cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6078/d14t49
title: Data from: Gene expression plasticity and desert adaptation in house mice

description: Understanding how organisms adapt to new environments is a key problem in
 evolution, yet it remains unclear whether phenotypic plasticity generally
 facilitates or hinders this process. Here we studied evolved and plastic
 responses to water-stress in lab-born descendants of wild house mice (Mus
 musculus domesticus) collected from desert and non-desert environments and
 measured gene expression and organismal phenotypes under control and
 water-stressed conditions. After many generations in the lab, desert mice
 consumed significantly less water than mice from other localities,
 indicating that this difference has a genetic basis. Under water-stress,
 desert mice maintained more weight than non-desert mice, and exhibited
 differences in blood chemistry related to osmoregulatory function. Gene
 expression in the kidney revealed evolved differences between mice from
 different environments as well as plastic responses between hydrated and
 dehydrated mice. Desert mice showed reduced expression plasticity under
 water-stress compared to non-desert mice. Importantly, non-desert mice
 under water-stress generally showed shifts towards desert-like expression,
 consistent with adaptive plasticity. Finally, we identify several
 co-expression modules linked to phenotypes of interest. These findings
 provide evidence for local adaptation after a recent invasion and suggest
 that adaptive plasticity may have facilitated colonization of the desert
 environment.
description: Phenotype data associated with study on plastic and evolved
 responses to water stress in <em>Mus musculus</em>. Files
 contain 1) water consumption measurements from inbred lines derived
 from five populations of North American house mice in a controlled lab
 environment and 2) phenotype data measured from control and water stressed
 treatment mice.
DOI: 10.5061/dryad.866t1g1pt
title: Data from: DNA methylation changes associated with type 2 diabetes and diabetic kidney disease in an East Asian population

description: Objective: There is growing body of evidence that epigenetic changes
 including DNA methylation influence the risk of type 2 diabetes and its
 microvascular complications. We conducted a methylome-wide association
 study (MWAS) to identify differentially methylated regions (DMRs) of type
 2 diabetes and diabetic kidney disease (DKD) in Korean population.
 Methods: We performed an initial MWAS in 232 participants in a
 case-control study design with type 2 diabetes and 197 non-diabetic
 controls with Illumina EPIC bead chip using peripheral blood leukocytes.
 Type 2 diabetes group was subdivided to 87 DKD cases and 80 non-DKD
 controls. Additional 819 individuals from two population-based cohorts
 were used to investigate the association of the identified DMRs with
 quantitative metabolic traits. We developed a DNA methylation score using
 identified DMRs to predict the occurrence of type 2 diabetes. To examine
 the causal relationship between the metabolic traits and differentially
 methylated status, we performed Mendelian randomization (MR) analyses.
 Results: We identified eight DMRs (each at BMP8A, NBPF20, STX18, ZNF365,
 CPT1A, and TRIM37, and two at TXNIP) which were significantly associated
 with risk of type 2 diabetes (P &lt; 9.0×10-8), including three that
 were previously known (DMRs in TXNIP and CPT1A), in 429 type 2 diabetes
 cases and controls. DNA methylation score consisted of these DMRs
 differentiated the risk of developing type 2 diabetes in an independent
 prospective cohort with a relative risk of 2.44 (95% confidence interval
 1.39–4.28) between the lowest and highest deciles of DNA methylation
 score. DMRs in CPT1A and TXNIP were associated with quantitative metabolic
 traits, including fasting glucose, HbA1c, and body mass index. We also
 identified three DMRs (on COMMD1, TMOD1, and FHOD1) associated with DKD in
 167 DKD cases and controls. The DMRs of DKD did not show meaningful
 overlap with those of type 2 diabetes. In MR analysis, the estimated
 glomerular filtration rate was causally associated with DNA methylation of
 these three DMRs. Conclusions: In an East Asian population, we identified
 eight DMRs, including five novel ones, associated with type 2 diabetes and
 three DMRs associated with DKD at methylome-wide statistical significance.
 Our findings suggest that epigenetics of DKD may share little with those
 responsible for the development of type 2 diabetes.
DOI: 10.5061/dryad.fttdz08rp
title: Ivermectin as a potential treatment for mild to moderate COVID-19 – A double blind randomized placebo-controlled trial

description: Objective: Ivermectin has been suggested as a treatment for COVID-19.This
 randomised control trial was conducted to test the efficacy of Ivermectin
 in the treatment of mild and moderate COVID-19. Design: Parallel, double
 blind, randomised, placebo controlled trial Setting: A tertiary care
 dedicated COVID-19 hospital in Bihar, India Participants: Adult patients
 (&gt; 18 years) admitted with mild to moderate COVID 19 disease
 (saturation &gt; 90% on room air, respiratory rate &lt; 30 and no
 features of shock) with no contraindications to ivermectin and willing to
 participate in the study Intervention: Patients in the intervention arm
 were given ivermectin 12 mg on day 1 and day 2 of admission. Patients in
 the placebo arm were given identical looking placebo tablets. Rest of the
 treatment was continued as per the existing protocol and the clinical
 judgment of the treating teams. Outcome Measures: The primary outcome
 measure was a negative RT-PCR test for SARS-CoV-2 on day 6 of admission.
 The secondary outcome measures were symptom status on day 6, discharge
 status on day 10, admission to ICU, need for invasive mechanical
 ventilation and in-hospital mortality. Results: A total of 115 patients
 were enrolled for the study of which 112 were included in the final
 analysis. Of them, 55 were randomised to the intervention arm while 57
 were randomised to the placebo arm. There was no significant difference in
 the baseline characteristics of the two arms. There was no significant
 difference in the primary outcome, i.e. negative RT-PCR status on day 6
 between the two groups. Similarly, there was no significant difference
 between the two groups in most of the secondary outcome measures, viz.
 symptom status on day 6, discharge status on day 10, admission to ICU, and
 need for invasive mechanical ventilation. However, while there was no
 in-hospital mortality in the intervention arm, there were 4 deaths in the
 placebo arm. As a result, all patients in the intervention arm (n=56) were
 successfully discharged as compared to 93.1% (n=54/58) in the placebo arm
 (RR 1.1, 95% CI 1.0 to 1.2, p=0.019). Conclusion: There was no difference
 in the primary outcome i.e. negative RT-PCR status on day 6 of admission
 with the use of ivermectin. However, a significantly higher proportion of
 patients were discharged alive from the hospital when they received
 ivermectin.
DOI: 10.5061/dryad.vt4b8gtr8
title: Risky movements? Natal dispersal does not decrease survival of a large herbivore

description: Natal dispersal is assumed to be a particularly risky movement behavior as
 individuals transfer, often long distances, from birth site to site of
 potential first reproduction. Though, because this behavior persists in
 populations, it is assumed that dispersal increases the fitness of
 individuals despite the potential for increased risk of mortality. The
 extent of dispersal risk, however, has rarely been tested, especially for
 large mammals. Therefore, we aimed to test the relationship between
 dispersal and survival for both males and females in a large herbivore.
 Using a radio-transmittered sample of 398 juvenile male and 277 juvenile
 female white-tailed deer (Odocoileus virginianus), we compared survival
 rates of dispersers and non-dispersers. We predicted that dispersing deer
 would experience greater overall mortality than philopatric deer due to
 direct transfer-related risks (e.g., vehicular collision), indirect
 immigration-related mortality attributable to colonization of unfamiliar
 habitat, and increased over-winter mortality associated with energetic
 costs of movement and unfamiliarity with recently colonized habitat. For
 both male and female yearlings, survival rates of dispersers (male =
 49.9%, female = 64.0%) did not differ from non-dispersers (male = 51.6%,
 female = 70.7%). Only two individuals (both female) were killed by
 vehicular collision during transfer, and over-winter survival patterns
 were similar between the two groups. Although dispersal movement likely
 incurs energetic costs on dispersers, these costs do not necessarily
 translate to decreased survival. In many species, including white-tailed
 deer, dispersal is likely condition-dependent, such that larger and
 healthier individuals are more likely to disperse; therefore, costs
 associated with dispersal are more likely to be borne successfully by
 those individuals that do disperse. Whether low-risk dispersal of large
 mammals is the rule or the exception will require additional research.
 Further, future research is needed to evaluate non-survival
 fitness-related costs and benefits of dispersal (e.g., increased
 reproductive opportunities for dispersers).
description: These data were collected on radio-transmittered white tailed
 deer in Pennsylvania.  Data files are input files (.inp) for known-fates
 analyses in Program MARK. We have also uploaded a .pdf file that further
 explains the data.
description: Explanation of data.pdf is a file that explains the format of the
 input files.
DOI: 10.5061/dryad.z8w9ghxb8
title: Mammalian intestinal allometry, phylogeny, trophic level and climate

description: An often-stated ecomorphological assumption that has the status of
 ‘textbook knowledge’ is that the dimensions of the digestive tract
 correlate with diet, where herbivores – consuming diets of lower
 digestibility – have longer intestinal tracts than faunivores – consuming
 diets of higher digestibility. However, statistical approaches have so far
 failed to demonstrate this link. Here, we collated data on the length of
 intestinal sections and body mass of 519 mammal species, and test for
 various relationships with trophic, climatic and other biological
 characteristics. All models showed a strong phylogenetic signal. Scaling
 relationships with body mass showed positive allometry at exponents
 &gt;0.33, except for the caecum, which is particularly large in
 smaller species. Body mass was more tightly linked to small intestine than
 to large intestine length. Adding a diet proxy to the relationships
 increased model fit for all intestinal sections, except for the small
 intestine when accounting for phylogeny. Thus, diet has a main effect on
 the components of the large intestine, with longer measures in herbivores.
 Additionally, measures of habitat aridity had a positive relationship with
 large intestine length. The small intestine was longer in species from
 colder habitats at higher latitudes, possibly facilitating the processing
 of peak intake rates during the growing season. This study corroborates
 intuitive expectations on digestive tract anatomy, while the dependence of
 significant results on large sample sizes and inclusion of specific
 taxonomic groups indicates that the relationships cannot be considered
 fixed biological laws.
description: Data on mammal intestinal length was collated as original data
 (MammalIntestine_Data.xlsx, first sheet) from the literature
 (MammalIntestine_Data_References.docx). Subsequently, weighted averages
 were calculated per species for each intestinal section separately, and
 supplemented with species-specific biological information
 (MammalIntestine_Data.xlsx, second sheet). This information contains a
 species label that corresponds to the species label in the phylogenetic
 tree (MammalIntestine_Phylogeny.txt).
description: Missing values correspond to missing values in the original
 literature and are indicated by empty cells.
DOI: 10.5061/dryad.1rn8pk0sh
title: Comparing ultraconserved elements and exons for phylogenomic analyses of Middle American cichlids: When data agree to disagree

description: Choosing among types of genomic markers to be used in a phylogenomic study
 can have a major influence on the cost, design, and results of a study.
 Yet few attempts have been made to compare categories of next-generation
 sequence markers limiting our ability to compare the suitability of these
 different genomic fragment types. Here we explore properties of different
 genomic markers to find if they vary in the accuracy of component
 phylogenetic trees and to clarify the causes of conflict obtained from
 different datasets or inference methods. As a test case, we explore the
 causes of discordance between phylogenetic hypotheses obtained using a
 novel dataset of ultraconserved elements (UCEs) and a recently published
 exon dataset of the cichlid tribe Heroini. Resolving relationships among
 heroine cichlids has historically been difficult, and the processes of
 diversification and colonization of Middle America and the Greater
 Antilles are not yet well understood. Despite differences in
 informativeness and levels of gene tree discordance between UCEs and
 exons, the resulting phylogenomic hypotheses generally agree on most
 relationships. The independent datasets disagreed in areas with low
 phylogenetic signal that were overwhelmed by noise and non-phylogenetic
 signals. For UCEs, high levels of incomplete lineage sorting (ILS) seem to
 be a major cause of noise, whereas, for exons, non-phylogenetic signal may
 be caused by a reduced number of highly informative loci. This paucity of
 informative loci in exons might be due to heterogeneous substitution rates
 that are problematic to model (i.e., computationally restrictive)
 resulting in systematic errors that UCEs (being less informative
 individually but more uniform) are less prone to. These results generally
 demonstrate the robustness of phylogenomic methods to accommodate genomic
 markers with different biological and phylogenetic properties. However, we
 identify common and unique pitfalls of different categories of genomic
 fragments when inferring enigmatic phylogenetic relationships.
DOI: 10.5061/dryad.0p2ngf20h
title: Species abundance along the railway of Kashmir Himalaya

description: 1. The significant portion of global terrestrial biodiversity
 harbored in mountains is under increasing threat from a variety of
 anthropogenic impacts. Protecting fragile mountain ecosystems requires
 understanding how these human disturbances affect biodiversity. As roads
 and railways are extended further into mountain ecosystems, understanding
 the long-term impacts of this infrastructure on community composition and
 diversity gains urgency. 2. We used railway corridors constructed across
 the mountainous landscapes of the Kashmir Himalaya from 1994-2013 to study
 the effects of anthropogenic disturbance on species’ distributions and
 community dynamics. In 2014 and 2017, we collected vegetation data along
 31 T-shaped transects laid perpendicular to the railway line, adopting the
 MIREN (Mountain Invasion Research Network) road survey
 methodology.  3. Plant communities shifted significantly
 from 2014 to 2017, potentially as a result of ongoing species’
 redistribution after railway construction, mostly driven by declines in
 both native and non-native species richness, and increasing abundance of a
 few non-native species, especially in areas away from the railway
 track.  4. These patterns indicate an advancing succession, where
 initial – rare – pioneering species are replaced by increasingly dominant
 and often non-native competitors, and potentially suggest a trend towards
 delayed local extinctions after the disturbance event. Native and
 non-native species richness were negatively correlated with elevation, but
 that relationship diminished over time, with the abundance of non-natives
 significantly increasing at high elevations.  5. Synthesis and
 applications: Transport corridors seem to facilitate the spread of
 non-native species to higher elevations, which has serious implications in
 light of the warming mountain tops. Our results indicate that plant
 communities next to railways do not reach equilibrium quickly after
 disturbance. More than 10 years after railway establishment succession
 continued, and signs pointed in the direction of a landscape increasingly
 dominated by non-native species. Our study indicates that the single
 disturbance event associated with construction of a railway in the
 Himalayas had large and long-lasting effects on plant communities at and
 around this transport corridor, and suggests the need for a long-term
 region-wide coordinated monitoring and management program. 
description: The entire stretch of the railway going through the Kashmir
 region was divided into 31 sites consisting of 16 stations and 15
 between-station sites, spanning an elevational gradient from 1591 to 1741
 m a.s.l. All these selected sites were first sampled during 2014 and then
 resampled during 2017.
DOI: 10.5061/dryad.g79cnp5p8
title: Highly porous Co-doped NiO nanorods: Facile hydrothermal synthesis and electrocatalytic oxygen evolution properties

description: Highly porous 3d transition metal oxide nanostructures are opening up the
 exciting area of oxygen evolution reaction (OER) catalysts in alkaline
 medium thanks to their good thermal and chemical stability, excellent
 physiochemical properties, high specific surface area and abundant
 nanopores. In this paper, highly porous Co-doped NiO nanorods were
 successfully synthesized by a simple hydrothermal method. The porous
 rod-like nanostructures were preserved with the added cobalt dopant
 ranging from 1 to 5 at% but were broken into aggregated nanoparticles at
 higher concentrations of additional cobalt. The catalytic activity of
 Co-doped NiO nanostructures for OER in an alkaline medium was assayed. The
 5%Co-NiO sample showed a drastically enhanced activity. This result could
 originate from the combination of advantageous characteristics of highly
 porous NiO nanorods such as large surface area and high porosity as well
 as the important role of Co dopant that could provide more catalytic
 active sites, leading to an enhanced catalytic activity of the
 nanocatalyst.
DOI: 10.5061/dryad.c2fqz6173
title: Risso’s dolphins perform spinning dives to target deep-dwelling prey

description: Foraging decisions of deep-diving cetaceans can provide fundamental
 insight into food web dynamics of the deep pelagic ocean. Cetacean optimal
 foraging entails a tight balance between oxygen-conserving dive strategies
 and access to deep-dwelling prey of sufficient energetic reward. Risso’s
 dolphins (Grampus griseus) displayed a thus far unknown dive strategy,
 which we termed the spin dive. Dives started with intense stroking and
 right-sided lateral rotation. This remarkable behaviour resulted in rapid
 descent. By tracking the fine-scale foraging behaviour of 7 tagged
 individuals, matched with prey-layer recordings, we tested the hypothesis
 that spin dives are foraging dives targeting deep-dwelling prey. Hunting
 depth traced the diel movement of the deep scattering layer, a dense
 aggregation of prey, that resides deep during the day and near-surface at
 night. Individuals shifted their foraging strategy from deep spin dives to
 shallow non-spin dives around dusk. Spin dives were significantly faster,
 steeper and deeper than non-spin dives, effectively minimizing transit
 time to bountiful mesopelagic prey, and were focussed on periods when the
 migratory prey might be easier to catch. Hence, whereas Risso’s dolphins
 were mostly shallow, nocturnal foragers, their spin dives enabled extended
 and rewarding diurnal foraging on deep-dwelling prey.
description: This data was collected using Dtags and analysed using (adapted)
 scripts from the dtag toolbox.
description: Data represent means per tag record per dive class.
DOI: 10.6086/d18d7b
title: Pre-dispersal seed predation obscures the detrimental effect of dust on wildflower reproduction - flowering and egg phenology

description:             Premise of the Research.  Seed production by flowering plants depends on abiotic and biotic factors whose interacting effects may be hidden. We previously reported that exposure to dust from unpaved roads reduced the average amount of pollen on flowers of Ipomopsis aggregata, but did not consistently reduce mean seed set per fruit.  Here we explore one possible explanation—that the expected detrimental effect of lower pollen loads on seed production was obscured because dust reduces not only pollination success but also attack by a pre-dispersal seed predator.              Methodology.  Over three consecutive summers we scored the fates of over 4,000 flowers, comparing those on hand-dusted I. aggregata plants to those on clean control plants in the same natural populations.  We censused plants throughout each flowering season, marking phenological cohorts of flowers and examining them for eggs of the Anthomyiid fly Hylemya sp.  We subsequently scored expanded fruits for seed loss to Hylemya larvae.             Pivotal Results.  Control plants consistently had higher egg loads and rates of seed loss to larvae than dusty plants.  Furthermore, most eggs appeared early in the season when flowers are most likely to set fruit and ovule numbers are highest.  In agreement with earlier studies, unparasitized fruits from dusty plants did not contain fewer seeds than fruits from control plants.  But when we simulated a system without Hylemya by assigning each parasitized fruit the average number of seeds for unparasitized flowers in the same phenological cohort, control plants out-produced dusty plants.             Conclusions.  Pre-dispersal seed predation likely contributed to the previous lack of a negative effect of dust on seed set in I. aggregata.  This study illustrates how exploring unexpected experimental outcomes can reveal important ecological interactions, and how the mechanistic understanding so gained can improve the ability to generalize results to other systems.  
description: During the summers of 2016, 2017, and 2018, pairs of bolting
 Ipomopsis plants in a natural population near the Rocky Mountain
 Biological Laboratory in West-Central Colorado, USA, were matched by
 proximity and size and randomly assigned to receive a hand-dusting or
 control treatment that was administered throughout the flowering period. 
 Once flowering began, plants were censused every 4 days to record the
 number of elongated buds and flowers present and their Hylemya egg loads. 
 The dataset summarizes, for each year, plant, and census, the total number
 of elongated buds, open flowers, and senesced flowers, and the number of
 each floral category with 1 egg or 2 eggs.  No flower was observed with
 more than 2 eggs.
description: Two files have been uploaded:
 Flower_and_Hylemya_Egg_CensusREADME.docx     
 This file contains variable definitions
 Flower_and_Hylemya_Egg_Census_DATA.txt     
 This text file contains the data.  Missing values are coded with a
 period.<br>