cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tdz08kq3f
title: Evolutionary conservation and diversification of auditory neural circuits that process courtship songs in Drosophila

description: Acoustic communication signals diversify even on short evolutionary time
 scales. To understand how the auditory system underlying acoustic
 communication could evolve, we conducted a systematic comparison of the
 early stages of the auditory neural circuit involved in song information
 processing between closely-related fruit-fly species. Male Drosophila
 melanogaster and D. simulans produce different sound signals during mating
 rituals, known as courtship songs. Female flies from these species
 selectively increase their receptivity when they hear songs with
 conspecific temporal patterns. Here, we first confirmed interspecific
 differences in temporal pattern preferences; D. simulans preferred pulse
 songs with longer intervals than D. melanogaster. Primary and secondary
 song-relay neurons, JO neurons and AMMC-B1 neurons, shared similar
 morphology and neurotransmitters between species. The temporal pattern
 preferences of AMMC-B1 neurons were also relatively similar between
 species, with slight but significant differences in their band-pass
 properties. Although the shift direction of the response property matched
 that of the behavior, these differences are not large enough to explain
 behavioral differences in song preferences. This study enhances our
 understanding of the conservation and diversification of the architecture
 of the early-stage neural circuit which processes acoustic communication
 signals.
DOI: 10.5061/dryad.w3r2280vc
title: Thesis: Morphological disparity across clades: Correlates, limitations and alternatives – Chapter 6: What determines disparity in avian clades?

description: Morphological disparity is an aspect of avian evolution that remains
 understudied and has rarely been quantified explicitly, despite its
 importance for inferring patterns of avian evolution. Morphological and
 molecular data are now routinely used both in combination and in isolation
 to infer phylogeny and to study evolutionary rates. Similarly, parallel
 studies of phylogeny, diversity and morphological disparity are now
 commonplace in both the neontological and palaeontological literature
 (Giribet, 2015; Bromham et al., 2002; Hopkins and Gerber, 2017; Deline et
 al., 2018; Prum et al., 2015). Most recently, the concept of molecular
 disparity has been introduced as an analogue of morphological disparity,
 although there are few studies that attempt to deploy it (Deline et al.,
 2018; van den Ende et al., 2022). This chapter addresses ten related
 questions using the largest available morphological and molecular data set
 for birds.
description: This dataset was collated from publicly available resources. All
 previously published datasets were extensively modified in order to ensure
 consistent sampling across orders and genera.  We
 obtained DNA sequences for 1104 loci of 104 bird species from https://b10k.genomics.cn/. The morphological data contained herein is a pruned matrix originally published by Livezey and Zusy (2006). https://doi.org/10.2992/0145-9058(2006)37[1:PON]2.0.CO;2 Annual temperature, latitude, body mass, geographic range and HWI were obtained from Sheard et al., (2020) https://doi.org/10.5281/zenodo.3747657 Evolutionary Distinctiveness scores were obtained from Jetz et al., (2014) https://doi.org/10.1016/j.cub.2014.03.011
description: The molecular sequence data
 with the .fas extension can be read in R using the package <em>Ape
 </em>and viewed with AliView. The morphological datasets with the
 .nex extension can be opened with Mesquite and read in R using the
 package <em>Claddis</em>.
DOI: 10.25338/b8264p
title: Data from: Measuring motivation for forage in feedlot cattle fed a high-concentrate diet using a short-term thwarting test

description: A thwarting test, where animals are able to interact with feed but not
 consume it, can be used to measure how valued the resource is. It is
 expected that feedlot cattle will be motivated to access additional
 roughage because of its potential to alleviate symptoms of ruminal
 acidosis caused by high-concentrate rations. The objective of this study
 was to measure how motivated cattle fed a high-concentrate diet are to
 access additional forage, when offered it freely for 8 short exposures
 before being prevented from consuming the resource, in a thwarting test.
 Eighteen animals, fed a finishing ration ad-libitum, were offered a small
 amount of either beardless wheat hay (WH; n=9) or their primary diet (TMR;
 n=9) in a plastic bin twice daily for a maximum of 1 h over 4 d (exposures
 1-8). Then on the 5th day (thwarting test), animals were given access to
 but prevented from consuming their treatment diet by covering it with wire
 for 30 min. There was no evidence of treatment differences detected during
 the thwarting test. This may indicate there was adequate roughage in the
 primary diet to satisfy motivation for thwarted WH. Animals were quick to
 approach the treatments (average latency less than 30 s) during the test,
 possibly indicating motivation to access both. Unlike the thwarting test,
 behavioural responses to the treatments differed in the exposures, when
 cattle showed more interest in the TMR than the WH. Interacting with the
 bin by moving it with their muzzles was observed more often for TMR
 animals than WH animals in exposures 7 and 8 (P=0.07 and 0.04,
 respectively). There was no evidence that latency to approach the bin
 differed by treatment or exposure (P&gt;0.1). These findings provide
 some evidence in support the theory that animals will seek out a
 high-energy diet such as the TMR, because it is more calorically-dense,
 and likely more palatable. However, these data do not support the
 hypothesis that finishing cattle will be more motivated to access WH than
 TMR when thwarted from doing so.
description: Please see the associated research publication for methodological
 details. 
description: Please see the assoicated README file.
DOI: 10.5061/dryad.g4f4qrftn
title: Ectopic expression of murine CD163 enables cell-culture isolation of lactate dehydrogenase-elevating (LDV) virus 63 years after its discovery

description: Arteriviruses are RNA viruses related to coronaviruses but have not yet
 been associated with human infection. A murine arterivirus (lactate
 dehydrogenase-elevating virus, LDV) was first described in 1960 and
 quickly became a promising model for understanding immune failure due to
 its unique ability to persist in immunocompetent adult mice. However,
 inability to culture LDV in vitro ultimately limited this system. Here, we
 demonstrate that the macrophage marker CD163 is essential for LDV
 infection. Expression of the murine homolog (mCD163) in otherwise
 mCD163-negative cell lines from mice and nonhuman primates enables
 productive LDV infection, creating the first immortalized cell-culture
 system. We also show that mCD163-knockout mice are completely resistant to
 LDV infection. These findings advance LDV as a model of arterivirus
 infection viral persistence and add to a growing body of literature
 suggesting that CD163 utilization is a broad feature of arteriviruses.
description: # Ectopic expression of murine CD163 enables cell-culture isolation of
 lactate dehydrogenase-elevating (LDV) virus 63 years after its discovery
 Raw data for plaque assay and qPCR experiments performed as part of this
 publication. ## Description of the data and file structure Each tab in the
 .csv file corresponds to the data from a figure. 1A: shows LDV N-gene
 copies per mL of supernatant generated from RT-qPCR with an RNA standard
 curve, expressed as a Log10 value, for 6 different cell types, with 3
 replicates. 1B: Shows RT-qPCR data for cell types shown in 1A measuring
 CD163 and beta-acin, expressed as raw Ct value. 2B: shows LDV N-gene
 copies per mL of supernatant generated from RT-qPCR with an RNA standard
 curve, expressed as a Log10 value, for different cell types with or
 without ectopic CD163, with 3 replicates. 2C: LDV N-gene copies per mL of
 supernatant generated from RT-qPCR with an RNA standard curve, expressed
 as a Log10 value, versus LDV plaque forming units, in triplicate. 3E: LDV
 strains p, c, and w plaque forming units per mL of supernatant generated
 on 3T3 cells with and without CD163 ectopic expression.  4C: LDV strains
 p, c, and w plaque forming units per mL of supernatant generated on MA-104
 cells with and without CD163 ectopic expression.  5B: LDVp viral loads,
 shown as N-gene copies per mL or plaque forming units per mL, on primary
 peritoneal macrophages. 5C: LDVp N-gene copies per mL of serum generated
 from RT-qPCR with an RNA standard curve, expressed as a Log10 value, in
 CD163 knockout or wild-type mice. 5D: LDV strains p, c, and w plaque
 forming units per mL of serum in CD163 knockout or wild-type mice. ##
 Sharing/Access information Published in the Journal of Virology. Data was
 derived from the following sources: Laboratory of Adam Bailey at
 UW-Madison
DOI: 10.15468/dl.9mvb6h
title: Occurrence Download

description: A dataset containing 179 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cherry leaf roll virus"
 ]
}

 The dataset includes 179 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003436-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.sbcc2frb4
title: Priority effects determine how dispersal affects biodiversity in seasonal metacommunities

description: The arrival order of species frequently determines the outcome of their
 interactions. This phenomenon, called the priority effect, is ubiquitous
 in nature and determines local community structure, but we know
 surprisingly little about how it influences biodiversity across different
 spatial scales. Here, we use a seasonal metacommunity model to show that
 biodiversity patterns and the homogenizing effect of high dispersal depend
 on the specific mechanisms underlying priority effects. When priority
 effects are only driven by positive frequency dependence,
 dispersal-diversity relationships are sensitive to initial conditions but
 generally show a hump-shaped relationship: biodiversity declines when
 dispersal rates become high and allow the dominant competitor to exclude
 other species across patches. When spatiotemporal variation in
 phenological differences alters species’ interaction strengths
 (trait-dependent priority effects), local, regional, and temporal
 diversity are surprisingly insensitive to variation in dispersal,
 regardless of the initial numeric advantage. Thus, trait-dependent
 priority effects can strongly reduce the effect of dispersal on
 biodiversity, preventing the homogenization of metacommunities. Our
 results suggest an alternative mechanism that maintains local and regional
 diversity without environmental heterogeneity, highlighting that
 accounting for the mechanisms underlying priority effects is fundamental
 to understanding patterns of biodiversity.
description: R code and a R markdown that generates all figures are deposited
 at Zenodo; please follow the link in the "Software"
 section.
DOI: 10.5061/dryad.qnk98sfm9
title: Data from: A mix of old British and modern European breeds: Genomic prediction of breed composition of smallholder pigs in Uganda

description: Pig herds in Africa comprise genotypes ranging from local ecotypes to
 commercial breeds. Many animals are composites of these two types and the
 best levels of crossbreeding for particular production systems are largely
 unknown. These pigs are managed without structured breeding programs and
 inbreeding is potentially limiting. The objective of this study was to
 quantify ancestry contributions and inbreeding levels in a population of
 smallholder pigs in Uganda. The study was set in the districts of Hoima
 and Kamuli in Uganda and involved 422 pigs. Pig hair samples were taken
 from adult and growing pigs in the framework of a longitudinal study
 investigating productivity and profitability of smallholder pig
 production. The samples were genotyped using the porcine GeneSeek Genomic
 Profiler (GGP) 50K SNP Chip. The SNP data was analyzed to infer breed
 ancestry and autozygosity of the Uganda pigs. The results showed that
 exotic breeds (modern European and old British) contributed an average of
 22.8% with a range of 2–50% while “local” blood contributed 69.2%
 (36.9–95.2%) to the ancestry of the pigs. Runs of homozygosity (ROH)
 greater than 2 megabase (Mb) quantified the average genomic inbreeding
 coefficient of the pigs as 0.043. The scarcity of long ROH indicated low
 recent inbreeding. We conclude that the genomic background of the pig
 population in the study is a mix of old British and modern pig ancestries.
 Best levels of admixture for smallholder pigs are yet to be determined, by
 linking genotypes and phenotypic records.
description: A sample of 422 pigs from the five districts in Uganda: Hoima
 (<em>n</em> = 163) Kamuli (<em>n</em> = 218), Kumi
 (<em>n</em> = 11), Pallisa (<em>n</em> = 12), and
 Soroti (<em>n</em> = 18) were involved in the study. A total
 of 41 animals, showing the characteristics of African pigs according to
 Blench (2000), were sampled from 41 households having been reported to
 keep local Uganda pigs by extension staff in the latter three districts.
 Prevalence of pigs with black coat color, long snout, short legs and
 popped ears, facing up and backward were criteria of selection of
 households keeping local pigs. Hair samples taken from the 422 pigs were
 genotyped using the Neogen GeneSeek Genomic Profiler (GGP) Porcine 50K
 array (Neogen Europe). The dataset is not qaulity controlled for both
 animals and SNPs.
description: The files can be accessed with any zip/unzip program and
 processed with PLINK and other software
DOI: 10.5061/dryad.41ns1rnj9
title: Data for: Wind speed that can effect increasing COVID-19

description: Several nations are currently experiencing a significant increase in
 coronavirus (COVID-19), including Indonesia. A total of
 34,874,744 confirmed cases with 1,097,497 deaths (case fatality rate (CFR)
 3.1%) were reported in 216 countries based on data from World Health
 Organization. COVID-19 remains public health problem around the world. It
 is possible the climate could affect the transmission of COVID-19. The
 wind is one of the climate factors besides temperature, humidity, and
 rainfall. Wind speed data can be used to study the spread of COVID-19
 cases.
description: The wind speed data was taken from the Meteorology, Climatology, and Geophysics
 Agency's data website (https://dataonline.bmkg.
 go.id/home). The wind speed (maximum and mean) in Jakarta
 from the pandemic inception, specifically between March and September
 2020. These records were obtained from the website of the Jakarta
 Provincial Health Office and the website of the Indonesian Meteorology,
 Climatology, and Geophysics Agency. Subsequently, the general information
 was converted into 31-week documentation. Furthermore, a basic map of
 Jakarta with neighboring community boundaries was obtained using the GADM
 Map and Data site.
 Coordinates for the weather monitoring stations were accessed online from
 (https://www.gps-latitude-longitude.com/).
DOI: 10.5061/dryad.stqjq2c74
title: Data from: Are Mediterranean marine threatened species at high risk by climate change?

description: Rapid anthropogenic climate change is driving threatened biodiversity one
 step closer to extinction. Effects on native biodiversity are determined
 by an interplay between species’ exposure to climate change and their
 specific ecological and life-history characteristics that render them even
 more susceptible. Impacts on biodiversity have already been reported;
 however, a systematic risk evaluation of threatened marine populations is
 lacking. Here, we employ a trait-based approach to assess the risk of 90
 threatened marine Mediterranean species to climate change, combining
 species’ exposure to increased sea temperature and intrinsic
 vulnerability. One-quarter of the threatened marine biodiversity of the
 Mediterranean Sea is predicted to be under elevated levels of climate
 risk, with various traits identified as key vulnerability traits. Climate
 risk, vulnerability and exposure hotspots are distributed along the
 Western Mediterranean, Alboran, Aegean, and Adriatic Seas. At each
 Mediterranean marine ecoregion, 21% to 31% of their threatened species
 have high climate risk. All Mediterranean Marine Protected Areas host
 threatened species with high risk to climate change, with 90% having a
 minimum of 4 up to 19 species of high climate risk, making the objective
 of a climate-smart conservation strategy a crucial task for immediate
 planning and action. Our findings aspire to offer new insights for
 systematic, spatially strategic planning and prioritization of vulnerable
 marine life in the face of accelerating climate change.
description: Data for the estimation of vulnerability ranks and exposure
 indices were collected from several free electronic databases cited in the
 article. They were processed in Microsoft Excel, in R studio and
 ArcGIS.
DOI: 10.15468/dl.tarjhk
title: Occurrence Download

description: A dataset containing 406 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Goniorrhachis marginata",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 406 records from 67 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003435-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2rbnzs7s9
title: Folding-unfolding asymmetry and a RetroFold computational algorithm

description: We treat protein folding as the molecular self-assembly, while unfolding
 is viewed as disassembly. Self-assembly and disassembly (fracture) are two
 opposite non-equilibrium dynamic processes; however, they cannot be
 converted to each other by a simple time variable reversal. Fracture is
 typically a much faster process than self-assembly. Self-assembly is often
 an exponentially decaying process, since energy relaxes due to
 dissipation, while fracture may be a constant rate process as the driving
 force is opposed by damping. Typically, protein folding takes two orders
 of magnitude longer time than unfolding, and it consumes a lot of
 computational resources to model folding. Based on energy dissipation
 rates, we suggest a mathematical transformation of variables, which makes
 it possible to view self-assembly as time-reversed disassembly, thus
 folding can be studied as reversed unfolding. We investigate the molecular
 dynamics modeling of folding and unfolding of the short Trp-cage protein.
 Folding time constitutes about 800 ns while unfolding (denaturation) takes
 only about 5.0 ns, and therefore, fewer computational resources are needed
 for its simulation. This “RetroFold” approach can be used for the design
 of a novel computation algorithm, which, while approximate, is less
 time-consuming than traditional folding algorithms.
description: We conducted the molecular dynamics (MD) simulation of both
 folding and unfolding using the Trp-Cage amino acid sequence with an
 extended initial conformation built by the LEaP module of AMBER. The
 linear conformation of this protein was designed using the Avogadro
 software. The 3D molecular structure (PDB ID: 1L2Y) of Trip-Cage was
 determined by the Nuclear Magnetic Resonance (NMR) method in the solution
 as a set (n =38) of stable conformations obtained from the RCSB Protein
 Data Bank. The MD simulations included the following phases: minimization
 (500 cycles), heating (50 ps), and equilibration (production) at 325 K
 (800 ns) for folding and at 473 K (5 ns) for unfolding according to the
 standard protocols published elsewhere. Our MD simulations were fully
 unrestrained and carried out in the canonical ensemble using the SANDER
 module available for Linux/Unix. The Berendsen thermostat was implemented
 for temperature control and the SHAKE algorithm to constrain the length of
 covalent bonds, including the hydrogen atoms. The ff99 force field was
 used as it was previously employed for similar modeling. Solvation effects
 were incorporated using the Generalized Born model, as implemented in
 AMBER. The Rosetta crystallographic refinement protocol was implemented to
 assess the conformational stability of the folded and unfolded protein
 conformations obtained from the previous MD simulations.
  
description: AMBER software
DOI: 10.5061/dryad.4xgxd25dv
title: Data for: Limited host availability disrupts the genetic correlation between virulence and transmission

description: Virulence is expected to be linked to parasite fitness via transmission.
 However, it is not clear whether this relationship is genetically
 determined, nor if it differs when transmission occurs continuously
 during, or only at the end of, the infection period. Here, we used inbred
 lines of the macro-parasitic spider mite Tetranychus urticae to
 disentangle genetic vs non-genetic correlations among traits, while
 varying parasite density and opportunities for transmission. A positive
 genetic correlation between virulence and the number of transmitting
 stages produced was found under continuous transmission. However, if
 transmission occurred only at the end of the infection period, this
 genetic correlation disappeared. Instead, we observed a negative
 relationship between virulence and the number of transmitting stages,
 driven by density dependence. Thus, within-host density dependence caused
 by reduced opportunities for transmission may hamper selection for higher
 virulence, providing a novel explanation as to why limited host
 availability leads to lower virulence.
description: This dataset was collected by infecting 4
 cm<sup>2</sup> leaf patches of bean plants (Phaseoulus
 vulgaris, variety Pongo) with different inbred lines of the macroparasite
 Tetranychus urticae (spider mites) at different densities (5, 10 or 20)
 for 4 days. After this period,  spider mites were removed, the number of
 eggs was measured and a photograph was taken to determine the percentage
 of host tissue damaged by spider mites. The offspring emerging from the
 eggs laid by the parasite was allowed to devolp until adulthood for 14
 days. Transmission to uninfected hosts was allowed during the infection
 period (experiment 1 - Continuous transmission) or not (experiment 2 -
 Transmission at the end of infection period). After 14 days, the total
 number of adult daughters (transmiting stage) produced was determined, as
 well as the number of daughters infection new hosts (for experiment
 1).