cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2v6wwpzjh
title: Molecular mechanisms underlying plasticity in a thermally varying environment

description: Adaptation to environmental variability is a prerequisite for species’
 persistence in their natural environments. With climate change predicted
 to increase the frequency and severity of temperature fluctuations,
 ectothermic organisms may increasingly depend on acclimation capacity to
 accommodate thermal variability. To elucidate the molecular basis of
 fluctuating temperature induced phenotypic plasticity, we investigated
 heat tolerance and the mechanisms induced by acclimation to thermal
 variability as compared to those seen at constant temperature. We ran
 genome-wide transcriptomic analysis on Drosophila melanogaster subjected
 to acclimation at constant (19 ± 0°C) and fluctuating (19 ± 8°C)
 temperatures and contrasted the induction of molecular mechanisms in adult
 males, adult females, and larvae. We found life stage and sex specific
 dynamics of the acclimation responses to fluctuating temperatures. Adult
 flies exposed to temperature fluctuations showed a constitutive
 improvement in heat tolerance while heat tolerance of larvae tracked
 thermal fluctuations. A constitutive down-regulation of gene expression
 was observed for several genes in the case of larvae exposed to
 fluctuations. Our results for adult females showed that, for several
 genes, fluctuating temperature acclimation resulted in canalization of
 gene expression. Both transcriptional and post-transcriptional machinery
 were greatly affected by fluctuations in the case of adult males. Gene
 ontology analysis showed enrichment of heat stress response involving
 several major heat shock proteins in both larvae and adults exposed to
 fluctuating temperatures, even though fluctuations were in a benign range
 of temperatures. Finally, molecular mechanisms related to environmental
 sensing seem to be an important component of insect response to thermal
 variability.
description: Phenotypic data from time to knock-down assays performed at
 different timepoints during larval and adult stage of Drosophila
 melanogaster. Experimental insects were placed in wells within
 experimental arenas which were further placed in an incubator set to
 a high temperature for recording the knock-down time. See the Materials
 and Methods section of the associated publication for further
 details.
description: There are some missing values in the dataset due to death by
 handling or missing experimental insect in wells within an
 arena. Information required to understand the data are
 explained in the README.txt file.
DOI: 10.5061/dryad.s7h44j14d
title: Sex-specific effects of cooperative breeding and colonial nesting on prosociality in corvids

description: The investigation of prosocial behavior is of particular interest from an
 evolutionary perspective. Comparisons of prosociality across non-human
 animal species have, however, so far largely focused on primates, and
 their interpretation is hampered by the diversity of paradigms and
 procedures used. Here we present the first systematic comparison of
 prosocial behavior across multiple species in a taxonomic group outside
 the primate order, namely the bird family Corvidae. We measured
 prosociality in 8 corvid species, which vary in the expression of
 cooperative breeding and colonial nesting. We show that cooperative
 breeding is positively associated with prosocial behavior across species.
 Also colonial nesting is associated with a stronger propensity for
 prosocial behavior, but only in males. The combined results of our study
 strongly suggest that both cooperative breeding and colonial nesting,
 which may both rely on heightened social tolerance at the nest, are likely
 evolutionary pathways to prosocial behavior in corvids.
description: Data are found in the file "Corvid_GSP_Data.csv".
 Labels and descriptions of the variables are found in the file
 "Corvid_GSP_Variables_Labels_Descriptions.txt". The file
 "Jetztree1.nex" contains the phylogenetic tree for the
 phylogenetically controlled model.
DOI: 10.5061/dryad.6wwpzgmvq
title: Do all roads lead to resistance? State road density is the main impediment to gene flow in a flagship species inhabiting a severely fragmented anthropogenic landscape

description: The wildcat population in Germany is currently estimated between 6,000 and
 15,000 individuals, and the European wildcat serves as an umbrella species
 due to its diverse habitat demands. Our study took place in the core range
 of the European wildcat in Germany, covering an area of ca.
 186.000 km², and we used genotypes of
 975 pure-bred wildcat individuals. Data were largely based on
 non-invasively sampled hair, but also included tissue, saliva, faeces and
 blood samples from different studies. We used pairwise genetic, geografic
 as well as effective distances of various landscape variables in different
 representations to determine effects of landscape variables on genetic
 distances.
description: See paper for methods.
description: The file contains pairwise straigt-line distance, genetic
 distance and effective distances in column-wise format with 474.825
 columns. Names of columns correspond to variable names.
DOI: 10.5061/dryad.w0vt4b8nb
title: Identification of a queen pheromone mediating the rearing of adult sexuals in the pharaoh ant Monomorium pharaonis

description: Division of labour between reproductive queens and mostly sterile workers
 is among the defining characteristics of social insects. Queen-produced
 chemical signals advertising her presence and fertility status, i.e. queen
 pheromones, are normally used to assert the queen’s reproductive dominance
 in the colony. Most queen pheromones identified to date are chemicals that
 stop the daughter workers from reproducing. Nevertheless, it has long been
 suggested that queen pheromones could also regulate reproduction in
 different ways. In some multiple-queen ants with obligately sterile
 workers, for example – such as fire ants and pharaoh ants – queen
 pheromones are thought to regulate reproduction by inhibiting the rearing
 of new sexuals. Here we identify the first such queen pheromone in the
 pharaoh ant Monomorium pharaonis and demonstrate its mode of action via
 bioassays with the pure biosynthesized compound. In particular, we show
 that the monocyclic diterpene neocembrene, which in different Monomorium
 species is produced solely by fertile, egg-laying queens, strongly
 inhibits the rearing of new sexuals (queens and males) and also exerts a
 weakly attractive “queen retinue”  effect on the workers. This is
 the first time that a queen pheromone with such a dual function has
 been identified in a social insect species with obligately
 sterile workers.
DOI: 10.5061/dryad.djh9w0vx5
title: Differentiation of parathyroid hormone expressing cells from human pluripotent stem cells

description: Abstract Differentiation of pluripotent stem cells into functional
 parathyroid-like cells would accelerate development of important
 therapeutic options for subjects with parathyroid-related disorders, from
 the design and screening of novel pharmaceutical agents to the development
 of durable cellular therapies. We have established a highly reproducible
 directed differentiation approach leading to parathyroid hormone (PTH)
 expressing cells from human embryonic stem cells (hESC) and induced
 pluripotent stem cells (iPSC). We accomplished this through the comparison
 of multiple different basal media, the inclusion of the CDK inhibitor
 PD0332991 in both definitive endoderm (DE) and anterior foregut endoderm
 (AFE) stages, and a 2-stage pharyngeal endoderm (PE) series. This is the
 first protocol to reproducibly establish PTH expressing-cells from human
 pluripotent stem cells and represents a first step towards the development
 of functional parathyroid cells with broad applicability for medicinal and
 scientific investigation.
DOI: 10.5061/dryad.gf1vhhmkw
title: Data from: Sampling schemes and drift can bias admixture proportions inferred by STRUCTURE

description: The interbreeding of individuals coming from genetically differentiated
 but incompletely isolated populations can lead to the formation of admixed
 populations, having important implications in ecology and evolution. In
 this simulation study, we evaluate how individual admixture proportions
 estimated by the software structure are quantitatively affected by
 different factors. Using various scenarios of admixture between two
 diverging populations, we found that unbalanced sampling from parental
 populations may seriously bias the inferred admixture proportions;
 moreover, proportionally large samples from the admixed population can
 also decrease the accuracy and precision of the inferences. As expected,
 weak differentiation between parental populations and drift after the
 admixture event strongly increase the biases caused by uneven sampling. We
 also show that admixture proportions are generally more biased when
 parental populations unequally contributed to the admixed population.
 Finally, with few exceptions, using a large number of markers reduces
 those biases, but using alternative priors for individual ancestry or the
 uncorrelated allele model only marginally affect the inference of
 admixture in most situations. We conclude that unbalanced sampling may
 cause important biases in the admixture proportions estimated by
 structure, especially when a small number of markers are used, and those
 biases can be worsened by the effect of drift and unequal genetic
 contribution of parental populations. Empirical studies should thus be
 careful with their sampling design and consider historical characteristics
 when using this software to estimate the ancestry of individuals from
 admixed populations.
DOI: 10.5061/dryad.3j9kd51fc
title: Changes in taxonomic and phylogenetic diversity in the Anthropocene

description: To better understand how ecosystems are changing, a multifaceted approach
 to measuring biodiversity that considers species richness and evolutionary
 history across spatial scales is needed. Here we compiled 162 datasets for
 fish, bird, and plant assemblages across the globe and measured how
 taxonomic and phylogenetic diversity changed at different spatial scales
 (within site α diversity and between sites spatial β diversity).
 Biodiversity change is measured from these datasets in three ways: across
 land use gradients, from species lists, and through sampling of the same
 locations across two time periods. We found that local species richness
 and phylogenetic α diversity (Faith’s PD) increased for all taxonomic
 groups. However, when measured with a metric that is independent of
 species richness (phylogenetic species variation, PSV), phylogenetic α
 diversity declined for all taxonomic groups. Land use datasets showed
 declines in species richness, Faith’s PD, and PSV. For all taxonomic
 groups and data types, spatial taxonomic and phylogenetic β diversity
 decreased when measured with Sorensen dissimilarity and phylogenetic
 Sorensen dissimilarity, respectively, providing strong evidence of global
 biotic homogenization. The decoupling of α and β diversity, as well as
 taxonomic and phylogenetic diversity, highlights the need for a broader
 perspective on contemporary biodiversity changes. Conservation and
 environmental policy decisions thus need to consider biodiversity beyond
 local species richness to protect biodiversity and ecosystem services.
description: Most column names are self-explaining. dat_1_n represents the
 number of sites of "time period" 1 for each dataset. `smd_logrr`
 represents the log response ratio of diversity, i.e.
 log(dat_2_ave/dat_1_ave). `signma_rr` represents the variance of log
 response ratio. See the paper for details.
DOI: 10.5061/dryad.n5tb2rbsp
title: Data from: Uneven missing data skew phylogenomic relationships within the lories and lorikeets

description: Inlcuded is the supplementary data for Smith, B. T., Mauck, W.
 M., Benz, B., & Andersen, M. J. (2018). Uneven missing data skews
 phylogenomic relationships within the lories and
 lorikeets. BioRxiv, 398297.  The resolution of the Tree
 of Life has accelerated with advances in DNA sequencing technology. To
 achieve dense taxon sampling, it is often necessary to obtain DNA from
 historical museum specimens to supplement modern genetic samples. However,
 DNA from historical material is generally degraded, which presents various
 challenges. In this study, we evaluated how the coverage at variant sites
 and missing data among historical and modern samples impacts phylogenomic
 inference. We explored these patterns in the brush-tongued parrots (lories
 and lorikeets) of Australasia by sampling ultraconserved elements in 105
 taxa. Trees estimated with low coverage characters had several clades
 where relationships appeared to be influenced by whether the sample came
 from historical or modern specimens, which were not observed when more
 stringent filtering was applied. To assess if the topologies were affected
 by missing data, we performed an outlier analysis of sites and loci, and a
 data reduction approach where we excluded sites based on data
 completeness. Depending on the outlier test, 0.15% of total sites or 38%
 of loci were driving the topological differences among trees, and at these
 sites, historical samples had 10.9x more missing data than modern ones. In
 contrast, 70% data completeness was necessary to avoid spurious
 relationships. Predictive modeling found that outlier analysis scores were
 correlated with parsimony informative sites in the clades whose topologies
 changed the most by filtering. After accounting for biased loci and
 understanding the stability of relationships, we inferred a more robust
 phylogenetic hypothesis for lories and lorikeets.
description: Included in the compresed file is supplementary data with four
 main directories: Filtered, Low_Coverage, final_consensus_trees_ and
 scripts. The Filtered and Low_Coverage directories contain the
 concatenated alignments and partition files for each likelihood threshold
 score. These directories also include the likelihodd scores for each of
 the six clades. The final_consensus_trees directories contain the
 consensus trees from the major phylogenetic analyses in the paper. The
 scripts directory contains two scripts for formatting concatenated
 alignments. Readme files are included in each subdirectory.
DOI: 10.5061/dryad.9ghx3fff5
title: Data from: Morphological innovation and biomechanical diversity in plunge-diving birds

description: Innovations in foraging behavior can drive morphological diversity by
 opening up new ways of interacting with the environment, or limit
 diversity through functional constraints associated with different
 foraging behaviors. Several classic examples of adaptive radiations in
 birds show increased variation in ecologically relevant traits. However,
 these cases primarily focus on geographically narrow adaptive radiations,
 consider only morphological evolution without a biomechanical approach, or
 do not investigate tradeoffs with other non-focal traits that might be
 affected by use of different foraging habitats. Here, we use X-ray
 micro-computed tomography (microCT), biomechanical modelling, and
 multivariate comparative methods to explore the interplay between foraging
 behavior and cranial morphology in kingfishers, a global radiation of
 birds with variable beaks and foraging behaviors, including the archetypal
 plunge-dive into water. Our results quantify covariation between the shape
 of the outer keratin covering (rhamphotheca) and the inner skeletal core
 of the beak, as well as highlight distinct patterns of morphospace
 occupation for different foraging behaviors and considerable rate
 variation among these skull regions. We anticipate these findings will
 have implications for inferring beak shapes in fossil taxa and inform
 biomimetic design of novel impact-reducing structures.
DOI: 10.25338/b8k33x
title: Data from: Gene flow in the anemone Anthopleura elegantissima limits signatures of local adaptation across an extensive geographic range

description: Species inhabiting marine environments face a wide range of environmental
 conditions that vary spatially across several orders of magnitude. The
 selective pressures that these conditions impose on marine organisms, in
 combination with potentially high rates of gene flow between distant
 populations, make it difficult to predict the extent to which these
 populations can locally adapt. Here, I identify how selection and gene
 flow influence the population genetic structure of the anemone Anthopleura
 elegantissima along the Pacific coast of North America.
 Isolation-by-distance is the dominant pattern across the range of this
 species, with a genetic break near Pt. Conception, CA. Furthermore,
 demographic modeling suggests that this species was historically confined
 to southerly latitudes before expanding northward. Outlier analyses
 identify 24 loci under selection (out of ~1,100), but the same analysis on
 simulated genetic data generated using the most likely demographic model
 erroneously identified the same number of loci under selection, if not
 more. Taken together, these results suggest that demographic processes are
 the dominant force shaping population genetic patterns in A. elegantissima
 along the Pacific coast of North America. I discuss these patterns in
 terms of the evolutionary history of A. elegantissima, the potential for
 local adaptation, and their consequences with respect to interactions with
 the endosymbiont Breviolum muscatinei across their geographic range.
description: Individuals were collected from Washington state to Baja
 California. After DNA extraction, RAD-seq libraries were produced using
 <em>sbfI  </em>and random shearing to achieve the desired
 insert size. Individuals were sequenced on the Illumina 2500 and 4000
 platforms. Subsequent SNP calls were made using the STACKS software
 pipeline after aligning reads to a draft A. sola genome assembly. Finally,
 loci were screened for contamination by BLASTing all loci to a database of
 bacteria and dinoflagellate genomes and were excluded if they had positive
 BLAST match e-values of 1 or less. All remaining loci were included in
 subsequent analyses and are included in the dataset uploaded here. Raw
 reads and the draft genome assembly are available on NCBI Bioproject
 PRJNA632874.
description: Individual metadata including latitude/longitude where they were
 collected are in an associated metafile.
DOI: 10.5061/dryad.ncjsxksrh
title: Data from: Dunnock social status correlates with sperm speed, but fast sperm does not always equal high fitness

description: Sperm competition theory predicts that males should modulate sperm
 investment according to their social status. Sperm speed, one proxy of
 sperm quality, also influences the outcome of sperm competition because
 fast sperm cells may fertilize eggs before slow sperm cells. We evaluated
 whether the social status of males predicted their sperm speed in a wild
 population of dunnocks (Prunella modularis). In addition to the
 traditional analysis of the average speed of sperm cells per sample, we
 also analyzed subsamples of the fastest sperm cells per sample. In other
 words, we systematically evaluated the effects of including different
 numbers of the fastest sperm in our analyses, ranging from the 5-fastest
 sperm cells to the 100-fastest sperm cells in a sample. We further
 evaluated whether fitness, defined here as the number of chicks sired per
 male per breeding season, relates to the sperm speed in the same
 population. We found that males in monogamous pairings (i.e. low levels of
 sperm competition), produced the slowest sperm cells whereas subordinate
 males in polyandrous male-male coalitions, (i.e. high levels of sperm
 competition), produced the fastest sperm cells. This result was consistent
 regardless of the number of fastest sperm included in our analyses, but
 statistical support was conditional on the number of sperm cells included
 in the analysis. Interestingly, we found no significant relationship
 between fitness and sperm speed, which suggests that it is possible that
 the differential mating opportunities across social status leveled out any
 possible difference. Our study also suggests that it is important to
 identify biologically meaningful subsets of fastest sperm and cutoffs for
 inclusions for assessing sperm competition via sperm speed
DOI: 10.5061/dryad.kwh70rz1j
title: Nonlinear Height-DBH model analysis for three tropical tree species in Mt. Makiling, Philippines

description: The study was conducted to develop the H-DBH models of three species in
 Mt. Makiling. Six H-DBH models (CR, EX, KF, ML, SC, and WE) were used to
 derive and estimate the height of three species in Mt. Makilingsix H-DBH
 models (CR, EX, KF, ML, SC, and WE) were used to derive and estimate the
 height of three species. Based on the evaluation criteria
 including R2, RMSE, Ē, AMD, AIC, and AICw, the performance of the WE model
 was determined to be the best in predicting the height of P. malaanonan
 species while the performance of the KL model was the best both for the D.
 paniculatus, and C. luzonica species. 
description: The dataset were collected using nondestructive sampling since
 cutting of trees in the study area is not allowed.
DOI: 10.5061/dryad.jsxksn06b
title: Drosophila wing disc cell morphology in timelapse

description: Here we provide measurements of cell morphology in the proliferating
 Drosophila larval wing disc, specifically the wing disc pouch, as it grows
 in ex vivo culture. The tables provided here include measurements of cell
 morphology (area and elongation) at each timepoint in each of 5 wing disc
 samples. For cell elongation, we report the elongation values for each of
 its component triangles (formed by connecting the cell to the center of
 its neighbors). We also provide a table that reports for each movie the
 x,y position of a point calculated as the center of radial cell elongation
 symmetry.
description: Timelapse movies of E-cadherin-GFP expressing wing discs were
 acquired as described in Dye et al 2017. Briefly, they were grown in
 Grace's media containing 20nM 20-hydroxyecdysone in a glass-bottom
 dish covered with a porous filter (using a double-stick tape spacer) at
 25C. A spinning disc microscope was used to acquire Z-stacks (0.5um
 Z-steps, 0.2x0.2 um/pixel in x and y) every 5min for ~13hr. For each
 timepoint, the apical surface was projected onto 2D. TissueAnalyzer (FIJI
 plugin) was used to segment and track each cell over time, and TissueMiner
 (Etournay et al 2016) was used for further analysis. We corrected cell
 area and elongation for local curvature as described in Dye et al 2017 and
 Dye et al 2020. For each movie, we also calculated the center of radial
 cell elongation symmetry, as described in Dye et al 2020.
description: See ReadMe file.