cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.12jm63xzr
title: Body temperature, evaporative water loss and resting metabolic rate data for six southern African bats

description: 1. The microsites that animals occupy during the rest phase of their
 circadian activity cycle influence their physiology and behaviour, but
 relatively few studies have examined correlations between interspecific
 variation in thermal physiology and roost microclimate. Among bats, there
 is some evidence that species exposed to high roost temperatures (Troost)
 possess greater heat tolerance and evaporative cooling capacity, but the
 small number of species for which both thermal physiology and roost
 microclimate data exist mean that the generality of this pattern remains
 unclear. 2. Here, we test the hypothesis that bat heat tolerance and
 evaporative cooling capacity have co-evolved with roost preferences. We
 predicted that species occupying roosts poorly buffered from high outside
 environmental temperature exhibit higher heat tolerance and evaporative
 cooling capacity compared to species inhabiting buffered roosts in which
 Troost remains well below outside conditions. 3. We used flow-through
 respirometry to investigate thermoregulation at air temperatures (Ta)
 approaching and exceeding normothermic body temperature (Tb) among six
 species with broadly similar body mass but differing in roost microclimate
 (hot versus cool roosts). We combined these data with empirical
 measurements of Troost for each study population. 4. Hot-roosting species
 tolerated Ta ~4 °C higher than cool-roosting bats before the onset of loss
 of coordinated locomotion and non-regulated hyperthermia. The evaporative
 scope [i.e., ratio of maximum evaporative water loss (EWL) to minimum
 thermoneutral EWL] of hot-roosting species (16.1 ± 2.4) was
 substantially higher than that of cool-roosting species (5.9 ±
 2.4). Maximum evaporative cooling capacities (i.e., evaporative heat loss
 / metabolic heat production) of hot-roosting species were &gt; 2,
 while the corresponding values for cool-roosting species were ≤1. 5. The
 greater heat tolerance and higher evaporative cooling capacity of
 hot-roosting species compared with those occupying cooler roosts reveal
 variation in bat evaporative cooling capacity correlated with roost
 microclimate, supporting the hypothesis that thermal physiology has
 co-evolved with roost preference.
DOI: 10.5061/dryad.5x69p8d40
title: Data archiving and sharing survey

description: Open data sharing improves the quality and reproducibility of scholarly
 research. Open data are defined as data that can be freely used, reused,
 and redistributed by anyone. Open data sharing democratizes science by
 making data more equitably available throughout the world regardless of
 funding or access to other resources necessary for generating cutting-edge
 data. For an interdisciplinary field like biological anthropology, data
 sharing is critical since one person cannot easily collect data across
 multiple domains. The goal of this paper is to encourage broader data
 sharing by exploring the state of data sharing in the field of biological
 anthropology. Our paper is divided into four parts: the first section
 describes the benefits, challenges, and emerging solutions to open data
 sharing; the second section presents the results of our data archiving and
 sharing survey that was completed by over 700 researchers; the third
 section presents personal experiences of data sharing by the authors; and
 the fourth section discusses the strengths of different types of data
 repositories and provides a list of recommended data repositories. The
 data archiving and sharing survey and the raw data collected from the
 survey are deposited here.
description: An online survey was developed to query researchers on their
 attitudes and practices with data archiving and sharing across biological
 anthropology and related fields. The survey was administered through
 Qualtrics and
 was open from May 23 – July 18, 2021. The link to the survey was sent via
 listserv and/or posted on the website of 19 professional societies and
 informal groups interested in data sharing. Responses from 722
 participants were received and the full Qualtrics survey
 report is available at https://ql.tc/4reI82. The raw
 data as exported from Qualtrics (Excel file) and the full survey (Word
 file) are deposited in this submission.
DOI: 10.5061/dryad.jsxksn0b0
title: Mutation of rpoB shifts the nutrient threshold triggering Myxococcus multicellular development

description: The ability to perceive and respond to environmental change is essential
 to all organisms. In response to nutrient depletion, cells of the
 soil-dwelling δ-proteobacterium Myxococcus xanthus undergo collective
 morphogenesis into multicellular fruiting bodies and transform into
 stress-resistant spores. This process is strictly regulated by gene
 networks that incorporate both inter- and intracellular signals. While
 commonly studied M. xanthus reference strains and some natural isolates
 undergo development only in nutrient-poor conditions, some lab mutants and
 other natural isolates commit to development at much higher nutrient
 levels, but mechanisms enabling such rich-medium development remain
 elusive. Here we investigate the genetic basis of rich-medium development
 in one mutant and find that a single amino-acid change (S534L) in RpoB,
 the β-subunit of RNA polymerase, is responsible for the phenotype. Ectopic
 expression of the mutant rpoB allele was sufficient to induce
 nutrient-rich development. These results suggest that the universal
 bacterial transcription machinery bearing the altered β-subunit can relax
 regulation of developmental genes that are normally strictly controlled by
 the bacterial stringent response. Moreover, the mutation also
 pleiotropically mediates a tradeoff in fitness during vegetative growth
 between high vs low nutrient conditions and generates resistance to
 exploitation by a developmental cheater. Our findings reveal a previously
 unknown connection between the universal transcription machinery and one
 of the most behaviorally complex responses to environmental stress found
 among bacteria.
DOI: 10.5061/dryad.fj6q573vv
title: Behavioural modification of range-extending coral reef fishes in temperate ecosystems

description: 1. Coral-reef fishes are shifting their distributions poleward in response
 to human-mediated ocean warming, yet the consequences for recipient
 temperate fish communities remain poorly understood. Behavioural
 modification is often the first response of species to environmental
 change, but we know little about how this might shape the ongoing
 colonisation by tropical fishes of temperate-latitude ecosystems under
 climate change. 2. In a global hotspot of ocean
 warming (southeast Australia), we quantified 14 behavioural
 traits of invading tropical and local co-occurring temperate fishes at 10
 sites across a 730 km latitudinal gradient as a proxy of species
 behavioural niche space in different climate ranges (subtropical,
 warm-temperate, cold-temperate). 3. We found that tropical fishes (4
 species) modified their behavioural niches as well as increased their
 overall behavioural niche breadth in their novel temperate ranges
 where temperate species predominate, but maintained a moderate to high
 niche segregation with native temperate species
 across latitudinal range position. Temperate species (3
 co-occurring species) also modified their niches, but in contrast to
 tropical species, experienced an increased niche breadth towards
 subtropical ranges. Alterations to feeding and
 shoaling behaviours contributed most to niche modifications in
 tropical and temperate species, while behaviours related to alertness and
 escape from potential threats contributed least. 4. We here show that at
 warmer and colder range edges where community structures are being
 reshuffled due to climate change, behavioural generalism and niche
 modification are potential mechanisms adopted by tropical range
 extenders and native-temperate fishes to adjust to novel species
 interactions under climate change.
DOI: 10.5061/dryad.8gtht76q8
title: Groping in the fog: Soaring migrants exhibit wider scatter in flight directions and respond differently to wind under low visibility conditions

description: Atmospheric conditions are known to affect flight propensity, behaviour
 during flight, and migration route in birds. Yet, the effects of fog have
 only rarely been studied although they could disrupt orientation and
 hamper flight. Fog could limit the visibility of migrating birds such that
 they might not be able to detect landmarks that guide them during their
 journey. Soaring migrants modulate their flight speed and direction in
 relation to the wind vector to optimise the cost of transport.
 Consequently, landmark-based orientation, as well as adjustments of flight
 speed and direction in relation to wind conditions, could be jeopardised
 when flying in fog. Using a radar system operated in a migration
 bottleneck (Strait of Messina, Italy), we studied the behaviour of soaring
 birds under variable wind and fog conditions over two consecutive springs
 (2016 and 2017), discovering that migrating birds exhibited a wider
 scatter of flight directions and responded differently to wind under fog
 conditions. Birds flying through fog deviated more from the mean migration
 direction and increased their speed with increasing crosswinds. In
 addition, airspeed and groundspeed increased in the direction of the
 crosswind, causing the individuals to drift laterally. Our findings
 represent the first quantitative empirical evidence of flight behaviour
 changes when birds migrate through fog and explain why low visibility
 conditions could risk their migration journey.
description: The dataset is a collection of summarised radar tracks. Raw
 tracks or collection of radar echoes labelled with unique IDs were reduced
 at one per line with average speed, length of the track, average direction
 of the track, etc. Associated with the tracks there are wind conditions
 per hour (u and v component at 10 m above the ground).
description: The readme file contains an explanation of each of the variables
 in the dataset, its measurement units. Information on how the measurements
 were done can be found in the associated manuscript referenced
 above.
DOI: 10.5061/dryad.47d7wm3f0
title: High resolution imaging as a tool for identifying quantitative trait loci that regulate photomorphogenesis in Arabidopsis thaliana

description: A primary component of seedling establishment is the photomorphogenic
 response as seedlings emerge from the soil. This process is characterized
 by a reduced growth rate in the hypocotyl, increased root growth, opening
 of the apical hook, and expansion of the cotyledons as photosynthetic
 organs. While fundamental to plant success, the photomorphogenic response
 can be highly variable. Additionally, studies of Arabidopsis thaliana are
 made difficult by subtle differences in growth rate between individuals.
 High-resolution imaging and computational processing have emerged as
 useful tools for quantification of such phenotypes. This study sought to:
 1) develop an imaging methodology which could capture changes in growth
 rate as seedlings transition from darkness to blue light in real time, and
 2) apply this methodology to single-QTL analysis using the Cvi x Ler RIL
 mapping population. Significant differences in the photomorphogenic
 response were observed between the parent lines and analysis of 158 RILs
 revealed a wide range of growth rate phenotypes. QTL analysis detected
 significant loci associated with dark growth rate on chromosome 5 and
 significant loci associated with light growth rate on chromosome 2.
 Candidate genes associated with these loci, such as the previously
 characterized ER locus, highlight the application of this approach for QTL
 analysis. Genetic analysis of Landsberg lines without the erecta mutation
 also supports a role for ER in modulating the photomorphogenic response,
 consistent with previous QTL analyses of this population. Strengths and
 limitations of this methodology are presented, as well as means of
 improvement.
description: Dark-grown 2d-old seedlings were imaged in darkness (T0), after 3
 hrs of growth in the darkness (T1) and after 5 hrs of growth in 20 µM
 m<sup>-2</sup> s<sup>-1</sup> blue light (T2).
 Images have not been processed.
description: Growth rate was determined by measuring hypocotyl length
 with ImageJ software. A calibration value of 35.509 pixels/mm was used for
 scale. Dark growth rate was determined based on the
 following formula: (Hypocotyl length (T1) - Hypocotyl length (T0))/3
 hrs Light growth rate was determined based on the
 following formula: (Hypocotyl length (T2) - Hypocotyl length
 (T1))/5 hrs Percent Reduction in growth rate was
 determined based on the following formula: 1 - (light growth rate)/(dark
 growth rate)
DOI: 10.5061/dryad.ghx3ffbpw
title: Quasipaa spinosa's genome assembly and annotation files

description: Quasipaa spinosa, an Asian commercial Dicroglossidae species, is noted for
 the spiny chest of adult male individuals. Here, we report the first
 chromosomal level Q. spinosa genome employing PacBio long read sequencing
 and High-through Chromosome Conformation Capture (Hi‐C) technology. The
 total length of the final assembled genome was 2,839,292,578 bp, with
 contig N50 of 3.79 Mb and scaffold N50 of 327.44 Mb. Approximately 99.30%
 of the length of the assembled genome sequences were anchored to 13
 chromosomes with the assistance of Hi-C reads. A total of 26,173
 protein‐coding genes were predicted, and 95.98% of the genes were
 functionally annotated. The annotated genes covered a total of 92.10% of
 the complete vertebrate core gene set according to the BUSCO pipeline
 evaluation. Approximately 41 million years ago, Q. spinosa began to
 diverge from its dicroglossid sister taxon Nanorana parkeri. The Q.
 spinosa genome revealed obvious chromosomal fissions compared with Xenopus
 tropicalis, which likely represented a specific chromosome evolutionary
 history within frogs. Population analysis showed that Chinese Q. spinosa
 could be divided into eastern and western genetic clusters, with the
 western population showing higher diversity than the eastern population.
 The effective population size of Q. spinosa showed a continuously
 decreasing trend from one million years ago to 10,000 years ago. In
 summary, this study sheds light on Q. spinosa evolution and population
 differentiation, providing a valuable genomic resource for further
 biological and genetic studies on this species, and other closely related
 frog taxa.
description: Quasipaa spinosa's genome assembly and annotation
 files.
DOI: 10.5061/dryad.5tb2rbp4w
title: Data from: Correlated evolution of larval development, egg size, and genome size across two genera of snapping shrimp

description: Across plants and animals, genome size is often correlated with life
 history traits: large genomes are correlated with larger seeds, slower
 development, larger body size, and slower cell division. Among decapod
 crustaceans, caridean shrimps are among the most variable both in terms of
 genome size variation and life history characteristics such as larval
 development mode and egg size, but the extent to which these traits are
 associated in a phylogenetic context is largely unknown. In this study, we
 examine correlations among egg size, larval development, and genome size
 in two different genera of snapping shrimp, Alpheus and Synalpheus, using
 phylogenetically informed analyses. In both Alpheus and Synalpheus, egg
 size is strongly linked to larval development mode: species with
 abbreviated development had significantly larger eggs than species with
 extended larval development. We produced the first comprehensive dataset
 of genome size in Alpheus (n = 37 species), and demonstrated that genome
 size was strongly and positively correlated with egg size in both Alpheus
 and Synalpheus. Correlated trait evolution analyses showed that in
 Alpheus, changes in genome size were clearly dependent on egg size. In
 Synalpheus, evolutionary path analyses suggest that changes in development
 mode (from extended to abbreviated) drove increases in egg volume; and
 larger eggs, in turn, resulted in larger genomes. These data suggest that
 variation in reproductive traits may underpin the high degree of variation
 in genome size seen in a wide variety of caridean shrimp groups more
 generally.
description: <strong>Egg size</strong>: Egg length and width were
 measured (and egg volume calculated) as described in the methods. Egg data
 were log-transformed. <strong>Development mode:
 </strong>Development mode was coded from the literature, and from
 examination of first-stage larval phases from collections or from the
 literature. <strong>Body size:
 </strong>Body size was measured as carapace length.
 <strong>Genome size: </strong>Genome size was
 measured using Feulgen Image Analysis Densitometry or flow cytometry, as
 detailed in the methods.
DOI: 10.5061/dryad.cfxpnvx5z
title: RNA sequencing of nuclease dead PET127 conditions

description: PET127, is thought to be a mitochondrial RNA exonuclease and loss
 of PET127 is thought to cause accumulation of untrimmed
 RNA in the mitochondria. Here we show RNA sequencing of
 Saccharomyces cerevisiae in four PET127 conditions:
 PET127 wild-type, pet127∆, pet127-nd (nuclease
 dead)/pet127∆, and pet127-nd/PET127. The resulting
 sequences show that regions of mitochondrial RNA accumulate in
 the pet127∆ background, and the RNA sequencing
 profile of PET127 containing disruptive mutations in the
 conserved exonuclease active site mimics that
 of pet127∆. 
description: RNA was isolated from 4.4 x 10<sup>7 </sup>log phase
 cells using acid phenol and purified using RNeasy kit (Qiagen) with on
 column DNAse treatment (Qiagen). Isolated total yeast RNA were processed
 using Ribozero rRNA removal for Yeast (Illumina). Sequencing was performed
 on NextSeq500 with 75 + 75 bases pair-end run with 6 + 6 nucleotide
 indexes.
DOI: 10.5061/dryad.9p8cz8wh6
title: Quantitative anatomy of the cerebellum on chickens and junglefowl

description: Domestication is the process by which wild organisms become adapted for
 human use. Many phenotypic changes are associated with animal
 domestication, including decreases in brain and brain region sizes. In
 contrast to this pattern, the chicken has a larger cerebellum compared
 with the wild red junglefowl, but what neuroanatomical changes are
 responsible for this difference have yet to be investigated. Here, we
 quantified cell layer volumes, neuron numbers and neuron sizes in the
 cerebella of chickens and junglefowl. Chickens have larger, more folded
 cerebella with more and larger granule cells than junglefowl, but neuron
 numbers and cerebellar folding were proportional to cerebellum size.
 However, chickens do have relatively larger granule cell layer volumes and
 relatively larger granule cells than junglefowl. Thus, the chicken
 cerebellum can be considered a scaled-up version of the junglefowl
 cerebellum, but with enlarged granule cells. The combination of scaling
 neuron number and disproportionate enlargement of cell bodies partially
 supports a recent theory that domestication does not affect neuronal
 density within brain regions. Whether the neuroanatomical changes we
 observed are typical of domestication or not requires similar quantitative
 analyses in other domesticated species and across multiple brain regions.
description: The data was collected using unbiased stereology, the parameters
 for which are described in the accompanying manuscript.
DOI: 10.5061/dryad.2547d7wrd
title: Prey-driven behavioral habitat use in a low-energy ambush predator

description: Food acquisition is an important modulator of animal behavior and habitat
 selection that can affect fitness. Optimal foraging theory predicts that
 predators should select habitat patches to maximize their foraging success
 and net energy gain, likely achieved by targeting areas with high prey
 availability. However, it is debated whether prey availability drives
 fine-scale habitat selection for predators. We assessed whether an ambush
 predator, the timber rattlesnake (Crotalus horridus), exhibits optimal
 foraging site selection based on the spatial distribution and availability
 of prey. We used passive infrared camera trap detections of potential
 small mammal prey (Peromyscus spp., Tamias striatus, and Sciurus spp.) to
 generate variables of prey availability across the study area and used
 whether a snake was observed in a foraging location or not to model
 optimal foraging in timber rattlesnakes. Our models of small mammal
 spatial distributions broadly predicted that prey availability was
 greatest in mature deciduous forests, but T. striatus and Sciurus spp.
 exhibited greater spatial heterogeneity compared to Peromyscus spp. We
 found the spatial distribution of cumulative small mammal encounters (i.e.
 overall prey availability), rather than the distribution of any one
 species, to be highly predictive of snake foraging. Timber rattlesnakes
 appear to forage where the probability of encountering prey is greatest.
 Our study provides evidence for fine-scale optimal foraging in a
 low-energy, ambush predator and offers new insights into drivers of snake
 foraging and habitat selection. 
description: (1) We quantified small mammal relative availability with
 widely-distributed camera traps, (2) projected small mammal encounters
 across the study area with landscape predictors, and (3)
 used radio-telemetry-derived timber rattlesnake foraging locations
 to model optimal foraging in timber rattlesnakes. We deployed game cameras
 to detect small mammals from 2017–2018 at
 242 randomly-chosen, unique sites. We positioned each game camera
 overlooking a log or downed woody debris to simulate a stereotyped ambush
 position of timber rattlesnakes (<em>Crotalus horridus</em>).
 We modeled counts of small mammal observations with
 remotely-sensed landscape characteristics to predict small mammal
 encounters across the study area. We modeled snake foraging using
 mixed-effects Bernoulli GLMs with foraging behavior as a binomial function
 of the spatially-explicit small mammal encounter rates.
DOI: 10.15468/dl.2puve2
title: Occurrence Download

description: A dataset containing 102081 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is India Biodiversity Portal publication grade dataset"
 ]
}

 The dataset includes 102081 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002952-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.