cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pvmcvdnhj
title: Data from: Modeling phylogenetic biome shifts on a planet with a past

description: The spatial distribution of biomes has changed considerably over deep
 time, so the geographical opportunity for an evolutionary lineage to shift
 into a new biome may depend on how the availability and connectivity of
 biomes has varied temporally. To better understand how lineages shift
 between biomes in space and time, we developed a phylogenetic biome shift
 model in which each lineage shifts between biomes and disperses between
 regions at rates that depend on the lineage’s biome affinity and location
 relative to the spatiotemporal distribution of biomes at any given time.
 To study the behavior of the biome shift model in an empirical setting, we
 developed a literature-based representation of paleobiome structure for
 three mesic forest biomes, six regions, and eight time strata, ranging
 from the Late Cretaceous (100 Ma) through the present. We then fitted the
 model to a time-calibrated phylogeny of 119 Viburnum species to compare
 how the results responded to various realistic or unrealistic assumptions
 about paleobiome structure. Ancestral biome estimates that account for
 paleobiome dynamics reconstructed a warm temperate (or tropical) origin of
 Viburnum, which is consistent with previous fossil-based estimates of
 ancestral biomes. Imposing unrealistic paleobiome distributions led to
 ancestral biome estimates that eliminated support for tropical origins,
 and instead inflated support for cold temperate ancestry throughout the
 warmer Paleocene and Eocene. The biome shift model we describe is
 applicable to the study of evolutionary systems beyond Viburnum, and the
 core mechanisms of our model are extensible to the design of richer
 phylogenetic models of historical biogeography and/or lineage
 diversification. We conclude that biome shift models that account for
 dynamic geographical opportunities are important for inferring ancestral
 biomes that are compatible with our understanding of Earth history.
description: This Dryad dataset includes the input data analyzed in the main
 text and the Supplemental Information described in the main text. The main
 text describes how the data were collected in detail. These data were
 derived from the Dryad dataset: https://doi.org/10.5061/dryad.hx3ffbgb1.
 The zip file containing the data also contains a README.md file that
 overviews its contents.
description: RevBayes code for the phylogenetic analysis and plotting scripts
 for the figures are hosted on GitHub:
 https://github.com/mlandis/biome_shift
DOI: 10.21223/p3/1get14
title: Dataset for: Advanced clones of group B3 cycle 1, population B (B3C1) in Comas-Peru

description: B3C1 is the first cycle of recombination of advanced B3C0 potato clones. These clones have high levels of horizontal resistance to late blight in absence of R-genes, and they also have high tuber yield. These clones were planted in a randomized complete block design (RCBD) with 2-4 replicates at Comas, located at 2400 to 2788 masl in Junin situated in the Central mountain ranges in Peru. The trials were established at Comas due to high disease pressure of late blight, disease endemic, highly favorable for disease development and severity during the rainy periods in these areas from 1999 to 2005.
DOI: 10.5061/dryad.3xsj3txcf
title: Acetylcholine is released in the basolateral amygdala in response to predictors of reward and enhances learning of cue-reward contingency

description: The basolateral amygdala (BLA) is critical for associating initially
 neutral cues with appetitive and aversive stimuli and receives dense
 neuromodulatory acetylcholine (ACh) projections. We measured BLA ACh
 signaling and activity of neurons expressing CaMKIIα (a marker for
 glutamatergic principal cells) in mice during cue-reward learning using a
 fluorescent ACh sensor and calcium indicators. We found that ACh levels
 and nucleus basalis of Meynert (NBM) cholinergic terminal activity in the
 BLA (NBM-BLA) increased sharply in response to reward-related events and
 shifted as mice learned the cue-reward contingency. BLA CaMKIIα neuron
 activity followed reward retrieval and moved to the reward-predictive cue
 after task acquisition. Optical stimulation of cholinergic NBM-BLA
 terminal fibers led to quicker acquisition of the cue-reward contingency.
 These results indicate BLA ACh signaling carries important information
 about salient events in cue-reward learning and provides a framework for
 understanding how ACh signaling contributes to shaping BLA responses to
 emotional stimuli.
description: See file: Crouse_et_al_2020_Dryad_Methods.docx
description: See file: 10.5061_dryad.3xsj3txcf.docx To read
 this document on the web, use the following link (Public README Crouse et
 al Source Data and Code):<br> https://docs.google.com/document/d/1x8ZXqY4HUcf6kfIUChyLuZpUhHWWlfYLCsG-CYIiK34/edit?usp=sharing
DOI: 10.5061/dryad.j6q573n9n
title: Impacts of global environmental change drivers on non-structural carbohydrates in terrestrial plants

description: 1. Non-structural carbohydrates (NSCs, including soluble sugars and
 starch) are essential to support the growth and survival of terrestrial
 plants. Starch and sugars play different roles in multiple plant
 ecological functions such as drought tolerance, growth, and plant defense,
 and several other processes which are being rapidly shaped by global
 environmental change. However, it is uncertain whether soluble sugars and
 starch show different responses across plant functional types, tissue
 types, and treatment conditions (i.e., the intensity and duration of
 environmental variability) to global-change drivers. 2. Here, based on a
 database of 275 plants (including 17 plant functional types), we conducted
 a meta-analysis to examine the effects of elevated atmospheric CO2
 concentration (eCO2), nitrogen (N) addition, drought and warming on NSCs
 and its components. 3. We found NSCs responses to global environmental
 change were mainly driven by i) soluble sugar changes in response to N
 addition and drought, as well as ii) starch changes in response to eCO2
 and warming. The different responses between soluble sugars and starch
 were more evident under eCO2 and drought, especially in herbs or leaves.
 Interactive effects of multiple environmental change drivers on soluble
 sugars and starch were mainly additive. The divergent main and interactive
 effects on soluble sugars and starch depend on experimental conditions.
 For example, the starch responses to eCO2 and its interaction with N
 addition were the strongest in short-term experiments. 4. Overall, our
 study shows the divergent responses of soluble sugars and starch in
 terrestrial plants to different global environmental change drivers,
 suggesting a changed carbon sink-source balance in plants under future
 global changes. The findings also highlight that predicting plant
 functional changes into the future requires a mechanistic understanding of
 how NSCs and its components are lined with specific environmental change
 drivers.
DOI: 10.15468/dl.jwp5kc
title: Occurrence Download

description: A dataset containing 766 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ophelimus maskelli"
 ]
}

 The dataset includes 766 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002316-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.zkh189375
title: Neuronal octopamine signaling regulates mating-induced germline stem cell increase in female Drosophila melanogaster

description: Stem cells fuel the development and maintenance of
 tissues. Many studies have addressed how local signals from
 neighboring niche cells regulate stem cell identity and their
 proliferative potential. However, the regulation of stem cells by
 tissue-extrinsic signals in response to environmental cues remains poorly
 understood. Here we report that efferent octopaminergic neurons
 projecting to the ovary are essential for germline stem cell (GSC)
 increase in response to mating in female Drosophila. The neuronal
 activity of the octopaminergic neurons is required for mating-induced GSC
 increase as they relay the mating signal from Sex peptide
 receptor-positive cholinergic neurons. Octopamine and its receptor Oamb
 are also required for mating-induced GSC increase via intracellular
 Ca2+ signaling. Moreover, we identified Matrix
 metalloproteinase-2 as a downstream component of the
 octopamine-Ca2+ signaling to induce GSC increase. Our study
 provides a mechanism describing how neuronal system couples stem cell
 behavior to environmental cues through stem cell niche signaling.
description: Source data file 1. Data of numbers of GSC and other cells. GSC
 numbers were determined based on the morphology and position of their
 anteriorly anchored spherical spectrosome visualized by immunostaining
 with mouse anti-Hts 1B1 (Developmental Studies Hybridoma Bank [DSHB];
 1:50), rat anti-DE-cadherin DCAD2 (DSHB; 1:50). Cap cells were visualized
 by immunostaining with mouse monoclonal anti-Lamin C antibody LC28.26
 (DSHB; 1:10). Source data file 2: Data of pMad and
 dad-lacZ signal intensity. pMad was visualized by immunostaining
 with rabbit monoclonal anti-pMad (Abcam #ab52903; 1:1000). LacZ was
 visualized by immunostaining with mouse monoclonal anti-LacZ antibody
 40-1a (DSHB; 1:50). The fluorescence intensity in confocal sections was
 measured via ImageJ. Source data file 3: Data of
 GCaMP6s intensity in escort cells. We monitored
 [Ca<sup>2+</sup>]<sub>i</sub> using a genetically
 encoded calcium sensor, GCaMP6s. <i>GCaMP6s</i> transgene was
 expressed driven
 by <i>tj-GAL4</i> or<i> c587-GAL4</i>, which are
 active in escort cells. GFP fluorescence intensity in confocal sections
 was measured via ImageJ. Source data file 4: Data of
 TRIC intensity in the abdominal ganglions. The transcriptional reporter of
 intracellular Ca<sup>2+</sup> (TRIC) is designed to increase
 the <i>GFP</i> expression in proportion to
 [Ca<sup>2+</sup>]<sub>i</sub>. The fly genotype
 was <i>Tdc2&gt;UAS-mCD8::RFP, UAS-p65AD::CaM LexAop2-mCD8::GFP;
 nSyb-MKII::nlsLexADBDo;UAS-p65AD::CaM. </i>GFP fluorescence
 intensity in confocal sections was measured via ImageJ.
DOI: 10.25338/b82g8z
title: Data from: The effect of early burn injury on sensitivity to future painful stimuli in dairy heifers

description: Animals that experience painful procedures as neonates are more sensitive
 to pain later in life. We evaluated whether disbudding with a heated iron
 at 3 (n=12), 35 (n=9), or 56 (n=20) d of age affected heifers’ pain
 responses to vaccine injections at 11 mo of age. Heifers responded to the
 injection procedure with struggling and changes in eye temperature and
 heart rate variability compared to a sham procedure the day before, and
 still had a heightened response 6 d later, regardless of disbudding age.
 However, some heart rate variability indices suggested increased
 sympathetic dominance in heifers disbudded at 35 d, compared to the other
 2 age groups, independent of the injection procedure. We also found that
 heifers disbudded at 3 or 35 d had a higher mean heart rate after the
 injection procedure compared to those disbudded at 56 d. We conclude that:
 (1) heifers find injections aversive; and (2) there is some evidence that
 disbudding age influences autonomic nervous system activity later in life.
description: Data were collected from the University of California Davis Dairy
 Facility on 41 heifers in 2017. Variables are defined in Sheet 2 of each
 Excel file. The R script used to analyze each dataset is
 provided.
DOI: 10.5061/dryad.j0zpc86b5
title: Genome complexity reduction and high throughput sequencing of green iguana (Iguana iguana) cause a paradigm shift in understanding sex chromosomal linkages on homomorphic X and Y sex chromosomes

description: Most lizards in the Superfamily Iguanoidea have an XX/XY sex determination
 system in which sex chromosomal linkage has homology with chicken (Gallus
 gallus) chromosome 15 (GGA15); however, sex chromosome genomics remains
 largely unexplored due to the presence of homomorphic sex chromosomes in
 many species. Recent advances in high-throughput sequencing with genome
 complexity reduction now provide an effective approach to identify
 sex-specific loci in both single nucleotide polymorphisms (SNPs) and
 restriction fragment presence/absence (PA), and a better understanding of
 sex chromosome dynamics in this lineage. Here, we applied Diversity Arrays
 Technology (DArTseq™) in 29 phenotypic sex assignments of green iguana
 (Iguana iguana). We confirmed a male heterogametic (XX/XY) sex
 determination mode in this species, identifying 29 perfectly sex-linked
 SNP/PA loci and 164 moderately sex-linked SNP/PA loci, likely serving as
 evidence indicative of XY recombination. 3 loci from perfectly sex-linked
 SNP/PA loci showed partial homology with several amniote sex chromosomal
 linkages. Our results support the hypothesis of an ancestral super-sex
 chromosome with overlaps of partial sex chromosomal linkages. However,
 only one locus from moderately sex-linked loci had homology with GGA15,
 suggesting that the specific region homologous to GGA15 was located
 outside the non-recombination region but very close to this region of sex
 chromosome in the green iguana. The location of GGA15 might, therefore, be
 further apart from the putative sex-determining locus in green iguana. The
 DArTseq platform provides an easy to use strategy for future research on
 sex chromosome evolution of lizards in Iguanoidea, particularly for
 non-model species with homomorphic or very cryptic sex chromosomes.
DOI: 10.5061/dryad.9ghx3ffdx
title: Consistent pattern of higher lability of leaves from high latitudes for both native Phragmites australis and exotic Spartina alterniflora

description: 1. Global variation in litter decomposition rates is driven by climate,
 decomposer taxa and litter quality. Most large-scale studies of litter
 quality have made comparisons across species, rather than within a species
 sourced from different latitudes. Here, we aim to explore latitudinal
 variation in leaf litter decomposition rate and litter quality within a
 species. 2. We investigated whether the typical interspecific pattern of
 increased litter lability at higher latitudes also holds within plant
 species, by comparing leaf litter decomposition rates and litter traits
 from stands of native Phragmites australis and exotic Spartina
 alterniflora in Chinese coastal wetlands spanning 20° of latitude using
 parallel greenhouse and field transplant experiments. 3. We found that
 leaf litter from high latitude plants decomposed 46.6±5.1% faster than
 that from low latitude conspecifics, with similar patterns in both plant
 species in both decomposition experiments. Higher lability of leaves from
 high latitudes was associated with lower levels of plant defensive
 compounds (phenolics and tannins) and higher levels of nutrients (Ca, Mg,
 Na). Litter from the exotic S. alterniflora decomposed faster than litter
 from the native P. australis, being consistent with lower defenses and
 higher nutrient concentrations in S. alterniflora litter. 4. Our results
 show that individual species follow the same pattern of increasing litter
 lability at higher latitudes previously reported in cross-species
 geographic comparisons. Moreover, this pattern can develop rapidly
 (&lt; 4 decades) in an introduced species, raising the question of
 whether it is caused by phenotypic plasticity or adaptation.
DOI: 10.5061/dryad.wdbrv15kb
title: Data from: Chemical signals from eggs facilitate cryptic female choice in humans

description: Mate choice can continue after mating via chemical communication between
 the female reproductive system and sperm. While there is a growing
 appreciation that females can bias sperm use and paternity by exerting
 cryptic female choice for preferred males, we know surprisingly little
 about the mechanisms underlying these post-mating choices. In particular,
 whether chemical signals released from eggs (chemoattractants) allow
 females to exert cryptic female choice to favour sperm from specific males
 remains an open question, particularly in species (including humans) where
 adults exercise pre-mating mate choice. Here, we adapt a classic
 dichotomous mate choice assay to the microscopic scale to assess
 gamete-mediated mate choice in humans. We examined how sperm respond to
 follicular fluid, a source of human sperm chemoattractants, from either
 their partner or a non-partner female when experiencing a simultaneous or
 non-simultaneous choice between follicular fluids. We report robust
 evidence under these two distinct experimental conditions that follicular
 fluid from different females consistently and differentially attracts
 sperm from specific males. This chemoattractant-moderated choice of sperm
 offers eggs an avenue to exercise independent mate preference. Indeed,
 gamete-mediated mate choice did not reinforce pre-mating human mate choice
 decisions. Our results demonstrate that chemoattractants facilitate
 gamete-mediated mate choice in humans, which offers females the
 opportunity to exert cryptic female choice for sperm from specific
 males. 
description: Samples were obtained from couples receiving assisted
 reproductive treatment at the Department of Reproductive Medicine at Old
 St. Mary’s Hospital in Manchester between 2015-2017. 
description: Raw data used in analyses. These data include: simultaneous
 choice sperm data, simultaneous choice clinical data, non-simultaneous
 choice sperm data, non-simultaneous choice clinical data, and sperm
 velocity data. A legend is included in each data file explaining what the
 column headings mean. Note that the dataset was updated after publication
 on 25/6/20 to clarify legend descriptions and details of male and female
 annonymized identities.
DOI: 10.5061/dryad.95x69p8gh
title: Data from: Adaptation to hand-tapping affects sensory processing of numerosity directly: evidence from reaction times and confidence

description: Like most perceptual attributes, the perception of numerosity is
 susceptible to adaptation, both to prolonged viewing of spatial arrays and
 to repeated motor actions such as hand-tapping. However, the possibility
 has been raised that adaptation may reflect response biases rather than
 modification of sensory processing. To disentangle these two
 possibilities, we studied visual and motor adaptation of numerosity
 perception while measuring confidence and reaction-times. Both sensory and
 motor adaptation robustly distorted numerosity estimates, and these shifts
 in perceived numerosity were accompanied by similar shifts in confidence
 and reaction-time distributions. After adaptation, maximum uncertainty and
 slowest response-times occurred at the point of subjective (rather than
 physical) equality of the matching task, suggesting that adaptation acts
 directly on the sensory representation of numerosity, before the
 decisional processes. On the other hand, making reward
 response-contingent, which also caused robust shifts in the psychometric
 function, caused no significant shifts in confidence or reaction-time
 distributions. These results reinforce evidence for shared mechanisms that
 encode the quantity of both internally and externally generated events,
 and advance a useful general technique to test whether contextual effects
 like adaptation and serial dependence really affect sensory processing.
description: The dataset was collected through customized psychophysical tests
 to assess the effect of numerosity adaptation in terms of change of PSEs,
 the confidence of the response and reaction-time.  PSEs
 were estimated from best fitting cumulative gaussian to the
 data.  Confidence and reaction-time via gaussian fits
 to the distributions of either aggregate or single subjects
 data.  Variability in the estimete of all statistics
 were measured through bootstrap simulations. Boostrap was also exploited
 to run no-assumption paired t-tests to asses wheter the results in the
 different conditions were statistically different.
DOI: 10.15468/dl.876evm
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Annea laxiflora",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 32 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002317-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.pk0p2ngk1
title: Supplementary tables S5, S7, S9, S10, original protein models fasta files used for alignments, aligned and manually curated protein modes files used for phylogenies (PHYLIP format), and phylogenetic trees of plant cell wall decomposition gene families from 44 basidiomycete genomes (.tre files)

description: Litter-decomposing Agaricales play key role in terrestrial carbon cycling,
 but little is known about their decomposition mechanisms. We assembled
 datasets of 42 gene families involved in plant-cell-wall decomposition
 from seven newly sequenced litter decomposers and 35 other Agaricomycotina
 members, mostly white-rot and brown-rot species. Using sequence similarity
 and phylogenetics, we split the families into phylogroups and compared
 their gene composition across nutritional strategies. Subsequently, we
 used Raman spectroscopy to examine the ability of litter decomposers,
 white-rot fungi, and brown-rot fungi to decompose crystalline cellulose.
 Both litter decomposers and white-rot fungi share the enzymatic cellulose
 decomposition, whereas brown-rot fungi possess a distinct mechanism that
 disrupts cellulose crystallinity. However, litter decomposers and
 white-rot fungi differ with respect to hemicellulose and lignin
 degradation phylogroups, suggesting adaptation of the former group to the
 litter environment. Litter decomposers show high phylogroup diversity,
 which is indicative of high functional versatility within the group,
 whereas a set of white-rot species shows adaptation to bulk-wood
 decomposition. In both groups, we detected species that have unique
 characteristics associated with hitherto unknown adaptations to diverse
 wood and litter substrates. Our results suggest that the terms white-rot
 fungi and litter decomposers mask a much larger functional diversity.
description: The four tables S5, S7, S9, S10 are part of the supplementary
 material containing data about gene copies across species and gene
 families (S5), statistical analyses results (S7), subclassification of
 gene families AA1, AA2, AA5, GH3 (S9), and the OrthoMCL results
 (S10).  The original protein datasets (.txt files) were
 collected using Pfam, IPR, superfamily domain information, and blastp
 searches. Those files starting with A_ were used for phylogenetic analyses
 and OrthoMCL, while those file starting with B_ were only analyzed on the
 first principal component analysis, but not further for phylogenetics and
 OrthoMCL.  After the initial alignments low quality
 models were manually removed. Those files have this format:
 FILENAME_excluded.txt The datasets were alignned
 using MAFFT (FFT-NS-i) and manually examined using AliView in order to
 remove poorly aligned regions. The final aligned files are those in PHYLIP
 format (.phy). The phylogenetic trees generated using
 RAxML at Cipres (PROTCAT and WAG) using 1000 bootstrap runs (.tre
 files)