cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.zjdvan
title: Occurrence Download

description: A dataset containing 406 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Catharus bicknelli",
 "GadmGid is one of (USA.33_1, USA.20_1, USA.46_1, USA.22_1, USA.30_1, CAN.11_1, CAN.7_1, CAN.4_1)",
 {
 "not" : {
 "DatasetKey" : [
 "is EOD – eBird Observation Dataset"
 ]
 }
 },
 "Month is one of (May, June, July, August, September)",
 "Year is greater than or equal to 2010",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 406 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003767-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.41ns1rnmg
title: Data from: Topological transitions of the generalized Pancharatnam-Berry phase

description: Distinct from the dynamical phase, in a cyclic evolution, a system’s state
 may acquire an additional component, a.k.a. geometric phase. Recently, it
 has been demonstrated that geometric phases can be induced by a sequence
 of generalized measurements implemented on a single qubit. Furthermore, it
 has been predicted that such geometric phases may exhibit a topological
 transition as a function of the measurement strength. We demonstrate and
 study this transition experimentally by employing an optical platform
 where the qubit is represented by the polarisation of light and the weak
 measurement is performed by means of coupling with the spatial degree of
 freedom. Our protocol can be interpreted in terms of environment-induced
 geometric phases, whose values are topologically determined by the
 environment-system coupling strength. Our results show that the two limits
 of geometric phase induced by either sequences of either weak or
 projective measurements are topologically distinct. 
description: # Detected interference intensities
 [https://doi.org/10.5061/dryad.41ns1rnmg](https://doi.org/10.5061/dryad.41ns1rnmg) ## Description of the data and file structure The uploaded data are the raw interference intensities detected in the experiment. Each file contains the dataset necessary to reproduce fig 3 b (one file for each panel). The file name specifies the waist value (also indicated in the figure panel). Data can be imported in Mathematica with the code string “Import[“w0_0.6mm.txt ”,”Data”]”. A Matrixplot will show a 20x40 matrix where the axis with 20 values corresponds to delta and the axis with 40 values to alpha. The geometric phase is obtained fitting, for each alpha, a function of delta of the form “A Cos(delta+phi)”, where the amplitude A and the geometric phase phi are fit parameters. The results and corresponding errors will yield the results in fig 3b ## Code/Software The GeneticAlgorithm.nb can be run on Mathematica13 and performs the genetic algorithm used to find the system imperfection parameters that better explain the data
DOI: 10.5061/dryad.70rxwdc4v
title: Western North American Temperature Atlas (WNATA)

description: Across western North America (WNA), 20th-21st century anthropogenic
 warming has increased the prevalence and severity of concurrent drought
 and heat events, also termed hot droughts. However, the lack of
 independent spatial reconstructions of both soil moisture and temperatures
 limits the potential to identify these events in the past and to place
 them in a long-term context. Here, we develop the Western North American
 Temperature Atlas (WNATA), a data-independent 0.5° gridded
 reconstruction of summer maximum temperatures back to the 16th century.
 Our evaluation of the WNATA with existing hydroclimate reconstructions
 reveals an increasing association between maximum temperature and drought
 severity in recent decades, relative to the past five centuries. The
 synthesis of these paleo-reconstructions indicates that the amplification
 of the modern WNA megadrought by increased temperatures, and the frequency
 and spatial extent of compound hot and dry conditions in the 21st century
 are likely unprecedented since at least 1553 CE.
description: The Western North American Temperature Atlas (WNATA), a 0.5°
 gridded reconstruction for western North America, was created using a
 nested, ensemble principal components regression approach, where a network
 of tree ring density and blue intensity chronologies were used as
 predictors to reconstruct June–August average maximum surface
 temperatures. The predicted climate data was CRU TS land 4.06 June–August
 maximum temperature data.  For the first of three total reconstruction
 nests, we calibrated and validated each of the 3029 grid point
 reconstructions over the period 1901-1980 CE (the common period shared
 between the instrumental temperature data and all tree-ring predictors in
 the WNATA network). We used a split calibration/verification approach,
 where we calibrated over the period spanning 1941-1980 CE and verified on
 the period spanning 1901-1940 CE. We repeated this approach for the
 remaining two forward nests: 1901-1990 CE and 1901-2000 CE. The
 verification period remained constant, but the calibration period varied
 for each nest (1941-1980; 1941-1990; 1941-2000 CE). For each
 reconstruction nest, we applied eight weights to each of the selected
 tree-ring predictors based on their correlations with temperature,
 resulting in a 24-member ensemble. 
description: # Western North American Temperature Atlas
 0.5° spatial field
 reconstruction of summer (June-August) average maximum temperatures for
 western North America, spanning 1553-2020 CE and based on tree ring
 density and blue intensity measurements. ## Description of the data and
 file structure The data consists of 3029 grid point reconstructions of
 summer average maximum temperatures. In the Excel file, rows 1 and 2 are
 the Latitude/Longitude coordinates for each reconstruction. Rows 3-470 are
 the annual reconstruction estimates. Estimates are displayed as z-scores,
 relative to the period 1553-2020 CE.
DOI: 10.15468/dl.femyg3
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bovichtus argentinus",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 2014"
 ]
}

 The dataset includes 13 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003768-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.prr4xgxst
title: Allele dataset of western grasswren for use in VORTEX (PVA analysis)

description: Conservation translocations have become an increasingly popular method to
 restore or secure vulnerable populations. However, translocations greatly
 vary in success. The use of population viability analysis (PVA) may
 increase the likelihood of meeting translocation goals. However, the
 quality of PVAs to inform translocations is dependent on the availability
 of ecological data and clear translocation objectives to guide them. Here,
 we used PVAs to inform the planned conservation translocation of the
 Western Grasswren (Amytornis textilis textilis) from mainland Shark Bay
 onto Dirk Hartog Island, Western Australia. A range of translocation
 scenarios was modelled and scored against success criteria as determined
 by translocation objectives. Simulations of 20-year outcomes found that a
 minimum founder population of 112 individuals meets all success criteria.
 PVA supported sourcing individuals from two subpopulations to maximise
 genetic diversity. No impact to source populations was detected for the
 proposed harvest quantities despite conservative estimates of initial
 source population sizes. Here we demonstrate that creating clear,
 measurable objectives alongside a PVA lessens ambiguity about which
 translocation scenarios could be viable. In doing so, we have identified
 the minimum translocation sizes needed to maintain genetic diversity and
 population growth, thus increasing the likelihood of translocation success
 without impacting the source population.
description: Allele dataset was generated through next generation SNP
 sequencing of blood samples from Western Grasswren (<em>Amytornis
 textilis textilis</em>). After filtering SNPs in the methods
 described in Gibson Vega et al. 2023, a subset of 1000 neutral loci were
 extracted for use in the program VORTEX to model population genetic
 mixing.  Gibson Vega, A., Hall, M. L., Ridley, A.,
 Cowen, S. J., Slender, A. L., Burbidge, A. H., Louter, M., and Kennington,
 W. J. (2023). Population genetic structure associated with a landscape
 barrier in the Western Grasswren (<em>Amytornis textilis
 textilis</em>). Ibis.
description: Description of the 'WGW allele freq\_Vortex1000\_v0.1.txt' file.
 This is an input file compatible with the program VORTEX to model genetic
 population mixing. Formatting is as such: 1st Row: number of loci (1000)
 2nd Row: number of alleles per loci Rows 3 to 2002: The allele frequencies
 at each loci, where the first 1000 of these rows represents frequencies at
 a subpopulation called Hamelin, and the following 1000 rows represents the
 allele frequencies at a subpopulation called Peron.
DOI: 10.15468/dl.pueetp
title: Occurrence Download

description: A dataset containing 31 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hymenostegia bakeriana",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 31 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003769-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.0rxwdbs6f
title: Amata variation analysis for Eco-geographic hypotheses do not explain variation in warning signals in diurnal Amata nigriceps wasp moths

description: Aposematic prey use conspicuous warning signals to advertise a secondary
 defense. To be effective, warning signals should be reliable throughout a
 prey population. However, warning signals vary considerably across and
 within populations, often for unknown causes. Here, the Australian diurnal
 moth Amata nigriceps, which has orange wing spots on a black background,
 was used to explore four ecogeographic hypotheses explaining warning
 signal variability: the thermal melanism, the photo-protection, the
 desiccation resistance, and the predator-loss hypotheses. We collected
 live moths from 29 populations across 746 km of coastal New South Wales,
 Australia, and sampled relevant museum collections from 1896 to 1982. We
 quantified the proportion of orange wing spots (warning signal size)
 relative to site-specific abiotic (temperature, precipitation, solar
 radiation) and biotic factors (diversity of bird predators). In museum
 specimens, warning signal size varied within the decade of collection,
 without a discernible temporal trend. Recent collections also varied in
 signal size, but we found no support for the four hypotheses. Our results
 are in contrast with studies that have found significant relationships
 between warning colours and eco-geographic factors. Local phenotypic
 responses in Amata nigriceps together with relaxed predator selection and
 genetic effects may explain the persistence of warning signal variation.
description: Fresh <em>Amata nigriceps</em> moths were collected
 from 29 sites across eastern Australia, preserved, and imaged.
 Historical specimens were imaged from 3 Australian museums,
 dating from 1896 to 1982. Proportion of warning signal
 size (orange wing spots on a black background) was quantified, and this
 'pSpot' value was used to compare changes in warning signal size
 over time in the historical collections, and compared with climate and
 bird diversity data in the fresh specimens.
description: Data and R code for the paper 'Eco-geographic hypotheses do not
 explain variation in warning signals in diurnal Amata nigriceps wasp
 moths' by Binns et al. This directory contains three folders: the
 data folder, the output folder and the R folder. The data folder contains
 various sub-folders. Each sub-folder contains a README.txt file that
 explains the folder contents. The output folder contains an updated
 dataset "20230405-fresh\_nigriceps\_all-updated.csv" that
 originates from the original dataset in the data/Moths folder. It contains
 new variable columns for climate and predator diversity. This folder also
 contains a README.txt file that describes the new variables and three
 graphical outputs included in the manuscript. The R folder contains the
 data analysis code and a README.txt file explaining the code.
DOI: 10.5061/dryad.z612jm6jg
title: Integrative species delimitation and five new species of lynx spiders (Araneae, Oxyopidae) in Taiwan

description: An accurate assessment of species diversity is a cornerstone of biology
 and conservation. The lynx spiders (Araneae: Oxyopidae) represent one of
 the most diverse and widespread cursorial spider groups, however their
 species richness in Asia is highly underestimated. In this study, we
 revised the species diversity with extensive taxon sampling in Taiwan and
 explored species boundaries based on morphological traits and genetic data
 using a two-step approach of molecular species delimitation. Firstly, we
 employed a single COI dataset and applied two genetic distance-based
 methods: ABGD and ASPA, and two topology-based methods: GMYC and bPTP.
 Secondly, we further analyzed the lineages that were not consistently
 delimited, incoporated H3 to the dataset for a coalescent-based analysis
 using BP&P. A total of eight morphological species were
 recognized, including five new species, Hamataliwa cordivulva sp. nov.,
 Hamat. lepusauris sp. nov., Tapponia auriola sp. nov., T. parvum sp. nov.
 and T. rarobulbus sp. nov., and three newly recorded species, Hamadruas
 hieroglyphica (Thorell, 1887), Hamat. Foveata Tang & Li, 2012 and
 Peucetia latikae Tikader, 1970. All eight morphological species exhibited
 reciprocally monophyletic lineages. The results of molecular-based
 delimitation analyses suggested a variety of species hypotheses which did
 not fully corresponding to the eight morphological species. We found that
 Hamat. cordivulva sp. nov. and Hamat. foveata showed shallow genetic
 differentiation in the COI, but they were unequivocally distinguishable
 according to their genitalia. In contrast, T. parvum sp. nov. represented
 a deep divergent lineage, while the difference of genitalia did not
 detected. This study highlights the need to comprehensively employ
 multiple evidences and methods to delineate species boundaries and the
 values of diagnostic morphological characters for taxonomic studies in
 lynx spiders.
DOI: 10.5061/dryad.1ns1rn91c
title: Data from: Cortical reactivation of spatial and non-spatial features coordinates with hippocampus to form a memory dialogue

description: Episodic memories comprise diverse attributes of experience distributed
 across neocortical areas. The hippocampus is integral to rapidly binding
 these diffuse representations, as they occur, to be later reinstated.
 However, the nature of the information exchanged during this
 hippocampal-cortical dialogue remains poorly understood. A recent study
 has shown that the secondary motor cortex carries two types of
 representations: place cell-like activity, which were impaired by
 hippocampal lesions, and responses tied to visuo-tactile cues, which
 became more pronounced following hippocampal lesions. Using two-photon
 Ca2+ imaging to record neuronal activities in the secondary motor cortex
 of male Thy1-GCaMP6s mice, we assessed the cortical retrieval of spatial
 and non-spatial attributes from previous explorations in a virtual
 environment. We show that, following navigation, spontaneous resting state
 reactivations convey varying degrees of spatial (trajectory sequences) and
 non-spatial (visuo-tactile attributes) information, while reactivations of
 non-spatial attributes tend to precede reactivations of spatial
 representations surrounding hippocampal sharp-wave ripples.
description: # Cortical reactivation of spatial and non-spatial features coordinates
 with hippocampus to form a memory dialogue
 [https://doi.org/10.5061/dryad.1ns1rn91c](https://doi.org/10.5061/dryad.1ns1rn91c) Deconvolved calcium traces, behavior, LFP and ROIs masks. ## Description of the data and file structure The data is organized as follow: `-- animal/ `-- yyyy_mm_dd/ |-- 1/ | `-- plane1/ | |-- deconv.mat | `-- masks_neurons.mat |-- 2/ | `-- plane1/ | |-- deconv.mat | `-- masks_neurons.mat |-- 3/ | `-- plane1/ | |-- deconv.mat | `-- masks_neurons.mat |-- yyyy_mm_dd_1.abf |-- yyyy_mm_dd_2.abf |-- yyyy_mm_dd_3.abf `-- channels.mat Starting from the top, we have the animal number, followed by the date of recording. REST1, RUN and REST2 then follow as directories `1`, `2` and `3`. Under the `plane1` folder, `deconv,mat` contains the matrix of deconvolved calcium transients (frames by neurons), while `masks_neurons.mat` contains the ROIs pixel identities of each neuron. The file `channels.mat` contains a vector defining the channels of the *abf* files. Specifically, we find `[frame pules, encoder A, encoder B, reward valve trigger, N/A, LFP, N/A]`. The associated *abf* files are suffixed by the recording block (i.e., 1, 2 and 3).
DOI: 10.15468/dl.zfq4gk
title: Occurrence Download

description: A dataset containing 395 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Leptonotus blainvilleanus",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 2014"
 ]
}

 The dataset includes 395 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003770-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.m0cfxpp97
title: Eggshell colour differences in a classic example of coevolved eggshell mimicry

description: Avian brood parasitism is a model system for understanding coevolutionary
 arms races, and the great reed warbler (Acrocephalus arundinaceus,
 hereafter ‘warbler’) and its parasite the common cuckoo (Cuculus canorus,
 hereafter ‘cuckoo’) are prime examples of this coevolutionary struggle.
 Here, warblers select for egg colour mimicry by rejecting poorly matched
 cuckoo eggs. Contrary to long-held assumptions, recent work showed that
 warblers tend to reject lighter and browner eggs but tended to accept
 darker and bluer eggs rather than basing rejection decisions solely on
 perceived colour differences (i.e., the degree of mimicry). This
 counter-intuitive, colour-biased rejection behaviour would select for
 bluer and darker cuckoo eggs, but would only be adaptive if cuckoos were
 consistently lighter and browner than warbler eggs. Therefore, we tested
 whether warbler eggs were consistently bluer and darker than the cuckoo
 eggs. To do so, we re-analysed eggshell reflectance spectra of warblers
 and the cuckoos that parasitized them in the Czech Republic. As expected,
 we found that warbler eggs were significantly bluer and darker than the
 cuckoo eggs at the population level. Thus, we demonstrate imperfect
 mimicry in a long-coevolved cuckoo host-race and provide insights for
 exploring the coevolutionary interactions among hosts and their brood
 parasites.
description: To replicate our results, you will need the attached R code
 (Villa\_etal\_2023.R) and the reflectance spectra data for the parasitized
 warbler nests previously published by Honza et al. 2014 (Reflectance
 data\_matching2013\_Suppl.csv). A complete version of the original data
 can be found in the supplemental material by Honza, M., Šulc, M., Jelínek,
 V., Požgayová, M., & Procházka, P. (2014). Brood parasites lay
 eggs matching the appearance of host clutches. Proceedings of the Royal
 Society B: Biological Sciences, 281(1774), 20132665. **Contents:** *
 ***Electronic supplementary material*** File name:
 esm\_Villa\_etal\_2023.doc * ***Analysis of egg colour information in R***
 File name: Villa\_etal2023.R Structure: 0\. libraries 1\. functions 2\.
 data preparation 3\. visual model 4\. circular analysis 5\. supplementary
 analysis * ***Parasitized great reed warblers by cuckoos, published by
 Honza et al. 2014*** File name: spectra\_Honza\_etal\_2014.csv Column A:
 'wl' : wavelength from 300 to 700 nm Column B to AM: reflectance
 values for 38 eggs (19 pairs) measured by Honza et al. 2014. Reflectance
 spectra of *Acrocephalus arundinaceus* eggs are indicated as
 'Aa' and *Cuculus canorus* eggs as c1
DOI: 10.5061/dryad.f7m0cfz36
title: The phenotypic and fitness response to the combination of copper and thermal stressors strongly varies within the ciliate species, Tetrahymena thermophila

description: Copper pollution can alter biological and trophic functions. Organisms can
 set up different tolerance strategies, including accumulation mechanisms
 (intracellular vacuoles, external chelation, etc.) to maintain themselves
 in copper-polluted environments. Accumulation mechanisms can influence the
 expression of other phenotypic traits, allowing organisms to improve their
 fitness. Whether copper effects on accumulation strategies interact with
 other environmental stressors such as temperature and how this may differ
 within species are still unsolved questions. Here, we tested
 experimentally whether the combined effect of copper and temperature
 modulates traits linked to fitness, morphology, movement and accumulation
 in six strains of the ciliate Tetrahymena thermophila. We also
 explored whether copper accumulation might modulate environmental copper
 concentration effects on phenotypic and fitness traits. Results showed
 high intraspecific variability in the phenotypic and fitness response to
 copper, with interactive effects between temperature and copper. In
 addition, they suggested an attenuation effect of copper accumulation on
 the sensitivity of traits to copper, but with great variation between
 strains, temperature and copper concentration. Diversity of responses
 among strains and their thermal dependencies pleads for the integration of
 intraspecific variability and multiple stressors approaches in
 ecotoxicological studies, thus improving the reliability of assessments of
 the effects of pollutants on biodiversity.
description: # The phenotypic and fitness response to the combination of copper and
 thermal stressors strongly varies within the ciliate species, Tetrahymena
 thermophila
 [https://doi.org/10.5061/dryad.f7m0cfz36](https://doi.org/10.5061/dryad.f7m0cfz36) These data consist of evaluating phenotypic traits of five strains of Tetrahymena thermophila exposed to copper and temperature. We quantified these phenotypic traits in monocultures for each of six strains at three temperatures: 15°C, 23°C and 31°C in laboratory conditions. The phenotype data contains: * strain: genotype designation. * Temperature: experimentally setup temperature * copper\_concentration (mg/L): Copper concentration in media before exposure * nb\_96h : cell density after 96h of exposure * nb\_inoculated: the number of cells inoculated at the beginning of the experiment * growth rate: nb\_96h – nb\_inoculated / nb\_inoculated * cell size(µm2): cell surface area * cell elongation: ratio major/minor axis * velocity(µm/S): total distance travelled by cells divided by the duration of the trajectory * accumulation concentration (mg/L): copper\_concentration - copper concentration remained after exposure * accumulation percentage: accumulation concentration / copper\_concentration