cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sn35910
title: Data from: Tetraconatan phylogeny with special focus on Malacostraca and Branchiopoda—Highlighting the strength of taxon-specific matrices in phylogenomics

description: Understanding the evolution of Tetraconata or Pancrustacea —the clade that
 includes crustaceans and insects—requires a well-resolved hypothesis
 regarding the relationships within and among its constituent taxa. Herein,
 we assembled a taxon-rich phylogenomic data set focusing on crustacean
 lineages based solely on genomes and new-generation Illumina-generated
 transcriptomes, including 89 representatives of Tetraconata. This
 constitutes the first phylogenomic study specifically addressing internal
 relationships of Malacostraca (with 26 species included) and Branchiopoda
 (36 species). Seven matrices comprising 81 to 684 orthogroups and 17,690
 to 242,530 amino acid positions were assembled and analysed under five
 different analytical approaches. To maximize gene occupancy and to improve
 resolution, taxon-specific matrices were designed for Malacostraca and
 Branchiopoda. Key tetraconatan taxa (i.e., Oligostraca, Multicrustacea,
 Branchiopoda, Malacostraca, Thecostraca, Copepoda, Hexapoda) were
 monophyletic and well supported. Within Branchiopoda Phyllopoda,
 Diplostraca, Cladoceromorpha and Cladocera were monophyletic. Within
 Malacostraca the clades Eumalacostraca, Decapoda and Reptantia were well
 supported. Recovery of Caridoida or Peracarida was highly depending on the
 analysis for the complete matrix but were consistently recovered
 monophyletic in the malacostracan-specific matrix. From such examples, we
 demonstrate that taxon-specific matrices and particular evolutionary
 models and analytical methods, namely CAT-GTR and Dayhoff recoding,
 outperform other approaches in resolving certain recalcitrant nodes in
 phylogenomic analyses.
description: trinity_assemblies_part_1This zip archive cotains one third of all trinity assemblies of the newly sequenced taxa. Assemblies were not further curated and mtDNA was largely removed prior to assemblytrinity_assemblies_1.ziptrinity_assemblies_2_part2This zip archive cotains one third of all trinity assemblies of the newly sequenced taxa. Assemblies were not further curated and mtDNA was largely removed prior to assemblytrinity_assemblies_2.ziptrinity_assemblies_part_3This zip archive cotains one third of all trinity assemblies of the newly sequenced taxa. Assemblies were not further curated and mtDNA was largely removed prior to assemblytrinity_assemblies_3.zipOMA_BranchiopodaThis zip archive contains the OMA output of the orthology assessement for the branchiopod specific matirces.OMA_all_taxaZip archive of the OMA output of the orthology assessemnt for all taxa. From this output the matrices including all taxa as well as the malacostracan specific matrices were derivedmatricesAll amino acid matrices used in the various phylogenetic analysespython scriptsAll custom python and perl scripts used to assemble and analysze the sequencing datatreesAll phylogenetic trees inferred in the course of this project. The title refers to the respective matrix and analytical method
DOI: 10.25345/c57w67k4c
title: MassIVE MSV000100598 - Metabolic plasticity and optimal redox homeostasis are essential for efficient metastatic colonization
title: Cancer cells must dynamically reprogram their metabolism to adapt to changing microenvironmental conditions during tumor growth and metastatic dissemination. This results in metabolic flexibility and plasticity, allowing the use of multiple metabolic routes. Metastasis of solid tumors, the principal cause of cancer-related mortality, is driven by cellular plasticity often through activation of an epithelial-mesenchymal transition (EMT). These processes are regulated by the transcription factor ZEB1, which is frequently upregulated during tumor progression. To investigate the role of metabolic plasticity in metastasis, we employed murine pancreatic ductal adenocarcinoma (PDAC) cell lines with distinct EMT states and lung colonization capacities. Highly plastic epithelial-type cancer cells (KPCepi) efficiently colonized the lung, whereas ZEB1-deficient cancer cells (KPCZ) lost their plasticity and showed markedly reduced colonization. This defect correlated with impaired glycolytic reserve, mitochondrial dysfunction, as well as reduced levels of detoxifying metabolites, including NADPH and reduced glutathione. Interestingly mesenchymal-type cancer cells (KPCmes) also exhibited poor lung colonization despite retaining normal glycolytic capacity and a high proportion of functional mitochondria; however, similar to KPCZ cells, they displayed diminished levels of detoxifying metabolites. Both KPCZ and KPCmes cells with low metastatic capacity were more susceptible to ferroptosis, indicating a limited ability to counteract reactive oxygen species under stress. Together, these findings demonstrate that metabolic plasticity and redox homeostasis are essential prerequisites for efficient lung colonization, and suggest that concurrent targeting of metabolic adaptability and redox buffering may represent a promising strategy to prevent metastasis in aggressive PDAC tumors.
DOI: 10.5061/dryad.k5k7n
title: Data from: Morphology-function relationships and repeatability in the sperm of Passer sparrows

description: Sperm performance is likely to be an important determinant of male
 reproductive success, especially when females copulate with multiple
 males. Understanding sperm performance is therefore crucial to fully
 understand the evolution of male reproductive strategies. In this study,
 we examined the repeatability of sperm morphology and motility measures
 over three breeding seasons, and we studied relationships between sperm
 morphology and function. We conducted this study in wild-derived captive
 house sparrows (Passer domesticus) and Spanish sparrows (P.
 hispaniolensis). Results for the two species were similar. As predicted
 from results in other passerine species, total sperm length was highly
 repeatable across ejaculates, and repeatability for the length of other
 components was moderate. The repeatability of sperm swimming speed across
 ejaculates was lower, but statistically significant, suggesting that sperm
 velocity may be a relatively dynamic trait. Surprisingly, swimming speed
 did not correlate with the relative length of the midpiece, and it
 correlated negatively with the relative length of the flagellum and with
 total sperm length. This pattern is the opposite of what theory predicts
 and differs from what has been found in house sparrows before. Also
 contrary to previous work, we found no evidence that total sperm length
 correlates with sperm longevity. These results therefore highlight the
 need for a better understanding of relationships between sperm morphology
 and function in passerine birds.
description: Sperm measurements
 (morphology and velocity) of two Passer speciesIncluded in this data
 set are three .csv files containing data, one .xlsx file with information
 on the naming of columns in the data files (information for each data file
 is in a separate tab in the .xlsx file), and R code. However, this R
 script should be sufficient to understand exactly how analyses were
 performed. Justification for analysis decisions is indicated in the
 manuscript.JMorph.7z
DOI: 10.5061/dryad.8p81b6h
title: Data from: Sexual selection across sensory modalities: female choice of male behavioral and gustatory displays

description: The role of cuticular hydrocarbons in sexual displays has received
 considerable interest over the last two decades. For example, multiple
 studies have documented significant directional and nonlinear sexual
 selection acting on the cuticular hydrocarbon profiles of both male and
 female insects. The majority of these studies have excluded other sensory
 modalities that may influence attractiveness, and measured selection using
 laboratory raised individuals. Furthermore, much of this work has been
 conducted using drosophilid fruit flies and crickets, and investigations
 using different taxa are necessary to improve our understanding of broader
 taxonomic trends. Here we extend our understanding of sexual selection on
 cuticular hydrocarbons by measuring selection imposed by female mate
 choice on male bull-horned dung beetles, Onthophagus taurus. Both male and
 female beetles used in our study were collected from the field, ensuring
 that our estimates of selection incorporated some degree of naturally
 occurring variation in both cuticular hydrocarbon profiles and female mate
 preferences. Consistent with previous studies on this species, we found
 significant directional selection on male courtship displays. We also
 found significant nonlinear selection on the male cuticular hydrocarbon
 profile acting independently of the influence of behavioral courtship. Our
 data are consistent with a role for cuticular hydrocarbons in the mating
 system of this species and suggest that female O. taurus use multiple
 sensory modalities to assess different aspects of male quality.
description: Berson and Simmons
 2018_BehEco_DataFile containing the
 mating success, courtship rate, and cuticular hydrocarbon (CHC)
 data.
DOI: 10.5061/dryad.d5vh1
title: Data from: Facial width predicts male fitness and rank but not survival in Second World War Finnish soldiers

description: We investigated fitness, military rank and survival of facial phenotypes
 in large scale warfare using 795 Finnish soldiers who fought in the Winter
 War (1939-40). We measured bizygomatic facial width vs. height - a trait
 known to predict aggressive behaviour in males - and assessed whether
 facial morphology could predict survival, lifetime reproductive success
 (LRS) and social status. We found no difference in survival along the
 phenotypic gradient, however, wider-faced individuals had greater LRS, but
 achieved a lower military rank.
description: Loehr OHara Finnish
 soldier dataLife history and
 morphological measurements of Finnish soldiers who fought in the Winter
 War (1939-1940). Photographs and individual data gathered from book and
 internet souces.
DOI: 10.5061/dryad.h6t7g
title: Data from: Asymmetric dispersal and colonization success of Amazonian plant-ants queens

description: Background: The dispersal ability of queens is central to understanding
 ant life-history evolution, and plays a fundamental role in ant population
 and community dynamics, the maintenance of genetic diversity, and the
 spread of invasive ants. In tropical ecosystems, species from over 40
 genera of ants establish colonies in the stems, hollow thorns, or leaf
 pouches of specialized plants. However, little is known about the relative
 dispersal ability of queens competing for access to the same host plants.
 Methodology/Principal Findings: We used empirical data and inverse
 modeling – a technique developed by plant ecologists to model seed
 dispersal – to quantify and compare the dispersal kernels of queens from
 three Amazonian ant species that compete for access to host-plants. We
 found that the modal colonization distance of queens varied 8-fold, with
 the generalist ant species (Crematogaster laevis) having a greater modal
 distance than two specialists (Pheidole minutula, Azteca sp.) that use the
 same host-plants. However, our results also suggest that queens of Azteca
 sp. have maximal distances that are four-sixteen times greater than those
 of its competitors. Conclusions/Significance: We found large differences
 between ant species in both the modal and maximal distance ant queens
 disperse to find vacant seedlings used to found new colonies. These
 differences could result from interspecific differences in queen body
 size, and hence wing musculature, or because queens differ in their
 ability to identify potential host plants while in flight. Our results
 provide support for one of the necessary conditions underlying several of
 the hypothesized mechanisms promoting coexistence in tropical plant-ants.
 They also suggest that for some ant species, limited dispersal capability
 could pose a significant barrier to the rescue of populations in isolated
 forest fragments. Finally, we demonstrate that inverse models
 parameterized with field data are an excellent means of quantifying the
 dispersal of ant queens.
description: AlatesxSizeData on the number of alate queens found in myrmecophytic plants of different sizes, where size is the number of domatia a plant has.EstablishedColonies_9haPlotX-Y locations of all established ant colonies found,i.e., the location of all myrmecophytic plants in a 9-ha study plot in the central Amazon and the identity of the ant resident.ExperimentalSeedlings_9haPlotData on the experimental seedlings used in our experiment, including size, location, and colonization history.
DOI: 10.5061/dryad.fd4m0
title: Data from: The influence of wing morphology upon the dispersal, geographical distributions and diversification of the Corvides (Aves; Passeriformes)

description: New species are sometimes known to arise as a consequence of the dispersal
 and establishment of populations in new areas. It has nevertheless been
 difficult to demonstrate an empirical link between rates of dispersal and
 diversification, partly because dispersal abilities are challenging to
 quantify. Here, using wing morphology as a proxy for dispersal ability, we
 assess this relationship among the global radiation of corvoid birds. We
 found that species distributions are associated with wing shape.
 Widespread species (occurring on both islands and continents), and those
 that are migratory, exhibit wing morphologies better adapted to
 long-distance flight compared with sedentary continental or insular forms.
 Habitat preferences also strongly predict wing form, with species that
 occur in canopies and/or areas of sparse vegetation possessing dispersive
 morphologies. By contrast, we found no significant differences in
 diversification rates among either the migratory or habitat
 classifications, but species distributed in island settings diversify at
 higher rates than those found on continents. This latter finding may
 reflect the elevated dispersal capabilities of widespread taxa,
 facilitating the radiation of these lineages across insular areas.
 However, as the correlations between wing morphology and diversification
 rates were consistently weak throughout our dataset, this suggests that
 historical patterns of diversification are not particularly well reflected
 by present-day wing morphology.
description: MCC phylogeny of 782
 species of the CorvidesThis phylogeny was
 largely based on that from the study Jønsson et al. (2016), which
 generated a time-calibrated tree using sequence data from 665 species of
 the Corvides. The remaining 124 species (as recognized by the IOC 2.7)
 which had no sequence data available at the time of the tree generation
 were added as polytomies to the maximum clade credibility (MCC) tree of
 Jønsson et al. (2016) using current taxonomic information. The branch
 lengths subtending these species were inferred using the polytomy
 resolution method. Subsequently, we pruned out 7 species for which wing
 measurements were unavailable.CC_782_Phylo.tre
DOI: 10.5061/dryad.27q59
title: Data from: Group formation, relatedness, and the evolution of multicellularity

description: The evolution of multicellular organisms represents one of approximately
 eight major evolutionary transitions that have occurred on earth. The
 major challenge raised by this transition is to explain why single cells
 should join together and become mutually dependent, in a way that leads to
 a more complex multicellular life form that can only replicate as a whole.
 It has been argued that a high genetic relatedness (r) between cells
 played a pivotal role in the evolutionary transition from single-celled to
 multicellular organisms, because it leads to reduced conflict and an
 alignment of interests between cells. We tested this hypothesis with a
 comparative study, comparing the form of multicellularity in species where
 groups are clonal (r = 1) to species where groups are potentially
 nonclonal (r ≤ 1). We found that species with clonal group formation were
 more likely to have undergone the major evolutionary transition to
 obligate multicellularity and had more cell types, a higher likelihood of
 sterile cells, and a trend toward higher numbers of cells in a group. More
 generally, our results unify the role of group formation and genetic
 relatedness across multiple evolutionary transitions and provide an
 unmistakable footprint of how natural selection has shaped the evolution
 of life.
description: Life-history and
 descriptive data on eukaryote and prokaryote multicellular
 species.Data collected from
 literature search (up to Feb 2013).curbio10341mmc2.xlsx
DOI: 10.15468/dl.em63ek
title: Occurrence Download

description: A dataset containing 49 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "IucnRedListCategory is VU",
 "TaxonKey is Davidia involucrata"
 ]
}

 The dataset includes 49 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001112-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8t026
title: Data from: The size at reproduction of canopy tree species in central Africa

description: Size at reproduction is a key aspect of species life history that has been
 little explored for long-lived tropical trees. In this study, we aimed to
 quantify reproductive diameter for 31 major timber species across 11 sites
 in Cameroon, Congo, and Central African Republic. Specifically, we
 examined (1) whether between-species variability can be explained by a set
 of seven species traits; (2) whether reproductive diameter varied
 within-species among sites; (3) whether reproductive status varied with
 crown exposure; and (4) whether the minimum cutting diameter limits (MCDL)
 imposed by national forest regulations enable the persistence of seed
 trees after logging operations. In accordance with studies conducted
 elsewhere in the tropics, we found a great variability in diameter at
 reproduction among species that was correlated with adult stature (maximum
 diameter and height). For some species, reproductive diameter thresholds
 showed substantial variation between sites, and crown exposure had a
 significant positive effect on reproductive status. The majority of MCDLs
 was found to be suitable, trees having high probability for being seed
 trees at MCDL. As the most complete assessment of size at reproduction for
 timber species in central Africa, the study has implications for the
 sustainable management of production forests, highlighting questionable
 MCDL for some species and between-site variation in reproductive diameter.
 The study also highlighted the need for long-term phenological monitoring
 of tree species spanning a large range of ecological strategies to address
 both theoretical (species life-history, allocation trade-offs) and
 practical questions (MCDL).
description: Data_OuedraogoEtAl2017_BiotropicaWe provide a zip file containing three txt files and one R script file used in the analyses presented in the article assessing the size at reproduction of 31 major timber species in central Africa. The ReproductiveSize_DATA.txt file contains the list of trees monitored for reproductive phenology in three central African countries (Cameroon, Congo, and Central African Republic) in 11 sites, with their species names, diameter, crown exposure index, and phenological status. The ReproductiveSize_TRAITS.txt file contains the list of the 31 studied species with their traits (regeneration guild, leaf habit, wood density, maximum diameter and height, dispersal mode, and maximum growth rate). The ReproductiveSize_MCDL.txt file contains the list of the 31 studied species with their minimum cutting diameter limits in the three studied contries. The ReproductiveSize_SCRIPT.r file contains the code used to perform the analyses and make the figures.
DOI: 10.5061/dryad.2np3s
title: Data from: Climate warming: a loss of variation in populations can accompany reproductive shifts

description: The most documented response of organisms to climate warming is a change
 in the average timing of seasonal activities (phenology). Although we know
 that these average changes can differ among species and populations, we do
 not know whether climate warming impacts within-population variation in
 phenology. Using data from five study sites collected during a 13-year
 survey, we found that the increase in spring temperatures is associated
 with a reproductive advance of 10 days in natural populations of common
 lizards (Zootoca vivipara). Interestingly, we show a correlated loss of
 variation in reproductive dates within populations. As illustrated by a
 model, this shortening of the reproductive period can have significant
 negative effects on population dynamics. Consequently, we encourage tests
 in other species to assess the generality of decreased variation in
 phenological responses to climate change.
description: Phenology of the common
 lizard on five study sitesThis file includes data
 collected on the phenology of the common lizard on five sites (variable
 SITE) of the Mont-Lozère. TEMPERATURE is the mean of daily maximum air
 temperature in June (°C). Parturition dates are described by the mean of
 the time interval since July 1 (MEAN in days) and its standard deviation
 (SD). The file also reports the sample size N (number of litters per site
 and year), the coefficient of variation CV (SD divided by the mean date),
 the SKEWNESS and KURTOSIS of the frequency distributions of parturition
 dates.Experimental
 testThis file includes data
 on the experiment performed in 2005. This experiment tested the influence
 of temperature during gestation on the parturition date of the common
 lizard. The variable DATE is the number of days since July 1, IDENTITY is
 the female identity, and TEMPERATURE reports the three experimental
 groups: A = warm group, B = intermediate-heat group, C = cold
 group.
DOI: 10.5061/dryad.5h3k3
title: Data from: Towards a mechanistic understanding of insect life history evolution: oxygen-dependent induction of moulting explains moulting sizes

description: Moults characterise insect growth trajectories, typically following a
 consistent pattern known as Dyar's rule; proportional size increments
 remain constant across inter-instar moults. Empirical work suggests that
 oxygen limitation triggers moulting. The insect respiratory system, and
 its oxygen supply capacity, grows primarily at moults. It is hypothesized
 that the oxygen demand increases with increasing body mass, eventually
 meeting the oxygen supply capacity at an instar-specific critical mass
 where moulting is triggered. Deriving from this hypothesis, we develop a
 novel mathematical model for moulting and growth in insect larvae. Our
 mechanistic model has great success in predicting moulting sizes in four
 butterfly species, indirectly supporting a size-dependent mechanism
 underlying moulting. The results demonstrate that an oxygen-dependent
 induction of moulting mechanism would be sufficient to explain moulting
 sizes in the study species. Model predictions deviated slightly from
 Dyar's rule, the deviations being typically negligible within the
 present data range. The developmental decisions (e.g. moulting) made by
 growing larvae significantly affect age and size at maturity, which has
 important life history implications. The successful modelling of moulting
 presented here provides a novel framework for the development of realistic
 insect growth models, which are required for a better understanding of
 life history evolution.
description: Kivelä et al.
 2015_BJLS_data