cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.td887
title: Data from: Conservation and modification of genetic and physiological toolkits underpinning diapause in bumble bee queens

description: Diapause is the key adaptation allowing insects to survive unfavorable
 conditions and inhabit an array of environments. Physiological changes
 during diapause are largely conserved across species, and are hypothesized
 to be regulated by a conserved suite of genes (a “toolkit”). Furthermore,
 it is hypothesized that in social insects, this toolkit was co-opted to
 mediate caste differentiation between long-lived, reproductive,
 diapause-capable queens and short-lived, sterile workers. Using Bombus
 terrestris queens we examined the physiological and transcriptomic changes
 associated with diapause and CO2 treatment, which causes queens to bypass
 diapause. We performed comparative analyses with genes previously
 identified to be associated with diapause in the Dipteran Sarcophaga
 crassipalpis and with caste differentiation in bumble bees. As in Diptera,
 diapause in bumble bees is associated with physiological and
 transcriptional changes related to nutrient storage, stress resistance and
 core metabolic pathways. There is a significant overlap, both at the level
 of transcript and gene ontology, between the genetic mechanisms mediating
 diapause in B. terrestris and S. crassipalpis, reaffirming the existence
 of a conserved insect diapause genetic toolkit. However, a substantial
 proportion (10%) of the differentially regulated transcripts in diapausing
 queens have no clear orthologs in other species, and key players
 regulating diapause in Diptera (juvenile hormone and vitellogenin) appear
 to have distinct functions in bumble bees. We also found a substantial
 overlap between genes related to caste determination and diapause in
 bumble bees. Thus, our studies demonstrate an intriguing interplay between
 pathways underpinning adaptation to environmental extremes and the
 evolution of sociality in insects.
description: Diapause Reads
 countstranscript counts from
 CufflinksDiapauseReadCounts.txtNormalized read counts for PCAnormalizedForPCA.txtPhenotype raw dataraw data for ovarian activation, juvenile hormone levels, lipid and glycogen content, queen weight and gene expression data (fold change) for 11 genes that were tested in the studyphysiological parameters and gene expression.xlsx
DOI: 10.5061/dryad.r6fr1
title: Data from: Field heritability of a plant adaptation to fire in heterogeneous landscapes

description: The strong association observed between fire regimes and variation in
 plant adaptations to fire suggests a rapid response to fire as an agent of
 selection. It also suggests that fire-related traits are heritable, a
 precondition for evolutionary change. One example is serotiny, the
 accumulation of seeds in unopened fruits or cones until the next fire, an
 important strategy for plant population persistence in fire-prone
 ecosystems. Here, we evaluate the potential of this trait to respond to
 natural selection in its natural setting. For this, we use a SNP marker
 approach to estimate genetic variance and heritability of serotiny
 directly in the field for two Mediterranean pine species. Study
 populations were large and heterogeneous in climatic conditions and fire
 regime. We first estimated the realized relatedness among trees from
 genotypes, and then partitioned the phenotypic variance in serotiny using
 Bayesian animal models that incorporated environmental predictors. As
 expected, field heritability was smaller (around 0.10 for both species)
 than previous estimates under common garden conditions (0.20). An estimate
 on a subset of stands with more homogeneous environmental conditions was
 not different from that in the complete set of stands, suggesting that our
 models correctly captured the environmental variation at the spatial scale
 of the study. Our results highlight the importance of measuring
 quantitative genetic parameters in natural populations, where
 environmental heterogeneity is a critical aspect. The heritability of
 serotiny, although not high, combined with high phenotypic variance within
 populations, confirms the potential of this fire-related trait for
 evolutionary change in the wild.
description: Pinus phenotypic data
 and locality descriptionsPhenotypes (serotiny and
 tree diameter) and locality descriptors (stand, coordinates, etc) for 367
 Pinus halpensis and 194 Pinus pinster individuals from SE Spain. Please
 note: these data are a subset of the dataset originally collected by
 Hernández-Serrano et al. (2013) Fire structures pine serotiny at different
 scales. American Journal of Botany 100, 2349-2356.Pinus_phenotypes_and_localities.txtGmatrix_P.halepensisTab-delimited text file with symetrical matrix showing pairwise relatedness estimates for 367 individuals of Pinus halepensis. Diagonal estimates are included. Estimates are based on 251 SNPs and were estimated with the synbreed package in R.Gmatrix P.pinasterTab-delimited text file with symetrical matrix showing pairwise relatedness estimates for 194 individuals of Pinus pinaster. Diagonal estimates are included. Estimates are based on 251 SNPs and were estimated with the synbreed package in R.Gmatrix_P.pinaster.txt
DOI: 10.5061/dryad.9sh82
title: Data from: Extensive recombination of a yeast diploid hybrid through meiotic reversion

description: In somatic cells, recombination between the homologous chromosomes
 followed by equational segregation leads to loss of heterozygosity events
 (LOH), allowing the expression of recessive alleles and the production of
 novel allele combinations that are potentially beneficial upon Darwinian
 selection. However, inter-homolog recombination in somatic cells is rare,
 thus reducing potential genetic variation. Here, we explored the property
 of S. cerevisiae to enter the meiotic developmental program, induce
 meiotic Spo11-dependent double-strand breaks genome-wide and return to
 mitotic growth, a process known as Return To Growth (RTG). Whole genome
 sequencing of 36 RTG strains derived from the hybrid S288c/SK1 diploid
 strain demonstrates that the RTGs are bona fide diploids with mosaic
 recombined genome, derived from either parental origin. Individual RTG
 genome-wide genotypes are comprised of 5 to 87 homozygous regions due to
 the loss of heterozygous (LOH) events of various lengths, varying between
 a few nucleotides up to several hundred kilobases. Furthermore, we show
 that reiteration of the RTG process shows incremental increases of
 homozygosity. Phenotype/genotype analysis of the RTG strains for the
 auxotrophic and arsenate resistance traits validates the potential of this
 procedure of genome diversification to rapidly map complex traits loci
 (QTLs) in diploid strains without undergoing sexual reproduction.
description: genotype_files_dryad_for_Laureau_et_algenotype files from Wild Type 4-spore tetrads and RTG from S288c/SK1 meiosis.genotype_files_dryad.zip
DOI: 10.5061/dryad.j78p5
title: Data from: Temperature-associated habitat selection in a cold-water marine fish

description: Habitat selection is a complex process, which involves behavioural
 decisions guided by the multiple needs and constraints faced by
 individuals. Climate-induced changes in environmental conditions may alter
 those trade-offs and resulting habitat use patterns. In this study we
 investigated the effect of sea temperature on habitat selection and
 habitat use of acoustically tagged Atlantic cod (Gadus morhua) at the
 Norwegian Skagerrak coast. Significant relationships between ocean
 temperature and habitat selection and use were found. Under favourable sea
 temperature thresholds (&lt; 16°C), cod selected vegetated habitats,
 such as eelgrass and macroalgae beds, available in shallow areas.
 Selection for those habitats was especially high at night, when cod tended
 to ascend to shallower areas, presumably to feed. Selection and use of
 those habitats decreased significantly as temperature rose. Under
 increased sea surface temperature conditions, cod were absent from
 vegetated shallow habitats, both during the day and night, and selected
 instead non-vegetated rocky bottoms and sand habitats, available in
 deeper, colder areas. This study shows the dynamic nature of habitat
 selection and strongly suggests that cod in this region have to trade off
 food availability against favourable temperature conditions. Future
 increases in ocean temperature are expected to further influence the
 spatial behaviour of marine fish, potentially affecting individual fitness
 and population dynamics.
description: Cod_positionsPosition data obtained from 40 acoustically tagged Atlantic cod in Tvedestrand, Norway from June to December 2013.Cod_daily_depth_dataDaily average depth used during daytime and nighttime by acoustically tagged Atlantic cod in Tvedestrand, Norway in June to December 2013. Average daily temperature at 1m depth is also provided.
DOI: 10.5061/dryad.dq1j6
title: Data from: The evolution of bat nucleic acid sensing Toll-like receptors

description: We characterized the nucleic acid sensing Toll-like receptors (TLR) of a
 New World bat species, the common vampire bat (Desmodus rotundus), and
 through a comparative molecular evolutionary approach searched for general
 adaptation patterns among the nucleic acid sensing TLRs of eight different
 bats species belonging to three families (Pteropodidae, Vespertilionidae
 and Phyllostomidae). We found that the bat TLRs are evolving slowly and
 mostly under purifying selection and that the divergence pattern of such
 receptors is overall congruent with the species tree, consistent with the
 evolution of many other mammalian nuclear genes. However, the chiropteran
 TLRs exhibited unique mutations fixed in ligand binding sites, some of
 which involved non-conservative amino acid changes and/or targets of
 positive selection. Such changes could potentially modify protein function
 and ligand biding properties, as some changes were predicted to alter
 nucleic acid binding motifs in TLR 9. Moreover, evidence for episodic
 diversifying selection acting specifically upon the bat lineage and sub
 lineages was detected. Thus, the long-term adaptation of chiropterans to a
 wide variety of environments and ecological niches with different pathogen
 profiles is likely to have shaped the evolution of the bat TLRs in an
 order-specific manner. The observed evolutionary patterns provide evidence
 for potential functional differences between bat and other mammalian TLRs
 in terms of resistance to specific pathogens or recognition of nucleic
 acids in general.
description: FileS1_Models3-D models for the D.rotundus nucleic acid sensing TLRs in PBD formatFileS2_Aln&TreesAlignments and trees for the nucleic acid sensing TLRs from bats and other mammalian sequences in Fasta and Newick formatsFileS3_PAMLComplete PAML results (in mlc files for the M1/M2, M8a/M8 and BSA test)
DOI: 10.5061/dryad.d4p7n
title: Data from: Deadwood structural properties may influence aye-aye (Daubentonia madagascariensis) extractive foraging behavior

description: The identification of critical, limited natural resources for different
 primate species is important for advancing our understanding of behavioral
 ecology and toward future conservation efforts. The aye-aye (Daubentonia
 madagascariensis) is an Endangered nocturnal lemur with adaptations for
 accessing structurally defended foods: continuously growing incisors; an
 elongated, flexible middle finger; and a specialized auditory system. In
 some seasons, ca. 90% of the aye-aye’s diet consists of two structurally
 defended resources: 1) the larvae of wood boring insects, extracted after
 the aye-aye gnaws through decomposing bark (deadwood), and 2) the seeds of
 Canarium trees. Aye-ayes have very large individual home ranges relative
 to most other lemurs, possibly owing to limited resource availability.
 Identification of limiting dietary factor(s) is critical for our
 understanding of aye-aye behavioral ecology and future conservation
 efforts. To investigate whether aye-ayes equally access all deadwood
 resources within their range, we surveyed two 100 × 100 m forest plots
 within the territories of two aye-ayes at Sangasanga, Kianjavato,
 Madagascar. Only 2 of 150 deadwood specimens within the plots (1.3%)
 appeared to have been accessed by the aye-ayes. To test whether any
 external or internal deadwood properties explain aye-aye foraging
 preferences we recorded species, height and diameter, and quantified the
 internal tree density using a 3D acoustic tomograph for each foraged and
 nonforaged deadwood resource within the plots, plus 13 specimens (5
 foraged and 8 nonforaged) outside the plots. We did not detect any
 statistically significant preferences for species, diameter, or height.
 However, results from the acoustic analysis tentatively indicated that
 aye-ayes are more likely to forage in trees with greater internal (≥6 cm
 from the bark) densities. This interior region may function as a sounding
 board in the tap-foraging process to help aye-ayes accurately identify
 potential grub-containing cavities in the outer 1–4 cm of deadwood.
description: Thompson et al. deadwood
 foraging and structural property dataThompson et al Deadwood
 structural property data.zip
DOI: 10.5061/dryad.v83fj
title: Data from: Regulatory RNA at the root of animals: dynamic expression of developmental lincRNAs in the calcisponge Sycon ciliatum

description: Long non-coding RNAs (lncRNAs) play important regulatory roles during
 animal development, and it has been hypothesized that an RNA-based gene
 regulation has been important for the evolution of developmental
 complexity in animals. However, most studies of lncRNA gene regulation
 have been performed using model animal species, and very little is known
 about this type of gene regulation in non-bilaterians. We have therefore
 analyzed RNA-Seq data derived from a comprehensive set of embryogenesis
 stages in the calcareous sponge Sycon ciliatum and identified hundreds of
 developmentally expressed intergenic lncRNAs (lincRNAs) in this species.
 In situ hybridization of selected lincRNAs revealed dynamic spatial and
 temporal expression during embryonic development. More than 600 lincRNAs
 constitute integral parts of differentially expressed gene modules, which
 also contain known developmental regulatory genes, e.g. transcription
 factors and signaling molecules. This study provides insight into the
 non-coding gene repertoire of one of the earliest evolved animal lineages,
 and suggests that RNA-based gene regulation was likely present in the last
 common ancestor of animals.
description: Non-coding-genes-raw-countsCoding-genes-raw-counts.txtCoding-genes-raw-countsnon-coding.gb.gff3coding-sequences.gb.gff3Primer sequences and lists of module genesPrimers_and_module_genes.xlsR commands used in this studyR-codes.RNames non correlated lincRNAsNames of the 1853 lincRNAs with no correlated gene expression with the nearest coding genenon.correlated.lincRNAs.txtNames lincRNAsThe names of the 2421 lincRNAs.lincRNAs.txt
DOI: 10.5061/dryad.707td
title: Data from: SimPhy: phylogenomic simulation of gene, locus and species trees

description: We present a fast and flexible software package—SimPhy—for the simulation
 of multiple gene families evolving under incomplete lineage sorting, gene
 duplication and loss, horizontal gene transfer—all three potentially
 leading to species tree/gene tree discordance—and gene conversion. SimPhy
 implements a hierarchical phylogenetic model in which the evolution of
 species, locus, and gene trees is governed by global and local parameters
 (e.g., genome-wide, species-specific, locus-specific), that can be fixed
 or be sampled from a priori statistical distributions. SimPhy also
 incorporates comprehensive models of substitution rate variation among
 lineages (uncorrelated relaxed clocks) and the capability of simulating
 partitioned nucleotide, codon, and protein multilocus sequence alignments
 under a plethora of substitution models using the program INDELible. We
 validate SimPhy's output using theoretical expectations and other
 programs, and show that it scales extremely well with complex models
 and/or large trees, being an order of magnitude faster than the most
 similar program (DLCoal-Sim). In addition, we demonstrate how SimPhy can
 be useful to understand interactions among different evolutionary
 processes, conducting a simulation study to characterize the systematic
 overestimation of the duplication time when using standard reconciliation
 methods. SimPhy is available at https://github.com/adamallo/SimPhy, where
 users can find the source code, precompiled executables, a detailed manual
 and example cases.
description: ScriptsScripts to replicate validation, benchmarking and test-case study.sup_files.tar.gzAppendix 1: Lineage counts sampling strategy implemented in SimPhySupplementary text describing the novel strategy used by SimPhy to sample lineage counts during the simulation of gene trees under the multilocus coalescent model.appendix1.pdfSupplementary figuresSupplementary materials.pdf
DOI: 10.5061/dryad.v13m6
title: Data from: First indications that northern bottlenose whales are sensitive to behavioural disturbance from anthropogenic noise

description: Although northern bottlenose whales were the most heavily hunted beaked
 whale, we have little information about this species in its remote habitat
 of the North Atlantic Ocean. Underwater anthropogenic noise and disruption
 of their natural habitat may be major threats, given the sensitivity of
 other beaked whales to such noise disturbance. We attached dataloggers to
 13 northern bottlenose whales and compared their natural sounds and
 movements to those of one individual exposed to escalating levels of
 1–2 kHz upsweep naval sonar signals. At a received sound pressure level
 (SPL) of 98 dB re 1 μPa, the whale turned to approach the sound source,
 but at a received SPL of 107 dB re 1 μPa, the whale began moving in an
 unusually straight course and then made a near 180° turn away from the
 source, and performed the longest and deepest dive (94 min, 2339 m)
 recorded for this species. Animal movement parameters differed
 significantly from baseline for more than 7 h until the tag fell off
 33–36 km away. No clicks were emitted during the response period,
 indicating cessation of normal echolocation-based foraging. A sharp
 decline in both acoustic and visual detections of conspecifics after
 exposure suggests other whales in the area responded similarly. Though
 more data are needed, our results indicate high sensitivity of this
 species to acoustic disturbance, with consequent risk from marine
 industrialization and naval activity.
description: ha13_176a_FineScaleTagDataTime-series data of northern bottlenose whale subject in the study.ha13_176a_FineScaleMahalanobisDistanceMahalanobis distance time series from the whale subject.DiveParametersMeasured dive parameters from tagged northern bottlenose whalesNBW_visual_and_acoustic_detectionsVisual and acoustic detection of northern bottlenose whales before and after the experimentsplDataModelled sound pressure levels of by distance and azimuth of the source locationvesselTrack_Sverdrup2GPRMC string of navigation data of the research vessel before and after the experiment
DOI: 10.35097/f01bks0yqymm80ar
title: Benchtop NMR Signal Enhancement of Metabolites in Urine Extract using SABRE

description: Metabolites in a urine extract are signal-enhanced by SABRE† hyperpolarization and detected using a benchtop NMR spectrometer. Quantification by standard addition is demonstrated for endogenic urinary nicotinamide (vitamin B3). Even higher sensitivity is achieved in an automated setup for multi-scan SABRE experiments. This hyperpolarization scheme is able to expedite biomarker detection and quantification, while maintaining low infrastructural requirements.
description: Included are 1H NMR data recorded on different spectrometers (Spinsolve 60 Ultra and Spinsolve 80, Magritek; 800 MHz Avance III spectrometer with He-cooled cryoprobe and 500 MHz Avance NEO spectrometer with conventional probe, Bruker) in their native formats. Spectra are sorted by their appearance in the associated manuscript and ESI. Most spectra are acquired on extracts of human urine for the detection and quantification of endogenous metabolites. The parahydrogen-based hyperpolarization techniques Signal Amplification By Reversible Exchange (SABRE) and non-hydrogenous Para-Hydrogen Induced Polarization (nh-PHIP) are used for signal enhancement.
DOI: 10.5061/dryad.2m6s2
title: Data from: Evolution of reduced postcopulatory molecular interactions in Drosophila populations lacking sperm competition

description: In many species with internal fertilization, molecules transferred in the
 male ejaculate trigger and interact with physiological changes in females.
 It is controversial to what extent these interactions between the sexes
 act synergistically to mediate the female switch to a reproductive state
 or instead reflect sexual antagonism evolved as a byproduct of sexual
 selection on males. To address this question, we eliminated sexual
 selection by enforcing monogamy in populations of Drosophila melanogaster
 for 65 generations and then measured the expression of male seminal fluid
 protein genes and genes involved in the female response to mating. In the
 absence of sperm competition, male and female reproductive interests are
 perfectly aligned and any antagonism should be reduced by natural
 selection. Consistent with this idea, males from monogamous populations
 showed reduced expression of seminal fluid protein genes, 16% less on
 average than in polygamous males. Further, we identified 428 genes that
 responded to mating in females. After mating, females with an evolutionary
 history of monogamy exhibited lower relative expression of genes that were
 upregulated in response to mating and higher expression of genes that were
 downregulated—in other words, their post-mating transcriptome appeared
 more virgin-like. Surprisingly, these genes showed a similar pattern even
 before mating, suggesting that monogamous females evolved to be less
 poised for mating and the accompanying receipt of male seminal fluid
 proteins. This reduced investment by both monogamous males and females in
 molecules involved in postcopulatory interactions points to a pervasive
 role of sexual conflict in shaping these interactions.
description: Gene expression for 6
 evolved populations x 2 sexes x 2 mating statusesThis text file contains
 the expression levels of 13995 genes from NimbleGen 12x135k arrays run for
 6 experimentally-evolved populations. Males (virgin) and females (virgin
 and females) from each of the 6 populations were profiled, for 18 total
 transcriptional profiles.evolved_expression.txt