cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m37pvmd0z
title: Data for: Coevolution fails to maintain genetic variation in a host-parasite model with constant finite population size

description: Coevolutionary negative frequency-dependent selection has been
 hypothesized to maintain genetic variation in host and parasites.
   Despite the extensive literature pertaining to host-parasite
 coevolution, the dynamics of genetic variation has not been examined in a
 matching-alleles model (MAM) with a finite population size relative to the
 expectation under neutral genetic drift alone.  The dynamics of
 the MA coevolution in an infinite population, in fact, suggests that
 genetic variation in these coevolving populations behaves neutrally.
   By comparing host heterozygosity to the expectation in
 a single-species model of neutral genetic drift we find that while this is
 also largely true in finite populations two additional phenomena arise.
  First, reciprocal natural selection acting on stochastic
 perturbations in host and pathogen allele frequencies results in a slight
 increase or decrease in genetic variation depending on the parameter
 conditions. Second, following the fixation of an allele in the
 parasite, selection in the MAM becomes directional, which then rapidly
 erodes genetic variation in the host.  Hence, rather than
 maintain it, we find that, on average, matching-alleles coevolution
 depletes genetic variation.
description: Mathematica notebooks for model analysis and individual-based
 simulations run in C++.
DOI: 10.5281/zenodo.18396268
title: Android Binary XV Diffing Code and Data

description: This paper presents XvDiff, a high-precision and high-performance cross-version diffing tool for Android binaries that integrates structural code-feature similarity with LLM-based semantic reasoning. XvDiff accurately identifies function-level changes even under heavy obfuscation, substantially outperforming state-of-the-art diffing approaches. Leveraging the diff results produced by XvDiff, we construct XvCKG, a multi-version Android code knowledge graph that unifies both intrinsic version-specific information and cross-version differential information into a single structured representation. Built upon this knowledge graph, we further develop an automated analysis framework that employs agentic retrieval-augmented generation to perform cross-version reasoning, enabling the detection of functional changes and the evolution of security properties throughout app development.
DOI: 10.5061/dryad.bk3j9kd9c
title: An aerodynamic perspective on hurricane-induced selection on Anolis lizards

description: Studies have demonstrated that hurricanes can drive selection in
 Neotropical anoles. In a recent study it was shown that post-hurricane
 survivors showed increased toepad areas, and surprisingly, shorter femurs.
 One potential explanation for the reduction in femur length is that
 increased drag on individuals with longer femurs causes them to be blown
 off their perch. Consequently, lizards with shorter femora might survive
 better in hurricanes. To gain insight into the form-function relationships
 of drag-reduction in perched lizards exposed to high-velocity winds, we
 quantified drag forces on Anolis lizard models in realistic grasping
 positions using computational fluid dynamics. We showed that overall drag,
 as well as the relatively high drag at the hind limbs strongly increases
 with the distance of the pelvic region from the perch. As optimal postures
 to resist sustained arboreal pulling involve extended limbs, longer hind
 limbs increase the chance of having the limbs and pelvic region positioned
 outside the zone in which efficient shielding from the wind by the perch
 occurs. Our study underlines the complexity of performance trade-offs on
 the evolution of limb morphology in arboreal lizards, and emphasizes the
 importance of generally ignored functions such as aerodynamic drag
 reduction in arboreal ecosystems. 
description: Case (.cas) and corresponding Data (-2000.dat) files
 from all simulations reported in the Results section of the article (Ansys
 Fluent version 19.1; also accessible with Ansys CFD Post). The five
 positions and inflow angle (0 or 20 degrees) are explained in Fig. 1a and
 Table 1. The original .stl (triangular surface mesh)
 file from laser scanning of an <em>Anolis carolinensis</em>
 individual is provided as well. The .out file gives
 time-dependent drag forces (N) for one posture (posture 1) from a
 transient simulation with a time-step size of 0.2 ms that was ran for 1000
 time steps.
description: Case (.cas) and corresponding Data (-2000.dat) files from all
 simulations reported in the Results section of the article (Ansys Fluent
 version 19.1; also accessible with Ansys CFD Post).
DOI: 10.5061/dryad.h18931zjm
title: External morphology measurements of several species of the plethodontid genus Aneides

description: While sexual dimorphism has long received special attention from
 biologists, derived monomorphism, the condition in which both males and
 females express similar derived features, has been less well
 studied.  Historically, the appearance of “male-like” features in
 females has been explained by the genetic correlation between the
 sexes.  Recent work emphasizes the importance of studying the
 independent selective forces on both females and males to understand
 sexual dimorphism.  Sexual dimorphism and derived monomorphism in
 the genus Aneides are examined in light of predictions of social
 selection.  Aneides hardii shows the greatest degree of sexual
 dimorphism in snout-vent length and head width, with the other species of
 Aneides less sexually dimorphic. This reduced dimorphism, however, is not
 a return to an ancestral monomorphic state, but rather exemplifies derived
 monomorphism because females express traits that were limited in
 expression to males of ancestral species.  Instead of calling
 these “male-typical” traits in females, I suggest the term “derived
 monomorphic” traits, as these traits are typical in these females and
 “derived monomorphic” can apply to both sexes. Increased attention to
 studying the patterns and ecological significance of derived monomorphism
 will shed light on the underlying selective forces, including sexual
 selection, on both females and males. 
description: Preserved animals were measured with calipers and some animals
 were weighed. 
description: README file for Aneides morphological data.
 All morphological measurements are in millimeters and weight is
 in grams. SM123 column<br>     1 = adult
 male<br>     2 = adult female<br>     3 = juvenile<br>
     7 = unknown Mature column<br>     8 =
 mature<br>     7 = not mature Morphological
 abbreviations<br>     SG = snout-gular length<br>     HW =
 head -width<br>     SVL = snout-vent length<br>     Tail =
 tail length<br>     AG = axilla-groin length<br>     WT =
 weight<br>     RHL = right hind limb length (excluding
 pes)<br>     RFL = right fore limb length (excluding
 manus)<br>     RG = regenerating tail These files
 may include some outliers/typos that were later removed.
DOI: 10.7272/q6x63k6c
title: Developing and validating the psychosocial burden among people seeking abortion scale (PB-SAS)

description: While there is a large body of research demonstrating that having an
 abortion is not associated with adverse mental health outcomes, less
 research has examined which factors may contribute to elevated levels of
 mental health symptoms at the time of abortion seeking. This study aims to
 develop and validate a novel tool to measure dimensions of psychosocial
 burden experienced by people seeking abortion in the United States. To
 develop scale items, we reviewed the literature including existing
 measures of stress and anxiety and conducted interviews with experts in
 abortion care and with patients seeking abortion. Thirty-five items were
 administered to 784 people seeking abortion at four facilities located in
 three U.S. states. We used exploratory factor analysis (EFA) to reduce
 items and identify key domains of psychosocial burden. We assessed the
 predictive validity of the overall scale and each sub-scale, by assessing
 their associations with validated measures of perceived stress, anxiety,
 and depression using multivariable linear regression models. 
 Factor analyses revealed a 12-item factor solution measuring psychosocial
 burden seeking abortion, with four subdomains: structural challenges,
 pregnancy decision-making, lack of autonomy, and others’ reactions to the
 pregnancy. The alpha reliability coefficients were acceptable for the
 overall scale (α=0.83) and each subscale (ranging from α= 0.82-0.85). In
 adjusted analyses, the overall scale was significantly associated with
 stress, anxiety and depression, and each subscale was significantly
 associated with each mental health outcome. This new scale offers a
 practical tool for providers and researchers to empirically document the
 factors associated with people’s psychological well-being at the time of
 seeking an abortion. Findings suggest that the same restrictions that
 claim to protect people from mental health harm may be increasing people’s
 psychosocial burden and contributing to adverse psychological outcomes at
 the time of seeking abortion.
description: We recruited study participants from four abortion facilities
 located in three U.S. states. To be eligible, people had to be seeking an
 abortion at the time of recruitment, aged 15 years or older, and able to
 speak and read English or Spanish. Research staff introduced the study to
 patients while they were waiting for their appointment, handed interested
 patients a tablet device to complete and confirm their eligibility, and
 consented those eligible and interested to participate in the study.
 Participants self-administered an anonymous survey which they could choose
 to complete in either English or Spanish, with research staff available to
 assist as needed.
DOI: 10.82294/dvnu5m6dg
title: Datos consolidados de eje medular. Territorio: Todos los territorios. Eje medular: Agenciamiento. Sector: Cultura, Educación, Total. Año: 2025

description: Datos consolidados de las observaciones semiestructuradas sobre el eje medular de agenciamiento, realizadas en todos los territorios. Este dataset reúne los archivos correspondientes a los educadores artísticos del sector Educación y del sector Cultura, así como un archivo consolidado que integra la información de ambos sectores.
DOI: 10.5061/dryad.v41ns1rtn
title: Breaking a species barrier by enabling hybrid recombination

description: Hybrid sterility maintains reproductive isolation between species by
 preventing them from exchanging genetic material. Anti-recombination can
 contribute to hybrid sterility when different species’ chromosome
 sequences are too diverged to cross-over efficiently during hybrid
 meiosis, resulting in chromosome mis-segregation and aneuploidy. The
 genome sequences of the yeasts Saccharomyces
 cerevisiae and Saccharomyces paradoxus have
 diverged by about 12% and their hybrids are sexually sterile: nearly all
 of their gametes are aneuploid and inviable. Previous methods to increase
 hybrid yeast fertility have targetted the anti-recombination machinery,
 enhancing meiotic crossing over but also having counteracting detrimental
 effects on gamete viability due to increased mutagenesis and
 ectopic recombination. Therefore the role of anti-recombination has not
 been fully revealed, and it is often dismissed as a minor player in
 speciation. By repressing two
 genes, SGS1 and MSH2, specifically during
 meiosis, whilst maintaining their mitotic expression we were able to
 increase hybrid fertility 70-fold, to the level of non-hybrid crosses,
 confirming that anti-recombination is the principal cause of hybrid
 sterility. Breaking this species barrier allows us to generate, for the
 first time, viable euploid gametes containing recombinant hybrid genomes
 from these two highly diverged parent species. 
description: ReadMe.txt
 file explains each data set.
DOI: 10.5061/dryad.zcrjdfn93
title: Stability in subtropical forests: the role of tree-species diversity, stand structure, environmental and socio-economic conditions

description: Aim: Tree species diversity can increase the stability of ecosystem
 productivity by increasing mean productivity and/or reducing the standard
 deviation in productivity. However, stand structure, environmental and
 socio-economic conditions influence plant diversity and may strongly
 influence the relationships between diversity and stability in natural
 forest communities. The relative importance of these factors on community
 stability remains poorly understood in complex (species-rich) subtropical
 forests. Location: Subtropical area of southern China. Time period:
 1999-2014. Major taxa studied: Forest trees. Methods: We conducted
 bivariate analyses to examine the mechanisms (overyielding and species
 asynchrony) underlying the effects of diversity on stability. Multiple
 regression models were then used to determine the relative importance of
 tree species diversity, stand structure, socio-economic factors and
 environmental conditions on stability. Structural equation modeling was
 used to disentangle how these variables directly and/or indirectly affect
 forest stability. Results: Tree species richness exerted a positive effect
 on stability through overyielding and species asynchrony and this effect
 was stronger in mountainous forests than that in hilly forests. Species
 richness positively affected the mean productivity whereas species
 asynchrony negatively affected the variability in productivity, and hence
 increased forest stability. Structural diversity also had a positive
 effect while population density had a negative effect on stability.
 Precipitation variability and slope mainly indirectly influenced stability
 through their effects on tree species richness. Main conclusions: Overall,
 tree species diversity governed stability; however stand structure,
 socio-economic and environmental conditions also played an important role
 in shaping stability in these forests. Our work highlights the importance
 of regulating stand structure and socio-economic factors in forest
 management and biodiversity conservation, to maintain and enhance their
 stability of providing the ecosystem services in the face of unprecedented
 anthropogenic activities and global climate change.
DOI: 10.5061/dryad.ns1rn8pr7
title: Dataset: Plant-plant facilitation increases with reduced phylogenetic relatedness along an elevation gradient

description: Environmental conditions can modify the intensity and sign of ecological
 interactions. The stress gradient hypothesis (SGH) predicts that
 facilitation becomes more important than competition under stressful
 conditions. To properly test this hypothesis, it is necessary to account
 for all (not a subset of) interactions occurring in the communities and
 consider that species do not interact at random but following a specific
 pattern. We aim to assess elevational changes in facilitation, in terms of
 species richness, frequency and intensity of the interaction as a function
 of the evolutionary relatedness between nurses and their associated
 species. We sampled nurse and their facilitated plant species in two
 1000-2000 m. elevation gradients in Mediterranean Chile where low
 temperature imposes a mortality filter on seedlings. We first estimated
 the relative importance of facilitation as a mechanism adding new species
 to communities distributed along these gradients. We then tested whether
 the frequency and intensity of facilitation increases with elevation,
 taking into account the evolutionary relatedness of the nurse species and
 the facilitated species. We found that nurses increase the species
 richness of the community by up to 35%. Facilitative interactions are more
 frequent than competitive interactions (56% vs. 44%) and facilitation
 intensity increased with elevation for interactions involving distantly
 related lineages. Our results highlight the importance of including an
 evolutionary dimension in the study of facilitation to have a clearer
 picture of the mechanisms enabling species to coexist and survive under
 stressful conditions. This knowledge is especially relevant to conserve
 vulnerable and threatened communities facing new climate scenarios, such
 as those located in Mediterranean-type ecosystems.
DOI: 10.15468/dl.cavk6m
title: Occurrence Download

description: A dataset containing 14964 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Chile",
 "DatasetKey is Pl@ntNet automatically identified occurrences"
 ]
}

 The dataset includes 14964 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002649-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7291/d1m96k
title: Elkhorn Slough eelgrass restoration

description: The global decline of marine foundation species (kelp forests, mangroves,
 salt marshes, and seagrasses) has contributed to the degradation of the
 coastal zone and threatens the loss of critical ecosystem services and
 functions. Restoration of marine foundation species has had variable
 success, especially for seagrasses, where a majority of restoration
 efforts have failed. While most seagrass restorations track structural
 attributes over time, rarely do restorations assess the suite of
 ecological functions that may be affected by restoration. Here we report
 on the results of two small-scale experimental seagrass restoration
 efforts in a central California estuary where we transplanted 117 0.25 m2
 plots (2,340 shoots) of the seagrass species Zostera marina. We quantified
 restoration success relative to persistent reference beds, and in
 comparison to unrestored, unvegetated areas. Within three years, our
 restored plots expanded ~8500%, from a total initial area of 29 m2 to 2513
 m2. The restored beds rapidly began to resemble the reference beds in 1)
 seagrass structural attributes (canopy height, shoot density, biomass), 2)
 ecological functions (macrofaunal species richness and abundance,
 epifaunal species richness, nursery function), and 3) biogeochemical
 functions (modulation of water quality). We also developed a
 multifunctionality index to assess cumulative functional performance,
 which revealed restored plots are intermediate between reference and
 unvegetated habitats, illustrating how rapidly multiple functions
 recovered over a short time period. Our comprehensive study is one of few
 published studies to quantify how seagrass restoration can enhance both
 biological and biogeochemical functions. Our study serves as a model for
 quantifying ecosystem services associated with the restoration of a
 foundation species and demonstrates the potential for rapid functional
 recovery that can be achieved through targeted restoration of fast-growing
 foundation species under suitable conditions.
description: Each of the datafiles has a ReadMe tab that is associated with
 that particular dataset.
DOI: 10.5061/dryad.pc866t1ms
title: A phylogenomic perspective on the evolutionary history of the stonefly genus Suwallia (Plecoptera: Chloroperlidae) revealed by ultraconserved genomic elements

description: Evolutionary biologists have long sought to disentangle phylogenetic
 relationships among taxa spanning the tree of life, an increasingly
 important task as anthropogenic influences have caused, and are expected
 to continue to cause, population declines and species extinctions,
 particularly in insects. Advances in DNA sequencing techniques have
 increasingly facilitated the ability of researchers to apply genomic
 methods to phylogenetic analyses, even for non-model organisms which have
 historically lacked the genomic resources to do so. Phylogenetic
 relationships within the stonefly genus Suwallia (Insecta: Plecoptera:
 Chloroperlidae) are poorly understood, and have never been assessed using
 molecular data. We used DNA sequence data from genome-wide ultraconserved
 element loci to generate the first molecular phylogeny for the group and
 assess its monophyly. Our results reveal that the monospecific
 chloroperlid Neaviperla forcipata renders Suwallia paraphyletic, and we
 recommend a taxonomic revision for its inclusion in Suwallia. We also
 found that Palearctic and Nearctic Suwallia do not form reciprocally
 monophyletic clades, and that a biogeographic history including dispersal,
 vicariance, and founder event speciation via jump dispersal best explains
 the geographic distribution of this group. Moreover, some Suwallia species
 (e.g., S. amoenacolens, S. kerzhneri, S. marginata, S. pallidula, and S.
 starki) exhibit pronounced cryptic diversity that is worthy of further
 investigation. These findings provide a first glimpse into the
 evolutionary history of Suwallia, improve our understanding of stonefly
 diversity, and highlight areas where additional research is needed.
description: We extracted genomic DNA from museum specimens (see Fig. 1 and
 Table S1 for sampling information). We captured UCEs using baits that were
 developed for Hemipterans and Hymenopterans, and sequenced them using an
 Illumina HiSeq (150 bp paired end reads). Raw data were processed using
 the PHYLUCE pipeline, and we generated a 50% matrix of UCE loci. We
 reconstructed a lineage tree from a concatenated UCE data set, and then
 used two coalescent-based phylogenetic approaches to estimate species
 trees. We also conducted a biogeographic analysis to evaluate various
 biogeographic models for these stoneflies. 
description: All trees and nexus files from our lineage tree reconstruction,
 and two species tree reconstructions (ASTRAL-III and SVDQuartets) are
 included herein, as are raw data and R scripts for BioGeoBEARs
 analysis.
DOI: 10.5061/dryad.s7h44j15f
title: A putative origin of the insect chemosensory receptor superfamily in the last common eukaryotic ancestor

description: The insect chemosensory repertoires of Odorant Receptors (ORs) and
 Gustatory Receptors (GRs) together represent one of the largest families
 of ligand-gated ion channels. Previous analyses have identified homologous
 'Gustatory Receptor-Like (GRL)' proteins across Animalia, but
 the evolutionary origin of this novel class of ion channels is unknown. We
 describe a survey of unicellular eukaryotic genomes for GRLs, identifying
 several candidates in fungi, protists and algae that contain many
 structural features characteristic of animal GRLs. The existence of these
 proteins in unicellular eukaryotes, together with ab initio protein
 structure predictions, provide evidence for homology between GRLs and a
 family of uncharacterized plant proteins containing the DUF3537 domain.
 Together, our analyses suggest an origin of this protein superfamily in
 the last common eukaryotic ancestor.
description: Output files of trRosetta and RaptorX analyses of selected insect
 Odorant Receptors (ORs) and Gustatory Receptors (GRs), other animal
 GR-like (GRL) proteins, unicellular eukaryotic GRL candidates and plant
 DUF3537 proteins. For each query, the results of a Dali full PDB search
 with the top model are included within the corresponding
 subfolder. In the trRosetta datasets, the
 .npz files - which containing the predicted inter-residue geometries - can
 be opened with NumPy.
DOI: 10.15468/dl.jcdnad
title: Occurrence Download

description: A dataset containing 1733 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Colutea arborescens",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 1733 records from 190 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002650-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.