cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qrfj6q5h2
title: Evolutionary allometry of sexual dimorphism of jumping performance in anurans

description: Sexual dimorphism is a common feature in animals, yet the degree of sexual
 dimorphism is not constant across taxa. Sometimes the magnitude of sexual
 dimorphism varies systematically with body size, resulting in evolutionary
 allometry of sexual dimorphism. While such patterns are commonly
 investigated for traits such as overall size, allometric variation in
 sexual dimorphism of other traits remains underexplored. Here, we
 characterize the evolutionary allometry of sexual dimorphism in a
 functional phenotypic trait (jumping performance) in anurans. Using
 morphology and anatomical approximations of jumping performance across 146
 species, we test for evidence of the correlated selection model of sexual
 dimorphism evolution. We analyze patterns of evolutionary allometry of
 sexual dimorphism in key phenotypic traits, including: body size
 (snout-vent length and mass), relative leg length, relative leg muscle
 volume, mass-specific peak jumping energy, and peak jumping velocity. We
 find that as previously reported, sexual size dimorphism scales
 isometrically between species and is independent of sexual dimorphism in
 jumping performance. Notably, however, we found significant trends in the
 evolutionary allometry of sexual dimorphism in relative limb length, and
 in two components of jumping performance. Additionally, we found greater
 rates of evolution for females versus males in relative limb length, but
 not jumping performance. We also observed that the allometric trends in
 limb length dimorphism were related to performance allometry. Sexual
 dimorphism in jumping performance increased in species with high
 performance while females in high performance species displayed increased
 relative limb length. Thus, we hypothesize that selection acting on
 functional performance explains allometric patterns of sexual dimorphism
 in morphology. We discuss biological implications of our findings in
 relation to natural and sexual selection. This study highlights the types
 of insights one may gain by studying the allometry of sexual dimorphism
 from a functional perspective to learn about both patterns and processes
 in evolution.
description: Anatomical data were obtained from museum specimens and
 microhabitat data were obtained from online databases and the literature.
 Please see original manuscript for details on several ways in which the
 data were filtered.
description: Raw values included here do not represent final values analyzed
 in the manuscript. Please see original manuscript for details. Some
 missing values are included, which are accounted for in the analyses,
 please see manuscript.
DOI: 10.5068/d1hx1d
title: Analysis of independent cohorts of outbred CFW mice reveals novel loci for behavioral and physiological traits and identifies factors determining reproducibility

description: Combining samples for genetic association is standard practice in human
 genetic analysis of complex traits, but is rarely undertaken in rodent
 genetics. Here, using 23 phenotypes and genotypes from two independent
 laboratories, we obtained a sample size of 3,076 commercially available
 outbred mice and identified 70 loci, more than double the number of loci
 identified in the component studies. Fine-mapping in the combined sample
 reduced the number of likely causal variants, with a median reduction in
 set size of 51%, and indicated novel gene associations, including Pnpo,
 Ttll6 and GM11545 with bone mineral density, and Psmb9 with weight.
 However replication at a nominal threshold of 0.05 between the two
 component studies was low, with less than a third of loci identified in
 one study replicated in the second.  In addition to overestimates
 in the effect size in the discovery sample (Winner’s Curse), we also found
 that heterogeneity between studies explained the poor replication, but the
 contribution of these two factors varied among traits. Available methods
 to control Winner’s Curse were contingent on the power of the discovery
 sample, and depending on the method used, both overestimated and
 underestimated the true effect.  Leveraging these observations we
 integrated information about replication rates, study-specific
 heterogeneity, and Winner’s Curse corrected estimates of power to assign
 variants to one of four confidence levels. Our approach addresses concerns
 about reproducibility, and demonstrates how to obtain robust results from
 mapping complex traits in any genome-wide association study.
DOI: 10.5061/dryad.12jm63xzt
title: Tspe_v1 (Telopea speciosissima) genome supplementary files for: Chromosome-level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long-reads, linked-reads and Hi-C

description: Telopea speciosissima, the New South Wales waratah, is an Australian
 endemic woody shrub in the family Proteaceae. Waratahs have great
 potential as a model clade to better understand processes of speciation,
 introgression and adaptation, and are significant from a horticultural
 perspective. Here, we report the first chromosome-level genome for T.
 speciosissima. Combining Oxford Nanopore long-reads, 10x Genomics Chromium
 linked-reads and Hi-C data, the assembly spans 823 Mb (scaffold N50 of
 69.0 Mb) with 97.8 % of Embryophyta BUSCOs ‘Complete’. We present a new
 method in Diploidocus (https://github.com/slimsuite/diploidocus) for
 classifying, curating and QC-filtering scaffolds, which combines read
 depths, k-mer frequencies and BUSCO predictions. We also present a new
 tool, DepthSizer (https://github.com/slimsuite/depthsizer), for genome
 size estimation from the read depth of single-copy orthologues and
 estimate the genome size to be approximately 900 Mb. The largest 11
 scaffolds contained 94.1 % of the assembly, conforming to the expected
 number of chromosomes (2n = 22). Genome annotation predicted 40,158
 protein-coding genes, 351 rRNAs and 728 tRNAs. We investigated CYCLOIDEA
 (CYC) genes, which have a role in determination of floral symmetry, and
 confirm the presence of two copies in the genome. Read depth analysis of
 180 ‘Duplicated’ BUSCO genes using a new tool, DepthKopy
 (https://github.com/slimsuite/depthkopy), suggests almost all are real
 duplications, increasing confidence in the annotation and highlighting a
 possible need to revise the BUSCO set for this lineage. The
 chromosome-level T. speciosissima reference genome (Tspe_v1) provides an
 important new genomic resource of Proteaceae to support the conservation
 of flora in Australia and further afield.
description: <strong>Chen et al. Molecular Ecology
 Resources</strong><br> Tspe_v1_Chen_et_al.zip. The zip
 directory contains files for tracks available on the Apollo genome browser
 (genome, gaps, mapped ONT and 10x reads and annotations), protein
 sequences from the GeMoMa genome annotation, BUSCOMP full html reports,
 and files from HAQESAC phylogenetic analysis of BUSCO genes.
DOI: 10.5061/dryad.bk3j9kdcz
title: Counting the bodies: estimating the numbers and spatial variation of Australian reptiles, birds and mammals killed by two invasive mesopredators

description: Aim: Introduced predators negatively impact biodiversity globally, with
 insular fauna often most severely affected. Here, we assess spatial
 variation in the number of terrestrial vertebrates (excluding amphibians)
 killed by two mammalian mesopredators introduced to Australia, the red fox
 (Vulpes vulpes) and feral cat (Felis catus). We aim to identify prey
 groups that suffer especially high rates of predation, and regions where
 losses to foxes and/or cats are most substantial. Location: Australia
 Methods: We draw information on the spatial variation in tallies of
 reptiles, birds and mammals killed by cats in Australia from published
 studies. We derive tallies for fox predation by (i) modelling
 continental-scale spatial variation in fox density, (ii) modelling spatial
 variation in the frequency of occurrence of prey groups in fox diet, (iii)
 analysing the number of prey individuals within dietary samples, and (iv)
 discounting animals taken as carrion. We derive point estimates of the
 numbers of individuals killed annually by foxes and by cats, and map
 spatial variation in these tallies. Results: Foxes kill more reptiles,
 birds and mammals (peaking at 1,071 km-2 yr-1) than cats (55 km-2 yr-1)
 across most of the unmodified temperate and forested areas of mainland
 Australia, reflecting the generally higher density of foxes than cats in
 these environments. However, across most of the continent – mainly the
 arid central and tropical northern regions (and on most Australian
 islands) – cats kill more animals than foxes. We estimate that foxes and
 cats together kill 697 million reptiles annually in Australia, 510 million
 birds and 1435 million mammals. Main conclusions: This continental-scale
 analysis demonstrates that predation by two introduced species takes a
 substantial and ongoing toll on Australian reptiles, birds and mammals.
 Continuing population declines and potential extinctions of some of these
 species threatens to further compound Australia’s poor contemporary
 conservation record.
description: See manuscript "Counting the bodies: estimating the numbers
 and spatial variation of Australian reptiles, birds and mammals killed by
 two invasive mesopredators" for Methods description.
DOI: 10.5061/dryad.3tx95x6h4
title: Inner hair cell dysfunction in Klhl18 mutant mice leads to low frequency progressive hearing loss

description: Age-related hearing loss in humans (presbycusis) typically involves
 impairment of high frequency sensitivity before becoming progressively
 more severe at lower frequencies. Pathologies initially affecting lower
 frequency regions of hearing are less common. Here we describe a
 progressive, predominantly low-frequency recessive hearing impairment in
 two mutant mouse lines carrying different mutant alleles of the Klhl18
 gene: a spontaneous missense mutation (Klhl18lowf) and a targeted mutation
 (Klhl18tm1a(KOMP)Wtsi). Both males and females were studied, and the two
 mutant lines showed similar phenotypes. Threshold for auditory brainstem
 responses (ABR; a measure of auditory nerve and brainstem neural activity)
 were normal at 3 weeks old but showed progressive increases from 4 weeks
 onwards. In contrast, distortion product otoacoustic emission (DPOAE)
 sensitivity and amplitudes (a reflection of cochlear outer hair cell
 function) remained normal in mutants. Electrophysiological recordings from
 the round window of Klhl18lowf mutants at 6 weeks old revealed 1) raised
 compound action potential thresholds that were similar to ABR thresholds,
 2) cochlear microphonic potentials that were normal compared with wildtype
 and heterozygous control mice and 3) summating potentials that were
 reduced in amplitude compared to control mice. Scanning electron
 microscopy showed that Klhl18lowf mutant mice had abnormally tapering of
 the tips of inner hair cell stereocilia in the apical half of the cochlea
 while their synapses appeared normal. These results suggest that Klhl18 is
 necessary to maintain inner hair cell stereocilia and normal inner hair
 cell function at low frequencies.
DOI: 10.5061/dryad.qv9s4mwfn
title: Supporting data and software for: Low-temperature open-air synthesis of PVP-coated NaYF4:Yb,Er,Mn upconversion nanoparticles with strong red emission

description: Upconversion nanoparticles (UCNPs) have unique photonic properties that
 make them ideally suited for many applications. They are excited by
 low-energy near-infrared photons and emit at higher energy (typically
 visible) wavebands. However, synthesis of UCNPs requires either high
 pressure reaction chambers or inert atmospheres. Combined with the
 requirements for high-temperatures (200 to 400 °C) and long reaction times
 (e.g. up to 24 hours), these place barriers to entry for UCNP research, in
 terms of both financial barriers and knowledge/"know how". These
 constraints may also limit the scale of UCNP production for end-user
 applications. We adapted and further developed a method for producing
 UCNPs with simple laboratory equipment, i.e. a hot-plate and beakers. No
 pressure vessel or inert atmosphere is required. The UCNPs produced have a
 polyvinylpyrrolidone (PVP) polymer coating, with strong red emission due
 to Mn2+ co-doping within the UCNP crystal lattice. It was found that UCNPs
 of composition NaYF4:Yb,Er,Mn  (Yb = 20 mol %, Er = 2 mol%, Mn =
 35 mol%) maximised the red emission whilst also minimising the diameter of
 the UCNPs to 36 ± 15 nm. These combination of optical and physical
 properties should make these UCNPs ideal for further development and
 exploitation, particularly for biological applications where red emission
 can penetrate over a centimetre of tissue. This dataset and software
 accompanies the manuscript 'Low-temperature open-air synthesis of
 PVP-coated NaYF4:Yb,Er,Mn upconversion nanoparticles with strong red
 emission', which was published in Royal Society Open Science on 19th
 January 2022. https://doi.org/10.1098/rsos.211508
description: The dataset comprises data characterising upconversion
 nanoparticles  synthesised  via the PVP40 route. The data is primarily
 transmission electron microscopy (TEM) images, scanning electron
 microscopy (SEM) images, powder x-ray diffraction (XRD) patterns, and
 upconversion luminesence emission spectra. Data is provided alongside
 custom-written Matlab scripts for processing and display of data where
 appropriate.
description: Please refer to README file.
DOI: 10.5061/dryad.p2ngf1vrg
title: Intracranial aneurysm risk scores, hemodynamics and vessel wall enhancement values

description: Vessel wall enhancement (VWE) in contrast-enhanced magnetic resonance
 imaging (MRI) is a potential biomarker for intracranial aneurysm (IA) risk
 stratification. In this study, we investigated the relationship between
 VWE features, risk metrics, morphology, and hemodynamics in 41 unruptured
 aneurysms. We reconstructed the IA geometries from MR angiography and
 mapped pituitary stalk-normalized MRI intensity on the aneurysm surface
 using an in-house tool. For each case, we calculated the maximum intensity
 (CRstalk) and IA risk (via size and the rupture resemblance score-RRS). We
 performed correlation analysis to assess relationships between CRstalk and
 IA risk metrics (size and RRS), as well as each parameter encompassed in
 RRS, i.e. aneurysmal Size Ratio (SR), normalized wall shear stress (WSS),
 and oscillatory shear index (OSI). We found that CRstalk had a strong
 correlation (Pearson correlation coefficient, PCC=0.630) with size and a
 moderate correlation (PCC=0.472) with RRS, indicating an association
 between VWE and IA risk. Furthermore, CRstalk had a weak negative
 correlation with normalized WSS (PCC=-0.320) and a weak positive
 correlation with SR (PCC= 0.390). Local voxel-based analysis showed only a
 weak negative correlation between normalized WSS and contrast-enhanced MRI
 signal intensity (PCC=-0.240), suggesting that if low normalized WSS
 induces enhancement-associated pathobiology, the effect is not localized.
DOI: 10.5061/dryad.5hqbzkh6m
title: Data for: Time at risk: Individual spatial behaviour drives effectiveness of marine protected areas and fitness

description: The effectiveness of Marine Protected Areas (MPAs) depends on the mobility
 of the populations that are the target of protection, with sedentary
 species likely to spend more time under protection even within small MPAs.
 However, little is understood about how individual variation in mobility
 may influence the risk of crossing an MPA border, as well as the fitness
 costs associated with being exposed to spillover fisheries. Here we
 investigated the repeatability of spatial behaviour, its role in
 determining the probability of being at risk (i.e. exposed to the fishery)
 and the fitness consequences for the individuals. We acoustically tracked
 the movements and fate of 282 individuals of three fish species during
 8 years in a southern Norwegian fjord. We found that for
 individuals with a home range centroid inside the MPA, the probability of
 being at risk outside the MPA increased rapidly with reduced distance from
 the home range centroid to MPA borders, particularly for individuals
 having larger and more dispersed home ranges. We also detected that the
 seasonal expansions of the home range are associated with increased time
 at risk. Last, we show that individuals spending more time at risk were
 also more likely to be harvested by the fishery operating outside the MPA.
 Our study provides clear links between individual fish behaviour,
 fisheries-induced selection, and the effectiveness of protected areas.
 These links highlight the importance of intraspecific trait variation for
 understanding the spatial dynamics of populations and emphasize the need
 to consider individual behaviour when designing and implementing MPAs.
description: Acoustic telemetry.
description: There is one file per species and year of tagging. Each file is
 an R object. Opening it with R, the estimated centers of activity for each
 group of fish will be shown. These centers of activity are then used for
 subsequent analyses. An excel file is also provided
 containing the biological characteristics of the tagged animals.
DOI: 10.5061/dryad.mpg4f4r16
title: Determinants of nest box local recruitment and natal dispersal in a declining bird population

description: Recruitment and dispersal are important demographic rates and studying
 their determinants is particularly important in the current context of
 global anthropogenic perturbations. In birds, and especially for migratory
 species, assessing these rates is challenging because of the difficulties
 involved in tracking individuals beyond fledging. Here we assessed the
 determinants of nest box local recruitment and natal dispersal distances
 in a declining aerial insectivore, the Tree swallow (Tachycineta bicolor).
 We used a 16-year dataset obtained from the long-term monitoring of a
 population breeding within a 10,200-km2 study system located along a
 gradient of agricultural intensification in southern Québec, Canada.
 Yearly nest box local recruitment rates ranged there in between 1.0% and
 3.2%. Heavier nestlings who fledged earlier were more likely to recruit.
 Natal dispersal distances were generally short (mean ± SD = 12.7 ± 13.8
 km) in the study system and were influenced by different factors depending
 on sex. Females dispersed over shorter distances when conspecific
 occupancy on breeding site was high, while males dispersed farther in the
 presence of competing House sparrows (Passer domesticus) and when their
 mother was young. Selection of breeding locations appeared to take place
 at multiple scales and individuals recruited in sites with characteristics
 similar to their natal sites. Our results provide important information
 concerning the factors influencing nest box local recruitment and natal
 dispersal dynamics of this migratory species. These factors should be
 considered in conservation practices for this species in order to support
 production of recruits in habitats favorable to their survival.
DOI: 10.6086/d1w10g
title: Isotopic signatures of methane emissions from dairy farms in California's San Joaquin Valley

description: In this study, we present seasonal atmospheric measurements of δ13CCH4
 from dairy farms in the San Joaquin Valley of California. We used δ13CCH4
 to characterize emissions from enteric fermentation by measuring downwind
 of cattle housing (e.g., freestall barns, corrals) and from manure
 management areas (e.g., anaerobic manure lagoons) with a mobile platform
 equipped with cavity ring-down spectrometers. Across seasons, the δ13CCH4
 from enteric fermentation source areas ranged from -69.7 ± 0.6 per mil (‰)
 to -51.6 ± 0.1‰ while the δ13CCH4 from manure lagoons ranged from -49.5 ±
 0.1‰ to -40.5 ± 0.2‰. Measurements of δ13CCH4 of enteric CH4 suggest a
 greater than 10‰ difference between cattle production groups in accordance
 with diet. Isotopic signatures of CH4 were used to characterize enteric
 and manure CH4 from downwind plume sampling of dairies. Our findings show
 that δ13CCH4 measurements could improve the attribution of CH4 emissions
 from dairy sources at scales ranging from individual facilities to regions
 and help constrain the relative contributions from these different sources
 of emissions to the CH4 budget.
DOI: 10.5061/dryad.g1jwstqrr
title: Plant-pollinator specialization: Origin and measurement of curvature

description: A feature of biodiversity is the abundance of curves displayed by organs
 and organisms. Curvature is a widespread, convergent trait that has
 important ecological and evolutionary implications. In pollination
 ecology, the curvature of flowers and pollinator mouthparts (e.g.
 hummingbird bills) along the dorsiventral plane has been associated with
 specialization, competition, and species co-existence. Six methods have
 historically been used to measure curvature in pollination systems; we
 provide a solution to this inconsistency by defining curvature using
 well-established concepts from differential geometry. Intuitively,
 curvature is the degree to which a line is not straight, but more
 formally, it is the rate at which the tangent of a curve changes direction
 with respect to arc length. Here, we establish a protocol wherein a line
 is fitted against landmarks placed on an image of a curved organ or
 organism, then curvature is computed at many points along the fitted line
 and the sum taken. The protocol is demonstrated by studying the
 development of nectar spur curvature in the flowering plant genus
 Epimedium (Berberidaceae). By clarifying the definition of curvature, our
 aim is to make the language of comparative morphology more precise and
 broadly applicable to capture other curved structures in nature.
description: This dataset is primarily an RStudio project. To run the .R
 files, we recommend first opening the .RProj file in RStudio and
 installing the package `here`. This will allow you to run all of the .R
 scripts without changing any of the working directories.
DOI: 10.5061/dryad.mgqnk990x
title: Data from: Comparison between the kinematics for kangaroo rat hopping on a solid versus sand surface

description: In their natural habitats, animals move on a variety of substrates,
 ranging from solid surfaces to those that yield and flow (e.g., sand).
 These substrates impose different mechanical demands on the
 musculoskeletal system and may therefore elicit different locomotion
 patterns. The goal of this study is to compare bipedal hopping by desert
 kangaroo rats (Dipodomys deserti) on a solid versus granular substrate
 under speed-controlled conditions. To accomplish this goal, we developed a
 rotary treadmill, which is able to have different substrates or uneven
 surfaces. We video recorded six kangaroo rats hopping on a solid surface
 versus sand at the same speed (1.8 m/s) and quantified the differences in
 the hopping kinematics between the two substrates. We found no significant
 differences in the hop period, hop length, or duty cycle, showing that the
 gross kinematics on the two substrates were similar. This similarity was
 surprising given that sand is a substrate that absorbs mechanical energy.
 Measurements of the penetration resistance of the sand showed that the
 combination of the sand properties, toeprint area, and kangaroo rat weight
 was likely the reason for the similarity.
description: Video data was digitized for joint centers. Joint angles were
 calculated from the digitized data. For the sand data, a penetrator was
 connected to a servo motor to measure force and penetration depth.
 Resistance to penetration was estimated by dividing change in force by
 change in depth.
description: Analysis code is in written in Matlab. Readme file contains
 description of data and analysis software.