonial width8 bicondylar width9 body length, left and right average10 ramus height, left and right average11 gonial angle, left and right average

fetal_metadata.csv | This matrix contains the age in days (first column) and biological sex (second column, 1 = male and 2 = female) for all samples (rows).