cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.b5mkkwhdv
title: Arthropod OTUs in fruit bodies of wood decay fungi

description: Biological communities within living organisms are structured by their
 host’s traits. How host traits affect biodiversity and community
 composition is poorly explored for some associations, such as arthropods
 within fungal fruit bodies. Using DNA metabarcoding, we revealed the
 arthropod communities in living fruit bodies of eleven wood-decay fungi
 from boreal forests and investigated how they were affected by different
 fungal traits. Arthropod diversity was higher in fruit bodies with a
 larger surface area-to-volume ratio, suggesting that colonisation is
 crucial to maintain arthropod populations. Diversity was not higher in
 long-lived fruit bodies, most likely because these fungi invest in
 physical or chemical defences against arthropods. Arthropod community
 composition was structured by all measured host traits, namely fruit body
 size, thickness, surface area, morphology and toughness. Notably, we
 identified a community gradient where soft and short-lived fruit bodies
 harboured more true flies, while tougher and long-lived fruit bodies had
 more oribatid mites and beetles, which might reflect different development
 times of the arthropods. Ultimately, close to 75% of the arthropods were
 specific to one or two fungal hosts. Besides revealing surprisingly
 diverse and host-specific arthropod communities within fungal fruit
 bodies, our study provided insight on how host traits structure
 communities.
DOI: 10.5061/dryad.k6djh9w74
title: Data from: High heritability of telomere length and low heritability of telomere shortening in wild birds

description: Telomere length and telomere shortening predict survival in many
 organisms. This raises the question of the contribution of genetic and
 environmental effects to variation in these traits, which is still poorly
 known, particularly for telomere shortening. We used experimental
 (cross-fostering) and statistical (quantitative genetic ‘animal’ models)
 means to disentangle and estimate genetic and environmental contributions
 to telomere length variation in pedigreed free-living jackdaws (Corvus
 monedula). Telomere length was measured twice in nestlings, at ages 4
 (n=715) and 29 days (n=474), using TRF-analysis, adapted to exclude
 interstitial telomeric sequences. Telomere length shortened significantly
 over the nestling period (10.4±0.3 bp/day) and was highly phenotypically
 (rP=0.95±0.01) and genetically (rG&gt;0.99±0.01) correlated within
 individuals. Additive genetic effects explained a major part of telomere
 length variation among individuals, with its heritability estimated at
 h2=0.74 on average. We note that TRF-based studies reported higher
 heritabilities than qPCR-based studies, and we discuss possible
 explanations. Parent-offspring regressions yielded similar heritability
 estimates for mothers and fathers when accounting for changes in paternal
 telomere length over life. Year effects explained a small but significant
 part of telomere length variation. Heritable variation for telomere
 shortening was low (h2=0.09±0.11). The difference in heritability between
 telomere length (high) and telomere shortening (low) agrees with
 evolutionary theory, in that telomere shortening has stronger fitness
 consequences in this population. Despite the high heritability of telomere
 length, its evolvability, which scales the additive genetic variance by
 mean telomere length, was on average 0.48%. Hence evolutionary change of
 telomere length due to selection is likely to be slow.
description: Both Excel files contain 2 sheets: 
 Data (data used in the analyses) ReadMe
 (explanation of variable names)
DOI: 10.5281/zenodo.15463948
title: 11111

description: HBDrug3D, the first benchmark dataset for accerating heterobifunctional drug linker design.
DOI: 10.5281/zenodo.15463949
title: HBDrug3D

description: HBDrug3D, the first benchmark dataset for accerating heterobifunctional drug linker design.
DOI: 10.5061/dryad.rfj6q57bm
title: Functional architecture of neural circuits for leg proprioception in Drosophila

description: To effectively control their bodies, animals rely on feedback from
 proprioceptive mechanosensory neurons. In the Drosophila leg,
 different proprioceptor subtypes monitor joint position, movement
 direction, and vibration. Here, we investigate how these diverse sensory
 signals are integrated by central proprioceptive circuits. We find
 that signals for leg joint position and directional movement
 converge in second-order neurons, revealing pathways for local
 feedback control of leg posture. Distinct populations of second-order
 neurons integrate tibia vibration signals across pairs of legs,
 suggesting a role in detecting external substrate vibration. In each
 pathway, the flow of sensory information is dynamically gated and
 sculpted by inhibition. Overall, our results reveal parallel pathways
 for processing of internal and external mechanosensory signals,
 which we propose mediate feedback control of leg movement and
 vibration sensing, respectively. The existence of a functional
 connectivity map also provides a resource for interpreting connectomic
 reconstruction of neural circuits for leg proprioception.
description: See manuscript
 (https://faculty.washington.edu/tuthill/docs/functionalconnectivity.pdf) for details.
description: Data description:
 This dataset includes
 calcium signals (quantified as DFF) of the downstream cell types labelled
 by LexA driver lines in the ventral nerve cord while optogenetically
 stimulating different sensory neurons subclasses in the
 <em>Drosophila</em> Femoral Chordotonal Organ (FeCO), which
 are club, claw, hook-f (short for hook-flexion) and hook-e (short for
 hook-extension). Lineage identity for each LexA lines can be found in
 Figure S2 in the paper. For each combination of sensory and central
 neurons, the following time series data are provided as *.mat files, which
 can be opened in Matlab: dff:  DF/F time series recorded
 from each fly. Imaging data was sampled at 8.9 frames per second
 (fps) dff_avg:
 mean DF/F from experimental flies (same as dff) image_vec: Imaging time. (same as
 dff) stim_ts:
 optogenetic stimulation intensity. The stimulus time series was sampled at
 100 samples per second. stim_vec: stimulation time (100
 Hz)  
 From Chen et al., 2021.
 https://doi.org/10.1016/j.cub.2021.09.035 For additional requests, contact
 tuthill@uw.edu.
DOI: 10.5061/dryad.9zw3r22fz
title: Cheating in mutualisms

description: Mutualisms such as those between flowering plants and their pollinators
 are common in nature. Yet, understanding their persistence in the face of
 cheaters and identifying the mechanisms behind their stunning diversity
 provide formidable challenges for evolutionary biologists. To shed light
 into these questions, we introduce an individual-based model of two
 coevolving species in which individuals of one species use a Boolean
 circuit to discriminate between cooperators and cheaters in the other
 species. This conveys the idea that interactions are often mediated by
 complex biological processes rather than simple trait matching, as often
 assumed in models of coevolution. Our results show that cheating promotes
 diversification and complex discrimination mechanisms at the cost of a
 higher risk for mutualism to collapse. This result is mediated by an
 inverse relationship between mutational robustness and organismal
 complexity.
DOI: 10.5061/dryad.qrfj6q5gx
title: Data from: Evolution of sociability by artificial selection

description: There has been extensive research on the ecology and evolution of social
 life in animals that live in groups. Less attention, however, has been
 devoted to apparently solitary species even though recent research
 indicates that they also possess complex social behaviors. To address this
 knowledge gap, we artificially selected on sociability, defined as the
 tendency to engage in non-aggressive activities with others, in fruit
 flies. Our goal was to quantify the factors that determine the level of
 sociability and the traits correlated with this feature. After 25
 generations of selection, the high sociability lineages showed sociability
 scores about 50% higher than did the low sociability lineages. Experiments
 using the evolved lineages indicated that there were no differences in
 mating success between flies from the low and high lineages. Both males
 and females from the low lineages, however, were more aggressive than
 males and females from the high lineages. Finally, the evolved lineages
 maintained their sociability scores after ten generations of relaxed
 selection, suggesting no costs to maintaining low and high sociability, at
 least under our settings. Sociability is a complex trait, which we
 currently assess through genomic work on the evolved lineages.
description: Please see attached README file for information about the data
 sets. Missing values indicated by "N/A" in
 those cells. See README for experiment-specific notes on missing
 values.
DOI: 10.5061/dryad.k0p2ngf91
title: Pasagshak River Sockeye Salmon (Oncorhynchus nerka) Escapement Monitoring 2019–2021

description: Since 2011, sockeye salmon (Oncorhynchus nerka) escapement through the
 Pasagshak River into Lake Rose Teed on the Kodiak Island road system has
 been estimated with a weir. A continuation of funding from the Alaska
 Sustainable Salmon Fund (AKSSF, Project #52009) allowed the Alaska
 Department of Fish and Game (ADF&G), Division of Commercial
 Fisheries to operate a PVC floating weir near the mouth of Lake Rose Teed
 during the 2019 through 2021 seasons. This data set includes the number
 and species of fish counted through the weir, and the age, sex, and length
 (ASL) information gathered from sockeye salmon captured and sampled at the
 weir.
description: Please refer to ReadMe file.
DOI: 10.5061/dryad.x95x69pk1
title: Genomic population reveals potential micro-refuge and riverine barriers in southern South American grasslands: An example in nightshade: VCF file (16,128 SNPs)

description: Aim: Pleistocene climate oscillations influenced the species distribution
 and genetic diversity in South American grasslands. Paleoclimate changes
 promoted expansion and contraction cycles that could lead to fragmentation
 and isolation of evolutionary lineages in refuges. Moreover, sea-level
 oscillations led to defrosting in some areas, affecting the river dynamics
 and influencing South American species' evolutionary history. This
 study aimed to infer which evolutionary processes most influenced the
 lineages differentiation in South American nightshade Petunia inhabiting
 subtropical grasslands in a phylogeographical context. Location: Pampa and
 Chaco. Taxon: The widely distributed herb Petunia axillaris subsp. parodii
 (Solanaceae) Methods: We obtained a high-density genome coverage
 throughout Petunia axillaris subsp . parodii geographic distribution. We
 estimated the genetic diversity and structure to evaluate population
 differentiation and applied a model-based demographic analysis to
 investigate the scenarios that could have influenced the species
 evolutionary history. We evaluated the association between neutral and
 outlier polymorphisms with environmental variables to distinguish the
 influence of the geographic distance and environmental differences between
 populations. Results: The results revealed three evolutionary lineages in
 P. axillaris subsp . parodii. The origin and differentiation of these
 lineages were related to the Pleistocene refuges and rivers acting as
 barriers to the gene flow. We also identified 496 outlier loci related to
 adaptation to environmental conditions. Main conclusion: The Pleistocene
 climate changes drove lineage diversification isolated in micro-refugia.
 Rivers and changes in their courses may have also acted on the population
 divergence, serving as barriers to gene flow or even as corridors for
 species range expansion. These findings contribute to the knowledge of the
 evolutionary processes that influenced the lineage diversification of
 South American subtropical grassland species.
description: This VCF file contains the 16,128 identified polymorphic SNPs
 throughout the <em>P. axillaris</em> reference genome, with no
 missing data and 100% of the reads mapped, as reported at Giudicelli et
 al. (2021).
DOI: 10.5061/dryad.4j0zpc8cb
title: A holocenic and dynamic hybrid zone between two cactophilic Drosophila species in a coastal lowland plain of the Brazilian Atlantic Forest

description: Hybridization and introgression are processes that contribute to shaping
 biological diversity. The factors promoting the formation of these
 processes are multiples but poorly explored in a biogeographical and
 ecological context. In the southeast coastal plain of the Brazilian
 Atlantic Forest, a hybrid zone was described between two closely related
 cactophilic species, Drosophila antonietae and D. serido. Here, we
 revisited and analyzed specimens from this hybrid zone to evaluate its
 temporal and spatial dynamic. We examined allopatric and sympatric
 populations of the flies using independent sources of data such as
 mitochondrial and nuclear sequences, microsatellite loci, morphometrics of
 wings and male genitalia, and climatic niche models. We also verified the
 emergence of the flies from necrotic tissues of collected cacti to verify
 the role of host association for the population dynamics. Our results
 support the existence of a hybrid zone due to secondary contact and
 limited to the localities where the two species are currently in contact.
 Furthermore, we detected asymmetric bidirectional introgression and the
 maintenance of the species integrity, ecological association, and
 morphological characters, suggesting selection and limited introgression.
 Considering our paleomodels, probably this hybrid zone is recent and the
 contact occurred during the Holocene to the present-day, favored by range
 expansion of their populations due to expansion of open and dry areas in
 eastern South America during palaeoclimatic and geomorphological events.
DOI: 10.5061/dryad.ns1rn8ptw
title: Genetic diversity and the origins of parthenogenesis in the teiid lizard Aspidoscelis laredoensis

description: Unisexual vertebrates typically form through hybridization events between
 sexual species in which reproductive mode transitions occur in the hybrid
 offspring. This evolutionary history is thought to have important
 consequences for the ecology of unisexual lineages and their interactions
 with congeners in natural communities. However, these consequences have
 proven challenging to study owing to uncertainty about patterns of
 population genetic diversity in unisexual lineages. Of particular interest
 is resolving the contribution of historical hybridization events vs.
 postformational mutation to patterns of genetic diversity in nature. Here
 we use restriction site associated DNA genotyping to evaluate genetic
 diversity and demographic history in Aspidoscelis laredoensis, a
 diploid unisexual lizard species from the vicinity of the Rio Grande River
 in southern Texas and northern Mexico. The sexual progenitor species from
 which one or more lineages are derived also occur in the Rio Grande Valley
 region, although patterns of distribution across individual sites are
 quite variable. Results from population genetic and phylogenetic analyses
 resolved the major axes of genetic variation in this species and highlight
 how these match predictions based on historical patterns of hybridization.
 We also found discordance between results of demographic modelling using
 different statistical approaches with the genomic data. We discuss these
 insights within the context of the ecological and evolutionary mechanisms
 that generate and maintain lineage diversity in unisexual species. As one
 of the most dynamic, intriguing, and geographically well investigated
 groups of whiptail lizards, these species hold substantial promise for
 future studies on the constraints of diversification in unisexual
 vertebrates.
description: This data was collected using a double digest restriction site
 associated DNA genotyping protocol and an Illumina NovaSeq
 sequencing platform. It was processed using the ipyrad assembly
 software.
description: The ReadMe.txt file contains a description of the datasets and
 scripts. The data and analyses performed are fully described in the
 associated manuscript.
DOI: 10.5061/dryad.0k6djhb1f
title: A non-parametric model-free analysis of actigraphic recordings of acute insomnia patients

description: Both parametric and non-parametric approaches to time series analysis have
 advantages and disadvantages. Parametric methods, although powerful and
 widely used, can yield inconsistent results due to the oversimplification
 of the observed phenomena, they require the setting of arbitrary constants
 for their creation and refinement, and, although these constants relate to
 assumptions about the observed systems, it can lead to erroneous results
 when treating a very complex problem with a sizable list of unknowns.
 Their non-parametric counterparts, instead, are more widely applicable but
 present a higher detrimental sensitivity to noise and low density in the
 data. For the case of approximately periodic phenomena, such as human
 actigraphic time series, parametric methods are widely used and concepts
 such as acrophase are staple in chronobiology; in this work we present a
 non-parametric method of analysis of actigraphic time series from
 insomniac patients and healthy age-matched controls, the method is fully
 data-driven, reproduces previous results in the context of sleep-onset
 delay and, crucially, extends the concept of acrophase not only to
 circadian but also for ultradian spectral components.
description: This is the set of code in matlab used to calculate fourier
 phases and amplitudes, probability distribution of motion, and to generate
 the corresponding figures in pdf format
description: a) Data files should exist in the same folder as code, otherwise,
 specifiy/modify main code b) Import all data files in
 matlab to save per-condition MAT files with obtained information
DOI: 10.5061/dryad.q573n5tjq
title: Dental measurement and diet data for mammals

description: Because teeth are the most easily preserved part of the vertebrate
 skeleton and are particularly morphologically variable in mammals, studies
 of fossil mammals rely heavily on dental morphology. Dental morphology is
 used both for systematics and phylogeny as well as for inferences about
 paleoecology, diet in particular. We analyze the influence of evolutionary
 history on our ability to reconstruct diet from dental morphology in the
 mammalian order Carnivora, and we find that much of our understanding of
 diet in carnivorans is dependent on the phylogenetic constraints on diet
 in this clade. Substantial error in estimating diet from dental morphology
 is present regardless of the morphological data used to make the
 inference, although more extensive morphological datasets are more
 accurate in predicting diet than more limited character sets.
 Unfortunately, including phylogeny in making dietary inferences actually
 decreases the accuracy of these predictions, showing that dietary
 predictions from morphology are substantially dependent on the
 evolutionary constraints on carnivore diet and tooth shape. The
 “evolutionary ratchet” that drives lineages of carnivorans to evolve
 greater degrees of hypercarnivory through time actually plays a role in
 allowing dietary inference from tooth shape, but consequently requires
 caution in interpreting dietary inference from the teeth fossil
 carnivores. These difficulties are another reminder of the differences in
 evolutionary tempo and mode between morphology and ecology.
description: Dental dimensions measured using digital calipers from specimens
 in the UC Museum of Vertebrate Zoology, with taxonomy corrected to MSW3
 for consistency with phylogenetic data. Specimen-level data includes 2
 specimens of each species where available; species-level data is simply
 one of the specimens with the most complete set of measurements or
 randomly chosen if both were equally complete. Diet data collected from
 primary literature as described in paper.
description: Missing values in measurement data represent specimens for which
 the dimension could not be measured, either because the image we took of
 it was not of adequate quality or because that part of the specimen was
 missing or damaged. See ReadMe file for additional information.
DOI: 10.5061/dryad.905qfttm9
title: Long-term litter removal rather than litter addition enhances ecosystem carbon sequestration in a temperate steppe

description: 1. Global change can greatly affect plant productivity and
 subsequently litter input to soil, with potential impacts on soil carbon
 (C) fluxes. However, the effects of litter layer in mediating C cycling
 and budget at an ecosystem scale is still not clear. 
 2. As part of a long-term litter fall manipulation
 experiment in a temperate steppe on the Mongolian
 Plateau, this study was conducted to explore effects of litter
 removal and addition on ecosystem C budget and the associated mechanisms.
 3. Overall, litter removal
 enhanced photosynthetic active radiation (PAR) at soil
 surface by 31.0%, but litter addition reduced it by 26.5%. Litter
 removal decreased soil inorganic nitrogen (SIN) content at the depth of
 0-10 cm by 13.6%, but litter addition enhanced it by 14.1%. Litter removal
 increased legume abundance by 131.1%, whereas litter addition enhanced
 grass abundance by 30.7% but decreased forb abundance by
 33.1%. Litter removal increased gross ecosystem productivity
 (GEP) through enhancing PAR and legume abundance,
 whereas litter addition elevated GEP by changing plant community
 composition mediated by decreasing PAR and increasing SIN. Litter removal
 did not affect ecosystem respiration (ER), but litter addition stimulated
 ER by 14.9%. Therefore, while litter addition did not affect net ecosystem
 productivity (NEP), litter removal surprisingly enhanced NEP by 23.9% over
 the later 7 years. 4. Our findings highlight that more
 aboveground litter input derived from biomass production may not
 necessarily result in a larger ecosystem C sink in grasslands under global
 change scenarios in the future. On the contrary, proper litter removal may
 be an effective way to increase the ecosystem C sink in grassland
 management.