cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15139/s3/wmvrxl
title: Data Management and Sharing Plan for: Prediction Autism from Brain MRI in the First Year of Life: A Critical Step Towards Presymptomatic Intervention

description: The Data Management and Sharing Plan describes the scientific data to be generated and/or used in the research and outlines a strategy for managing and sharing project data.
description: Data Management and Sharing Plan
DOI: 10.5061/dryad.hdr7sqvdr
title: Draft genomes of two Atlantic bay scallop subspecies Argopecten irradians irradians and A. i. concentricus

description: The two subspecies of Atlantic bay scallop (Argopecten irradians), A. i.
 irradians and A. i. concentricus, are economically important aquacultural
 species in northern and southern China. Here, we performed the
 whole-genome sequencing, assembly, and gene annotation and produced draft
 genomes for both subspecies. In total, 253.17 and 272.97 gigabases (Gb) of
 raw reads were generated from Illumina Hiseq and PacBio platforms for A.
 i. irradians and A. i. concentricus, respectively. Draft genomes of 835.7
 Mb and 874.82 Mb were assembled for the two subspecies, accounting for
 83.9% and 89.79% of the estimated sizes of their corresponding genomes.
 The contig N50 was 78.54 kb and the scaffold N50 was 1.53 Mb for the A. i.
 irradians genome, and the contig and scaffold N50s were 63.73 kb and 1.25
 Mb, respectively, for the A. i. concentricus genome. Moreover, 26,777 and
 25,979 protein-coding genes were predicted for A. i. irradians and A. i.
 concentricus, respectively. These genomes lay foundation for future
 studies and provide guidances for scallop breeding.
DOI: 10.7280/d1295x
title: What explains vast differences in jumping power within a clade? diversity, ecology, and evolution of anuran jumping power

description: 1. Anuran (frog and toad) jumping power varies greatly across
 species, yet muscle power does not. Given that the jumping power of some
 species is up to five times higher than typical muscle power, power
 amplification by elastic elements is suggested to explain this
 discrepancy. However, the ecological reasons for this variation in jumping
 power are unclear. One hypothesis is that small jumpers are limited by the
 time available to accelerate their body during take-off, leading to small
 species needing greater power production than larger species to achieve
 similar jumping performance. Another (non-mutually exclusive) hypothesis
 is that the microhabitat species inhabit may drive variation through
 trade-offs with performance in microhabitat-specific, non-jumping
 behaviors.  2. We compared jumping power across 68
 anuran species that were diverse in evolutionary relationships,
 microhabitat use, and body mass. We used phylogenetic comparative methods
 to compare the role of microhabitat and body mass in explaining variation
 in jumping power across species.  3. We found the
 strongest support for a model that included two factors and their
 interaction. First, as body mass increased, jumping power decreased.
 Second, species that burrowed showed lower jumping power than species that
 did not burrow. Third, the interaction between body mass and burrowing
 behavior showed that jumping power declines more rapidly with body mass in
 burrowing species than non-burrowing species.  4. The
 effect of body mass suggests that interspecific variation in jumping power
 might be partly explained by scaling relationships. Anurans with small
 body mass may be able to achieve similar locomotor performance (e.g.
 takeoff velocity) as those with larger body mass, by more effectively
 amplifying muscle power. Additionally, the effect of burrowing behavior
 suggests that species that use hindlimbs to burrow may experience a
 reduction in their ability to generate jumping power. This may indicate a
 functional trade-off between jumping and burrowing performance.
description: Frogs jumps were recorded with a high-speed video camera at 500
 frames per second. Each individual's video with their best effort was
 digitized with ImageJ. We digitized from the beginning of movement until
 three frames post take-off. We took the derivate of the displacement
 profile to get velocity and the derivate of the velocity profile to get
 acceleration. Body-mass-specific power was calculated by multiplying the
 velocity profile by the acceleration profile. Muscle-mass-specific power
 was calculated by dividing the body-mass-specific power by the muscle-mass
 to body-mass ratio.
DOI: 10.5061/dryad.kh189322k
title: Phylogenetic signal and evolutionary correlates of urban tolerance in a widespread neotropical lizard clade

description: Urbanization is intensifying worldwide, and while some species tolerate
 and even exploit urban environments, many others are excluded entirely
 from this new habitat. Understanding the factors that underlie tolerance
 of urbanization is thus of rapidly growing importance. Here we examine
 urban tolerance across a diverse group of lizards: Caribbean members of
 the neotropical genus Anolis. Our analyses reveal that urban
 tolerance has strong phylogenetic signal, suggesting that closely related
 species tend to respond similarly to urban environments. We propose that
 this characteristic of urban tolerance in anoles may be used to forecast
 the possible responses of species to increasing urbanization. In addition,
 we identified several key ecological and morphological traits that tend to
 be associated with tolerance in Anolis. Specifically, species experiencing
 hot and dry conditions in their natural environment and those that
 maintain higher body temperatures tend to have greater tolerance of urban
 habitats. We also found that tolerance of urbanization is positively
 associated with toepad lamella number, and negatively associated with
 ventral scale density and relative hindlimb length. The
 identification of factors that predispose a species to be more or less
 urban tolerant can provide a starting point for conservation and
 sustainable development in our increasingly urbanized world.
description: See supplementary materials of the associated manuscript for
 detailed description of data collection. 
description: Please see supplementary materials of the associated manuscript
 for detailed data collection information and for sources of trait data
 used in PGLS analyses. Edited tree is derived
 from: Gamble, Tony; Geneva, Anthony J.; Glor, Richard E.; Zarkower, David
 (2014), Data from: Anolis sex chromosomes are derived from a single
 ancestral pair, v2, Dryad, Dataset, https://doi.org/10.5061/dryad.dp848
DOI: 10.5281/zenodo.17657022
title: Inputs and outputs for: Direct Spectroscopic Evidence of an Atom-Transfer Mechanism during Copper Electrodeposition on Gold

description: This compressed file contains the inputs/outputs for the spectra calculated in OCEAN v.3.0 for the paper: "Direct Spectroscopic Evidence of an Atom-Transfer Mechanism during Copper Electrodeposition on Gold".
DOI: 10.5281/zenodo.17657023
title: Inputs and outputs for: Direct Spectroscopic Evidence of an Atom-Transfer Mechanism during Copper Electrodeposition on Gold

description: This compressed file contains the inputs/outputs for the spectra calculated in OCEAN v.3.0 for the paper: "Direct Spectroscopic Evidence of an Atom-Transfer Mechanism during Copper Electrodeposition on Gold".
DOI: 10.5061/dryad.g79cnp5m8
title: Can behaviour impede evolution? persistence of singing effort after morphological song loss in crickets

description: Evolutionary loss of sexual signals is widespread. Examining the
 consequences for behaviours associated with such signals can provide
 insight into factors promoting or inhibiting trait loss. We tested whether
 a behavioural component of a sexual trait, male calling effort, has been
 evolutionary reduced in silent populations of Hawaiian field crickets
 (Teleogryllus oceanicus). Cricket song requires energetically costly wing
 movements, but ‘flatwing’ males have feminised wings that preclude song
 and protect against a lethal, eavesdropping parasitoid. Flatwing males
 express wing movement patterns associated with singing but, in contrast to
 normal-wing males, sustained periods of wing movement cannot confer sexual
 selection benefits and should be subject to strong negative selection. We
 developed an automated technique to quantify how long males spend
 expressing wing movements associated with song. We compared calling effort
 among populations of Hawaiian crickets with differing proportions of
 silent males, and between male morphs. Contrary to expectation, silent
 populations invested as much in calling effort as non-silent populations.
 Additionally, flatwing and normal-wing males did not differ in calling
 effort. The lack of evolved behavioural adjustment following morphological
 change in silent Hawaiian crickets illustrates how behaviour might
 sometimes impede, rather than facilitate, evolution.
description: Sining effort data was produced by automatic video tracking of
 adult male crickets with reflectors on their wings. The csv files were
 produced by MATLAB using custom scripts. Two files are provided, clearly
 labelled: one in which singing bouts are defined by 10-second intervals,
 the other by 5-second intervals. The variable canSing refers to whether
 each individual was able to sing, and 'pl' refers to pronotum
 length in mm.
DOI: 10.5061/dryad.xpnvx0kbs
title: Conservation status assessment of banana crop wild relatives using species distribution modelling

description: Aim: Crop wild relatives (CWR) are an essential source of genetic material
 for the improvement of certain traits in related crop species. Despite
 their importance, increasing public, scientific and political support,
 large gaps exist in the amount of genetic material collected and conserved
 of many CWR. Here, we construct a dataset on the distribution of wild
 banana species (Musa spp.) and assess their risk and conservation status.
 We deal with the questions (1) what areas are potentially suitable for
 wild banana species (2) how much of the wild banana diversity is currently
 at risk or insufficiently conserved ex- and in-situ. Location: Native
 distribution area of wild banana species, ranging from the northeastern
 states of India to northeastern Australia. Methods: We assessed the
 potential environmental range of wild species using a species distribution
 modelling approach with MaxEnt. Extinction risk was evaluated following
 IUCN criterion B and the ex- and in-situ conservation status was assessed
 using an indicator for biodiversity and sustainable development targets.
 Results: We found that 11 out of 59 assessed species can be considered as
 vulnerable and nine as endangered. Highest species richness was found
 along the border of south China and northern Vietnam, in the northeastern
 states of India and on the Malayan peninsula. Our distribution modelling
 approach indicates that the northern Indo-Burmese region has the highest
 environmental suitability for most wild banana species and that lowland
 rainforests in general are highly suitable for bananas. Assessment of in-
 and ex-situ conservation status indicates that 56 out of 59 assessed
 species are currently insufficiently conserved ex-situ and that 49 are of
 high priority for further conservation. Additional in-situ conservation is
 of high priority for six species and of medium priority for 40 species.
 Main Conclusions: To date, little of the banana CWR are sufficiently
 conserved both in- and ex-situ.
DOI: 10.5061/dryad.8gtht76kc
title: Data from: Distinct epileptiform abnormalities are associated with clinical seizures in Alzheimer’s disease

description: Objective: Examine the relationship between scalp EEG biomarkers of
 hyperexcitability in Alzheimer’s disease (AD) and determine how these
 electrical biomarkers relate to the clinical expression of seizures in AD.
 Methods: In this cross-sectional study, we performed 24-hour ambulatory
 scalp EEGs on 43 cognitively normal elderly healthy controls (HC), 41
 early-stage AD participants with no history or risk factors for epilepsy
 (AD-NoEp), and 15 early-stage AD participants with late-onset epilepsy
 related to AD (AD-Ep). Two epileptologists, blinded to diagnosis, visually
 reviewed all EEGs and annotated all potential epileptiform abnormalities.
 A panel of 9 epileptologists, blinded to diagnosis, was then surveyed to
 generate a consensus interpretation of epileptiform abnormalities in each
 EEG. Results: Epileptiform abnormalities were seen in 53% of AD-Ep, 22% of
 AD-NoEp, and 4.7% of HC participants. Specific features of epileptiform
 discharges, including high frequency, robust morphology, right temporal
 location, and occurrence during wakefulness and REM, were associated with
 clinical seizures in AD. Multiple electrical biomarkers concordantly
 demonstrated a pattern of left temporal lobe hyperexcitability in early
 stages of AD, whereas clinical seizures in AD were often associated with
 bi-temporal hyperexcitability. Frequent small sharp spikes were
 specifically associated with epileptiform EEGs and thus identified as a
 potential biomarker of hyperexcitability in AD. Conclusion: Epileptiform
 abnormalities are common in AD, but not all equivalent. Specific features
 of epileptiform discharges are associated with clinical seizures in AD.
 Given the difficulty recognizing clinical seizures in AD, these EEG
 features could provide guidance on which AD patients are at high risk for
 clinical seizures.
description: This file contains Supplementary Data for the manuscript
 "Distinct epileptiform abnormalities are associated with clinical
 seizures in Alzheimer's disease."    Included
 are: - Figure e-1:   Recruitment flow chart for this
 study - Table e-1:  Comparison of epileptiform
 discharge morphological features - Table e-2:  Summary
 of Alzheimer's disease biomarkers for study participants
DOI: 10.6078/d1n10h
title: Numerical data of hydrodynamics and sediment transport for three reference scenarios: N1, P, and N2

description: The residual sediment transport in tidally energetic estuarine channels is
 investigated by means of idealized cross‐sectional modeling. The lateral
 bathymetric variation follows a Gaussian profile, assuming longitudinal
 uniformity. The total along‐channel residual sediment flux is decomposed
 into contributions from an advective flux and a tidal pumping flux. Two
 important mechanisms are found to modify the tidal covariance between
 sediment concentration and current velocity, thereby contributing to the
 tidal pumping of sediment. First, longitudinal and lateral straining of
 salinity leads to tidal asymmetries in stratification and thus sediment
 resuspension. Second, lateral circulations directly redistribute suspended
 sediments within the cross section, which are then differentially
 transported by the along‐channel tidal currents. A general relationship
 between the phasing of the lateral circulations and the resulting
 lateral‐advection‐driven tidal pumping is proposed. Reduced‐physics
 experiments with lateral sediment advection turned off provide the first
 evidence that lateral‐advection‐driven tidal pumping plays a leading role
 in sediment transport for tidally energetic estuaries with nonnegligible
 lateral depth gradients. Additionally, a temporal decomposition breaks
 down the cross‐sectionally averaged tidal pumping flux into individual
 contributions from different tidal phases (early tide, peak tide, late
 tide), providing a new perspective on tidal asymmetry in sediment
 resuspension and settling. The direction and strength of tidal pumping
 (both stratification‐driven and lateral‐advection‐driven) are shown to
 depend on lateral bathymetry, sediment grain size, and longitudinal
 buoyancy gradient forcing.
description: The three NetCDF files contain the numerical data generated by
 GETM simulations which can be used to reproduce certain key figures in the
 manuscript. Reference scenario N1 (seaward tidal pumping of fine sediment
 in wide channel): channel width = 20 km, d = 44 micron (variable name:
 iow_spm05 concentration of SPM); Reference scenario P (landward tidal
 pumping of fine sediment in medium channel): channel width = 1 km, d =
 50 micron (variable name: iow_spm06 concentration of SPM); Reference
 scenario N2 (seaward tidal pumping of coarse sediment in narrow channel):
 channel width = 0.2 km, d = 80 micron (variable name:
 iow_spm11 concentration of SPM).
DOI: 10.5061/dryad.c866t1g3q
title: Predators and dispersers: Context-dependent outcomes of the interactions between rodents and a megafaunal fruit plant

description: Many plant species bear fruits that suggest adaptation to seed dispersal
 by extinct megafauna. Present-day seed dispersal of these megafaunal
 plants is carried out by rodents, which can act as predators or
 dispersers; whether this interaction is primarily positive or negative can
 depend on the context. Here, we parameterized a stochastic model using
 data from the field and experimental arenas to estimate the effect of
 rodents on the recruitment of Myrcianthes
 coquimbensis -an Atacama Desert shrub with megafaunal fruits- and
 examine whether environmental conditions can alter the sign and strength
 of these rodent-plant interactions. We show that the outcome of
 these interactions is context-dependent: in wet conditions seed
 removal by rodents negatively impacts the recruitment probability
 of M. coquimbensis; in contrast, in dry conditions, the
 interaction with rodents increases recruitment success. In all cases, the
 strength of the effect of rodents on the recruitment success was
 determined mainly by their role as dispersers, which could be positive or
 negative. This study demonstrates that by caching seeds, rodents can be
 effective dispersers of a megafaunal fruit plant, but that the sign and
 magnitude of their effect on recruitment changes as a function of the
 environmental context in which the interaction occurs.
description: Seed processing by rodents was collected from experimental
 arenas. Seedling emergence was monitored in field
 conditions during 2015.
DOI: 10.5061/dryad.xksn02vbw
title: Data from: Comparative phylogeographic inference with genome-wide data from aggregated population-pairs

description: Comparing divergences across multiple sister population-pairs has been a
 focus in phylogeography since its inception. Initial approaches utilized
 organelle genetic data and involved qualitative comparisons of
 phylogenetic patterns to evaluate hypotheses of shared and variable
 evolutionary responses. This endeavor has progressed with coalescent
 model-based statistical techniques and advances in next-generation
 sequencing, yet there remains a need for methods that can exploit
 aggregated genomic-scale data within a unified analytical framework. To
 this end, we introduce the aggregate joint site frequency spectrum (ajSFS)
 by validating its use within a hierarchical Bayesian framework through
 several in silico experiments. Subsequently, we applied our method against
 two published restriction site associated DNA marker datasets consisting
 of eight local replicates of a lamprey species-pair and six co-distributed
 passerine taxon-pairs respectively, with the aim of inferring variability
 in co-divergence and co-migration histories. We found that the lamprey
 population-pairs exhibited temporal synchrony in both co-divergence and
 collective secondary contact times, yet an idiosyncratic pattern in
 secondary migration intensities. In contrast, the bird population-pairs
 displayed thoroughly asynchronous co-divergence histories. Our results
 demonstrate that the ajSFS can be exploited for complex and flexible
 co-demographic inference, opening up new possibilities for comparative
 phylogeography and population genomic studies.
description: Simulated datasets via Multi-DICE and fastsimcoal2
DOI: 10.5061/dryad.d7wm37pxr
title: Diurnal foraging ant–tree co-occurrence networks are similar between canopy and understorey in a Neotropical rain forest

description: Discussion of the vertical stratification of organisms in tropical forests
 has traditionally focused on species distribution. Most studies have shown
 that, due to differences in abiotic conditions and resource distribution,
 species can be distributed along the vertical gradient according to their
 eco-physiological needs. However, the network structure between distinct
 vertical strata remains little-explored. To fill this gap in knowledge, we
 used baits to sample ants in the canopy and understorey trees of a Mexican
 tropical rainforest to record the ant–tree co-occurrences. We examined the
 ant–tree co-occurrences in the canopy and understorey using complementary
 network metrics (i.e., specialization, interaction diversity, modularity,
 and nestedness). In addition, we evaluated co-occurrence patterns between
 ant species on trees, using C-score analysis. In general, we found no
 differences in the network structure, although the interaction diversity
 was greater in the understorey than in the canopy networks. We also
 observed that co-occurrence networks of each vertical stratum featured
 four ant species in the central core of highly co-occurring species, with
 three species unique to each stratum. Moreover, we found a similar trend
 towards ant species segregation in the both strata. These findings reveal
 a similar pattern of ant–ant co-occurrences in both vertical strata,
 probably due to the presence of arboreal nesting ants in the understorey.
 Overall, we showed that despite the marked differences in species
 composition and environmental conditions between understorey and canopy
 strata, ant–tree co-occurrences in these habitats could be governed by
 similar mechanisms, related to dominance and resource monopolization by
 ants.
description: This study was carried out at the <i>Estación de Biología
 Tropical Los Tuxtlas</i>, on the coast of the Gulf of Mexico in the
 state of Veracruz (18°34’ N, 95°04’ W; 200 – 350 m a.s.l.).  At each
 sampling site (n= 6) we chose the tallest canopy tree to serve as the
 central sampling point of each plot. This central canopy tree was the
 starting point for the delineation of six circular plots with a radius of
 30 meters. Once we defined the canopy trees of each plot, we chose a
 posteriori one understorey woody plant for each canopy tree, i.e., they
 were paired.