cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.818ms
title: Data from: Phylogenetic composition of host plant communities drives plant-herbivore food web structure

description: 1. Insects tend to feed on related hosts. The phylogenetic composition of
 host plant communities thus plays a prominent role in determining insect
 specialization, food web structure, and diversity. Previous studies showed
 a high preference of insect herbivores for congeneric and confamilial
 hosts suggesting that some levels of host plant relationships may play
 more prominent role that others. 2. We aim to quantify the effects of host
 phylogeny on the structure of quantitative plant-herbivore food webs.
 Further, we identify specific patterns in three insect guilds with
 different life histories and discuss the role of host plant phylogeny in
 maintaining their diversity. 3. We studied herbivore assemblages in three
 temperate forests in Japan and the Czech Republic. Sampling from a canopy
 crane, a cherry picker and felled trees allowed a complete census of
 plant-herbivore interactions within three 0.1 ha plots for leaf chewing
 larvae, miners, and gallers. We analyzed the effects of host phylogeny by
 comparing the observed food webs with randomized models of host selection.
 4. Larval leaf chewers exhibited high generality at all three sites,
 whereas gallers and miners were almost exclusively monophagous. Leaf
 chewer generality dropped rapidly when older host lineages (5-80 myr) were
 collated into a single lineage but only decreased slightly when the most
 closely related congeneric hosts were collated. This shows that leaf
 chewer generality has been maintained by feeding on confamilial hosts
 while only a few herbivores were shared between more distant plant
 lineages and, surprisingly, between some congeneric hosts. In contrast,
 miner and galler generality was maintained mainly by the terminal nodes of
 the host phylogeny and dropped immediately after collating congeneric
 hosts into single lineages. 5. We show that not all levels of host plant
 phylogeny are equal in their effect on structuring plant-herbivore food
 webs. In the case of generalist guilds, it is the phylogeny of deeper
 plant lineages that drives the food web structure whereas the terminal
 relationships play minor roles. In contrast, the specialization and
 abundance of monophagous guilds is affected mainly by the terminal parts
 of the plant phylogeny and does not generally reflect deeper host
 phylogeny.
description: Insect data and host
 plant associationsInsect data from our
 sampling sites used in the food-web analysis.Insect_data_corrected_gallers.xlsx
DOI: 10.5061/dryad.78h38
title: Data from: Adaptive radiation driven by the interplay of eco-evolutionary and landscape dynamics

description: We investigate an individual-based model of adaptive radiation based on
 the biogeographical changes of the Great African Lakes where cichlid
 fishes radiated. In our model, the landscape consists of a mosaic of three
 habitat types which may or may not be separated by geographic barriers. We
 study the effect of the alternation between allopatry and sympatry called
 landscape dynamics. We show that landscape dynamics can generate a
 significantly higher diversity than allopatric or sympatric speciation
 alone. Diversification is mainly due to the joint action of allopatric,
 ecological divergence, and of disruptive selection increasing assortative
 mating and allowing for the coexistence in sympatry of species following
 reinforcement or character displacement. Landscape dynamics possibly
 increase diversity at each landscape change. The characteristics of the
 radiation depend on the speed of landscape dynamics and of the number of
 geographically isolated regions at steady state. Under fast dynamics of a
 landscape with many fragments, the model predicts a high diversity,
 possibly subject to the temporary collapse of all species into a hybrid
 swarm. When fast landscape dynamics induce the recurrent fusion of several
 sites, diversity is moderate but very stable over time. Under slow
 landscape dynamics, diversification proceeds similarly, although at a
 slower pace.
description: revised_simul_DLCode for simulation and diversity estimation. NOTE: Please use revised_simul_DL.zip and not simul_DL.zip. Version 1 was uploaded by mistake, and this is not the simulation code corresponding to the published paper. Version 2 is the correct simulation code.
DOI: 10.5061/dryad.82vr1
title: Data from: Is diagnosability an indicator of speciation? Response to ‘Why one century of phenetics is enough’

description: Recently (Heller et al. 2013; H&A), we commented on a revision of
 the bovid taxonomy, which proposes a doubling in the number of recognized
 species (Groves and Grubb 2011; G&G). The subsequent response by
 Cotterill et al. (2014; C&A) contains a number of
 misunderstandings and leaves much of the critique voiced in our paper
 unanswered, focusing instead on species ontologies and taxonomic history.
 C&A argue strongly against phenetics, morphospecies and taxonomic
 conservatism, ascribing us views that we do not hold and hence confusing
 the substance of our disagreement. These misconceptions oblige us to
 clarify our views on certain key issues to avoid being misrepresented.
 More seriously, however, the authors fail to respond to, or acknowledge,
 some of our crucial practical concerns, notably the risk of taxonomic
 inflation (Isaac & Mace 2004) posed by their diagnostic
 phylogenetic species concept (dPSC). Here we restate a number of our
 concerns regarding the proposed bovid taxonomy of G&G and discuss
 their treatment in C&A.
description: Appendix
 1UNSUPPORTED SPLITS IN
 G&GAppendix
 2EXAMPLES OF
 INTRASPECIFIC DIAGNOSABILITY BASED ON GENETIC DATA
DOI: 10.5061/dryad.86p82f43
title: Data from: Spatial and temporal patterns of neutral and adaptive genetic variation in the endangered African wild dog (Lycaon pictus)

description: Deciphering patterns of genetic variation within a species is essential
 for understanding population structure, local adaptation and differences
 in diversity between populations. Whilst neutrally evolving genetic
 markers can be used to elucidate demographic processes and genetic
 structure, they are not subject to selection and therefore are not
 informative about patterns of adaptive variation. As such, assessments of
 pertinent adaptive loci, such as the immunity genes of the Major
 Histocompatibility Complex (MHC), are increasingly being incorporated into
 genetic studies. In this study we combined neutral (microsatellite, mtDNA)
 and adaptive (MHC class II DLA-DRB1 locus) markers to elucidate the
 factors influencing patterns of genetic variation in the African wild dog
 (Lycaon pictus); an endangered canid that has suffered extensive declines
 in distribution and abundance. Our genetic analyses found all extant wild
 dog populations to be relatively small (Ne &lt; 30). Furthermore,
 through coalescent modelling, we detected a genetic signature of a recent
 and substantial demographic decline, which correlates with human
 expansion, but contrasts with findings in some other African mammals. We
 found strong structure of wild dog populations, indicating the negative
 influence of extensive habitat fragmentation and loss of gene flow between
 habitat patches. Across populations we found that the spatial and temporal
 structure of microsatellite and MHC diversity were correlated, and
 strongly influenced by demographic stability and population size,
 indicating the effects of genetic drift in these small populations.
 Despite this correlation, we detected signatures of selection at the MHC,
 implying that selection has not been completely overwhelmed by genetic
 drift.
description: Dryad_MolEcolSheet1 - Microsatellite data for free ranging African wild dog samples collected in Eastern Africa. Sheet 2 - Note on microsatellite allele sizes. Sheet 3 - Primer details.Dryad_molecol_mtDNAmtDNA sheet: Individual level mtDNA haplotype data for free ranging populations of African wild dogs in Eastern and Southern Africa. mtDNA notes sheet: Information about the data, primer details, and accession numbers.Dryad_molecol_MHCMHC data sheet: Individual level MHC class II DLA-DRB1 data for free ranging African wild dogs from populations in Eastern and Southern Africa. Included are both official names, and local names of alleles. MHC alleles sheet: Table of local and official names for alleles and corresponding publication source.
DOI: 10.5061/dryad.pj319sn
title: Data from: Pollination on the dark side: acoustic monitoring reveals impacts of a total solar eclipse on flight behavior and activity schedule of foraging bees

description: The total solar eclipse of 21 August 2017 traversed ~5000 km from coast to
 coast of North America. In its 90-min span, sunlight dropped by three
 orders of magnitude and temperature by 10–15°C. To investigate impacts of
 these changes on bee (Hymenoptera: Apoidea) pollinators, we monitored
 their flights acoustically in natural habitats of Pacific Coast, Rocky
 Mountain, and Midwest regions. Temperature changes during the eclipse had
 little impact on bee activity. Most of the explained variation (R2) in
 buzzing rate was attributable to changes in light intensity. Bees ceased
 flying during complete darkness at totality, but flight activity was
 unaffected by dim light in partial phases before and after totality.
 Flights of bees during partial phases of the eclipse lasted longer than
 flights made under full sun, showing that behavioral plasticity matched
 bee flight properties to changes in light intensity during the eclipse.
 Efforts of citizen scientists, including hundreds of school children,
 contributed to the scope and educational impact of this study.
description: MetadataDescribes abbreviations, units, sampling details and indicates sources of additional information in the publication for the three data files.Fig 2 data-flight buzz volume over time during eclipsebee flight buzz counts referenced by eclipse phases.Fig 2 data corrected.xlsxFig 3 DataBee flight buzz density and light intensity during the eclipse in two regions used for environmental monitoringFigure 4 dataData from seven sites showing minutes elapsed from totality (before or after) and flight buzz duration by site.
DOI: 10.5061/dryad.g9049
title: Data from: No evidence for a trade-off between sperm length and male premating weaponry

description: Male ornaments and armaments that mediate success in mate acquisition and
 ejaculate traits influencing competitive fertilization success are under
 intense sexual selection. However, relative investment in these pre- and
 postcopulatory traits depends on the relative importance of either
 selection episode and on the energetic costs and fitness gains of
 investing in these traits. Theoretical and empirical work has improved our
 understanding of how precopulatory sexual traits and investments in sperm
 production covary in this context. It has recently also been suggested
 that male weapon size may trade off with sperm length as another
 postcopulatory sexual trait, but the theoretical framework for this
 suggestion remains unclear. We evaluated the relationship between
 precopulatory armaments and sperm length, previously reported in
 ungulates, in five taxa as well as meta-analytically. Within and between
 taxa, we found no evidence for a negative or positive relationship between
 sperm length and male traits that are important in male-male contest
 competition. It is important to consider pre- and postcopulatory sexual
 selection together to understand fitness, and to study investments in
 different reproductive traits jointly rather than separately. A trade-off
 between pre- and postcopulatory sexual traits may not manifest itself in
 sperm length but rather in sperm number or function. Particularly in
 large-bodied taxa such as ungulates, sperm number is more variable
 interspecifically and likely to be under more intense selection than sperm
 length. We discuss our and the previous results in this context.
description: Data of Primates,
 Ungluates, Pheasants, Stalk-eyed flies and Onthophagine dung
 beetlesComplete data sets of
 all species of Primates, Ungluates, Pheasants, Stalk-eyed flies and
 Onthophagine dung beetles used in this study, including data on male and
 female body size, testes size, male weapon size and/or sexual size
 dimorphism, as well as sperm length.Datafiles.zipPhylogenies of the Primates, Ungluates, Pheasants, Stalk-eyed flies and Onthophagine dung beetlesPhylogenies in NEXUS format of all species of Primates, Ungluates, Pheasants, Stalk-eyed flies and Onthophagine dung beetles used in this study. All phylogenies are based on published molecular phylogenies. Since no branch lengths were available for most phylogenies, all branch lengths are set to 1 for consistency.Phylogenies.zipReferencesReferences accompanying the data flies and phylogenies
DOI: 10.5061/dryad.3rj81
title: Data from: Different phylogenetic and environmental controls of first-order root morphological and nutrient traits: evidence of multidimensional root traits

description: 1. Although fine roots are essential for the water and nutrient uptake of
 plants, there is limited understanding of root trait variation and the
 underlying mechanism. 2. Here, six first-order root morphological and
 chemical traits were measured for 181 species from eight subtropical and
 boreal forests to test the hypothesis of different phylogenetic and
 environmental regulations of root morphological and nutrient traits result
 in the multidimensions of root traits. 3. Two independent root trait
 dimensions between root thickness and nutrient traits were detected at
 both species and community levels. At the species level, diameter-related
 traits were mainly restricted by phylogenetic structure and showed little
 plasticity to the changing environments, whereas the variation in woody
 root nutrient was influenced significantly by soil variables. For
 community-level traits, the diameter-related axis scores of principal
 component analysis (PCA) were mainly driven by mean annual temperature
 (MAT) through shifting species composition, whereas the root
 nutrient-related axis scores were strongly influenced by soil P
 availability. 4. From both species and community levels, our study
 confirms, that the root-thickness-related dimension and root nutrient
 dimension represent new support for the multidimensionality of root traits
 which are driven by different selection pressure. This study also
 underlines that the community-aggregated traits might serve as a promising
 avenue to improve our understanding of community assemblage processes,
 allowing us to predict changes of vegetation distributions in a changing
 climate.
description: Data of first-order root
 trait in eastern ChinaThe data file contains
 six first-order root traits, including root diameter (RD), specific root
 length (SRL), root tissue density (RTD), root carbon and nitrogen
 concentration (RC and RN) and C:N ratio, of 181 plant species from eight
 subtropical and boreal forests in eastern China.Root trait data-revised the RTD
 unit.xlsx
DOI: 10.5061/dryad.nt898
title: Data from: Probabilistic graphical model representation in phylogenetics

description: Recent years have seen a rapid expansion of the model space explored in
 statistical phylogenetics, emphasizing the need for new approaches to
 statistical model representation and software development. Clear
 communication and representation of the chosen model is crucial for: (1)
 reproducibility of an analysis, (2) model development and (3) software
 design. Moreover, a unified, clear and understandable framework for model
 representation lowers the barrier for beginners and non-specialists to
 grasp complex phylogenetic models, including their assumptions and
 parameter/variable dependencies. Graphical modeling is a unifying
 framework that has gained in popularity in the statistical literature in
 recent years. The core idea is to break complex models into conditionally
 independent distributions. The strength lies in the comprehensibility,
 flexibility, and adaptability of this formalism, and the large body of
 computational work based on it. Graphical models are well-suited to teach
 statistical models, to facilitate communication among phylogeneticists and
 in the development of generic software for simulation and statistical
 inference. Here, we provide an introduction to graphical models for
 phylogeneticists and extend the standard graphical model representation to
 the realm of phylogenetics. We introduce a new graphical model component,
 tree plates, to capture the changing structure of the subgraph
 corresponding to a phylogenetic tree. We describe a range of phylogenetic
 models using the graphical model framework and introduce modules to
 simplify the representation of standard components in large and complex
 models. Phylogenetic model graphs can be readily used in simulation,
 maximum likelihood inference, and Bayesian inference using, for example,
 Metropolis-Hastings or Gibbs sampling of the posterior distribution.
description: baculum (absent/present)
 datamorphology of
 absence/presence of a baculum in mammals.baculumData01.nexMammal PhylogenyMammal phylogeny published by dos Reis et al. (2012) Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny Proceedings of the Royal Society B: Biological Sciences, The Royal Society, 2012, 279, 3491-3500mammalia_dosReis.treeGraphicalModels_Example_1aRevBayes example file for analysis shown in Figure 1.a.GraphicalModels_Example_1bRevBayes example file for analysis shown in Figure 1.b.GraphicalModels_Example_2RevBayes example file for analysis shown in Figure 2.Supplementary InformationProbabilistic Graphical Model Representation in Phylogenetics supplementary information, including additional phylogenetic graphical models and RevBayes implementation and examples.Hohna_etal_GM_SM.pdf
DOI: 10.5061/dryad.gn95r
title: Data from: A systematic review and meta-analysis of seroprevalence surveys of ebolavirus infection

description: Asymptomatic ebolavirus infection could greatly influence transmission
 dynamics, but there is little consensus on how frequently it occurs or
 even if it exists. This paper summarises the available evidence on
 seroprevalence of Ebola, Sudan and Bundibugyo virus IgG in people without
 known ebolavirus disease. Through systematic review, we identified 51
 studies with seroprevalence results in sera collected from 1961 to 2016.
 We tabulated findings by study population, contact, assay, antigen and
 positivity threshold used, and present seroprevalence point estimates and
 95% confidence intervals. We classified sampled populations in three
 groups: those with household or known case-contact; those living in
 outbreak or epidemic areas but without reported case-contact; and those
 living in areas with no recorded cases of ebolavirus disease. We performed
 meta-analysis only in the known case-contact group since this is the only
 group with comparable exposures between studies. Eight contact studies
 fitted our inclusion criteria, giving an overall estimate of
 seroprevalence in contacts with no reported symptoms of 3.3% (95% CI
 2.4-4.4, p&lt;0.001), but with substantial heterogeneity.
description: Findings from a
 systematic review of ebolavirus serology in subjects without known ebola
 virus diseaseThe dataset contains
 findings and information from 51 seroprevelance studies performed from on
 samples collected from 1961 to 2016. These investigated 84
 exposure-defined subgroups of subjects reported to have had no symptoms of
 EVD during the outbreak period, or to have come from populations with no
 known outbreaks. The data covers more than 44,000 people. The dataset
 records the sample locations, exposure type, numbers investigated,
 number/% considered positive and the cut-off used to define positivity.
 The data comes from a systematic review of published papers:
 DOI/PMCID?PMIDs are recorded. Information on antigens tested, any
 validation work and other notes are in the ReadMe file, as are
 explanations of the variablesScidata EV Asymp Serology
 Dataset 061216.csvScidata EV Asymp Full
 Findings Table 061216Table 1: detailed
 breakdown of the study populations, test methods and
 results.
DOI: 10.5061/dryad.dv15kp5
title: Data from: Phylogenetic analysis of the genus Retrotapes del Río, 1997 (Bivalvia: Veneridae) and systematic analysis of its taxa from Chile

description: Since the genus Retrotapes was erected, some authors have been in favor or
 against its validity, or argued the assignment of the extant species R.
 exalbidus and R. lenticularis to Retrotapes. Some authors synonymized
 Retrotapes with the Miocene genus Frigichione, and others with the extant
 genus Eurhomalea to which most of the species that belong to Retrotapes
 were previously assigned. In the present contribution, a phylogenetic
 analysis of the genus is performed to test these controversies. Besides, a
 systematic revision of the Chilean species of the genus is performed to
 complete the analysis of the Retrotapes taxa from Patagonia and Antarctica
 started by previous authors. This study demonstrates that Retrotapes is a
 monophyletic genus, which is not closely related to Frigichione or
 Eurhomalea. But instead, it is closely related to some Austral taxa from
 Kerguelen Island (Paleomarcia), New Zealand (Atamarcia) and Australia
 (Katelysia), a relationship previously unknown. Besides, the extant
 species R. lenticularis and R. exalbidus belong to Retrotapes and were
 recovered as part of a clade closely related to the type species of the
 genus, R. ninfasiensis (Miocene, Patagonia). Retrotapes is registered in
 Chile since the late Eocene, where it was represented by R. difficilis
 nov. comb., a taxon that resembles some Eocene species of the same genus
 from Antarctica. In the late Oligocene–early Miocene it was represented by
 R. navidadis and later in the Pliocene by three species, the fossil R.
 fuenzalidae and the two extant ones.
description: Supplementary Data Set
 1List
 of the reviewed materials.Supplementary Data Set
 2List
 of several taxa used for comparison and performed the phylogenetic
 analysis.Appendix
 1List
 of characters used to build the matrix.Appendix1_Characters.pdfAppendix 2Matrix used to perform the phylogenetic analysis.Appendix2_Matrix.pdf
DOI: 10.5061/dryad.d6jk5
title: Data from: A new specimen of Agorophius pygmaeus (Agorophiidae, Odontoceti, Cetacea) from the Early Oligocene Ashley Formation of South Carolina, USA

description: The holotype partial skull of Agorophius pygmaeus (the monotypic form for
 both the genus Agorophius and the Family Agorophiidae) has been missing
 for approximately 140 years. Since the discovery of Agorophius pygmaeus,
 many additional taxa and specimens have been placed in the Family
 Agorophiidae, only to be reclassified and removed later. This has created
 confusion as to what is and what is not an agorophiid and a lack of
 clarity as to what characteristics delimit the Agorophiidae. A newly
 discovered skull of an agorophiid recently collected from an underwater
 cliff face of the Ashley River, South Carolina, USA, is assigned to
 Agorophius pygmaeus. It derives from the base of the Ashley Formation
 (early Oligocene). The new specimen consists of most of the skull and
 periotics, which are well preserved and described for the first time in an
 agorophiid. The new specimen provides an opportunity to diagnose the
 Agorophiidae and place the genus and species within the phylogenetic
 context of the early odontocete radiation in the Oligocene, along with
 other taxa such as the Ashleycetidae, Mirocetidae, Patriocetidae,
 Simocetidae, Waipatiidae, and Xenorophidae. Based on this new
 understanding, Agorophiidae are known with certainty only from the early
 Oligocene of South Carolina, with other undescribed, potential agorophiid
 specimens from the Oligocene of the North Pacific region (Japan, Mexico,
 and Washington State).
description: Godfrey et al Agorophius
 matrixNEXUS format data file
 used for phylogenetic analysis.Supplementary
 DataAdditional drawings,
 dinoflagellate data, and phylogenetic data