cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.brv15dv5v
title: Phylogenomic species delimitation, taxonomy, and "bird guide" identification for the Neotropical ant genus Rasopone (Hymenoptera: Formicidae)

description: Rasopone Schmidt & Shattuck is a poorly known lineage of ants that
 live in Neotropical forests. Informed by phylogenetic results from
 thousands of ultraconserved elements (UCEs) and mitochondrial DNA
 barcodes, we revise the genus, providing a new morphological diagnosis and
 a species-level treatment. Analysis of UCE data from many Rasopone samples
 and select outgroups revealed non-monophyly of the genus. Monophyly of
 Rasopone was restored by transferring several species to the unrelated
 genus Mayaponera Schmidt & Shattuck. Within Rasopone, species are
 morphologically very similar, and we provide a "bird guide"
 approach to identification rather than the traditional dichotomous key.
 Species are arranged by size in a table, along with geographic range and
 standard images. Additional diagnostic information is then provided in
 individual species accounts. We recognize a total of 15 named species, of
 which the following are described as new species: R. costaricensis, R.
 cryptergates, R. cubitalis, R. guatemalensis, R. mesoamericana, R.
 pluviselva, R. politognatha, R. subcubitalis, and R. titanis. An
 additional 12 morphospecies are described but not formally named due to
 insufficient material. Rasopone panamensis (Forel, 1899) is removed from
 synonymy and elevated to species. The following species are removed from
 Rasopone and made new combinations in Mayaponera: M. arhuaca (Forel,
 1901), M. becculata (Mackay & Mackay, 2010), M. cernua (Mackay
 & Mackay, 2010), M. conicula (Mackay & Mackay, 2010), M.
 longidentata (Mackay & Mackay, 2010), and M. pergandei (Forel,
 1909).
DOI: 10.5061/dryad.sf7m0cg2c
title: Predation risks of signalling and searching: bats prefer moving katydids

description: Males signalling their attractiveness to females are at risk from
 predators that exploit mating signals to detect and locate prey.
 Signalling, however, is not the only risky activity in sexual
 interactions: mate searching can incur risk as well. Male Neotropical
 pseudophylline katydids produce both acoustic and vibrational signals
 (tremulations). Females reply to male signals with tremulations of their
 own, and both sexes walk to find one another. We asked if movement
 increases predation risk, and whether tremulation or walking was more
 attractive to predators. We offered the Neotropical gleaning bat
 Micronycteris microtis a series of two-choice tests, presenting the bats
 with katydid models that were motionless or moved in a way to mimic either
 tremulating or walking. We found that prey movements do put prey at risk.
 Although M. microtis can detect motionless prey on leaves, they preferred
 moving prey. Our study shows that movement can put searching or signalling
 prey in danger, potentially explaining why silent female katydids are
 frequently consumed by gleaning bats.
description: Model katydids were presented to bats. The bat behaviour was
 recorded via video cameras.
DOI: 10.5061/dryad.jsxksn05t
title: A novel method for detecting extra-home range movements (EHRMs) by animals and recommendations for future EHRM studies

description: Infrequent, long-distance animal movements outside of typical home range
 areas provide useful insights into resource acquisition, gene flow, and
 disease transmission within the fields of conservation and wildlife
 management, yet understanding of these movements is still limited across
 taxa. To detect these extra-home range movements (EHRMs) in spatial
 relocation datasets, most previous studies compare relocation points
 against fixed spatial and temporal bounds, typified by seasonal home
 ranges (referred to here as the “Fixed-Period” method). However, utilizing
 home ranges modelled over fixed time periods to detect EHRMs within those
 periods likely results in many EHRMs going undocumented, particularly when
 an animal’s space use changes within that period of time. To address this,
 we propose a novel, “Moving-Window” method of detecting EHRMs through an
 iterative process, comparing each day’s relocation data to the preceding
 period of space use only. We compared the number and characteristics of
 EHRM detections by both the Moving-Window and Fixed-Period methods using
 GPS relocations from 33 white-tailed deer (Odocoileus virginianus) in
 Alabama, USA. The Moving-Window method detected 1.5 times as many EHRMs as
 the Fixed-Period method and identified 120 unique movements that were
 undetected by the Fixed-Period method, including some movements that
 extended nearly 5 km outside of home range boundaries. Additionally, we
 utilized our EHRM dataset to highlight and evaluate potential sources of
 variation in EHRM summary statistics stemming from differences in
 definition criteria among previous EHRM literature. We found that this
 spectrum of criteria identified between 15.6% and 100.0% of the EHRMs
 within our dataset. We conclude that variability in terminology and
 definition criteria previously used for EHRM detection hinders useful
 comparisons between studies. The Moving-Window approach to EHRM detection
 introduced here, along with proposed methodology guidelines for future
 EHRM studies, should allow researchers to better investigate and
 understand these behaviors across a variety of taxa.
description: This dataset was collected by deploying store-on-board GPS
 collars on free-ranging white-tailed deer in Alabama. Data was collected
 from the collars and compiled. Raw data (included here in the repository)
 were processed in R to create home ranges for both the
 Moving-Window method and the Fixed-Period method described in the article.
 Home ranges and associated point data were analyzed to detect extra-home
 range movements. Processed data from the extra-home range movement
 analysis were used to perform statistical analyses as well as create
 tables and figures.
description: There are no missing values in this dataset.
DOI: 10.5061/dryad.02v6wwq05
title: Medicare Shared Savings Program and readmission rate among ischemic stroke patients

description: Objective Hospitals participating in the Medicare Shared Savings Program
 (MSSP) share with the Centers for Medicare and Medicaid Services (CMS) the
 savings generated by reducing readmissions. Our aim was to determine
 whether MSSP is associated with changes in readmissions and mortality for
 Medicare patients hospitalized with ischemic stroke, and whether MSSP has
 a different impact on safety-net hospitals (SNHs) compared to
 non-SNHs.    Methods This study was based on
 the CMS Hospital Compare data for risk-standardized 30-day readmission and
 mortality rates for Medicare patients hospitalized with ischemic strokes
 between 2010 and 2017. With propensity score matched sample,
 hospital-level difference-in-difference (DID) analysis was used to
 determine whether MSSP was associated with changes in hospital readmission
 and mortality as well as to examine the impact of MSSP on SNHs compared to
 non-SNHs.  Results MSSP-participating hospitals had slightly
 greater reductions in readmission rates compared to matched
 non-participating hospitals (difference, 0.25 percentage points; 95% CI:
 -0.42, -0.08). Mortality rates decreased among all hospitals, but
 mortality reduction was not significantly different between
 MSSP-participating hospitals and matched hospitals (difference, 0.06
 percentage points; 95% CI: -0.28, 0.17). Prior to MSSP, readmission rates
 in SNHs were higher compared to non-SNH, but MSSP did not have a
 significantly different impact on hospital readmission and mortality rates
 for SNH and non-SNHs. Conclusion MSSP led to slightly fewer readmissions
 without increases in mortality in patients hospitalized with ischemic
 stroke. Similar reductions in readmission rates were observed in SNHs and
 non-SNHs participating in MSSP, indicating persistent gaps between SNHs
 and non-SNHs.
DOI: 10.5061/dryad.p5hqbzkm4
title: Using a coalescent approach to assess gene flow and effective population size of Acrocomia aculeata (Jacq.) Lodd. Ex Mart. in the Brazilian Atlantic Forest

description: Acrocomia aculeata is a tropical palm tree native to Central and South
 America that has significant economic, social, and environmental
 potential. However, land encroachment due to the expansion of
 agribusiness, and other factors such as urban sprawl, have resulted in the
 fragmentation and destruction of its habitat, leading to the loss of genes
 and genotypes in A. aculeata populations. In this context, the objective
 of this study was to characterize the genetic variability of A. aculeata
 populations by estimating gene flow and effective population size using an
 approach based on coalescent theory. Four populations located in the
 municipalities of Teodoro Sampaio (TSI and TSII), Rosana (RA), and Amparo
 (AP) in São Paulo State, Brazil, were genotyped with nine microsatellite
 markers. Gene flow and effective population size were estimated using a
 coalescent-based Bayesian inference implemented in the MIGRATE-N software.
 The effective population size (Ne) was obtained considering an assumed
 mutation rate of 5x10-5. Gene flow (Nm) for pairwise populations ranged
 from 0.28 to 1.17, with higher levels of migration between the three
 geographically proximal locations (TSI, TSII, and RA). The estimates of
 effective population size (Ne) were 444, 835, 838, and 874 for AP, TSII,
 RA, and TSI, respectively, showing that the effects caused by genetic
 drift may be more pronounced when Ne is smaller. The coalescent-based
 results add to our understanding of A. aculeata population genetics and
 suggest that some traditional assessment methods may be ineffective in
 characterizing historical evolutionary processes.
description: This file contains the genotype data of four subpopulations of
 <em>A. aculeata</em> (microsatellites loci).
DOI: 10.5061/dryad.x3ffbg7fb
title: Data from: Trait plasticity alters the range of possible coexistence conditions in a competition-colonization trade-off

description: Most of the classical theory on species coexistence has been based on
 species-level competitive trade-offs. However, it is becoming apparent
 that plant species display high levels of trait plasticity. The
 implications of this plasticity are almost completely unknown for most
 coexistence theory. Here, we model a competition-colonization trade-off
 and incorporate trait plasticity to evaluate its effects on coexistence.
 Our simulations show that the classic competition-colonization trade-off
 is highly sensitive to environmental circumstances and coexistence only
 occurs in narrow ranges of conditions. The inclusion of plasticity, which
 allows shifts in competitive hierarchies across the landscape, leads to
 coexistence across a much broader range of competitive and environmental
 conditions including disturbance levels, the magnitude of competitive
 differences between species, and landscape spatial patterning. Plasticity
 also increases the number of species that persist in simulations of
 multispecies assemblages. Plasticity may generally increase the robustness
 of coexistence mechanisms and be an important component of scaling
 coexistence theory to higher diversity communities.
description: This data set includes the scripts required to recreate and run
 the simulation model described in the associated manuscript. In addition,
 data files from simulations that were run to explore model dynamics in the
 manuscript are also included. Manuscript figures can be recreated using
 the included script and datafiles.
description: See the included README.txt file and model description in the
 associated manuscript (Muthukrishnan, R., L.L. Sullivan, A.K. Shaw, and
 J.D. Forester. 2020. Trait plasticity alters the range of possible
 coexistence conditions in a competition–colonisation trade-off. Ecology
 Letters)
DOI: 10.5061/dryad.0zpc866tw
title: Impact of soil temperature-difference on desert carbon-sink

description: The global carbon-cycle is crucial for climate change. Desert, which has
 long been neglected in the global carbon-cycle, may sequester enormous
 volumes of CO2 and play the role of a carbon-sink. As the world's
 second-largest shifting desert, the Taklimakan Desert (TD) contributes
 substantially to desert carbon-sinks. However, the contributions of the
 internal processes of the TD to its carbon-sink and the long-term trend of
 the carbon-sink under climate change are still unclear. This study will
 address this important knowledge gap. Through field observations, we found
 that the expansion/contraction of soil air containing CO2 caused by heat
 fluctuation in shifting sand, in combination with salts/alkali chemistry
 dominates the release/absorption processes of CO2 in shifting sand. The
 mutual counteraction of these processes means that the TD shifting sand
 acts as a stable carbon-sink that had a CO2 annual uptake of 1.60×106
 t·a-1 during 2004–2017. It suggests that global shifting deserts maybe
 uptake of ~2.125×108 t of CO2 per year. However, an increasing soil
 temperature-difference will stimulate soil air expansion of desert and
 release more CO2 into the atmosphere under climate change, causing the
 shifting sand carbon-sink decrease in the TD gradually in the future.
 These processes will be accelerated by positive feedback effect under
 climate change and enhance regional warming. These conclusions are very
 important for re-recognizing the status of deserts in the carbon-cycle,
 narrowing the gap in the missing carbon-sink and assessing the global
 carbon-cycle.
description: Through experiments of dismantling and temperature-controlled, we
 found that the expansion/contraction of soil air containing
 CO<sub>2</sub> caused by heat fluctuation, in combination with
 salts/alkali chemistry dominates the release/absorption processes of
 CO<sub>2</sub> in shifting sand. Finally, combined with
 historical soil temperature data and the Fifth Coupled Model
 Intercomparison Project (CMIP5) simulations, we reveal a stable
 carbon-sink property of the TD shifting sand.
description: The data file contains all the data of the corresponding
 manuscript, and there is no missing value.
DOI: 10.5061/dryad.3n5tb2rd1
title: Quality-quantity tradeoffs drive functional trait evolution in a model microalgal “climate change winner”

description: Phytoplankton are the unicellular photosynthetic microbes that form the
 base of aquatic ecosystems, and their responses to global change will
 impact everything from food web dynamics to global nutrient cycles. Some
 taxa respond to environmental change by increasing population growth rates
 in the short-term, and are projected to increase in frequency over
 decades. To gain insight into how these projected “climate change winners”
 evolve, we grew populations of microalgae in ameliorated environments for
 several hundred generations. Most populations evolved to allocate a
 smaller proportion of carbon to growth while increasing their ability to
 tolerate and metabolise reactive oxygen species (ROS). This tradeoff
 drives the evolution of traits that underlie the ecological and
 biogeochemical roles of phytoplankton. This offers evolutionary and a
 metabolic frameworks for understanding trait evolution in projected
 “climate change winners”, and suggests that short-term population booms
 have the potential to be dampened or reversed when environmental
 amelioration persists.
description: All methods are in the published paper.
DOI: 10.5061/dryad.dz08kprth
title: Paternal exposure to a common herbicide alters the behavior and serotonergic system of zebrafish offspring

description: Increasingly, studies are revealing that endocrine disrupting chemicals
 (EDCs) can alter animal behavior. Early life exposure to EDCs may
 permanently alter phenotypes through to adulthood. In addition, the
 effects of EDCs may not be isolated to a single generation − offspring may
 indirectly be impacted, via non-genetic processes. Here, we analyzed the
 effects of paternal atrazine exposure on behavioral traits (distance
 moved, exploration, bottom-dwelling time, latency to enter the top zone,
 and interaction with a mirror) and whole-brain mRNA of genes involved in
 the serotonergic system regulation (slc6a4a, slc6a4b, htr1Aa, htr1B,
 htr2B) of zebrafish (Danio rerio). F0 male zebraﬁsh were exposed to
 atrazine at 0.3, 3 or 30 part per billion (ppb) during early juvenile
 development, the behavior of F1 progeny was tested at adulthood, and the
 effect of 0.3 ppb atrazine treatment on mRNA transcription was quantified.
 Paternal exposure to atrazine significantly reduced interactions with a
 mirror (a proxy for aggression) and altered the latency to enter the top
 zone of a tank in unexposed F1 offspring. Bottom-dwelling time (a proxy
 for anxiety) also appeared to be somewhat affected, and activity (distance
 moved) was reduced in the context of aggression. slc6a4a and htr1Aa mRNA
 transcript levels were found to correlate positively with anxiety levels
 in controls, but we found that this relationship was disrupted in the 0.3
 ppb atrazine treatment group. Overall, paternal atrazine exposure resulted
 in alterations across a variety of behavioral traits and showed signs of
 serotonergic system dysregulation, demonstrating intergenerational
 effects. Further research is needed to explore transgenerational effects
 on behavior and possible mechanisms underpinning behavioral effects.
description: <b>Paternal atrazine exposure on F1 zebrafish behavior.xlsx
 </b> Behavioral data collected from adult F1
 zebrafish during the three behavioral tests, the novel arena assay, novel
 object assay and mirror exposure assay.
 <b>Paternal atrazine exposure on F1 zebrafish serotonergic
 mRNA.xlsx</b> mRNA transcript number data on
 several genes involved in serotonergic regulation collected from
 whole-brain.
DOI: 10.15139/s3/uaol9v
title: Data Management and Sharing Plan for: Understanding the Selective Mechanism of Tau Propagation in Alzheimer's Disease Through Multi-layer Spreading Pathways

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: 10.7283/522b-n573
title: NOTA Affiliated GPS Network - BBWY-biscuitbasin2025 P.S.
DOI: 10.5061/dryad.w3r2280m9
title: Limited mass-independent individual variation in resting metabolic rate in a wild population of snow voles (Chionomys nivalis)

description: Resting metabolic rate (RMR) is a potentially important axis of
 physiological adaptation to the thermal environment. However, our
 understanding of the causes and consequences of individual variation in
 RMR in the wild is hampered by a lack of data, as well as analytical
 challenges. RMR measurements in the wild are generally characterized by
 large measurement errors and a strong dependency on mass. The latter is
 problematic when assessing the ability of RMR to evolve independently of
 mass. Mixed models provide a powerful and flexible tool to tackle these
 challenges, but they have rarely been used to estimate repeatability of
 mass-independent RMR from field data. We used respirometry to obtain
 repeated measurements of RMR in a long-term study population of snow voles
 (Chionomys nivalis) inhabiting an environment subject to large circadian
 and seasonal fluctuations in temperature. Using both uni- and bivariate
 mixed models, we quantify individual repeatability in RMR and decompose
 repeatability into mass-dependent and mass-independent components, while
 accounting for measurement error. RMR varies among individuals, i.e. is
 repeatable (R=0.46), and strongly co-varies with BM. Indeed, much of the
 repeatability of RMR is attributable to individual variation in BM, and
 the repeatability of mass-independent RMR is reduced by 41% to R=0.27.
 These empirical results suggest that the evolutionary potential of RMR
 independent of mass may be severely constrained. This study illustrates
 how to leverage bivariate mixed models to model field data for metabolic
 traits, correct for measurement error, and decompose the relative
 importance of mass-dependent and mass-independent physiological variation.
DOI: 10.5061/dryad.6m905qfwc
title: Offspring phenotype is shaped by the non-sperm fraction of semen

description: In a large majority of animal species, the only contribution of males to
 the next generation has been assumed to be their genes (sperm). However,
 along with sperm, seminal plasma contains a wide array of extracellular
 factors that have many important functions in reproduction. Yet, the
 potential intergenerational effects of these factors are virtually
 unknown. We investigated these effects in European whitefish (Coregonus
 lavaretus) by experimentally manipulating the presence and identity of
 seminal plasma and by fertilizing the eggs of multiple females with the
 manipulated and unmanipulated semen of several males in a full-factorial
 breeding design. Presence of both own and foreign seminal plasma inhibited
 sperm motility and removal of own seminal plasma decreased embryo
 survival. Embryos hatched significantly earlier after both semen
 manipulations than in control fertilizations; foreign seminal plasma also
 increased offspring aerobic swimming performance. Given that our
 experimental design allowed us to control potentially confounding
 sperm-mediated (sire) effects and maternal effects, our results indicate
 that seminal plasma may have direct intergenerational consequences for
 offspring phenotype and performance. This novel source of offspring
 phenotypic variance may provide new insights into the evolution of
 polyandry and mechanisms that maintain heritable variation in fitness and
 associated female mating preferences.
DOI: 10.5061/dryad.1jwstqjr4
title: Data from: Molecular mapping and identification of quantitative trait loci for domestication traits in field cress (Lepidium campestre L.) genome

description: Lepidium campestre (L.) or field cress is a multifaceted oilseed
 plant, which has not been domesticated yet. Moreover, the molecular and
 genetic mechanisms underlying the domestication traits of field cress
 remain largely elusive. The overarching goal is to identify quantitative
 trait loci (QTL) that are fundamental for domestication of field cress.
 Mapping and dissecting quantitative trait variation may provide important
 insights into genomic trajectories underlying field cress domestication.
 We used 7624 single nucleotide polymorphism (SNP) markers for QTL mapping
 in 428 F2 interspecific hybrid individuals, whilst field
 phenotyping was conducted in F2:3 segregating families. We
 applied multiple QTL mapping algorithms to detect and estimate QTL effects
 for seven important domestication traits of field cress. Verification of
 pod shattering across sites revealed that the non-shattering lines
 declined drastically whereas the shattering lines increased sharply,
 possibly due to inbreeding followed by selection events. In total, 1461 of
 the 7624 SNP loci mapped to eight linkage groups (LGs), spanning 571.9
 cM map length. We identified 27 QTL across all LGs of field cress
 genome, which captured medium to high heritability, implying that
 genomics-assisted selection could deliver domesticated lines in field
 cress breeding. The use of high throughput genotyping can accelerate the
 process of domestication in novel crop species. This is the first QTL
 mapping analyses in field cress genome that may lay a foundational
 framework for positional or functional QTL cloning, introgression, as well
 as genomics-assisted breeding in field cress domestication.
description: Phenotype and genotype data records for field cress