cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3n5tb2rjt
title: Florida Freshwater Fish Life History Data

description: This dataset contains life history data for 31 non-native freshwater
 fishes that have been successfully established in peninsular Florida, 33
 non-native freshwater fish species that have failed to establish in
 peninsular Florida as of the year 2021, and 61 native freshwater
 fish species. The dataset contains a total of 21 traits that span
 reproductive characteristics, size and shape, and habitat preferences and
 requirements.
description: Data were mined from the published literature, grey literature,
 and publicly available databases. We conducted multiple searches for each
 species using both common name and scientific name, both with and without
 “life history” included in the search bar. These searches were conducted
 using Google Scholar and the Web of Science. Primary literature was used
 whenever possible, but databases, including Fishbase, FishTraits (Frimpong
 & Angermeier, 2009), and gray literature were used to fill in any
 data gaps. Some traits were not available for some species, in which case
 congener data for similar species were used to fill in data gaps. Species
 lacking data that could not be determined using biologist expertise or
 congener data were removed from the lists and not included in analyses.
 Life history data for some species is more plentiful than others,
 therefore data quality is variable. 
description: There are no missing values, but new or higher quality traits
 data may be available for some species.
DOI: 10.5061/dryad.0cfxpnw3q
title: Urban runoff and stream channel incision interact to influence riparian soils and understory vegetation

description: Riparian soil processes and vegetation are sensitive to water
 availability. Urbanization can alter riparian water availability by
 modifying stream flows and stream channel morphology. In cities, runoff
 from impervious surfaces tends to increase stormflow magnitudes, causing
 stream channels to incise, or downcut. This change in channel morphology
 has been linked to lowered water tables and drier conditions in temperate
 urban riparian zones, leading to shifts in riparian nitrogen (N) cycling
 and vegetation communities. In Mediterranean climates with distinct wet
 and dry periods, there is an additional dynamic to consider: runoff from
 urban water use can cause streams to flow when they would otherwise be
 dry. This dry-season stream flow could create increased, rather than
 decreased, water availability in urban riparian zones. However, channel
 incision may counteract this effect. We asked whether dry-season stream
 flow interacted with channel incision to influence riparian soil
 characteristics and understory vegetation along streams in Sacramento,
 California, which has a Mediterranean climate with an intense summer dry
 season. At 40 stream reaches that varied by severity of downcutting and
 presence of dry-season flow, we sampled soils and vegetation on top of
 stream banks and at the margin of the low-flow channel, an important
 location for nutrient cycling in dry climates. We measured soil moisture,
 organic matter, and ∂15N, as well as total and perennial understory
 vegetation cover. We found that channel characteristics associated with
 incision limited the influence of dry-season stream flow on soil moisture,
 and this interaction appears to have lasting effects on soil organic
 matter and perennial vegetation on bank tops. At the stream margin,
 channel downcutting was associated with reduced soil organic matter and
 vegetation cover, while dry-season flow was associated with increased
 vegetation cover. Values of soil ∂15N pointed to limited hydrologic
 linkage between stream flows and riparian bank soils along incised
 streams. Our findings suggest that channel incision could limit the
 ability of urban riparian ecosystems to mitigate low-flow water quality.
 However, where streams are not incised in Mediterranean climates,
 dry-season flows from urban runoff may actually increase riparian
 productivity and N cycling above historical levels. 
description: Please see methods and information in the publication and in the
 ReadMe file.
DOI: 10.25338/b83627
title: The biogeography of community assembly: latitude and predation drive variation in community trait distribution in a guild of epifaunal crustaceans

description: While considerable evidence exists of biogeographic patterns in the
 intensity of species interactions, the influence of these patterns on
 variation in community structure is less clear. Using a model selection
 approach on measures of trait dispersion in crustaceans associated with
 eelgrass (Zostera marina) spanning 30º of latitude in two oceans, we found
 that dispersion strongly increased with increasing predation and
 decreasing latitude. Ocean and epiphyte load appeared as secondary
 predictors; Pacific communities were more overdispersed while Atlantic
 communities were more clustered, and increasing epiphytes were associated
 with increased clustering. By examining how species interactions and
 environmental filters influence community structure across biogeographic
 regions, we demonstrate how both latitudinal variation in species
 interactions and historical contingency shape these responses. Community
 trait distributions have implications for ecosystem stability and
 functioning, and integrating large-scale observations of environmental
 filters, species interactions, and traits can help us predict how
 communities may respond to environmental change.
description: See main manuscript for details.
DOI: 10.7272/q64f1p0f
title: Data from: Influence of periaqueductal gray on other salience network nodes predicts social sensitivity

description: The intrinsic connectivity of the salience network (SN) plays an important
 role in social behavior, however the directional influence that individual
 nodes have on each other has not yet been fully determined. In this study,
 we used spectral Dynamic Causal Modeling to characterize the effective
 connectivity patterns in the SN for 44 healthy older adults and for 44
 patients with behavioral variant frontotemporal dementia (bvFTD) who have
 focal SN dysfunction. We examined the relationship of SN effective
 connections with individuals’ socioemotional sensitivity, using the
 Revised Self-Monitoring Scale, an informant-facing questionnaire that
 assesses sensitivity to expressive behavior. Overall, average SN effective
 connectivity for bvFTD patients differs from healthy older adults in
 cortical, hypothalamic, and thalamic nodes. For the majority of healthy
 individuals, strong periaqueductal gray (PAG) output to right cortical
 (p&lt;.01) and thalamic nodes (p&lt;.05), but not PAG output to
 other central pattern generators contributed to sensitivity to
 socioemotional cues. This effect did not exist for the majority of bvFTD
 patients; PAG output towards other SN nodes was weak, and this lack of
 output negatively influenced socioemotional sensitivity. Instead, input to
 the left vAI from other SN nodes supported patients’ sensitivity to
 others’ socioemotional behavior (p&lt;.05), though less effectively.
 The key role of PAG output to cortical and thalamic nodes for
 socioemotional sensitivity suggests that its core functions, i.e.,
 generating autonomic changes in the body, and moreover representing the
 internal state of the body, is necessary for optimal social
 responsiveness, and its breakdown is central to bvFTD patients’ social
 behavior deficits.
description: This data includes
 individuals' first level DCM results ordered by patient group. Please
 refer to the article for materials and methods description.
description: All code used for analyses after preprocessing is available at
 https://github.com/MyrtheGwenRijpma/DCM.
DOI: 10.5061/dryad.547d7wm9c
title: Male courtship reduces the risk of cannibalism in web-building spiders but varies in structure

description: Male courtship serves multiple functions in addition to inducing females
 to accept them as a mate. In predatory species, male courtship can
 function to reduce the risk of sexual cannibalism. This is particularly
 important in web-building spiders in which males risk being mistaken for
 prey when they enter the female’s predatory trap – the web – in order to
 commence courtship. Male spiders generate vibrations by shuddering in the
 female’s web. Shudder vibrations can delay female aggression, even toward
 prey struggling in the web. We predicted that shudder vibrations are
 highly conserved across species of web-building spider as males all face
 the same constraint of not being mistaken for prey by females. We examined
 how conserved shudder vibrations are across web-building spiders by
 testing whether female Trichonephila plumipes delay aggressive behaviour
 toward real prey struggling in the web during playback of conspecific or
 heterospecific (Argiope keyserlingi) male shudder vibrations. We found
 that while conspecific shudder vibrations do indeed delay female predatory
 behaviour, heterospecific male shudder vibrations do not. There is
 evidence of shudder or shudder-like vibrations in male courtship behaviour
 across web-building spider families, but these vary in structure. This
 suggests that despite strong constraints on courtship signal design to
 separate predatory responses from sexual responses, there is additional
 selection driving the divergence of signals across distantly related
 spider species.
description: Experiment 1: Female <em>Trichonephila
 plumipes</em> were presented with live crickets in their webs
 during playbacks of male <em>T. plumipes </em>shudder
 vibrations, white noise or a silent control. Their responses were
 compared. Experiment 2: Female <em>Trichonephila
 plumipes</em> were presented with live crickets in their webs
 during playbacks of male <em>A. keyserlingi </em>shudder
 vibrations, white noise or a silent control. Their responses were
 compared. Shudder recordings: Recordings of male
 shudders from 8 species of web-building spider were analysed for peak
 frequency (Hz), duration (ms) and inter-shudder duration (s). Species
 included were: <i>Argiope aetherea, A. katherina, A.
 keyserlingi </i>(note, recordings from Wignall & Herberstein
 2013a), <i>A. radon, Cryptachaea</i>
 sp.,  <i>Phonognaetha graffei, Plebs eburnus, Trichonephila
 plumipes. </i>A subset of these recordings were compared in a linear
 discriminant analysis.
description: Response latencies of female spiders in Experiments 1 and 2 are
 censored (females were given a maximum of 10 minutes to respond to
 prey). Recordings of male courtship were used to test
 for the presence of shudder courtship elements, rather than to
 comprehensively characterise male courtship behaviour. 
 Cells marked 'NA' indicate measurements that were not
 applicable.
DOI: 10.5061/dryad.w9ghx3fqr
title: Integrative taxonomy of two thrush complexes (Aves: Turdidae) reveals introgression across sister species

description: The classification of some Turdus species, such as the
 Naumann’s and dusky thrush complexes and
 the red-throated
 and black-throated thrush complexes, is
 controversial. Herein, we used molecular data and morphological
 characters to review the taxonomy of these thrush complexes and analyze
 the genetic differentiation between them. Herein, we examined
 the genetic characteristics of 13 microsatellite loci in
 all individuals and total of 129 alleles were detected. In
 parallel, we have a further judgment on their classification
 status by measuring 5 morphological features (tail length, wing length,
 toe length, claw length and instep length).
description: Collection of microsatellite loci  We
 characterized 13 microsatellite loci for the targeted thrush species; the
 loci were identified originally isolated from therelated
 species <i>Turdus merula</i>. The 5' end of each forward
 primer was connected to a fluorescent dye-labeled M13, and the fluorescent
 label was FAM or JOE. The amplification profile of the microsatellite loci
 was standardized as follows: 5.0 μl of Ex Taq DNA polymerase (TaKaRa,
 Dalian), 3.5 μl of H<sub>2</sub>O, 0.2 μl of BSA, 0.1 μl (10
 pmol/μl) of each primer, 0.1 μl (10 pmol/μl) of M13 and 3.5 μl (20 ng) of
 genomic DNA. The PCR conditions were as follows: initial denaturation at
 94°C for 3 min; 20 cycles of 94°C for 30 s, the annealing temperature for
 30 s and 72°C for 45 s; 15 cycles of 94°C for 30 s, 60°C for 30 s and 72°C
 for 45 s; and a final extension at 72°C for 10 min. Amplicons were sized
 by a service provider (Shenggong BioTech) using capillary electrophoresis
 with an ABI 3730xl DNA analyzer. Alleles were scored using GeneMapper
 software version 4.0 (Applied Biosystems Inc.).
 Morphometric data A total of 77 individuals,
 including Naumann’s thrush (<i>N</i>=33), the dusky
 thrush (<i>N</i>=8),
 the red-throated thrush (<i>N=</i>33), and
 the black-throated thrush (<i>N=</i>3), were used in the
 morphometric analysis. Five morphological features, tail length, wing
 length (maximum chord), toe length, claw length and instep length, were
 measured using an electronic vernier caliper (with an accuracy
 of 0.001).
description: All lengths are measured in cm.
DOI: 10.5061/dryad.h9w0vt4jz
title: The complete chloroplast genome of Mimusops elengi (Sapotaceae)

description: The first complete chloroplast genome sequences of Mimusops
 elengi (Sapotaceae) were reported in this study. The
 cpDNA of M. elengi is 159,719 bp in length, contains a
 large single-copy region (LSC) of 88,935 bp and a small
 single-copy region (SSC) of 18,606 bp, which were separated by a pair of
 inverted repeat (IR) regions of 26,089 bp. The genome contains
 132 genes, including 87 protein-coding genes, 8
 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of
 the whole genome is 36.8%. Phylogenetic analysis of
 12 chloroplast genomes within the family
 Sapotaceae suggests that the sister relationship of
 Autranella and Tieghemella is strongly supported.
 Minusops genus is close to Autranella and Tieghemella,
 although the support value is still low.
description: Total genomic DNA was
 extracted using Tiangen Plant Genomic DNA Kit (Tiangen Biotech Co.,
 Beijing, China). DNA was sequenced using
 the Illumina HiSeq 2000 platform at Novogene Co.,
 Ltd (Beijing, China). The complete chloroplast genome was assembled,
 circularized, and annotated using GENIOUS 2019.1.1 (Kearse et
 al. 2012).
DOI: 10.5061/dryad.zw3r2288t
title: Impacts of taxon-sampling schemes on Bayesian tip dating under the fossilized birth-death process

description: Evolutionary timescales can be inferred by molecular-clock analyses of
 genetic data and fossil evidence. Bayesian phylogenetic methods such as
 tip dating provide a powerful framework for inferring evolutionary
 timescales, but the most widely used priors for tree topologies and node
 times often assume that present-day taxa have been sampled randomly or
 exhaustively. In practice, taxon sampling is often carried out so as to
 include representatives of major lineages, such as orders or families. We
 examined the impacts of different densities of diversified sampling on
 Bayesian tip dating on unresolved fossilized birth-death (FBD) trees, in
 which fossil taxa are topologically constrained but their exact placements
 are averaged out. We used synthetic data generated by simulations of
 nucleotide sequence evolution, fossil occurrences, and diversified taxon
 sampling. Our analyses under the diversified-sampling FBD process show
 that increasing taxon-sampling density does not necessarily improve
 divergence-time estimates. However, when informative priors were specified
 for the root age or when tree topologies were fixed to those used for
 simulation, the performance of tip dating on unresolved FBD trees
 maintains its accuracy and precision or improves with taxon-sampling
 density. By exploring three situations in which models are mismatched, we
 find that including all relevant fossils, without pruning off those that
 are incompatible with the diversified-sampling FBD process, can lead to
 underestimation of divergence times. Our reanalysis of a eutherian mammal
 data set confirms some of the findings from our simulation study, and
 reveals the complexity of diversified taxon sampling in phylogenomic data
 sets. In highlighting the interplay of taxon-sampling density and other
 factors, the results of our study have practical implications for using
 Bayesian tip dating to infer evolutionary timescales across the Tree of
 Life.
DOI: 10.7272/q60p0x95
title: Therapeutic Deep Brain Stimulation Disrupts Subthalamic Nucleus Activity Dynamics in Parkinsonian Mice

description: Subthalamic nucleus deep brain stimulation (STN DBS) relieves many motor
 symptoms of Parkinson’s Disease (PD), but its underlying therapeutic
 mechanisms remain unclear. Since its advent, three major theories have
 been proposed: (1) DBS inhibits the STN and basal ganglia output; (2) DBS
 antidromically activates motor cortex; and (3) DBS disrupts firing
 dynamics within the STN. Previously, stimulation-related electrical
 artifacts limited mechanistic investigations using electrophysiology. We
 used electrical artifact-free calcium imaging to investigate activity in
 basal ganglia nuclei during STN DBS in parkinsonian mice. To test whether
 the observed changes in activity were sufficient to relieve motor
 symptoms, we then combined electrophysiological recording with targeted
 optical DBS protocols. Our findings suggest that STN DBS exerts its
 therapeutic effect through the disruption of STN dynamics, rather than
 inhibition or antidromic activation. These results provide insight into
 optimizing PD treatments and establish an approach for investigating DBS
 in other neuropsychiatric conditions.
description: Collected from a large cohort of hemiparkinsonian (6OHDA) mice.
 Consists of a combination of fiberphotometry recordings + STN DBS or
 LDopa, optical stimulation, and invivo electrophysiology.
DOI: 10.5061/dryad.7sqv9s4t5
title: Data supporting: Success of post-fire plant recovery strategies varies with shifting fire seasonality

description: Wildfires are increasing in size and severity and fire seasons are
 lengthening, largely driven by climate and land use change. Many plant
 species from fire prone ecosystems are adapted to specific fire regimes
 corresponding to historical conditions and shifts beyond these bounds may
 have severe impacts on vegetation recovery and long-term species
 persistence. Here, we conduct a meta-analysis of field-based studies
 across different vegetation types and climate regions to investigate how
 post-fire plant recruitment, reproduction and survival are affected by
 fires that occur outside of the historical fire season. We find that fires
 outside of the historical fire season may lead to decreased post-fire
 recruitment for many species, particularly obligate seeding species.
 Conversely, we find a general increase of post-fire survival in
 resprouting species. Our results highlight the trade-offs that exist when
 considering the effects of changes in the seasonal timing of fire, an
 already present aspect of climate-related global fire regime change.
DOI: 10.5061/dryad.mgqnk9918
title: Characteristics of COVID-19 patients predicting hospital readmission after ED discharge

description: Objective: We aimed at identifying baseline predictive factors for
 emergency department (ED) readmission, with hospitalization/death, in
 COVID-19 patients previously discharged from the ED. We also developed a
 disease progression velocity index. Design and setting: Retrospective
 cohort study of prospectively collected data. The charts of consecutive
 COVID-19 patients discharged from the Reggio Emilia (Italy) ED (March 2 -
 March 31, 2020) were retrospectively examined. Clinical, laboratory, and
 computed tomography (CT) findings at first ED admission were tested as
 predictive factors using multivariable logistic models. We divided CT
 extension by days from symptom onset to build a synthetic velocity index.
 Participants: 450 patients discharged from the ED with diagnosis of
 COVID-19. Main outcome measure: ED readmission within 14 days, followed by
 hospitalization/death. Results: Of the discharged patients, 84 (18.7%)
 were readmitted to the ED and 61 (13.6%) were hospitalized and 10 (2.2%)
 died. Age (OR=1.05; 95% CI 1.03-1.08), Charlson Comorbidity Index 3 vs 0
 (OR=11.61; 95% CI 1.76-76.58), days from symptom onset (OR for one day
 increase=0.81; 95% CI 0.73-0.90), and CT extension (OR for 1%
 increase=1.03; 95% CI 1.01-1.06) were associated in a multivariable model
 for readmission with hospitalization/death. A 2-day lag velocity index was
 a strong predictor (OR for unit increase=1.21, 95% CI 1.08-1.36); the
 model including this index resulted in less information loss. Conclusions:
 A velocity index combining CT extension and days from symptom onset
 predicts disease progression in COVID-19 patients. For example, a 20% CT
 extension 3 days after symptom onset has the same risk as does 50% after
 10 days.
description: Age and sex are standard parameters routinely collected for all
 patients. Charlson index was calculated based on hospital admissions in
 the previous 10 years. Date of COVID-19-related admission to the ED, date
 of symptom onset, diagnosis, hospitalization, and death, were retrieved
 from the COVID-19 Surveillance Registry, coordinated by the National
 Institute of Health and implemented in each Local Health Authority.
 Radiologist completed a routine CT report that included the extension
 of pulmonary lesions using a visual scoring system (&lt; 20%, 20-39%,
 40-59%, ≥ 60%). We built a synthetic indicator of the velocity of disease
 progression at ED admission, ie, the ratio of CT involvement and days from
 symptom onset to first ED admission, with 2 days lag and we approximate
 it without decimals. Then we collapse the dataset for
 these varaibles and report the frequency in the "freq"
 variable.
description: There are 14 missing in extension of pulmonary lesions and
 consequentially in the velocity index.
DOI: 10.5061/dryad.1c59zw3wh
title: Supplementary data to: Trapped in the morphospace: the trade-off between morphological integration and functional performance can limit adaptation

description: The evolution of complex morphological structures can be seen as the
 result of interplay between different anatomical units evolving in a
 coordinated fashion. These can be influenced by genetic, developmental
 and/or functional integration in response to selective pressures. Using
 the highly derived humeral morphology of talpid moles as model, here we
 test whether functional specialization (measured as performance) can be
 linked to increased levels of morphological integration and, if so, what
 is the extent of the relationship. Combining 2D geometric morphometrics,
 phylogenetic comparative methods and functional landscape modelling, we
 demonstrate that the high biomechanical performance of subterranean moles
 was coupled with a high degree of integration, whereas less specialized
 taxa displayed intermediate or low magnitudes of integration. Theoretical
 morphs occurring in high-performance areas of the functional landscape not
 covered by any species showed a marked drop in covariation levels,
 suggesting the existence of a genuine tradeoff between integration and
 performance in the evolution of talpid moles. We argue that the remarkable
 stability of the subterranean environment may have helped constraining
 humeral morphology over a restricted area of the functional landscape,
 trapping subterranean moles in a narrow region of the landscape, impeding
 any attempt to reposition on a new ascending slope.
description: We present a dataset including 2D landmark coordinates. These are
 aligned Procrustes coordinates averaged per species. In total, we sampled
 36 landmarks on 84 species encompassing the known variation of talpid
 moles. The phylogenetic tree is the strict consensus
 topology generated from a cladistic analysis performed on 171
 morphological characters.