cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.12jj3sv
title: Data from: All-trans retinoic acid disrupts development in ex vivo cultured fetal rat testes. I: altered seminiferous cord maturation and testicular cell fate

description: Exposure to excess retinoic acid disrupts the development of the mammalian
 testicular seminiferous cord. However, the molecular events surrounding
 retinoic acid-driven loss of cord structure have not previously been
 examined. To investigate the mechanisms associated with this adverse
 developmental effect, fetal rat testes were isolated on gestational day
 15, after testis determination and the initiation of cord development, and
 cultured in media containing all-trans retinoic acid (ATRA; 10-8 to 10-6
 M) or vehicle for 3 days. ATRA exposure resulted in a
 concentration-dependent decrease in the number of seminiferous cords per
 testis section and number of germ cells, assessed by histopathology and
 immunohistochemistry. Following 1 day of culture, genome-wide expression
 profiling by microarray demonstrated that ATRA exposure altered biological
 processes related to retinoid metabolism and gonadal sex determination.
 Real-time RT-PCR analysis confirmed that ATRA enhanced the expression of
 the key ovarian development gene Wnt4 and the anti-testis gene Nr0b1 in a
 concentration-dependent manner. After 3 days of culture, ATRA-treated
 testes contained both immunohistochemically DMRT1-positive and
 FOXL2-positive somatic cells, providing evidence of disrupted testicular
 cell fate maintenance following ATRA exposure. We conclude that exogenous
 retinoic acid disrupts seminiferous cord development in ex vivo cultured
 fetal rat testes, resulting in a reduction in seminiferous cord number,
 and interferes with maintenance of somatic cell fate by enhancing
 expression of factors that promote ovarian development.
description: Supplemental Tables
 S1-S7Supplemental tables
 pertaining to microarray analysis of gestation day 15 rat testes cultured
 for 24 h in media containing 10^-6 M ATRA or DMSO vehicle, including gene
 lists and pertinent results of Gene Set Enrichment Analysis and Ingenuity
 Pathway Analysis2018-06-21_I-ATRA_supplemental-tables.xlsx2018-06-21_I-ATRA_supplemental-figuresSupplemental Figures S1-S2
DOI: 10.5061/dryad.53m6f5n
title: Data from: The evolution of anti-bat sensory illusions in moths

description: Prey transmit sensory illusions to redirect predatory strikes, creating a
 discrepancy between what a predator perceives and reality. We use the
 acoustic arms race between bats and moths to investigate the evolution and
 function of a sensory illusion. The spinning hindwing tails of silk moths
 (Saturniidae) divert bat attack by reflecting sonar to create a misleading
 echoic target. We characterized geometric morphometrics of moth hindwings
 across silk moths, mapped these traits onto a new, robust phylogeny, and
 found that elaborated hindwing structures have converged on four adaptive
 shape peaks. To test the mechanism underlying these anti-bat traits, we
 pit bats against three species of silk moths with experimentally altered
 hindwings that created a representative gradient of ancestral and extant
 hindwing shapes. High-speed videography of battles reveals that moths with
 longer hindwings and tails more successfully divert bat attack. We
 postulate that sensory illusions are widespread and are underappreciated
 drivers of diversity across systems.
description: Rubin et al. -
 phylogenomic and morphometric data filesPhylogenomic and
 morphometric data sets and coding scriptsRubin et al. -
 behavioral data sheetsBehavioral data files:
 Bat-moth interactions, kinematics and echolocation
DOI: 10.5061/dryad.kp275f9
title: Data from: Long-tailed macaques (Macaca fascicularis) can use simple heuristics but fail at drawing statistical inferences from populations to samples

description: Human infants, apes, and capuchin monkeys engage in intuitive statistics:
 they generate predictions from populations of objects to samples based on
 proportional information. This suggests that statistical reasoning might
 depend on some core knowledge that humans share with other primate
 species. To aid the reconstruction of the evolution of this capacity, we
 investigated whether intuitive statistical reasoning is also present in a
 species of Old World monkey. In a series of 4 experiments, 11 long-tailed
 macaques were offered different pairs of populations containing varying
 proportions of preferred vs. neutral food items. One population always
 contained a higher proportion of preferred items than the other. An
 experimenter simultaneously drew one item out of each population, hid them
 in her fists and presented them to the monkeys to choose. Although some
 individuals performed well across most experiments, our results imply that
 long-tailed macaques as a group did not make statistical inferences from
 populations of food items to samples but rather relied on heuristics.
 These findings suggest that there may have been convergent evolution of
 this ability in New World monkeys and apes (including humans).
description: RawDataThis is the excel file used during data collection and for the data analyses. For each step and each experiment of the study, it provides information about the day of testing, the name of the subjects tested, the session and trial number, the side on which each population was presented, and the choice of the monkeys.IndividualScoresCSV file containing the data to calculate means, SD, effect sizes and used for the t.test, the binomial tests, and Fig. 2.EffectHandsCSV file used for the analyses to check the effect of the state of the arms on monkeys' choices.TTest_BinomialTest_BoxPlot_PlacìR code used to calculate means, SD, effect sizes, t-tests, binomial tests and plot Fig. 2.EffectHands_PlacìR code to test the effect of the state of the arms on monkeys' choices.LearningCurves_PlacìR code to test whether monkeys learnt to associate a proportion to a favourable sample across trials and to plot Fig. S1 of the supplementary material.
DOI: 10.5061/dryad.8s444dr
title: Data from: Glucocorticoid-environment relationships align with responses to environmental change in two co-occurring congeners

description: As more species undergo range shifts in response to climate change, it is
 increasingly important to understand the factors that determine an
 organism’s realized niche. Physiological limits imposed by abiotic factors
 constrain the distributions of many species. Because glucocorticoids are
 essential to the maintenance of physiological homeostasis, identifying
 glucocorticoid-environment relationships may generate critical insights
 into both limits on species distributions and potential responses to
 environmental change. We explored relationships between variability in
 baseline glucocorticoids and sensitivity to environmental conditions in
 two chipmunk species characterized by divergent patterns of spatial,
 genetic, and morphological change over the past century. Specifically, we
 investigated whether the alpine chipmunk (Tamias alpinus), which has
 undergone pronounced changes, displays greater glucocorticoid sensitivity
 to environmental parameters than the lodgepole chipmunk (T. speciosus),
 which has exhibited little change over the same interval. From 2013-2015,
 we collected environmental data and fecal glucocorticoid metabolite (FGM)
 samples from these species. Using generalized linear mixed models and a
 model averaging approach, we examined the impacts of environmental and
 individual phenotypic parameters on FGMs. We found pronounced
 interspecific differences, with environmental parameters being better
 predictors of FGMs in T. alpinus. FGMs in this species were particularly
 elevated in less climatically suitable habitats and in areas with higher
 maximum daily temperatures. Individual phenotypic traits were not
 predictive of FGMs in T. alpinus, although they were highly predictive for
 T. speciosus. Collectively, these findings support the hypothesis that T.
 alpinus is more sensitive to environmental change. More generally, our
 results suggest that both phenotypic attributes and environmental
 conditions contribute to FGM responses but that the relative contributions
 of these factors differ among taxa, including among closely related
 species. Finally, our analyses underscore the value of glucocorticoids as
 bioindicators of sensitivity to environmental change in species for which
 the factors affecting stress physiology have been assessed.
description: yosemite_weather_data_2Weather data for 2013-2015 from a Yosemite weather station downloaded from NOAAspeciosus_data_ecolapp_dryadTamias speciosus glucocorticoid data and associated biological and environmental data collected 2013-2015 in Yosemite National Park and surrounding areas.alpinus_data_ecolapp_dryadTamias alpinus glucocorticoid data and associated biological and environmental data collected 2013-2015 in Yosemite National Park and surrounding areas.
DOI: 10.5061/dryad.6f50rb0
title: Data from: Supplementation stocking of lake trout (Salvelinus namaycush) in small boreal lakes: ecotypes influence on growth and condition

description: Supplementation stocking is a commonly used management tool to sustain
 exploited fish populations. Possible negative consequences of
 supplementation on local stocks are a concern for the conservation of wild
 fish populations. However, the direct impacts of supplementation on life
 history traits of local populations have rarely been investigated. In
 addition, intraspecific hybridization between contrasting ecotypes
 (planktivorous and piscivorous) has been seldom considered in
 supplementation plans. Here, we combined genetic (genotype-by-sequencing
 analysis) and life history traits to document the effects of
 supplementation on maximum length, growth rates, body condition and
 genetic admixture in stocked populations of two Lake Trout ecotypes from
 small boreal lakes in Quebec and Ontario, Canada. In both ecotypes, the
 length of stocked individuals was greater than local individuals and, in
 planktivorous-stocked populations, most stocked fish exhibited a
 planktivorous-like growth while 20% of fish exhibited piscivorous-like
 growth. The body condition index was positively related to the proportion
 of local genetic background, but this pattern was only observed in stocked
 planktivorous populations. We conclude that interactions and hybridization
 between contrasting ecotypes is a risk that could result in deleterious
 impacts and possible outbreeding depression. We discuss the implications
 of these findings for supplementation stocking.
description: Figure - files and
 codesThis file combine all
 original figures (.tiff) published in the article and the codes (R script)
 to generate them.Figures.zipCode - R scriptsThis file provides all codes (R scripts) that accompany this article. Those codes are necessary to all analyses related to growth parameters estimation and linear mixed effect models.Codes.zipData - Backcalculation and Growth parametersThis file provide all the datafiles needed to run the R codes and generate the analyses published in the article.Data.zipGenomics - Admixture analysesThis file provides all of genomics data (vcf) and code that accompany this publication and that are needed to run the ADMIXTURE analyses.Genomics.zip
DOI: 10.5061/dryad.2710pk5
title: Data from: Evolution of floral traits and impact of reproductive mode on diversification in the phlox family (Polemoniaceae)

description: Pollinator-mediated selection is a major driver of evolution in flowering
 plants, contributing to the vast diversity of floral features. Despite
 long-standing interest in floral variation and the evolution of
 pollination syndromes in Polemoniaceae, the evolution of floral traits and
 known pollinators has not been investigated in an explicit phylogenetic
 context. Here we explore macroevolutionary patterns of both pollinator
 specificity and three floral traits long considered important determinants
 of pollinator attraction across a nearly complete species-level
 phylogenetic tree for the family. This phylogenetic tree is the most
 comprehensive yet produced for Polemoniaceae. The presence of floral
 chlorophyll is reconstructed as the ancestral character state of the
 family, even though the presence of floral anthocyanins is the most
 prevalent floral pigment in extant taxa. Mean corolla length and width of
 the opening of the floral tube are correlated, and both appear to vary
 with pollinator type. The evolution of pollination systems appears labile,
 with multiple gains and losses of selfing and conflicting implications for
 patterns of diversification. Explicit testing of diversification models
 rejects the hypothesis that selfing is an evolutionary dead-end. This
 study begins to disentangle the individual components that comprise
 pollination syndromes and lays the foundation for future work on the
 genetic mechanisms that control each trait.
description: Alignment_filesAlignment files in Nexus format for each of the 7 loci used in the study, and two concatenated files, one of chloroplast and one with all loci.Phenotypic data filesExcel spreadsheets of flower size measurements and flower color for the included taxa.Data_files.zipTree_filesTree files, including the MCC tree from the Beast run and 1,000 trees from the posterior distribution used in analyses.
DOI: 10.5061/dryad.pp39377
title: Data from: The cotton stainer’s gut microbiota suppresses infection of a co-transmitted trypanosomatid parasite

description: The evolutionary and ecological success of many insects is attributed to
 mutualistic partnerships with bacteria that confer hosts with novel traits
 including food digestion, nutrient supplementation, detoxification of
 harmful compounds and defense against natural enemies. Dysdercus fasciatus
 firebugs (Hemiptera: Pyrrhocoridae), commonly known as cotton stainers,
 possess a simple but distinctive gut bacterial community including
 B-vitamin supplementing Coriobacteriaceae symbionts. In addition, their
 guts are often infested with the intestinal trypanosomatid parasite
 Leptomonas pyrrhocoris (Kinetoplastida: Trypanosomatidae). In this study,
 using experimental bioassays and fluorescence in situ hybridization
 (FISH), we report on the protective role of the D. fasciatus gut bacteria
 against L. pyrrhocoris. We artificially infected 2nd instars of dysbiotic
 and symbiotic insects with a parasite culture and measured parasite
 titers, developmental time and survival rates. Our results show that L.
 pyrrhocoris infection increases developmental time and slightly modifies
 the quantitative composition of the gut microbiota. More importantly, we
 found significantly higher parasite titers and a tendency towards lower
 survival rates in parasite infected dysbiotic insects compared to
 symbiotic controls, indicating that the gut bacteria successfully
 interferes with the establishment or proliferation of L. pyrrhocoris. The
 colonization of symbiotic bacteria on the peritrophic matrix along the gut
 wall, as revealed by FISH, likely acts as a barrier blocking parasite
 attachment or entry into the peritrophic matrix. Our findings show that in
 addition to being nutritionally important, D. fasciatus’ gut bacteria
 complement the host’s immune system in preventing parasite invasions and
 that a stable gut microbial community is integral for the host’s health.
description: Dysdercus developmental
 success and microbiota composition upon parasite
 infectionDevelopmental times,
 survivorship, parasite and symbiont titers (qPCR), and microbiota
 composition (Illumina 16S microbiota profiling) of symbiotic (S+) and
 dysbiotic (S-) Dysdercus fasciatus with (P+) and without (P-) infection by
 the trypanosomatid parasite Leptomonas pyrrhocoris,
 respectively.Onchuru_et_al_MolEcol_Data.xlsxDysdercus microbiota profiling data (with and without parasite infection)Raw Illumina sequencing reads, QIIME2 analysis pipeline, and output files (OTU table, representative sequence set) for bacterial community profiling of symbiotic Dysdercus fasciatus, infected or not with Leptomonas pyrrhocoris trypanosomes.Dysdercus_sequencing_data.7z
DOI: 10.5061/dryad.5pv4qm3
title: Data from: Cambrian petalonamid Stromatoveris phylogenetically links Ediacaran biota to later animals

description: Macro-organisms of the Ediacaran period (635-541 Ma) were large and
 morphologically complex, with some living in aphotic habitats, presenting
 the possibility that they were early animals. However, ‘bizarre’ Ediacaran
 morphologies and mouldic preservation have frustrated comparison to later
 taxa. Consequently, both the positions of Ediacaran biota in the tree of
 life and the origins of the Metazoa have been unresolved. Here we provide
 phylogenetic evidence to identify Ediacaran macro-biota as animals, based
 on 206 new fossils of Stromatoveris psygmoglena from the Lower Cambrian
 Chengjiang Lagerstätte. Exceptionally preserved soft-tissue anatomy shows
 that Stromatoveris was a soft-bodied, radially symmetric animal with
 multiple, sub-branched petaloids and a differentiated holdfast.
 Photo-referenced morphological character analysis enables phylogenetic
 reconstruction of a monophyletic clade designated Petalonamae, following
 Pflug, 1970, that unites Stromatoveris with iconic Ediacaran genera
 (Rangea, Pteridinium, Ernietta, Swartpuntia, Arborea, Pambikalbae and
 Dickinsonia), placed as sister-group to the Eumetazoa. Therefore the
 Ediacaran petalonamids are established as animals, based on phylogenetic
 bracketing within the Metazoa. From these findings, it follows that
 petalonamids remained an important component of Cambrian marine ecosystems
 and that the metazoan radiation can be dated to a minimum age of between
 558 and 571 Ma.
description: Supporting Information
 Cambrian petalonamid Stromatoveris phylogenetically links Ediacaran biota
 to later animals (Hoyal Cuthill and Han)Figs S1-S3, Appendix S1
 Phylogenetic character-taxon matrix in nexus file format, Appendix S2
 Reconstructed phylogenetic trees in Newick format.SI_Hoyal_Cuthill_and_Han.docx
DOI: 10.5061/dryad.k7jm5hp
title: Data from: The fitness landscape of the codon space across environments

description: Fitness landscapes map the relationship between genotypes and fitness.
 However, most fitness landscape studies ignore the genetic architecture
 imposed by the codon table and thereby neglect the potential role of
 synonymous mutations. To quantify the fitness effects of synonymous
 mutations and their potential impact on adaptation on a fitness landscape,
 we use a new software based on Bayesian Monte Carlo Markov Chain methods
 and re-estimate selection coefficients of all possible codon mutations
 across 9 amino-acid positions in Saccharomyces cerevisiae Hsp90 across 6
 environments. We quantify the distribution of fitness effects of
 synonymous mutations and show that it is dominated by many mutations of
 small or no effect and few mutations of larger effect. We then compare the
 shape of the codon fitness landscape across amino-acid positions and
 environments, and quantify how the consideration of synonymous fitness
 effects changes the evolutionary dynamics on these fitness landscapes.
 Together these results highlight a possible role of synonymous mutations
 in adaptation and indicate the potential mis-inference when they are
 neglected in fitness landscape studies.
description: Mathematica Notebook
 Fitness landscapes statistics and adaptive walkThis notebook allows to
 replicate the data analyses corresponding to the section of the manuscript
 called "The shape of the codon fitness landscape with and without
 synonymous effects". Please note that the data set necessary to run
 the analyses is obtained through the R notebooks also available within
 this repository.Mathematica_notebook_finalVersionJune2018.nbR notebooks for data formatting, data normalisation and statistical analysesThese R notebooks were done using R studio. They allow 1) to format the data sets after running empiricIST; 2) to do data normalisation for all the analyses performed in the manuscript; 3) to perform all statistical analyses and create the plots for the manuscript. Please note that these notebooks assume that you have run the empiricIST in the data set (the empiricIST is available at https://github.com/Matu2083/ empiricIST). The data analysed here, as indicated in the manuscript, is available from the publication: Bank C, Hietpas RT, Wong A, Bolon DN, Jensen JD (2014). A Bayesian MCMC approach to assess the complete distribution of fitness effects of new mutations: Uncovering the potential for adaptive walks in challenging environments. Genetics 196: 841–852.R_notebooks.zip
DOI: 10.5061/dryad.fq8c217
title: Data from: Herbicides and herbivory interact to drive plant community and crop-tree establishment

description: Land management practices often directly alter vegetation structure and
 composition, but the degree to which ecological processes such as
 herbivory interact with management to influence biodiversity is less well
 understood. We hypothesized that large herbivores compound the effects of
 intensive forest management on early-seral plant communities and
 plantation establishment (i.e., tree survival and growth), and the degree
 of such effects is dependent on the intensity of management practices. We
 established 225 m2 wild ungulate (deer and elk) exclosures, nested within
 a manipulated gradient of management intensity (no-herbicide Control,
 Light herbicide, Moderate herbicide and Intensive herbicide treatments),
 replicated at the scale of whole harvest units (10-19 ha). Vegetation
 structure, composition and crop-tree responses to herbivory varied across
 the gradient of herbicide application during the first two years of stand
 establishment, with herbivory effects most evident at intermediate
 herbicide treatments. In the Moderate herbicide treatment – which
 approximates treatments applied to &gt; 2.5 million hectares in
 Pacific Northwest U.S.A. – foraging by deer and elk resulted in
 simplified, low-cover plant communities more closely resembling the
 Intensive herbicide treatment. Herbivory further suppressed the growth of
 competing vegetation in the Light herbicide treatment, improving crop-tree
 survival, and providing early evidence of an ecosystem service. By
 changing community composition and vegetation structure, intensive forest
 management alters foraging selectivity and subsequent plant-herbivore
 interactions; initial shifts in early-seral communities are likely to
 influence understory plant communities and tree growth in later stages of
 forest development.
description: DataS1Plant community
 dataDataS2Douglas-fir
 dataDataS3Camera trap
 data