cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sd5hv94
title: Data from: MHC-mediated sexual selection on bird song: generic polymorphism, particular alleles and acoustic signals

description: Several hypotheses predict that the major histocompatibility complex (MHC)
 drives mating preference in females. Olfactory, color or morphological
 traits are often found as reliable signals of the MHC profile, but the
 role of avian song mediating MHC-based female choice remains largely
 unexplored. We investigated the relationship between several MHC and
 acoustic features in the collared flycatcher (Ficedula albicollis) a
 European passerine with complex songs. We screened a fragment of the class
 IIB 2nd exon of the MHC molecule, of which individuals harbor 4-15
 alleles, while considerable sequence diversity is maintained at the
 population level. To make statistical inferences from a large number of
 comparisons, we adopted both null-hypothesis testing and effect size
 framework in combination with randomization procedures. After controlling
 for potential confounding factors, neither MHC allelic diversity nor the
 presence of particular alleles was associated remarkably to the
 investigated qualitative and quantitative song traits. Furthermore,
 genetic similarity among males based on MHC sequences was not reflected by
 the similarity in their song based on syllable content. Overall, these
 results suggest that the relationship between features of song and the
 allelic composition and diversity of MHC is not strong in the studied
 species. However, a biologically-motivated analysis revealed that
 individuals that harbor an MHC allele that impairs survival perform songs
 with broader frequency range. This finding suggests that certain aspects
 of the song may bear reliable information concerning the MHC profile of
 the individuals, which can be used by females to optimize mate choice.
description: quantitative_song_traitsIndividual-specific estimates of quantitative song traits, number of MHC alleles, and the presence of particular MHC alleles. This dataset was used to test if quantitative song traits reflect MHC allelic diversity or the presence of particular allelesqualitative_song_traitsIndividual-specific estimates of syllable content (presence of particular syllables), and the number of MHC alleles. This dataset was used to test if qualitative song traits reflect MHC allelic diversity. To test if the presence of particular syllables are associated with the presence of particular alleles, this dataset should be merged with "quantitative_song_traits.xlsx" based on ring numbersgenetic_distanceGenetic distance of individuals (with information on qualitative song traits) based on their MHC sequencessong_distanceDissimilarity in song content among males based on the frequency of use of particular syllables
DOI: 10.5061/dryad.33nd74t
title: Data from: Venom gland size and venom complexity – essential trophic adaptations of venomous predators: a case study using spiders

description: Specialised predators possess variety of adaptations. In the venomous
 predators this may include size of the venom gland and venom composition.
 It is expected that due to different foraging strategies predators with a
 wide trophic niche (generalists) should possess larger venom glands that
 contain more diversified components than species with a narrow niche
 (specialists). We focused on spiders, as the most diversified group of
 venomous predators, in which a wide variety of trophic strategies has
 evolved. We conducted a comparative analysis using 40 spider species, in
 which we measured the size of their venom gland and its complexity using
 proteome profiling methods. The species were classified into three trophic
 groups: generalists, facultative specialists, and obligatory specialists.
 We found that the venom glands of generalists are larger than those of
 obligatory specialists, which is presumably due to more frequent prey
 capture by the former. The complexity of venom, of peptides (2-15 kDa) and
 proteins (15-250 kDa), was more diverse in generalists than in
 specialists. Multivariate analysis of venom revealed significant
 differences among the three trophic categories only in the complexity of
 peptides. Our study thus shows that venom gland size and its content have
 taken different pathways during the evolution of trophic strategies in
 spiders. Generalists evolved larger venom glands with more complex
 composition, whereas obligatory specialists possess smaller glands with
 less diverse chemical structures, presumably containing prey-specific
 toxins.
description: data-archiveGland volumes, MALDI-TOF profiles, and SDS-PAGE relative intensities
DOI: 10.5061/dryad.j1828
title: Data from: Characterisation of microsatellite and SNP markers from Miseq and genotyping-by-sequencing data among parapatric Urophora cardui (Tephritidae) populations

description: Phylogeographic analyses of the gall fly Urophora cardui have in earlier
 studies based on allozymes and mtDNA identified small-scale,
 parapatrically diverged populations within an expanding Western Palearctic
 population. However, the low polymorphism of these markers prohibited an
 accurate delimitation of the evolutionary origin of the parapatric
 divergence. Urophora cardui from the Western Palearctic have been
 introduced into Canada as biological control agents of the host plant
 Cirsium arvense. Here, we characterise 12 microsatellite loci with hexa-,
 penta- and tetra-nucleotide repeat motifs and report a
 genotyping-by-sequencing SNP protocol. We test the markers for genetic
 variation among three parapatric U. cardui populations. Microsatellite
 variability (N=59 individuals) was high: expected
 heterozygosity/locus/population (0.60-0.90), allele
 number/locus/population (5-21). One locus was alternatively sex-linked in
 males or females. Cross-species amplification in the sister species U.
 stylata was successful or partially successful for seven loci. For
 genotyping-by-sequencing (N=18 individuals), different DNA extraction
 methods did not affect data quality. Depending on sequence sorting
 criteria, 1177-2347 unlinked SNPs and 1750-4469 parsimony informative
 sites were found in 3514-5767 loci recovered after paralog filtering. Both
 marker systems quantified the same population partitions with high
 probabilities. Many and highly differentiated loci in both marker systems
 indicate genome-wide diversification and genetically distinct populations.
description: peerj-16427-Uc_GBS_14-6_StructureStructure file (1492 unlinked SNPs) generated by pyRAD for parameter set 14-6 (14 “minimum coverage of individuals” (mincov) and 6 “maximum number of heterozygote samples” (maxSH). The file contains data from N=18 individuals sampled in three parapatric U. cardui populations (each N=6).peerj-16427-Uc_GBS_14-6.vcf.xlsxGBS loci and genotypes recovered with pyRAD from parameter set 14-6 (mincov = 14, maxSH = 6).Uc_microsats_GenepopGenepop file. Genetic variation at 12 microsatellite loci in three parapatric U. cardui populations. N=59.
DOI: 10.5061/dryad.rh29r
title: Data from: Ecological consequences of the Guadalupian extinction and its role in the brachiopod-mollusk transition

description: The Guadalupian (middle Permian) extinction may have triggered substantial
 ecological restructuring in level-bottom communities, such as turnover in
 dominant brachiopod genera or a shift from abundant brachiopods to
 mollusks, despite comparatively minor taxonomic losses. However,
 ecological changes in relative abundance have been inferred from limited
 data; as a result, constraints on important shifts like the
 brachiopod-mollusk transition are imprecise. Here, I reevaluate the
 magnitude of ecological shifts during the Guadalupian–Lopingian (G-L)
 interval by supplementing previous census counts of silicified assemblages
 with counts from non-silicified assemblages and global occurrence data,
 both sourced from the Paleobiology Database. Brachiopod occurrences are
 consistent with more pronounced faunal composition changes from the
 Guadalupian to Lopingian than among stages within those intervals, but
 only in Iran and South China, and not in Pakistan or a Tethys-wide data
 set. In Iran and South China, Bray-Curtis dissimilarity values comparing
 occurrence frequencies between adjacent stages were elevated across the
 G-L transition, although other intervals exhibited similarly large shifts.
 However, genus occurrence frequencies were less strongly correlated or
 were anti-correlated across the G-L transition, suggesting moderate faunal
 turnover among dominant brachiopod genera. In contrast to previous
 inferences from silicified faunas, abundances of brachiopods, bivalves,
 and gastropods remained consistent from the Guadalupian to Lopingian in
 non-silicified local counts and global occurrences, implying that the
 brachiopod-mollusk shift did not occur until the end-Permian extinction.
 Ecological and taxonomic consequences were both minor in level-bottom
 settings, suggesting that severe environmental perturbations may not be
 necessary to explain biotic changes during the Guadalupian-Lopingian
 transition.
description: PT_abundance_dataAbundance counts of bivalves, brachiopods, and gastropods in non-silicified collections with ages between the Early Permian and Early Triassic. Only collections containing at least 30 specimens from marine environments are included. Columns contain the Paleobiology Database collection number ("collection_no"), name of the taxonomic class ("class_name"), name of the genus ("occurrence.genus_name"), abundance value and unit, Paleobiology Database reference number ("collection.reference_no"), and time interval data ("epoch", "stage", and Paleobiology Database "10_my_bin").pt_abund_data.csv
DOI: 10.5061/dryad.81tf9
title: Data from: The fragmentation of Pangaea and Mesozoic terrestrial vertebrate biodiversity

description: During the Mesozoic (242–66 million years ago), terrestrial regions
 underwent a massive shift in their size, position and connectivity. At the
 beginning of the era, the land masses were joined into a single
 supercontinent called Pangaea. However, by the end of the Mesozoic,
 terrestrial regions had become highly fragmented, both owing to the
 drifting apart of the continental plates and the extremely high sea levels
 that flooded and divided many regions. How terrestrial biodiversity was
 affected by this fragmentation and large-scale flooding of the
 Earth's landmasses is uncertain. Based on a model using the
 species–area relationship (SAR), terrestrial vertebrate biodiversity would
 be expected to nearly double through the Mesozoic owing to continental
 fragmentation, despite a decrease of 24% in total terrestrial area.
 Previous studies of Mesozoic vertebrates have generally found increases in
 terrestrial diversity towards the end of the era, although these increases
 are often attributed to intrinsic or climatic factors. Instead,
 continental fragmentation over this time may largely explain any observed
 increase in terrestrial biodiversity. This study demonstrates the
 importance that non-intrinsic effects can have on the taxonomic success of
 a group, and the importance of geography to understanding past
 biodiversity.
description: Supplementary_materials_S2Complete R code for all analyses and figures used in the paper.Supplementary_materials_S3RData file containing polygon data for all land regions through the Mesozoic. Use in conjunction with R code contained in Supplementary_materials_S2.R in this same repository.Supplementary_materials_S4Individual areas for each terrestrial region through the Mesozoic, as used to create figure 1a in original paper. Please consult Supplementary_materials_S2.R for R code to create this dataset from the original polygon data.
DOI: 10.5061/dryad.72mr1
title: Data from: Evolution of plasticity and adaptive responses to climate change along climate gradients

description: The relative contributions of phenotypic plasticity and adaptive evolution
 to the responses of species to recent and future climate change are poorly
 understood. We combine recent (1960–2010) climate and phenotypic data with
 microclimate, heat balance, demographic and evolutionary models to address
 this issue for a montane butterfly, Colias eriphyle, along an elevational
 gradient. Our focal phenotype, wing solar absorptivity, responds
 plastically to developmental (pupal) temperatures and plays a central role
 in thermoregulatory adaptation in adults. Here, we show that both the
 phenotypic and adaptive consequences of plasticity vary with elevation.
 Seasonal changes in weather generate seasonal variation in phenotypic
 selection on mean and plasticity of absorptivity, especially at lower
 elevations. In response to climate change in the past 60 years, our models
 predict evolutionary declines in mean absorptivity (but little change in
 plasticity) at high elevations, and evolutionary increases in plasticity
 (but little change in mean) at low elevation. The importance of plasticity
 depends on the magnitude of seasonal variation in climate relative to
 interannual variation. Our results suggest that selection and evolution of
 both trait means and plasticity can contribute to adaptive response to
 climate change in this system. They also illustrate how plasticity can
 facilitate rather than retard adaptive evolutionary responses to
 directional climate change in seasonal environments.
description: Kingsolver&Buckley.PRSb.Supplement_13June2017Description of the set of models used in the studies and simulations, and climatic data for each study site during the time period of the simulations (1960-2010).
DOI: 10.5061/dryad.ht529
title: Data from: Preparation, characterization and luminescence properties of core–shell ternary terbium composites SiO2(600)@Tb(MABA-Si)•L

description: Two novel core-shell structure ternary terbium composites
 SiO2(600)@Tb(MABA-Si)•L(L:dipy/phen) nanometer luminescence materials were
 prepared by ternary terbium complexes Tb(MABA-Si)•L2•(ClO4)3•2H2O shell
 grafted onto the surface of SiO2 microspheres. And corresponding ternary
 terbium complexes were synthesized using (CONH(CH2)3Si(OCH2CH3)3)2
 (denoted as MABA-Si) as first ligand and L as second ligand coordinated
 with terbium perchlorate. The as-synthesized products were characterized
 by means of IR spectra, 1HNMR, element analysis, molar conductivity, SEM
 and TEM. It found that the first ligand MABA-Si of terbium ternary complex
 hydrolysed to generate the Si-OH and the Si-OH condensate with the Si-OH
 on the surface of SiO2 microspheres, then ligand MABA-Si grafted onto the
 surface of SiO2 microspheres. The diameter of SiO2 core of
 SiO2(600)@Tb(MABA-Si)•L was about 600 nm.. Interestingly, the luminescence
 properties demonstrate that the two core-shell structure ternary terbium
 composites SiO2(600)Tb(MABA-Si)•L(dipy/phen) exhibit strong emission
 intensity, which are 2.49 and 3.35 times higher than that of the
 corresponding complexes Tb(MABA-Si)•L2•(ClO4)3•2H2O, respectively.
 Luminescence decay curves show that core-shell structure ternary terbium
 composites have longer lifetime. Excellent luminescence properties enable
 the core-shell materials to have potential applications in medicine,
 industry, luminescent fibres and various biomaterials filed.
description: Figuresnew
DOI: 10.5061/dryad.c459h
title: Data from: PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment

description: Modeling across site variation of the substitution process is increasingly
 recognized as important for obtaining more accurate phylogenetic
 reconstructions. Both finite and infinite mixture models have been
 proposed, and have been shown to significantly improve on classical
 single-matrix models. Compared to their finite counterparts, infinite
 mixtures have a greater expressivity. However, they are computationally
 more challenging. This has resulted in practical compromises in the design
 of infinite mixture models. In particular, a fast but simplified version
 of a Dirichlet process model over equilibirum frequency profiles
 implemented in PhyloBayes (Lartillot et al, 2007) has often been used in
 recent phylogenomics studies, while more refined model structures, more
 realistic and empirically more fit, have been practically out of reach. We
 introduce an Message Passing Interface (MPI) version of PhyloBayes,
 implementing the Dirichlet process mixture models as well as more
 classical empirical matrices and finite mixtures. The parallelization is
 made efficient thanks to the combination of two algorithmic strategies: a
 partial Gibbs sampling update of the tree topology, and the use of a
 truncated stick-breaking representation for the Dirichlet process prior.
 The implementation shows close to linear gains in computational speed for
 up to 64 cores, thus allowing faster phylogenetic reconstruction under
 complex mixture models. PhyloBayes MPI is freely available from our
 website www.phylobayes.org.
description: LartillotSB2013suppmatSupplementary information
DOI: 10.5061/dryad.s0d20
title: Data from: A continental scale trophic cascade from wolves through coyotes to foxes

description: Top-down processes, via the direct and indirect effects of interspecific
 competitive killing (no consumption of the kill) or intraguild predation
 (consumption of the kill), can potentially influence the spatial
 distribution of terrestrial predators, but few studies have demonstrated
 the phenomenon at a continental scale. For example, in North America, grey
 wolves (Canis lupus) are known to kill coyotes (Canis latrans), and
 coyotes, in turn, may kill foxes (Vulpes spp.), but the spatial effects of
 these competitive interactions at large scales are unknown. Here, we
 analyse fur return data across eight jurisdictions in North America to
 test whether the presence or absence of wolves has caused a continent-wide
 shift in coyote and red fox (Vulpes vulpes) density. Our results support
 the existence of a continental scale cascade whereby coyotes outnumber red
 foxes in areas where wolves have been extirpated by humans, whereas red
 foxes outnumber coyotes in areas where wolves are present. However, for a
 distance of up to 200 km on the edge of wolf distribution, there is a
 transition zone where the effects of top-down control are weakened,
 possibly due to the rapid dispersal and reinvasion capabilities of coyotes
 into areas where wolves are sporadically distributed or at low densities.
 Our results have implications for understanding how the restoration of
 wolf populations across North America could potentially affect
 co-occurring predators and prey. We conclude that large carnivores may
 need to occupy large continuous areas to facilitate among-carnivore
 cascades and that studies of small areas may not be indicative of the
 effects of top-down mesopredator control.
description: JAEDataArchiveNewsomeRipple
DOI: 10.5061/dryad.5cn37rr
title: Data from: Plant water use affects competition for nitrogen: why drought favors invasive species in California

description: Classic resource competition theory typically treats resource supply rates
 as independent; however, nutrient supplies can be affected by plants
 indirectly, with important consequences for model predictions. We
 demonstrate this general phenomenon by using a model in which competition
 for nitrogen is mediated by soil moisture, with competitive outcomes
 including coexistence and multiple stable states as well as competitive
 exclusion. In the model, soil moisture regulates nitrogen availability
 through soil moisture dependence of microbial processes, leaching, and
 plant uptake. By affecting water availability, plants also indirectly
 affect nitrogen availability and may therefore alter the competitive
 outcome. Exotic annual species from the Mediterranean have displaced much
 of the native perennial grasses in California. Nitrogen and water have
 been shown to be potentially limiting in this system. We parameterize the
 model for a Californian grassland and show that soil moisture–mediated
 competition for nitrogen can explain the annual species’ dominance in
 drier areas, with coexistence expected in wetter regions. These results
 are concordant with larger biogeographic patterns of grassland invasion in
 the Pacific states of the United States, in which annual grasses have
 invaded most of the hot, dry grasslands in California but perennial
 grasses dominate the moister prairies of northern California, Oregon, and
 Washington.
description: invade-exp-data-output-annual-seedsSeed data for grassesinvade-exp-data-output-full-plant-biomassPlant biomass datainvade-exp-data-output-taxa-table-biomassTaxa description tableinvade-exp-file-descriptionsFile descriptions
DOI: 10.5061/dryad.vr20p
title: Data from: Fear of feces? Trade-offs between disease risk and foraging drive animal activity around raccoon latrines

description: Fear of predation alters prey behavior, which can indirectly alter entire
 landscapes. A parasite-induced ecology of fear might also exist if animals
 avoid parasite-contaminated resources when infection costs outweigh
 foraging benefits. To investigate whether animals avoid parasite
 contaminated sites, and if such avoidance balances disease costs and
 foraging gains, we monitored animal behavior at raccoon latrines — sites
 that concentrate both seeds and pathogenic parasite eggs. Using wildlife
 cameras, we documented over 40 potentially susceptible vertebrate species
 in latrines and adjacent habitat. Latrine contact rates reflected
 background activity, diet preferences and disease risk. Disease-tolerant
 raccoons and rats displayed significant site attraction, while susceptible
 birds and small mammals avoided these high-risk sites. This suggests that
 parasites, like predators, might create a landscape of fear for vulnerable
 hosts. Such non-consumptive parasite effects could alter disease
 transmission, population dynamics, and even ecosystem structure.
description: Latrine_CamerasWe monitored animal activity at Coal Oil Point Reserve in Santa Barbara County, California using wildlife camera traps. We set camera traps (Moultrie models: MFH-DGS-M80XT, MCG-12594, MCG-12631) at raccoon latrines and latrine-adjacent habitat to examine wildlife contact rates with raccoon latrines and exposure risk to the raccoon parasite, Baylisascaris procyonis. We mapped latrines and then monitored animal behavior at latrines and paired latrine-adjacent sites from December 2012 through April 2015. We identified vertebrate animals in camera trap photos and recorded when animals were in contact with or foraging in latrines. The “latrine cameras” data set includes three sheets with (1) set data for each camera deployment, (2) animal observations from each camera, and (3) latrine habitat surveys. Field attributes for each sheet are described in the “Metadata ReadMe” file. Contact S. Weinstein for access to original camera trap photos.