cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dncjsxkvs
title: Molecular basis for the evolved instability of a human G-protein coupled receptor

description: Membrane proteins are prone to misfolding and degradation. This is
 particularly true for mammalian forms of the gonadotropin-releasing
 hormone receptor (GnRHR). Although they function at the plasma membrane,
 mammalian GnRHRs accumulate within the secretory pathway. Their apparent
 instability is believed to have evolved through selection for attenuated
 GnRHR activity. Nevertheless, the molecular basis of this adaptation
 remains unclear. We show that adaptation coincides with a C-terminal
 truncation that compromises the translocon-mediated membrane integration
 of its seventh transmembrane domain (TM7). We also identify a series of
 polar residues in mammalian GnRHRs that compromise the membrane
 integration of TM2 and TM6. Reverting a lipid-exposed polar residue in TM6
 to an ancestral hydrophobic residue restores expression with no impact on
 function. Evolutionary trends suggest variations in the polarity of this
 residue track with reproductive phenotypes. Our findings suggest that the
 marginal energetics of cotranslational folding can be exploited to tune
 membrane protein fitness.
DOI: 10.5061/dryad.905qfttgm
title: The allometry of daily energy expenditure in hummingbirds: an energy budget approach

description: 1. Within-clade allometric relationships represent standard laws of
 scaling between energy and size, and their outliers provide new avenues
 for physiological and ecological research. According to the metabolic
 level boundaries hypothesis, metabolic rates as a function of mass are
 expected to scale closer to 0.67 when driven by surface-related processes
 (e.g., heat or water flux), while volume-related processes (e.g.,
 activity) generate slopes closer to one. 2. In birds, daily energy
 expenditure (DEE) scales with body mass (M) in the relationship
 log⁡(DEE)=2.35+0.68log⁡(M), consistent with surface-level processes
 driving the relationship. However, taxon-specific patterns differ from the
 scaling slope of all birds. 3. Hummingbirds have the highest mass-specific
 metabolic rates among all vertebrates. Previous studies on a few
 hummingbird species, without accounting for the phylogeny, estimated that
 the DEE-body mass relationship for hummingbirds was log⁡(DEE) =
 1.72+1.21log⁡(M). Contrary to theoretical expectations, this slope greater
 than 1 indicates that larger hummingbirds are less metabolically efficient
 than smaller hummingbirds. 4. We collected DEE and mass data for 12
 hummingbird species, which, combined with published data, represented 17
 hummingbird species in eight of nine hummingbird clades over a six-fold
 size range of body size (2.7 - 17.5 g). 5. After accounting for
 phylogenetic relatedness, we found daily energy expenditure scales with
 body mass as log⁡(DEE) = 2.04+0.95log⁡(M). This slope of 0.95 is lower
 than previously estimated for hummingbirds, but much higher than the slope
 for all birds (0.68). The high slopes of torpor, hovering and flight
 potentially explain the high interspecific DEE slope for hummingbirds
 compared to other endotherms. 08-Jan-2020
description: Doubly labeled water data compiled from this study and the
 literature (Powers & Nagy 1988, Weathers & Stiles 1991,
 Powers & Conley 1994,  Fernandez et al. 2011).
description: See Metadata file.
DOI: 10.5061/dryad.8sf7m0chv
title: An automated sensitive approach for measuring whole gut transit time

description: Background Commonly used methods to measure whole gut transit time in
 rodents have yet to combine high sensitivity, objectivity and automation.
 We have developed a novel method using oral gavage of non-toxic
 fluorescent dye particles and their detection by fluorescence imaging to
 enable unbiased automated detection of gut transit time simultaneously in
 8 cages. Methods Naïve mice (n=20) were gavaged with a 4.4% suspension of
 fluorescent dye in CMC in 3 groups on 2 occasions. Each group was imaged
 in 8 cages at 5-minute intervals using blue LEDs for illumination and a
 Sony full-frame mirrorless camera with a green band-pass emission filter.
 Custom Matlab code counted the number of fluorescent boli per cage
 post-hoc and provided graphical and spreadsheet output. Boli counts across
 a wide range of parameters were compared to blind assessments by an
 experimenter. Results Fluorescent boli were detected with high
 sensitivity, while unstained boli were readily rejected. All cages showed
 no fluorescent boli for the first ~20 frames (120 minutes), after which
 many cages gradually show a rise to 1-6 fluorescent boli. The mean time to
 first fluorescent bolus in each session was 264±141 and 223±81 minutes
 post-gavage, with no within subject consistency. There was high
 correlation between automated scores and that of experimenter
 (r=0.95±0.02), being robust to parameter changes. Conclusions &
 Inferences This novel approach provides a reliable, automatic and low-cost
 method of measuring gastrointestinal transit time in mice.
description: Images (jpg) are sequentially numbered and were taked at 5min
 intervals. Matlab code automatically counts fluorescent
 boli.
description: See extensive notes within matlab m file:
 automated_gut_transit_measure_1_9_20.m
DOI: 10.15468/dl.fteeff
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "PublishingOrg is one of (c2ecae57-6701-485e-9ebd-5f87b2945cb2, f9b67ad0-9c9b-11d9-b9db-b8a03c50a862, 6ea87510-0561-11d8-b851-b8a03c50a862)",
 "TaxonKey is Melanoplus carolinensis",
 "Year 1900-2026"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002150-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mgvbs8
title: Occurrence Download

description: A dataset containing 5573 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Canada",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Lontra canadensis"
 ]
}

 The dataset includes 5573 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002148-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.jm63xsj6k
title: Management of urban wetlands for conservation can reduce aquatic biodiversity and increase mosquito risk

description: 1. Global wetland loss means constructed urban wetlands are an
 increasingly valuable resource for conservation. However, priorities for
 managing urban wetlands for conservation are often seen to conflict with
 management to reduce potential mosquito risks. Understanding the
 ecological and public health consequences of wetland management practices
 is vital to maximise the conservation value of urban wetlands without
 negatively impacting public health, however are often untested. 2. We
 conducted a landscape-scale experiment to test the ecological impacts of
 an existing urban wetland management regime, in which a group of urban
 wetlands are drained annually to reduce the abundance of an invasive fish
 Gambusia holbrooki, and then refilled to provide breeding habitat for a
 threatened frog Litoria aurea. We collected and compared aquatic
 macroinvertebrates and mosquito larvae from these refilled wetlands, and
 adjacent undrained wetlands, as well as sampling adult mosquito
 populations on four occasions across summer and autumn. 3. Wetland
 draining had a significant effect on aquatic macroinvertebrates and larval
 mosquitoes. Twice as many macroinvertebrates were collected from drained
 wetlands compared to undrained wetlands, and almost all mosquito larvae
 were collected from drained wetlands. Differences in macroinvertebrate
 assemblages and larval mosquitoes at drained and undrained wetlands
 decreased over time, but total macroinvertebrate abundance and taxa
 richness did not. Draining did not affect adult mosquito assemblages. 4.
 Synthesis and applications. While conserving threatened habitats and
 species is imperative, our results highlight how wetland management
 practices can have unintended consequences for non-target species, with
 potentially negative effects on humans. As constructed urban wetlands
 become more common, so too does the need for both routine maintenance and
 management of threatened and invasive species. It is vital that future
 design and management of urban wetlands considers the impact mosquitoes
 might have on humans. Pre-emptive, targeted action for control of
 geographically-relevant nuisance-biting species or vectors of
 mosquito-borne pathogens would reduce negative impacts on public health
 and increase positive conservation outcomes associated with urban
 wetlands.07-Jan-2020
DOI: 10.5066/p14grawg
title: Data for dam passage analysis of Silver Carp at three locks and dams on the Tennessee and Cumberland rivers from 2016–2019

description: Acoustic telemetry data (Innovasea, Inc.) were collected on invasive Silver Carp (Hypophthalmichthys molitrix) in the lower reaches of the Tennessee and Cumberland river systems to determine timing and environmental conditions associated with dam passages by Silver Carp during 2016–2019. Data also include water level. dam discharge, and lock use data for three dams within these river systems. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.
DOI: 10.5061/dryad.cnp5hqc1w
title: β-Elemene derivatives produced from SeO2-mediated oxidation reaction

description: We report herein the first access of ß-elemene derivatives through the
 SeO2-mediated oxidation reaction. Several new compounds were isolated
 through such one-step reaction, and their structures were elucidated using
 various 2D-NMR techniques. This method provides easy access to multiple
 oxidative ß-elemene derivatives in one single step, and represents the
 first cyclohexyl ring modifications of ß-elemene. It’s expected to open up
 the opportunity for future derivatization on cyclohexyl ring of ß-elemene.
 The new compounds obtained above showed better anti-proliferation
 activities on several cancer cell lines than ß-elemene itself.
description: The <sup>1</sup>H NMR, <sup>13</sup>C
 NMR, <sup>1</sup>H-<sup>1</sup>H COSY,
 <sup>1</sup>H-<sup>1</sup>H NOESY, HMBC, HSQC are
 recorded in 500 MHz NMR machine. The data were processed in MestReNova
 software.
description: There is no any special instruction to obtain the data. Anyone in
 this field knows how to record NMR experience and how to interpret
 data.
DOI: 10.5061/dryad.3r2280gcc
title: Data from: Behavioral evidence for memory replay of video episodes in the macaque

description: Humans recall the past by replaying fragments of events temporally. Here,
 we demonstrate a similar effect in macaques. We trained six rhesus monkeys
 with a temporal-order judgement (TOJ) task and collected 5000 TOJ trials.
 In each trial, they watched a naturalistic video of about 10 s comprising
 two across-context clips, and after a 2-s delay, performed TOJ between two
 frames from the video. The monkeys apply a non-linear forward,
 time-compressed replay mechanism during the temporal-order judgement. In
 contrast with humans, such compression of replay is however not
 sophisticated enough to allow them to skip over irrelevant information by
 compressing the encoded video globally. We also reveal that the monkeys
 detect event contextual boundaries and such detection facilitates recall
 by an increased rate of information accumulation. Demonstration of a
 time-compressed, forward replay like pattern in the macaque monkeys
 provides insights into the evolution of episodic memory in our lineage
description: We collected the data from six rhesus macaques and seven human
 subjects. Trials with RT longer than 10 s (1.45%) or faster
 than 0.7 s (2.47%) were excluded from the analyses. Both correct and
 incorrect trials were entered for all analyses, except those reported in
 the GLMs. For Neptune, data of one day of primate list 5 (exposure 4) and
 two days of primate lists 4 and 5 (exposure 5) were lost due to machine
 breakdown and thus only 4,700 trials are included for Neptune.
DOI: 10.5061/dryad.f1vhhmgsx
title: Manipulation of trait expression and pollination regime reveal the adaptive significance of spur length

description: Understanding the mechanisms of adaptive population differentiation
 requires that both the functional and adaptive significance of divergent
 traits are characterized in contrasting environments. Here, we (a)
 determined the effects of floral spur length on pollen removal and receipt
 using plants with artificial spurs representing the species-wide variation
 in length, and (b) quantified pollinator-mediated selection on spur length
 and three traits contributing to floral display in two populations each of
 the short-spurred and the long-spurred ecotype of the orchid Platanthera
 bifolia. Both pollen receipt and removal reached a maximum at 28-29 mm
 long spurs in a short-spurred population visited by short-tongued moths.
 In contrast, pollen receipt increased linearly across the tested range
 (4-52 mm) and pollen removal was unrelated to spur length in a
 long-spurred population predominantly visited by a long-tongued moth.
  The experimentally documented effects on pollen transfer were
 not reflected in pollinator-mediated selection through female fitness or
 pollen removal indicating that the natural within-population variation in
 spur length was insufficient to result in detectable variation in pollen
 limitation. Our study illustrates how combining trait manipulation with
 analysis of causes and strength of phenotypic selection can illuminate the
 functional and adaptive significance of trait expression when trait
 variation is limited.
description: The excel files provide data on:  (1)
 Pollination success (pollen removal and pollen receipt) collected in a
 field experiment conducted in a short-spurred grassland and in a
 long-spurred woodland population of the orchid <em>Platanhera
 bifolia</em> on the island Öland in southeastern Sweden in 2017. In
 this experiment, artificial nectar spurs were used to vary the spur length
 of experimental plants. (2) Data on sugar concentration
 in nectar produced by  flowers in a short-spurred grassland and in a
 long-spurred woodland population. This information was used to decide
 the sugar concentration to be used in "nectar" added to
 artificial spurs. (3) Pollen removal and receipt in
 flowers with intact nectar spurs and in flowers with artificial nectar
 spurs in plants included in the artificial-spur experiment. These data
 were used to check that pollination success was similar in intact and
 manipulated flowers within the natural range of spur lengths in each of
 the two study populations. (4) Data on pollen removal,
 female fitness, and floral traits in two grassland and in two woodland
 populations of <em>P. bifolia</em> on the island Öland in
 southeastern Sweden in 2016. These data were used to quantify phenotypic
 selection among open-pollinated control plants and among plants receiving
 supplemental hand-pollination, and from these results estimate
 pollnator-mediated selection, non-pollinator mediated selection, and net
 selection on spur length, plant height, number of flowers, and flower
 size.
DOI: 10.5061/dryad.kd51c5b2g
title: A large-scale assessment of plant dispersal mode and seed traits across human-modified Amazonian forests

description: 1. Quantifying the impact of habitat disturbance on ecosystem function is
 critical for understanding and predicting the future of tropical forests.
 Many studies have examined post-disturbance changes in animal traits
 related to mutualistic interactions with plants, but the effect of
 disturbance on plant traits in diverse forests has received much less
 attention. 2. Focusing on two study regions in the eastern Brazilian
 Amazon, we used a trait-based approach to examine how seed dispersal
 functionality within tropical plant communities changes across a
 landscape-scale gradient of human modification, including both
 regenerating secondary forests and primary forests disturbed by burning
 and selective logging. 3. Surveys of 230 forest plots recorded 26,533 live
 stems from 846 tree species. Using herbarium material and literature, we
 compiled trait information for each tree species, focusing on dispersal
 mode and seed size. 4. Disturbance reduced tree diversity and increased
 the proportion of lower wood-density and smaller-seeded tree species in
 study plots. Unexpectedly, disturbance also increased the proportion of
 stems with seeds that are ingested by animals and reduced those dispersed
 by other mechanisms (e.g. wind). Older secondary forests had functionally
 similar plant communities to the most heavily disturbed primary forests.
 5. Synthesis. Anthropogenic disturbance has major effects on the seed
 traits of tree communities, with implications for mutualistic interactions
 with animals. The higher importance of animal-mediated seed dispersal in
 disturbed and recovering forests highlights the importance of avoiding
 defaunation or promoting faunal recovery. The changes in mean seed width
 suggest larger vertebrates hold especially important functional roles in
 these human-modified forests. Monitoring fruit and seed traits can provide
 a valuable indicator of ecosystem condition, emphasising the importance of
 developing a comprehensive plant traits database for the Amazon and other
 biomes.
description: This spreadsheet contains three tabs to present the data used in
 the article 'A large-scale assessment of plant dispersal mode and
 seed traits across human-modified Amazonian forests' (Hawes et al.
 Journal of Ecology). The first tab, labelled Legend, describes the column
 headers for the next two tabs. The second tab, labelled Plots, contains
 predictor and response variables for each of the 230 forest plots
 surveyed. The third tab, labelled Species, contains fruit type, dispersal
 mode, seed width and wood density for each of the tree species recorded.
 Data on fruit and seed measurements from herbarium collections were also
 contributed to the TRY Plant Trait Database (Kattge et al.
 2020).
DOI: 10.5061/dryad.vq83bk3pb
title: Experimental variation in the spatial deposition of trace metals in feathers revealed using synchrotron x-ray fluorescence

description: Feathers can be used to investigate exposure to pollution in birds because
 they are a secondary route for the excretion of trace elements.
 Evidence based on analytical imaging and spectroscopy suggests
 that the spatial distribution of the essential trace element zinc
 within feathers is related to melanin pigmentation. However, our
 understanding of how trace elements are deposited into growing
 feathers is poor and has been hampered by a lack of analytical tools
 to examine the localization of trace elements within a feather.
 Here, synchrotron micro X-ray fluorescence spectroscopy was used
 to map zinc directly within the barb and barbules of lesser scaup
 (Aythya affinis) feathers grown after experimental increases in
 dietary zinc. The results showed distinct spatial variation in zinc within
 barbs and barbules, with higher levels observed in the latter.
 Furthermore, increases in dietary zinc were found to increase the
 relative levels of zinc throughout the barbules from the base to
 the tip of the feather. Finally, analysis of feather cross
 sections revealed that regions of the feather barb and barbules
 with higher melanosome density also contained higher levels of
 zinc. These results provide a more detailed understanding of zinc
 and melanosome arrangement within the feather barb and barbules.
 Moreover, these results provide further support for the use of
 feathers as a noninvasive tool to study exposure to trace
 elements and highlight the utility of X-ray spectroscopy in studies
 investigating impacts of a rapidly changing environment on wild bird
 health. 
description: This data is associated with Akhter et al., 2020.
 Reference: Akhter F, Fairhurst GD, Blanchard PER, Machin KL, Blyth RIR,
 Thompson J, McLeod J, Feng R, Soos C. Experimental variation in the
 spatial deposition of trace metals in feathers revealed using synchrotron
 X-ray fluorescence. X-Ray Spectrom. 2020;1–9. Available at:
 https://doi.org/10.1002/xrs.3140.<br>   Please
 see the materials and methods section for details.
DOI: 10.5061/dryad.t4b8gthz1
title: Tracking the near Eastern origins and European dispersal of the Western house mouse

description: The house mouse (Mus musculus) represents the extreme of globalization of
 invasive mammals. However, the timing and basis of its origin and early
 phases of dispersal remain poorly documented. To track its
 synanthropisation and subsequent invasive spread during the develoment of
 complex human societies, we analyzed 829 Mus specimens from 43
 archaeological contexts in Southwestern Asia and Southeastern Europe,
 between 40,000 and 3,000 cal. BP, combining geometric morphometrics
 numerical taxonomy, ancient mitochondrial DNA and direct radiocarbon
 dating. We found that large late hunter-gatherer sedentary settlements in
 the Levant, c. 14,500 cal. BP, promoted the commensal behaviour of the
 house mouse, which probably led the commensal pathway to cat
 domestication. House mouse invasive spread was then fostered through the
 emergence of agriculture throughout the Near East 12,000 years ago.
 Stowaway transport of house mice to Cyprus can be inferred as early as
 10,800 years ago. However, the house mouse invasion of Europe did not
 happen until the development of proto urbanism and exchange networks —
 6,500 years ago in Eastern Europe and 4000 years ago in Southern Europe —
 which in turn may have driven the first human mediated dispersal of cats
 in Europe.
description: The acquisition of GMM data for the molar shape analysis of the
 first lower molars (m1) was performed on 2D images of the occlusal view of
 the m1, following Cucchi el al. (2013). The images were acquired by a
 Leica EZ4D stereoscope digital camera and the LAS operating software. The
 2D external outline of the occlusal view of the m1 was recorded using
 tpsDig v. 2.30 Cucchi, T., Kovács, Z.E.,
 Berthon, R., Orth, A., Bonhomme, F., Evin, A., Siahsarvie, R., Darvish,
 J., Bakhshaliyev, V., Marro, C., 2013. On the trail of Neolithic mice and
 men towards Transcaucasia: zooarchaeological clues from Nakhchivan
 (Azerbaijan). Biological Journal of the Linnean Society 108, 917–928.
 https://doi.org/10.1111/bij.12004
description: This dataset include the shape variables (procrustes coordinates)
 of the 1341 modern and archaeological m1 teeth of the genus <em>Mus
 </em>studied. These shapes coordinates have been obtained after
 Procrustes superposition using Bending Energy Minimization method
 follonwing Cucchi et al. (2013)
DOI: 10.5061/dryad.bk3j9kd73
title: Allele frequency files for population genomic and phenotypic association analyses

description: Adaptation to local environments involves evolution of ecologically
 important traits and underlying physiological processes. One challenge in
 studying the genetic architecture of local adaptation is to achieve high
 marker density to detect candidate genes in natural populations that often
 have small blocks of linkage disequilibrium.  Here, we used low
 coverage whole-genome resequencing (lcWGR) to identify genome regions
 involved in thermal adaptation in wild redband trout Oncorhynchus mykiss
 gairdneri, a subspecies of rainbow trout that inhabits ecosystems ranging
 from cold montane forests to high elevation deserts.