cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.b5mkkwhfm
title: Dataset for: Smith et al., Phylogenomic analysis of the parrots of the world distinguishes artifactual from biological sources of gene tree discordance

description: Gene tree discordance is expected in phylogenomic trees and biological
 processes are often invoked to explain it. However, heterogeneous levels
 of phylogenetic signal among individuals within datasets may cause
 artifactual sources of topological discordance. We examined how the
 information content in tips and subclades impacts topological discordance
 in the parrots (Order: Psittaciformes), a diverse and highly threatened
 clade of nearly 400 species. Using ultraconserved elements from 96% of the
 clade's species-level diversity, we estimated concatenated and
 species trees for 382 ingroup taxa. We found that discordance among tree
 topologies was most common at nodes dating between the late Miocene and
 Pliocene, and often at the taxonomic level of genus. Accordingly, we used
 two metrics to characterize information content in tips and assess the
 degree to which conflict between trees was being driven by lower quality
 samples. Most instances of topological conflict and non-monophyletic
 genera in the species tree could be objectively identified using these
 metrics. For subclades still discordant after tip-based filtering, we used
 a machine learning approach to determine whether phylogenetic signal or
 noise was the more important predictor of metrics supporting the
 alternative topologies. We found that when signal favored one of the
 topologies, noise was the most important variable in poorly performing
 models that favored the alternative topology. In sum, we show that
 artifactual sources of gene tree discordance, which are likely a common
 phenomenon in many datasets, can be distinguished from biological sources
 by quantifying the information content in each tip and modeling which
 factors support each topology.
description: Please see Materials and Methods section of the main text and
 Parrots_UCE_variant_calling_and_other_methods.txt.
description: See README.txt
DOI: 10.5061/dryad.9kd51c5kb
title: Data from: Temporal factors and distance to human settlement affect nest survival of the endangered Yellow-headed Parrot in Belize, Central America

description: The endangered Yellow-headed Parrot (Amazona oratrix) has experienced a
 considerable reduction in abundance and distribution. Identifying natural
 and anthropogenic causes of nest failure is a critical step towards
 developing conservation actions that increase nest survival. In this
 study, we examined daily nest survival in relation to temporal, habitat
 and anthropogenic factors, as well as nest site properties. We monitored
 nests (n = 124) across six study sites in Belize during 2017 and 2018 and
 independently modeled the effects of predation, abandonment and poaching
 on daily nest survival rates. Overall, the estimated cumulative nest
 survival probability was 0.18 (95% CI = 0.12 – 0.25). Predation was the
 main cause of nest failure, followed by abandonment and poaching. Our
 results showed that nest predation and abandonment usually occurred early
 in the nesting cycle. Day within the nesting season negatively influenced
 daily survival for abandoned nests and had a quadratic effect on survival
 for poached nests. Poaching events occurred at a specific date range later
 in the season, with nests farther from the nearest human settlement having
 higher daily survival. Findings from this study highlight the additive
 mortality effect that nest poaching is having on Yellow-headed Parrot
 populations in Belize and show that managers can anticipate the timing and
 location of nests most vulnerable to poaching.
description: This data was collected by monitoring Yellow-headed Parrot
 (<em>Amazona oratrix)</em> nests during the 2017-2018 breeding
 seasons in Belize. Dataset includes nests that failed due to predation,
 abandonment and poaching, as well as nests that were successful during the
 two breeding seasons. Associated with them are covariates included in the models used to evaluate daily nest survival. Names of covariates follow those needed to perform survival analysis in RMark. 
description: Dataset does not contain missing values. Please contact the
 author for any additional inquiries of how data was collected and
 analyzed.
DOI: 10.5061/dryad.931zcrjn0
title: Pyrophilic ground beetle rearing study

description: Many insects are drawn to the heat, ash, and smoke produced by forest
 fires and arrive in large numbers at recent burns, often while the fire is
 still active. Some of these insects are pyrophilic and reproduce
 exclusively in the immediate aftermath of fire but are rarely, if ever,
 collected from unburnt habitats. Numerous observations made at active
 fires note an apparent preference among some pyrophilic insects to
 oviposit exclusively in the burnt portions of trees, raising broader
 questions about the adaptive benefits of reproduction in the post-burn
 environment. Here, we tested whether the reproductive output of pyrophilic
 ground-beetles (i.e., Sericoda spp.) increased in heat-sterilized soils.
 In the first experiment, eggs of Sericoda quadripunctata were reared in
 three types of soil collected from burnt forests: recently burnt soil
 (collected 1-2 weeks after the fire), soil collected one year after burn,
 and soil from an unburnt patch of forest adjacent to the fire. Daily
 monitoring through a dissecting microscope documented extensive predation
 of eggs by soil microarthropods (mites, springtails, and nematodes),
 especially in 1-year old and unburnt soil treatments. This led to a second
 experiment that included the same three treatments and an additional
 fourth soil treatment: recently burnt soil reheated to 100 °C for 2 hours
 (i.e., reheated soil). In this experiment, male and female pairs (n = 100)
 of Sericoda obsoleta were reared for 14 days in jars containing 90 g of
 soil corresponding to each of the four soil treatments. Reproductive
 output, measured as the number of larvae produced by each breeding pair,
 was significantly higher in the reheated soil, suggesting that
 heat-sterilization and removal of soil-dwelling predators improved egg
 survival. Our findings suggest that pyrophily in insects may have evolved
 as a means of increasing reproductive output in the post-burn environment
 through access to heat-sterilized ovipositing substrates. Furthermore, the
 abrupt disappearance of Sericoda and other pyrophilic insects following
 fire may be explained by the sub-optimal reproductive conditions as the
 burn is colonized by other organisms and by local emigration in favor of
 other recent burns on the landscape.
DOI: 10.5061/dryad.95x69p8n3
title: Biogeographic distribution and divergent assembly process of cyanobacterial morphotypes in biocrusts across northwestern China

description: The patterns of biogeographical distribution and assembly processes of
 microbiota are of vital importance for understanding ecological adaptation
 and functioning maintenance. However, the role of their morphological
 characteristics in microbial assembly is still poorly ascertained. Here,
 by integrating high-throughput sequencing and robust extrapolation of
 traits, we investigated taxonomic and phylogenetic turnovers of various
 cyanobacterial morphotypes in biocrusts to evaluate the contributions of
 deterministic and stochastic processes across a large scale of drylands.
 The results showed that the non-heterocyst filamentous category dominated
 biocrusts in the arid ecosystem and exhibited strong tolerance against
 environmental fluctuations. Despite thesignificant distance-decay
 relationship of β-diversity detected in all categories, both species
 composition and phylogenetic turnover rates of coccoid cyanobacteria were
 higher than non-heterocyst filamentous and heterocystous morphotypes.
 Moreover, the assembly of cyanobacteria was driven by different ecological
 processes that the entire community and non-heterocyst filamentous
 morphotype were governed by deterministic processes, while stochasticity
 prevailed in heterocystous and coccoid cyanobacteria. However, aridity can
 modulate the balance between determinism and stochasticity and prompt a
 shifting threshold among morphotypes, generating an alteration in
 community composition. Our findings provide a unique perspective to
 understanding the role of microbial morphology in community assembly,
 highlighting the differentiation of biogeographic distribution,
 environmental response, and species preference between cyanobacterial
 morphotypes with consideration of potential functional consequences.
DOI: 10.5061/dryad.nk98sf7vp
title: Identification of an arthropod molecular target for plant-derived natural repellents

description: Arthropods maintain ecosystem balance, while also contribute to disease
 spreading. Plant-derived natural repellents represent an ecological way of
 pest control, but their direct molecular targets in arthropods remain to
 be further elucidated. Occupying a critical phylogenetic niche in
 arthropod evolution, scorpions retain an ancestral genetic profile. Here,
 using a behavior-guided screening of the Mesobuthus martensii genome, we
 identified a scorpion transient receptor potential (sTRP1) channel that
 senses Cymbopogon-derived natural repellents, while insensitive to the
 synthetic chemical pesticide DEET. Scrutinizing orthologs of sTRP1 in
 Drosophila melanogaster, we further demonstrated dTRPϒ ion channel also as
 a chemosensory receptor of natural repellents to mediate avoidance
 behavior. This study sheds light on arthropod molecular targets of natural
 repellents, exemplifying the arthropod-plant adaptation. It should also
 help the rational design of insect control strategy and conserve
 biodiversity.
description: Electrophysiological data were mainly collected
 from traditional patch-clamp recordings and Ca2+ imaging. All behavioral
 experiments with scorpions or flies were conducted in a double-blind
 manner.
DOI: 10.25338/b8h352
title: Effects of parental experience and age on expression of prolactin, vasoactive intestinal peptide and their receptors in a biparental bird, Columba livia

description: As animals gain parental experience, they often show more rapid and
 efficient parental care responses that likely improve offspring survival
 and fitness. Changes in circulating hormones that underlie reproductive
 behaviors, including prolactin, have been found to correlate with parental
 experience in birds and mammals. Altered responsiveness to prolactin in
 key behavioral centers of the brain may also underlie the effects of
 experience on parental behaviors. Further, experience may also affect
 responsiveness to prolactin stimulatory hormones, such as hypothalamic
 vasoactive intestinal peptide (VIP). While experience has been shown to
 upregulate neural prolactin receptors and responsiveness in rodents, its
 effects on prolactin receptor gene expression remain unstudied in birds.
 To address this, we examined gene expression of pituitary prolactin,
 hypothalamic prolactin receptors in the preoptic area, hypothalamic VIP,
 and pituitary VIP receptors in both sexes of the biparental rock dove
 (Columba livia) when birds were not actively nesting. As age and parental
 experience are often confounded (i.e.,experienced parents tend to be older
 than their inexperienced counterparts), we measured gene expression in
 birds of varying combinations of age (0.6–3 years) and prior reproductive
 experience (0–12 chicks raised). We found that increasing experience with
 chicks correlated with lower PRLR expression in the preoptic area, and age
 correlated with lower VIP expression in birds of both sexes. Pituitary PRL
 and VIPR expression was not associated with parental experience or age.
 These results suggest there may be persistent effects of experience and
 age on neural responsiveness to, and regulation of, prolactin in birds.
description: This data was collected by running quantitative PCR on RNA
 extracted from pituitaries and microdissected hypothalami of rock doves
 (Columba livia).
DOI: 10.5061/dryad.xwdbrv1fr
title: Functional integration of multiple sexual ornaments: signal coherence and sexual selection

description: The sexual ornamentation of animals typically consists of multiple
 distinct traits. The classical research approach focuses on differences
 among these traits, but this approach may often be misleading because of
 correlations among distinct sexual traits of similar origins. There are
 many published studies on the correlation structures of sexual traits, but
 the way receivers take into account the components of an integrated,
 multi-component trait system remains mostly unknown. Here we propose a
 general analytical framework to assess the possible sexual selection
 consequences of within-individual coherence in the expression of multiple
 correlated sexual traits. We then apply this framework to a long-term
 mutual plumage coloration data set from a wild bird population. The
 results suggest that the coherence of component plumage color traits is
 not sexually selected. However, component trait coherence affects sexual
 selection on integrated plumage color. When assessing across-spectrum
 plumage reflectance, receivers choosing mates apparently disregard a
 component trait if it is inconsistent with the overall expression of other
 components. This indicates that separately examining and manipulating
 distinct sexual traits may often be misleading. Theoretical and empirical
 studies should further explore the effects of coherence on the
 ornament-preference co-evolution.
description: ReadMe file attached to the dataset.
DOI: 10.5061/dryad.n5tb2rbxm
title: Phylogeny and biogeography of the northern temperate genus Dracocephalum s.l. (Lamiaceae)

description: The northern temperate genus
 Dracocephalum consists of approximately 70 species mainly
 distributed in the steppe-desert biomes of Central and
 West Asia and the alpine region of the Qinghai-Tibetan
 Plateau (QTP). Previous work has shown that
 Dracocephalum is not monophyletic and might include
 Hyssopus and Lallemantia. This study attempts
 to clarify the phylogenetic relationships, diversification
 patterns, and the biogeographical history of the three
 genera (defined as Dracocephalum s.l.). Based on a
 sampling of 66 taxa comprising more than 80%
 from extant species of Dracocephalum s.l., morphological, phylogenetic (maximum parsimony, likelihood, and Bayesian inference based on nuclear ITS and ETS, plastid rpl32-trnL, trnL-trnF, ycf1, and ycf1-rps15, and two low-copy nuclear markers AT3G09060 and AT1G09680), molecular dating, diversification, and ancestral range estimation analyses were carried out. Our results demonstrate that both Hyssopus and Lallemantia are embedded within Dracocephalum and nine well-supported clades can be recognized within Dracocephalum s.l. Analyses of divergence times suggest that the genus experienced an early rapid radiation during the middle to late Miocene with major lineages diversifying within a relatively narrow timescale. Ancestral area reconstruction analyses indicate that Dracocephalum s.l. originated in Central and West Asia and southern Siberia, and dispersed from Central and West Asia into the QTP and adjacent areas twice independently during the Pliocene. The aridification of the Asian interior possibly promoted the rapid radiation of Dracocephalum within this region, and the uplift of the QTP appears to have triggered the dispersal and recent rapid diversification of the genus in the QTP and adjacent regions. Combining molecular phylogenetic and morphological evidence, a revised infrageneric classification of Dracocephalum s.l. is proposed, which recognized nine sections within the genus.
DOI: 10.5061/dryad.j3tx95xgp
title: Made-up mouths with preen oil reveal genetic and phenotypic conditions of starling nestlings

description: Animal colouration are due to pigments, nanostructures, or to the cosmetic
 use of natural products, and plays a central role in social communication.
 The role of cosmetic colouration has traditionally been focussed on
 scenarios of sexual selection, but it could also be used in other
 contexts. Here, by using spotless starling (Sturnus unicolor) as a model
 system, we explore the possibility that nestlings cosmetically used their
 intensely yellow coloured uropygial secretion to signal their genetic
 and/or phenotypic quality to their parents. In agreement with the
 hypothetical cosmetic use of the uropygial secretion, (i) video recorded
 nestlings collected secretion with the bill at the age of feathering, (ii)
 cotton swabs turned to the colour of secretion after rubbing with them
 nestlings’ gape, and (iii) gape and skin colourations correlated
 positively with that of secretion. Furthermore, we found that (iv)
 secretion colouration has a genetic component, and (v) associated
 positively with Vitamin-E supplementation and (vi) with plasma carotenoid
 concentration, which highlights the informative value of nestling
 secretion. Finally, (vii) colouration of begging related traits and of
 secretion of nestlings predicted parental feeding preferences.
 Consequently, all these results strongly suggest that the cosmetic use of
 coloured uropygial secretion might also play a role in parent-offspring
 communication, complementing or amplifying information provided by the
 flamboyant coloured gapes and skin of nestlings. The use of makeups by
 offspring to communicate with parents has been scarcely explored and we
 hope that these results will encourage further investigations in birds and
 some other taxa with parental care. Keywords: Antioxidants, Begging,
 Makeup hypothesis, Parent-offspring communication, Uropygium --
DOI: 10.5061/dryad.v6wwpzgxw
title: Induction and potential role of summer dormancy to enhance persistence of perennial grasses under warmer climates

description: The persistence of perennial herbaceous species is threatened by
 increasing aridity. However, summer dormancy is a strategy conferring
 superior survival to grasses adapted to hot and dry summers. The role of
 temperature on the induction of summer dormancy was investigated in the
 perennial grass Dactylis glomerata to analyse the potential expression of
 this strategy under warmer climates. We tested seven populations of D.
 glomerata originating from Morocco to Norway across the same latitudinal
 gradient in a five-site experiment. One population of the highly
 summer-dormant grass Poa bulbosa was used as a reference. Plants were
 grown from autumn in pots under full irrigation for one year mostly under
 open-air shelters.  Heading date (ear emergence preceding
 flowering) was recorded and foliage senescence was assessed from end of
 spring until autumn. The maximum plant senescence under summer irrigation
 indicated the level of dormancy expression. Summer dormancy onset,
 release, expression and duration were modelled as a function of climatic
 variables. From north to south, the duration of summer dormancy of the
 Mediterranean populations of D. glomerata and P. bulbosa ranged from 0 to
 122 days, and 79 to 200 days respectively. P. bulbosa was always
 completely dormant, while dormancy expression of D. glomerata was
 positively correlated with the sum of temperatures from winter onset
 (R²=0.57) and with the mean of minimum temperatures in summer (R²=0.73).
 Dormancy onset, release and duration were also positively correlated with
 thermal time from winter onset, while the duration of summer dormancy was
 longer as maximum temperatures increased. Mapping the European regions
 with climates allowing the expression of summer dormancy in D. glomerata,
 showed that the potentially inductive areas for this strategy may expand
 in parallel with increasing summer aridity under a future climate warming
 scenario.
description: We tested 7 populations of cocksfoot and 1 population of Poa
 bulbosa in 5 sites from Morocco to Norway. Plants were grown for 1 year
 under irrigation. Summer maximum foliage senescence allowed to detect
 plants that were summer dormant (over 70% summer maximum foliage
 senescence under irrigation). Dates of onset and release of summer
 dormancy were calculated accordingly as well as dormancy
 duration.
description: We provide a READ ME file
DOI: 10.6078/d1xd8t
title: Data from: Genetic and genomic architecture of species-specific cuticular hydrocarbon variation in parasitoid wasps

description: Cuticular hydrocarbons (CHCs) serve two fundamental functions in
 insects: protection against desiccation and
 chemical signaling. How the interaction of genes shapes
 CHC profiles, which are essential for insect survival, adaptation, and
 reproductive success, is still poorly understood. Here
 we investigate the genetic and genomic basis of CHC biosynthesis
 and variation in parasitoid wasps of the genus Nasonia. We mapped
 91 quantitative trait loci (QTL) explaining variation of a total of 43
 CHCs in F2 hybrid males from interspecific crosses between
 three Nasonia species. To identify candidate genes, we
 localized orthologs of CHC biosynthesis-related genes in
 the Nasonia genomes. We discovered multiple genomic
 regions where the location of QTL coincides with the location of CHC
 biosynthesis-related candidate genes. Most conspicuously, on a region on
 chromosome 1 close to the centromere, multiple CHC biosynthesis-related
 candidate genes co-localize with several QTL explaining variation in
 methyl-branched alkanes. The genetic underpinnings behind this compound
 class are not well understood so far, despite their high potential for
 encoding chemical information as well as their prevalence in hymenopteran
 CHC profiles. Our study considerably extends our knowledge on the genetic
 architecture governing this fundamental compound class, establishing a
 model for methyl-branched alkane genetics in the Hymenoptera in general.
DOI: 10.15468/dl.3yemku
title: Occurrence Download

description: A dataset containing 187 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((105 20,170 20,170 70,105 70,105 20))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Harrimanella stelleriana"
 ]
}

 The dataset includes 187 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003066-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.9w0vt4bhj
title: Kcnma1-tdtomato floxed allele sequence

description: BK large conductance calcium-activated K+ channels (KCa1.1) are
 expressed widely across many tissues, contributing to systemic regulation
 of cardiovascular, neurological, and other specialized physiological
 functions. The pore-forming α subunit is encoded by
 the Kcnma1 gene, originally
 named mSlo1 in mouse
 and slowpoke in Drosophila. Global deletion in
 mouse (Kcnma1−/−) produces a plethora of defects in neuron and muscle
 excitability, as well as other phenotypes related to channel function in
 nonexcitable cells. While homozygous null mice are viable, the ubiquitous
 loss of BK function has complicated the interpretation of phenotypes
 involving the interaction of multiple cell types which independently
 express BK channels. Here, we report the generation of a targeted allele
 for conditional inactivation of Kcnma1 using the
 Cre-loxP system (Kcnma1fl-tdTomato). Cre-mediated recombination generates
 a null allele, and BK currents were not detectable in neurons and muscle
 cells from Nestin-Cre; Kcnma1fl/fl and
 SM22α-Cre; Kcnma1fl/fl mice, respectively. tdTomato
 expression was detected in Cre-expressing tissues, but not in Cre-negative
 controls. These data demonstrate the utility
 of Kcnma1fl-tdTomato for conditional deletion of the BK
 channel, facilitating the understanding of tissue-specific contributions
 to physiological function in vivo.
description: The file contains the annotated Kcnma1-tdtomato floxed allele
 sequence.