cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8f6d2
title: Data from: Recognizing sexual dimorphism in the fossil record: lessons from nonavian dinosaurs

description: The demonstration of sexual dimorphism in the fossil record can provide
 vital information about the role that sexual selection has played in the
 evolution of life. However, statistically robust inferences of sexual
 dimorphism in fossil organisms are exceedingly difficult to establish,
 owing to issues of sample size, experimental control, and methodology.
 This is particularly so in the case of dinosaurs, for which sexual
 dimorphism has been posited in many species, yet quantifiable data are
 often lacking. This study presents the first statistical investigation of
 sexual dimorphism across Dinosauria. It revisits prior analyses that
 purport to find quantitative evidence for sexual dimorphism in nine
 dinosaur species. After the available morphological data were subjected to
 a suite of statistical tests (normality and unimodality tests and mixture
 modeling), no evidence for sexual dimorphism was found in any of the
 examined taxa, contrary to conventional wisdom. This is not to say that
 dinosaurs were not sexually dimorphic (phylogenetic inference suggests
 they may well have been), only that the available evidence precludes its
 detection. A priori knowledge of the sexes would greatly facilitate the
 assessment of sexual dimorphism in the fossil record, and it is suggested
 that unambiguous indicators of sex (e.g., presence of eggs, embryos,
 medullary bone) be used to this end.
description: Supplementary File
 1Summary of
 results.Supplementary File
 2Raw
 data used in study.
DOI: 10.15468/dl.d5sa2e
title: Occurrence Download

description: A dataset containing 65 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "RecordedBy is one of (Du Chaillu, Du Chaillu Coll., Du Chaillu P.B., Du Chaillu P.B.?, du Chaillu)"
 ]
}

 The dataset includes 65 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001485-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.4539d
title: Data from: Inferring fitness landscapes and selection on phenotypic states from single-cell genealogical data

description: Recent advances in single-cell time-lapse microscopy have revealed
 non-genetic heterogeneity and temporal fluctuations of cellular
 phenotypes. While different phenotypic traits such as abundance of
 growth-related proteins in single cells may have differential effects on
 the reproductive success of cells, rigorous experimental quantification of
 this process has remained elusive due to the complexity of single cell
 physiology within the context of a proliferating population. We introduce
 and apply a practical empirical method to quantify the fitness landscapes
 of arbitrary phenotypic traits, using genealogical data in the form of
 population lineage trees which can include phenotypic data of various
 kinds. Our inference methodology for fitness landscapes determines how
 reproductivity is correlated to cellular phenotypes, and provides a
 natural generalization of bulk growth rate measures for single-cell
 histories. Using this technique, we quantify the strength of selection
 acting on different cellular phenotypic traits within populations, which
 allows us to determine whether a change in population growth is caused by
 individual cells' response, selection within a population, or by a
 mixture of these two processes. By applying these methods to single-cell
 time-lapse data of growing bacterial populations that express a
 resistance-conferring protein under antibiotic stress, we show how the
 distributions, fitness landscapes, and selection strength of single-cell
 phenotypes are affected by the drug. Our work provides a unified and
 practical framework for quantitative measurements of fitness landscapes
 and selection strength for any statistical quantities definable on
 lineages, and thus elucidates the adaptive significance of phenotypic
 states in time series data. The method is applicable in diverse fields,
 from single cell biology to stem cell differentiation and viral evolution.
description: Data for the
 figures.This file includes the
 data used to make the plots in the main and supplemental
 figures.DataForFigures.xlsExperimental dataThe file contains the raw data from the time-lapse experiments. The details on the data structures are described in the ReadMe file.ExperimentalData.zipPlasmid sequencesThe file contains the plasmid sequences of pLVK3, pLVSK4, pTmcherryK4, pTN001, and pTN002.PlasmidSeq.zip
DOI: 10.15468/dl.46zk8q
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Kazakhstan",
 "TaxonKey is Ferula soongarica"
 ]
}

 The dataset includes 16 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001484-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.fv4b5
title: Data from: Experimental measurements of water molecule binding energies for the second and third solvation shells of [Ca(H2O)n]2+ complexes

description: Further understanding of the biological role of the Ca2+ ion in an aqueous
 environment requires quantitative measurements of both the short- and
 long-range interactions experienced by the ion in an aqueous medium. Here,
 we present experimental measurements of binding energies for water
 molecules occupying the second and, quite possibly, the third solvation
 shell surrounding a central Ca2+ ion in [Ca(H2O)n]2+ complexes. Results
 for these large, previously inaccessible, complexes have come from the
 application of finite heat bath theory to kinetic energy measurements
 following unimolecular decay. Even at n = 20, the results show water
 molecules to be more strongly bound to Ca2+ than would be expected just
 from the presence of an extended network of hydrogen bonds. For
 n &gt; 10, there is very good agreement between the experimental
 binding energies and recently published density functional theory
 calculations. Comparisons are made with similar data recorded for
 [Ca(NH3)n]2+ and [Ca(CH3OH)n]2+ complexes.
description: CalciumWaterDetails of the individual experimental measurements made in order to extract binding energy results.
DOI: 10.5061/dryad.m5kk3
title: Data from: Genomic and phenotypic evidence for an incomplete domestication of South American grain amaranth (Amaranthus caudatus)

description: The domestication syndrome comprises phenotypic changes that differentiate
 crops from their wild ancestors. We compared the genomic variation and
 phenotypic differentiation of the two putative domestication traits seed
 size and seed colour of the grain amaranth Amaranthus caudatus, which is
 an ancient crop of South America, and its two close wild relatives and
 putative ancestors A. hybridus and A. quitensis. Genotyping 119 accessions
 of the three species from the Andean region using genotyping by sequencing
 (GBS) resulted in 9485 SNPs that revealed a strong genetic differentiation
 of cultivated A. caudatus from its two relatives. A. quitensis and A.
 hybridus accessions did not cluster by their species assignment but formed
 mixed groups according to their geographic origin in Ecuador and Peru,
 respectively. A. caudatus had a higher genetic diversity than its close
 relatives and shared a high proportion of polymorphisms with their wild
 relatives consistent with the absence of a strong bottleneck or a high
 level of recent gene flow. Genome sizes and seed sizes were not
 significantly different between A. caudatus and its relatives, although a
 genetically distinct group of A. caudatus from Bolivia had significantly
 larger seeds. We conclude that despite a long history of human cultivation
 and selection for white grain colour, A. caudatus shows a weak genomic and
 phenotypic domestication syndrome and proposes that it is an incompletely
 domesticated crop species either because of weak selection or high levels
 of gene flow from its sympatric close undomesticated relatives that
 counteracted the fixation of key domestication traits.
description: Raw data and
 scriptsdata_and_scripts.zip
DOI: 10.5061/dryad.5nk5n
title: Data from: Untangling the roles of microclimate, behaviour and physiological polymorphism in governing vulnerability of intertidal snails to heat stress

description: Biogeographic distributions are driven by cumulative effects of smaller
 scale processes. Thus, vulnerability of animals to thermal stress is the
 result of physiological sensitivities to body temperature (Tb),
 microclimatic conditions, and behavioural thermoregulation. To understand
 interactions among these variables, we analysed the thermal tolerances of
 three species of intertidal snails from different latitudes along the
 Chinese coast, and estimated potential Tb in different microhabitats at
 each site. We then empirically determined the temperatures at which heart
 rate decreased sharply with rising temperature (Arrhenius breakpoint
 temperature, ABT) and at which it fell to zero (flat line temperature,
 FLT) to calculate thermal safety margins (TSM). Regular exceedance of FLT
 in sun-exposed microhabitats, a lethal effect, was predicted for only one
 mid-latitude site. However, ABTs of some individuals were exceeded at
 sun-exposed microhabitats in most sites, suggesting physiological
 impairment for snails with poor behavioural thermoregulation and revealing
 inter-individual variations (physiological polymorphism) of thermal
 limits. An autocorrelation analysis of Tb showed that predictability of
 extreme temperatures was lowest at the hottest sites, indicating that the
 effectiveness of behavioural thermoregulation is potentially lowest at
 these sites. These results illustrate the critical roles of mechanistic
 studies at small spatial scales when predicting effects of climate change.
description: TPC modelling results
 for littoraria sinensisResults of thermal
 performance curve models using an exponential modified Gaussian model for
 Littoraria sinensis along the coast of ChinaTPC_modelling_results_littoraria_sinensis.txtTPC modelling results littorina breviculaResults of thermal performance curve models using an exponential modified Gaussian model for Littorina brevicula along the coast of ChinaTPC_modelling_results_littorina_brevicula.txtTPC modelling results Nerita yoldiiResults of thermal performance curve models using an exponential modified Gaussian model for Nerita yoldii along the coast of ChinaTPC_modelling_results_nerita_yoldii.txt
DOI: 10.5061/dryad.9n42p
title: Data from: Nutrient limitation in tropical secondary forests following different management practices

description: Secondary forests now make up more than half of all tropical forests, and
 constraints on their biomass accumulation will influence the strength of
 the terrestrial carbon (C) sink in the coming decades. However the
 variance in secondary tropical forest biomass for a given stand age and
 climate is high and our understanding of why is limited. We constructed a
 model of terrestrial C, nitrogen (N), and phosphorus (P) cycling to
 examine the influence of disturbance and management practices on nutrient
 limitation and biomass recovery in secondary tropical forests. The model
 predicted that N limited the rate of forest recovery in the first few
 decades following harvest, but that this limitation switched to P
 approximately 30-40 years after abandonment, consistent with field data on
 N and P cycling from secondary tropical forest chronosequences. Simulated
 biomass recovery agreed well with field data of biomass accumulation
 following harvest (R2=0.80). Model results showed that if all biomass
 remained on site following a severe disturbance such as blowdown, regrowth
 approached pre-disturbance biomass in 80-90 years, and recovery was faster
 following smaller disturbances such as selective logging. Field data from
 regrowth on abandoned pastures were consistent with simulated losses of
 nutrients in soil organic matter, particularly P. Following any forest
 disturbance that involved the removal of nutrients (i.e., except
 blowdown), forest regrowth produced reduced biomass relative to the
 initial state as a result of nutrient loss through harvest, leaching
 and/or sequestration by secondary minerals. Differences in nutrient
 availability accounted for 49-94% of the variance in secondary forest
 biomass C at a given stand age. Management lessons from this study are the
 importance of strategies that help retain nutrients on site, recognizing
 the role of coarse woody debris in immobilization and subsequent release
 of nutrients, and the potential for nutrient additions to enhance biomass
 growth and recovery in secondary tropical forests.
description: data_for_dryadThis zip archive contains parameter files, model output files, driver files, model structure files, an R script, keys to the files used to make the figures and tables, and a ReadMe file.
DOI: 10.5061/dryad.934fg
title: Data from: Here and there, but not everywhere: repeated loss of uncoupling protein 1 in amniotes

description: Endothermy is an evolutionary innovation in eutherian mammals and birds.
 In eutherian mammals, UCP1 is a key protein in adaptive nonshivering
 thermogenesis (NST). Although ucp1 arose early in the vertebrate lineage,
 the loss of ucp1 was previously documented in several reptile species
 (including birds). Here we determine that ucp1 was lost at the base of the
 reptile lineage, as we fail to find ucp1 in every major reptile lineage.
 Furthermore, though UCP1 plays a key role in mammalian NST, we confirm
 that pig has lost several exons from ucp1 and conclude that pig is not a
 sole outlier as the only eutherian mammal lineage to do so. Through
 similarity searches and synteny analysis, we show that ucp1 has also been
 lost/pseudogenized in Delphinidae (dolphin, orca) and potentially
 Xenarthra (sloth, armadillo) and Afrotheria (hyrax). These lineages
 provide models for investigating alternate mechanisms of thermoregulation
 and energy metabolism in the absence of functional UCP1. Further, the
 repeated losses of a functional UCP1 suggest the pervasiveness of NST via
 UCP1 across the mammalian lineage needs re-evaluation.
description: Supplemental_File1_Methods_Results_FiguresDetailed description of methods and results including figures S1 and S2.Supplemental_File2_TablesThis is a summary of results for each species analyzed in our study, including presence of ucp1 annotation, synteny analysis, and blasting of raw reads. This table also includes the ftp links to the sequence data used for each species. Species highlighted in purple had no evidence of ucp1 in Ensembl and were investigated further through synteny analysis and BLAST search of their raw data.Supplemental_File3_BlastQUERY_SyntenyThe exon sequences for ucp1 and six flanking genes used in the BLASTn for synteny analysis.Supplemental_File4_Protein_UCP1_Query_for_TBLASTNThe UCP1 protein sequences used for tBLASTn against the genomes.Supplemental_File5_BlastQUERY_for_raw_reads_mammalsThe ucp1 gene sequences used for BLASTn against the raw sequence data for reptiles.Supplemental_File6_BlastQUERY_for_raw_reads_reptiles_birdsThe ucp1 gene sequences used for BLASTn against the raw sequence data for reptiles.
DOI: 10.5061/dryad.t5m22
title: Data from: Regression commonality analyses on hierarchical genetic distances.

description: Landscape genetics is emerging as an important way of supporting
 decision-making in landscape management, in response to the deterioration
 of matrix permeability due to habitat loss and fragmentation. In line with
 unremitting methodological developments in landscape genetics, a new
 analytical procedure was recently proposed as a way of evaluating the
 effects of landscape gradients on genetic structures. This procedure is
 based on the computation of inter-individual hierarchical genetic
 distances (HGD), a metric of genetic differentiation taking into account
 the hierarchical structure in populations as inferred from clustering
 algorithms. HGD can be used as dependent variables in multivariate
 regressions to assess the effects of various landscape predictors on
 spatial patterns of genetic differentiation. However, multicollinearity
 may obscure the interpretation of multivariate regressions. We illustrate
 how regression commonality analyses (CA), a detailed variance partitioning
 procedure that can be used to deal with multicollinearity issues, can
 thoroughly improve our understanding of landscape connectivity when HGD
 are used as a dependent variable, with the red deer (Cervus elaphus) as an
 empirical example. Using logistic regression commonality analyses on HGD,
 we showed that semi-natural open areas, transportation infrastructures
 and, to a lesser extent, urban areas and rivers, were associated with an
 increase in hierarchical genetic differentiation in red deer. Regressions
 based on HGD provided detailed results that could not have been obtained
 with regressions based on standard genetic distances, with notably
 additional insights as to the possible influence of linear features such
 as roads and highways on landscape connectivity. Furthermore, CA helped
 identify synergistic associations among variables as well as suppressors,
 thus resolving inconsistencies among hierarchical levels and revealing
 spurious correlations that may have gone unnoticed in the course of
 classical regression analyses. We thus recommend the use of regression
 commonality analysis on hierarchical genetic distances as a promising
 statistical tool for landscape geneticists.
description: Pairwise matrices of
 genetic distancesPairwise
 inter-individual classical and hierarchical genetic distances for the 669
 individuals retained in main analyses.Genetic_Distances.zipPairwise matrices of landscape distancesPairwise inter-individual landscape distances for the 669 individuals retained in main analyses.Landscape_Distances.zip
DOI: 10.5061/dryad.j0226
title: Data from: Validating two-dimensional leadership models on three-dimensionally structured fish schools

description: Identifying leader-follower interactions is crucial for understanding how
 a group decides where or when to move, and how this information is
 transferred between members. Although many animal groups have a
 three-dimensional structure, previous studies investigating
 leader-follower interactions have often ignored vertical information. This
 raises the question whether commonly used two-dimensional leader-follower
 analyses can be used justifiably on groups that interact in three
 dimensions. To address this we quantified the individual movements of
 banded tetra fish (Astyanax mexicanus) within shoals by computing the
 three-dimensional trajectories of all individuals using a stereo-camera
 technique. We used these data firstly to identify and compare
 leader-follower interactions in two and three dimensions, and secondly to
 analyse leadership with respect to an individual’s spatial position in
 three dimensions. We show that for 95% of all pairwise interactions
 leadership identified through two-dimensional analysis matches that
 identified through three-dimensional analysis, and we reveal that fish
 attend to the same shoalmates for vertical information as they do for
 horizontal information. Our results therefore highlight that
 three-dimensional analyses are not always required to identify
 leader-follower relationships in species that move freely in
 three-dimensions. We discuss our results in terms of the importance of
 taking species’ sensory capacities into account when studying interaction
 networks within groups.
description: Data:Validating
 two-dimensional leadership models on three-dimensionally structured fish
 schoolsThe data for all fish of
 each shoal, indicated in the name. The data is in a csv file, with column
 one X, column two Y, column three Z, and column 4 Time.Data
 Dryad.zip
DOI: 10.5061/dryad.80724
title: Data from: Low abundant soil bacteria can be metabolically versatile and fast growing

description: The abundance of species is assumed to depend on their life history
 traits, such as growth rate and resource specialization. However, this
 assumption has not been tested for bacteria. Here we investigate how
 abundance of soil bacteria relates to slow growth and substrate
 specialization (oligotrophy) versus fast growth and substrate
 generalization (copiotrophy). We collected 47 saprotrophic soil bacterial
 isolates of differing abundances and measured their growth rate and the
 ability to use a variety of single carbon sources. Opposite to our
 expectation, there was no relationship between abundance in soil and the
 measured growth rate or substrate utilization profile (SUP). However,
 isolates with lower growth rates used fewer substrates than faster growing
 ones supporting the assumption that growth rate may relate to substrate
 specialization. Interestingly, growth rate and SUP were correlated with
 phylogeny, rather than with abundance in soil. Most markedly,
 Gammaproteobacteria on average grew significantly faster and were able to
 use more substrates than other bacterial classes, whereas
 Alphaproteobacteria were growing relatively slowly and used fewer
 substrates. This finding suggests that growth and substrate utilization
 are phylogenetically deeply conserved. We conclude that growth rate and
 substrate utilization of soil bacteria are not general determinants of
 their abundance. Future studies on explaining bacterial abundance need to
 determine how other factors, such as competition, predation and abiotic
 factors may contribute to rarity or abundance in soil bacteria.
description: Low abundant soil
 bacteria can be metabolically versatile and fast growingMeasurement data on
 bacterial isolates; further description see metasheet
DOI: 10.15468/dl.dsk25b
title: Occurrence Download

description: A dataset containing 39067 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Diveboard - Scuba diving citizen science observations"
 ]
}

 The dataset includes 39067 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001481-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m2udz4
title: Occurrence Download

description: A dataset containing 34927 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Helianthus tuberosus)",
 "OccurrenceStatus is Present",
 "SpeciesKey is not null",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2026",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 },
 "BasisOfRecord is one of (Human Observation, Machine Observation, Observation)"
 ]
}

 The dataset includes 34927 records from 343 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001486-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.