cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.382k1
title: Data from: Earthworms affect plant growth and resistance against herbivores: a meta-analysis

description: 1. Subterranean detritivores such as earthworms can increase soil nutrient
 availability through their burrowing and casting activities. A number of
 recent studies have explored whether these changes caused by earthworms
 may in turn affect plant performance and resistance to herbivores, but no
 formal synthesis of this literature has been conducted to date. 2. We here
 formally tested for the effects of earthworms on plant growth, resistance
 and chemical defence against insect herbivores by performing a
 meta-analysis of the existing literature up to 2016. We also explored
 ecological factors that might explain among-studies variation in the
 magnitude of the earthworm effects on plant growth and resistance. 3. We
 found that earthworm presence increases plant growth (by 20 %) and
 nitrogen content (by 11 %). Overall, earthworms did not affect plant
 resistance against chewing herbivores (caterpillars, slugs and rootworms),
 and even led to a 22 % decrease in plant resistance against phloem-feeding
 herbivores (aphids). However, earthworm presence increased production of
 chemical defences by 31% when plants where attacked by cell-feeders
 (thrips), and resulted in an 81 % increase in resistance against thrips.
 The magnitude of earthworm effects was stronger when earthworm
 inoculations consisted of a mix of species and ecological types, and when
 densities of earthworms were high. 4. These results suggest that earthworm
 presence is an important factor underlying natural variation in plant
 defences against herbivores, and call for a better integration of the soil
 fauna in the studies of plant-herbivore interaction, both for applied and
 fundamental research.
description: Dataset and list of
 studies used in the meta-analysis (Appendix S1)Appendix
 S1.xlsx
DOI: 10.5061/dryad.p8066hd
title: Data from: Rethinking phylogenetic comparative methods

description: As a result of the process of descent with modification, closely related
 species tend to be similar to one another in a myriad different ways. In
 statistical terms, this means that traits measured on one species will not
 be independent of traits measured on others. Since their introduction in
 the 1980s, phylogenetic comparative methods (PCMs) have been framed as a
 solution to this problem. In this paper, we argue that this way of
 thinking about PCMs is deeply misleading. Not only has this sowed
 widespread confusion in the literature about what PCMs are doing but has
 led us to develop methods that are susceptible to the very thing we sought
 to build defenses against --- unreplicated evolutionary events. Through
 three Case Studies, we demonstrate that the susceptibility to singular
 events is indeed a recurring problem in comparative biology that links
 several seemingly unrelated controversies. In each Case Study we propose a
 potential solution to the problem. While the details of our proposed
 solutions differ, they share a common theme: unifying hypothesis testing
 with data-driven approaches (which we term ``phylogenetic natural
 history'') to disentangle the impact of singular evolutionary
 events from that of the factors we are investigating. More broadly, we
 argue that our field has, at times, been sloppy when weighing evidence in
 support of causal hypotheses. We suggest that one way to refine our
 inferences is to re-imagine phylogenies as probabilistic graphical models;
 adopting this way of thinking will help clarify precisely what we are
 testing and what evidence supports our claims.
description: Supplementary
 MethodsSupplementary methods,
 derivations and results for the manuscript "Rethinking phylogenetic
 comparative methods".pnh-ms_supplement.pdf
DOI: 10.15468/dl.wrvhaw
title: Occurrence Download

description: A dataset containing 268 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((105 20,170 20,170 70,105 70,105 20))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Salix nakamurana"
 ]
}

 The dataset includes 268 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000743-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.c1d1f8h
title: Data from: Diversification by host switching and dispersal shaped the diversity and distribution of avian malaria parasites in Amazonia

description: Understanding how pathogens and parasites diversify through time and space
 is fundamental to predicting emerging infectious diseases. Here, we use
 biogeographic, coevolutionary and phylogenetic analyses to describe the
 origin, diversity, and distribution of avian malaria parasites in the most
 diverse avifauna on Earth. We first performed phylogenetic analyses using
 the mitochondrial cytochrome b (cyt b) gene to determine relationships
 among parasite lineages. Then, we estimated divergence times and
 reconstructed ancestral areas to uncover how landscape evolution has
 shaped the diversification of Parahaemoproteus and Plasmodium in Amazonia.
 Finally, we assessed the coevolutionary patterns of diversification in
 this host–parasite system to determine how coevolution may have influenced
 the contemporary diversity of avian malaria parasites and their
 distribution among Amazonian birds. Biogeographic analysis of 324
 haemosporidian parasite lineages recovered from 4178 individual birds
 provided strong evidence that these pathogens readily disperse across
 major Amazonian rivers and this has occurred with increasing frequency
 over the last five million years. We also recovered many duplication
 events within areas of endemism in Amazonia. Cophylogenetic analyses of
 these blood parasites and their avian hosts support a diversification
 history dominated by host switching. The ability of avian malaria
 parasites to disperse geographically and shift among avian hosts has
 played a major role in their radiation and has shaped the current
 distribution and diversity of these parasites across Amazonia.
description: Amazonia
 Lineages_PlasmodiumLineages used in
 phylogeny reconstruction for Plasmodium.Amazonia
 Lineages_ParahaemoproteusLineages used in
 phylogeny reconstruction for Parahaemoproteus.
DOI: 10.5061/dryad.8q9v6mv
title: Data from: Seeing is believing? comparing plant-herbivore networks constructed by field co-occurrence and DNA barcoding methods for gaining insights into network structures

description: Plant-herbivore interaction networks provide information about community
 organization. Two methods are currently used to document pairwise
 interactions among plants and insect herbivores. One is the traditional
 method that collects plant-herbivore interaction data by field observation
 of insect occurrence on host plants. The other is the increasing
 application of newly developed molecular techniques based on DNA barcodes
 to the analysis of gut contents. The second method is more appealing
 because it documents realized interactions. To construct complete
 networks, each technique of network construction is urgent to be assessed.
 We addressed this question by comparing the effectiveness and reliability
 of the two methods in constructing plant-Lepidoptera larval network in a
 50 ha subtropical forest in China. Our results showed that the accuracy of
 diet identification by observation method increased with the number of
 observed insect occurrences on food plants. In contrast, the molecular
 method using three plant DNA markers were able to identify food residues
 for 35.6% larvae and correctly resolved 77.3% plant (diet) species.
 Network analysis showed molecular networks had three-fold more unique host
 plant species but fewer links than the traditional networks had. The
 molecular method detected plants that were not sampled by the traditional
 method, e.g., bamboos, bryophytes and lianas in the diets of insect
 herbivores. The two networks also possessed significantly different
 structural properties. Our study indicates the traditional observation of
 co-occurrence is inadequate, while molecular method can provide higher
 species resolution of ecological interactions.
description: Plant-Lepidoptera larval
 interaction matrix constructed by molecular methodIn this interaction
 matrix, 239 Lepidoptera species associated with 102 plant species/species
 complexes.catplspmat.mori.csvTaxonomic labels of 406 Lepidoptera speciesThis file describes Genbank accession ID and taxonomic label of each Lepidoptera species.Dryad_file1_Taxonomic labels of 406 Lepidoptera species.docxLink similarity and dissimilarity identified by molecular and observation methodLink similarities and dissimilarities for 795 Lepidoptera larvae identified by the molecular method and the traditional observation method, respectively.Dryad_file2_Link similarity and disimilarity identified by molecular and observation method.docx
DOI: 10.5061/dryad.9rv1h
title: Data from: Contrasting patterns of selection on the size and coloration of a female plumage ornament in common yellowthroats

description: Females often possess ornaments that appear smaller and duller than
 homologous traits in males. These ornaments may arise as nonfunctional
 by-products of sexual selection in males and cause negative viability or
 fecundity selection in females in proportion to the cost of their
 production and maintenance. Alternatively, female ornaments may function
 as signals of quality that are maintained by sexual or social selection.
 In a 4-year study of 83 female common yellowthroats (Geothlypis trichas)
 and their 222 young, we found strong viability and fecundity selection on
 the yellow bib, a carotenoid-based plumage ornament that is a target of
 sexual selection in males. Females with larger bibs were older, larger and
 more fecund than females with smaller bibs. However, bib size positively
 covaried with bib total brightness and carotenoid chroma, aspects of bib
 coloration that were under negative viability and fecundity selection.
 Females with more colourful bibs laid fewer eggs in their first clutch,
 were more likely to suffer total brood loss due to predation and were less
 likely to return to the study area. Selection against bib coloration
 limits the value of bib size as a quality indicator in females and may
 constrain the elaboration of bib attributes in males.
description: Common Yellowthroat
 Female Ornamentation Data SetFecundity, survival,
 standard morphometrics (body size), plumage ornamentation, and breeding
 experience for female Common Yellowthroats nesting in Saratoga County, New
 York, USA (2005-2008).Female Orn Data
 Set.xlsx
DOI: 10.5061/dryad.4572v
title: Data from: Climate-related environmental variation in a visual signalling device: the male and female dewlap in Anolis sagrei lizards

description: Animals communicate using a variety of signals that differ dramatically
 among and within species. The astonishing dewlap diversity in anoles has
 attracted considerable attention in this respect. Yet, the evolutionary
 processes behind it remain elusive and have mostly been explored for males
 only. Here, we considered Anolis sagrei males and females to study signal
 divergence among populations. First, we assessed the degree of variation
 in dewlap design (size, pattern, colour) and displays by comparing 17
 populations distributed across the Caribbean. Second, we assessed whether
 the observed dewlap diversity is associated to variation in
 climate-related environmental conditions. Results showed that populations
 differed in all dewlap characteristics, with the exception of display rate
 in females. We further found that males and females occurring in ‘xeric’
 environments had a higher proportion of solid dewlaps with higher
 UV-reflectance. In addition, lizards inhabiting ‘mesic’ environments had
 primarily marginal dewlaps showing high reflectance in red. For dewlap
 display, a correlation with environment was only observed in males. Our
 study provides evidence for a strong relationship between signal design
 and prevailing environmental conditions, which may result from
 differential selection on signal efficacy. Moreover, our study highlights
 the importance of including females when studying dewlaps in an
 evolutionary context.
description: Climatic and
 morphological data of Anolis sagrei populationsDescriptive statistics
 for dewlap measurements in male and female brown anoles, with additional
 information on climatic variables of the populations
 sampled.Dryad_data_JEB.pdf
DOI: 10.5061/dryad.8866
title: Data from: Brain plasticity over the metamorphic boundary: carry-over effect of larval environment on froglet brain development

description: Brain development shows high plasticity in response to environmental
 heterogeneity. However, it is unknown how environmental variation during
 development may affect brain architecture across life history switch
 points in species with complex life cycles. Previously, we showed that
 predation and competition affect brain development in common frog (Rana
 temporaria) tadpoles. Here, we studied if larval environment had
 carry-over effects in brains of metamorphs. Tadpoles grown at high density
 had large optic tecta at metamorphosis, while tadpoles grown under
 predation risk had small diencephala. We found that larval density had a
 carry-over effect on froglet optic tectum size, while the effect of larval
 predation risk had vanished by metamorphosis. We discuss the possibility
 that the observed changes may be adaptive, reflecting the needs of an
 organism in given environmental and developmental contexts.
description: metamorph
 brainsExperimental treatments
 included low and high larval density, crossed with the presence and
 absence of a caged predator. 100 tadpoles from each of the 12 clutches
 were pooled into a bucket and allocated to each tank (high density = 50
 tadpoles/tank; low density = 10 tadpoles/tank). In tanks with the predator
 treatments, one dragonfly larva (Aeshna sp.) was placed in a cylindrical
 cage (diameter 8 cm; height 21 cm) made of transparent plastic film with a
 double net bottom (mesh size 1.5 mm) and hung 6 cm over the tank bottom.
 This allowed tadpoles to receive both visual and chemical cues from the
 predator, while the predator was unable to actually prey on tadpoles. In
 the no-predator treatment, the cage was left empty. During the experiment,
 tadpoles relied on the initial resources provided (leaves, rabbit
 pellets), as well as subsequent algal growth. Each treatment combination
 was replicated eight times, resulting in a total of 32 experimental units.
 143 metamorphs (four to five per tank) were used for analyses. Formalin
 fixed metamorphs were weighed with a digital balance. After dissection,
 dorsal and right lateral views of brains were photographed with a digital
 camera connected to a dissecting microscope. We could only measure two
 dimensions for each brain part (length and width of telencephalon,
 diencephalon and optic tectum, and height and width of medulla oblongata)
 because some of the borders of the brain parts could not be identified
 accurately. Measurements were taken from digital photographs using tpsDig
 1.37 software, and were defined as the greatest distance enclosed by the
 given structure in the given direction. All brains were photographed and
 measured three times. Repeatability of different brain measurements was
 high (R = 0.71 – 0.96 [mean = 0.86]).ALL metamorph
 brains.xlsMetamorphs body
 weight143 metamorphs (four to
 five per tank) were used for analyses. Formalin fixed metamorphs were
 weighed with a digital balance.bodySizeWeightMetamorphs1.xls
DOI: 10.5061/dryad.96pr7
title: Data from: Thermal adaptation of cellular membranes in natural populations of Drosophila melanogaster

description: 1. Changes in temperature disrupt the fluidity of cellular membranes,
 which can negatively impact membrane integrity and cellular processes.
 Many ectotherms, including Drosophila melanogaster (Meigen), adjust the
 glycerophospholipid composition of their membranes to restore optimal
 fluidity when temperatures change, a type of trait plasticity termed
 homeoviscous adaptation. 2. Existing data suggest that plasticity in the
 relative abundances of the glycerophospholipids phosphatidylethanolamine
 (PE) and phosphatidylcholine (PC) underlies cellular adaptation to
 temporal variability in the thermal environment. For example, laboratory
 populations of D. melanogaster evolved in the presence of temporally
 variable temperatures have greater developmental plasticity of the ratio
 of PE to PC (PE/PC) and greater fecundity than do populations evolved at
 constant temperatures. 3. Here, we extend this work to natural populations
 of D. melanogaster by evaluating thermal plasticity of glycerophospholipid
 composition at different life stages, in genotypes isolated from Vermont,
 Indiana and North Carolina, USA. We also quantify the covariance between
 developmental and adult (reversible) plasticity, and between adult
 responses of the membrane to cool and warm thermal shifts. 4. As predicted
 by physiological models of homeoviscous adaptation, flies from all
 populations decrease PE/PC and the degree of lipid unsaturation in
 response to warm temperatures. Furthermore, these populations have
 diverged in their degree of membrane plasticity. Flies from the most
 variable thermal environment (Vermont, USA) decrease PE/PC to a greater
 extent than do other populations when developed at a warm temperature, a
 pattern that matches our previous observation in laboratory-evolved
 populations. We also find that developmental plasticity and adult
 plasticity of PE/PC covary across genotypes, but that adult responses to
 cool and warm thermal shifts do not. 5. When combined with our previous
 observations of laboratory-evolved populations, our findings implicate
 developmental plasticity of PE/PC as a mechanism of thermal adaptation in
 temporally variable environments. While little is known about the genetic
 bases of plastic responses to temperature, our observations suggest that
 both environmentally sensitive and environmentally specific alleles
 contribute to thermal adaptation of membranes, and that costs of
 plasticity may arise when the adult environment differs from that
 experienced during development.
description: Cooper_et_al_FE_dataSheet one contains the full data set from Cooper et al. Sheet two contains a key that matches the lipid identifiers (l1 to l23) to the actual lipids. Any questions about these data should be sent to Brandon S. Cooper (brandonscooper@gmail.com).
DOI: 10.5061/dryad.5h51p
title: Data from: Cannibalism as an interacting phenotype: pre-cannibalistic aggression is influenced by social partners in the endangered Socorro isopod (Thermosphaeroma thermophilum)

description: Models for the evolution of cannibalism highlight the importance of
 asymmetries between individuals in initiating cannibalistic attacks.
 Studies may include measures of body size but typically group individuals
 into size/age classes or compare populations. Such broad comparisons may
 obscure the details of interactions that ultimately determine how socially
 contingent characteristics evolve. We propose that understanding
 cannibalism is facilitated by using an interacting phenotypes perspective
 that includes the influences of the phenotype of a social partner on the
 behaviour of a focal individual and focuses on variation in individual
 pairwise interactions. We investigated how relative body size, a composite
 trait between a focal individual and its social partner, and the sex of
 the partners influenced precannibalistic aggression in the endangered
 Socorro isopod, Thermosphaeroma thermophilum. We also investigated whether
 differences in mating interest among males and females influenced
 cannibalism in mixed sex pairs. We studied these questions in three
 populations that differ markedly in range of body size and opportunities
 for interactions among individuals. We found that relative body size
 influences the probability of and latency to attack. We observed
 differences in the likelihood of and latency to attack based on both an
 individual's sex and the sex of its partner but found no evidence of
 sexual conflict. The instigation of precannibalistic aggression in these
 isopods is therefore a property of both an individual and its social
 partner. Our results suggest that interacting phenotype models would be
 improved by incorporating a new conditional ψ, which describes the
 strength of a social partner's influence on focal behaviour.
description: Body size and aggressive
 attack latency data for Socorro isopodsData collected in the
 field in May 2009 in Socorro, NM. Data archived in Excel, JMP 9.0.2 was
 used to create principle component measure of body size and transform
 data.dryad
 data sharing.xlsx
DOI: 10.5061/dryad.778hc71
title: Data from: Overall seed dispersal effectiveness is lower in endemic Trillium species than in their widespread congeners

description: PREMISE OF THE STUDY: Comparing ecological attributes of endemic species
 with related, widespread species can reveal differences accounting for
 rarity. Forests of the southeastern US are home to many range-restricted
 endemic and widespread species of Trillium, a genus of ant-dispersed
 herbs. Evidence suggests that aspects of seed-related life history stages
 are often correlated with plant rarity, but few studies have tested
 whether the process of seed dispersal differs for endemic and widespread
 species. To address this question, we compare aspects of seed dispersal
 effectiveness (SDE) for three sympatric widespread-endemic Trillium
 species pairs. METHODS: We observed ant seed dispersal for Trillium
 species pairs at eight sites, recorded numbers of seeds dispersed and
 dispersal distances, and described disperser interactions. To test
 disperser preference, we presented seeds of each pair to captive colonies
 of Aphaenogaster picea, a keystone disperser. Seeds were assigned scores
 based on worker behavior, and we recorded proportions of seeds dispersed
 after 60 minutes and 24 hours. KEY RESULTS: Field observations yielded
 some significant within-pair differences. Ants dispersed more seeds of
 widespread species for all pairs, although dispersal distances did not
 differ. In laboratory experiments, after 24 hours, ants dispersed more
 seeds of widespread species into nests. CONCLUSIONS: Endemic Trillium
 species exhibited lower overall SDE than their widespread congeners. These
 findings add to the list of ecological and demographic challenges that
 face endemic plants when compared to common congeners. Lower SDE may
 negatively impact reproductive rates and the colonization of new habitats,
 which may contribute to patterns of endemism. If you would like your
 personal information to be removed from the database, please contact the
 publication office.
description: The master data file for
 AJB-D-18-00217R1This is a .xlsx file
 containing the raw and metadata from our study. The first sheet
 (AJB-D-18-00217R1_Field_2016_raw) contains field observations of ant-seed
 dispersal distances and rates for endemic-widespread Trillium pairs across
 9 study sites. The second sheet (AJB-D-18-00217R1_Cafeteria_raw) contains
 data from laboratory cafeteria experiments of ant preference. The third
 sheet (Cafeteria_metadata) contains metadata on the cafeteria raw data.
 The fourth sheet (Field_metadata) contains metadata on the field raw
 data.AJB-D-18-00217R1_MasterFile.xlsx