cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2bvq83bmd
title: Leaf-cutting ants negatively impact the regeneration of the Caatinga dry forest across abandoned pastures

description: The mechanisms affecting forest regeneration in human-modified landscapes
 are attracting increasing attention as tropical forests have been
 recognized as key habitats for biodiversity conservation, provision of
 ecosystem services and human well-being. Here we investigate the effect of
 the leaf-cutting ants (LCA) Atta opaciceps on regenerating plant
 assemblages in Caatinga dry forest. Our study encompassed 15 Atta
 opaciceps colonies located in landscape patches with a gradient of forest
 cover from 8.7% to 87.8%, where we monitored regenerating individuals
 (seedlings and saplings of woody and herbaceous plants) in different
 habitats (nests, foraging areas and control areas) over one year. We
 recorded 2977 regenerating plant individuals, distributed among 55 species
 from 23 families. Herbaceous plants represented 82.1% and 58.2% of the
 total number of individuals and species, respectively. Species richness of
 both the whole and herbaceous plant assemblages increased along the forest
 cover gradient, but without difference between the habitats. Total plant
 abundance was highest in control areas followed by foraging areas and
 nests and this pattern held for both woody and herbaceous plants. Although
 forest cover did not influence the abundance of herbaceous plants and the
 whole plant assemblage, it positively affects woody plant abundance across
 control areas. Forest cover and habitat changed species composition of
 both the entire regenerating and the herbaceous assemblages. These results
 together indicate that LCA negatively impact regenerating plant
 assemblages, particularly in those sites with increased forest cover. As
 LCA proliferate in human modified landscapes, they may prevent plant
 regeneration of disturbed areas.
DOI: 10.5061/dryad.866t1g1n2
title: False holes as camouflage

description: Long noted by naturalists, leaf mimicry provides some of the most
 impressive examples of camouflage through masquerade. Many species of
 leaf-mimicking Lepidoptera also sport wing markings that closely resemble
 irregularly shaped holes caused by decay or insect damage. Despite
 proposals that such markings can either enhance resemblance to damaged
 leaves or act to disrupt surface appearance through false depth cues, to
 our knowledge, no attempt has been made to establish exactly how these
 markings function, or even whether they confer a survival benefit to prey.
 Here, in two field experiments using artificial butterfly-like targets, we
 show that false hole markings provide significant survival benefits
 against avian predation. Furthermore, in a computer-based visual search
 experiment, we demonstrate that detection of such targets by humans is
 impeded in a similar fashion. Equally contrasting light marks do not have
 the same effect; indeed, they lead to increased detection. We conclude
 that the mechanism is the disruption of the otherwise homogeneous wing
 surface (surface disruptive camouflage) and that, by resembling the holes
 sometimes found in real leaves, the disruptive benefits are not offset by
 conspicuousness costs.
DOI: 10.5061/dryad.9kd51c5d6
title: Was the Devonian placoderm Titanichthys a suspension-feeder?

description: Large nektonic suspension-feeders have evolved multiple times. The
 apparent trend among apex predators for some evolving into feeding on
 small zooplankton is of interest for understanding the associated shifts
 in anatomy and behaviour while the spatial and temporal distribution gives
 clues to an inherent relationship with ocean primary productivity and how
 past and future perturbations to these may impact on the different tiers
 of the food web. The evolution of large nektonic suspension-feeders -
 'gentle giants’ - occurred 4 times among chondrichthyan fishes (e.g.
 whale sharks, basking sharks and manta rays), as well as in baleen whales
 (mysticetes), the Mesozoic pachycormid fishes and at least twice in
 radiodontan stem group arthropods (Anomalocaridids) during the Cambrian
 Explosion. The Late Devonian placoderm Titanichthys has tentatively been
 considered to have been a megaplanktivore, primarily due to its gigantic
 size and narrow, edentulous jaws while no suspension-feeding apparatus
 have ever been reported. Here the potential for microphagy and other
 feeding behaviours in Titanichthys is assessed via a comparative study of
 jaw mechanics in Titanichthys and other placoderms with presumably
 differing feeding habits (macrophagy and durophagy). Finite element models
 of the lower jaws of Titanichthys termieri in comparison to Dunkleosteus
 terrelli and Tafilalichthys lavocati reveal considerably less resistance
 to von Mises stress in this taxon. Comparisons with a selection of
 large-bodied extant taxa of similar ecological diversity reveals similar
 disparities in jaw stress resistance. Our results therefore conform to the
 hypothesis that Titanichthys was a suspension-feeder with jaws ill-suited
 for biting and crushing but well suited for gaping ram feeding.
DOI: 10.5061/dryad.n2z34tmsv
title: Data from: Intraspecific and biogeographic variation in foliar fungal communities and pathogen damage of native and invasive Phragmites australis

description: Aim Recent research has highlighted that the relationship between species
 interactions and latitude can differ between native and invasive plant
 taxa, generating biogeographical heterogeneity in community resistance to
 plant invasions. In the first study with foliar pathogens, we tested
 whether co-occurring native and invasive lineages of common reed
 (Phragmites australis) exhibit nonparallel latitudinal gradients in foliar
 fungi communities, pathogen susceptibility and damage, and whether these
 biogeographic patterns can influence invasion success. Location North
 America. Time period 2015-2017. Major taxa studied Perennial grass
 Phragmites australis. Methods We surveyed 35 P. australis field
 populations, spanning 17° latitude and comprising four phylogeographic
 lineages, including one endemic to North America and one invasive from
 Europe. For each population, we quantified percent leaf pathogen damage
 and cultured fungi from diseased leaves, that we identified using
 molecular tools. To assess whether latitudinal gradients in pathogen
 damage were genetically-based, we inoculated plants from 73 populations
 with four putative pathogens in a complementary common garden experiment,
 and measured P. australis susceptibility (i.e., diseased leaf area).
 Results We isolated 84 foliar fungi morphospecies. Phragmites australis
 lineage influenced fungal community composition but not diversity. Despite
 the invasive European P. australis lineage being the least susceptible to
 three of the four pathogens tested in the common garden experiment,
 pathogen damage in the field was similar between native and invasive
 lineages, providing no evidence that release from foliar pathogens
 contributes to invasion success. Genetically-based latitudinal gradients
 in pathogen susceptibility observed in the common garden were
 isolate-specific and obscured by local environmental conditions in the
 field, where pathogen damage was threefold higher for northern than
 southern populations, regardless of lineage. Main conclusions Our results
 highlight that host plant lineage and genetically-based biogeographic
 gradients strongly influence foliar fungi communities and pathogen
 susceptibility, but do not translate to pathogen damage patterns observed
 in the field.
description: Methods provided in corresponding paper.
description: Please contact corresponding author if further information is
 required.
DOI: 10.6078/d1pq5m
title: Data from: Exploring density and frequency dependent interactions experimentally: an R program for generating hexagonal fan designs.

description: Species interactions and diversity are strongly impacted by local
 processes, with both the density of a focal species and its frequency in
 the community having an impact on its growth, survival, and fecundity.
 Yet, studies that attempt to control for variation in both frequency and
 density have traditionally required a large number of
 replicates.  Hexagonal fan designs can include a range of both
 densities and frequencies in a single plot, providing large economies in
 space and material for studying local interactions such as competition and
 disease transmission. However, in practice such experiments can be
 difficult to plan and implement. This study presents an R program whereby
 the user can rapidly view a variety of designs and determine the
 configurations that work best with their space and material constraints.
 Simple instructions for implementing the fan in any design setting are
 also provided. We illustrate the implementation of a simple form of the
 hexagonal fan design in a field experiment to assess the impact of host
 density on pollinator movement and disease transmission.
description: Healthy host plants <em>Silene latifolia</em> were
 grown from seed under greenhouse conditions, and diseased plants were
 produced by inoculating the pathogen onto plants at the seedling stage.
 Pathogen transmission was assessed under field conditions in experimental
 hexagonal fan arrays containing healthy and diseased flowers, cut from
 adult flowering plants and supported individually in 12cm tall plastic
 floral tubes that were wedged in the ground. The <i>hex()</i>
 function (https://github.com/crozins/Hexagonalfan) was used to design a
 hexagonal fan array that spanned a wide range of host densities, but which
 was of a sufficient size to fit into open space available for the study.
 For each replicate of the hexagonal fan array, 34 healthy flowers were
 included in an expanding series of eight hexagons with a diseased flower
 in the center of each. Distances from healthy to diseased flowers ranged
 from 0.25 to 9.01m. In order to check whether variation in pathogen
 movement with plant density may be a consequence of the connected nature
 of the hexagonal fan array, spore transmission was also assessed in a
 single run of regular, non-expanding designs, where different densities
 were fixed as arrays of regularly-shaped hexagon. In three separate
 arrays, interplant spacing was set equal to the most-dense, middle, and
 least-dense thirds of the hexagonal fan array. Each array consisted of a
 line of three contiguous hexagons with a diseased flower in the center.
 The hexagons were separated by at least 20m and placed in the same field
 but on different days.
DOI: 10.5061/dryad.j0zpc869v
title: Assessing zinc tolerance in two butterfly species: consequences for conservation in polluted environments

description: 1. Zinc is a widespread pollutant released from industrial combustion,
 auto- mobile residue, and mining. Zinc accumulates in soils and mobilises
 into plant tissue where it may be consumed to potentially toxic levels by
 leaf feeding insects, including developing pollinators. 2. While zinc
 tolerance thresholds have been previously assessed in insect pollinators,
 most observations are limited to model organisms and pest species. We lack
 understand- ing of zinc tolerance in insects of conservation concern. 3.
 We assess dietary zinc tolerance of developing caterpillars from wild
 populations of the monarch butterfly (Danaus plexippus), a species of
 conservation concern, whose caterpillars are commonly exposed to elevated
 dietary zinc exposure in milkweed plants along roadsides. We contrast
 monarch zinc tolerance with that of cabbage white butterfly caterpillars
 (Pieris rapae), a non-native pest species. Tolerance was assessed by
 rearing caterpillars on artificial diets containing varying levels of
 zinc. 4. Zinc reduced monarch survival at levels as low as 344 mg kg−1 but
 positively impacted cabbage white survival at 227 and 738 mg kg−1. Cabbage
 whites also displayed prolonged development time, smaller adult body size,
 and slower growth rate, consistent with the possibility that zinc
 tolerance had fitness costs. 5. Our results support previous observations
 that heavy metal tolerance varies between species and highlight the
 importance of broadening our understanding of toler- ance to insect
 species of conservation concern before drawing general conclusions about
 insect susceptibility to heavy metal pollution. Nonetheless, our results
 suggest that zinc pollution alone is unlikely a risk in developing
 roadside habitat for monarch butterflies.
description: Empirical data.
DOI: 10.15468/dl.5rrqya
title: Occurrence Download

description: A dataset containing 136 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Adesmia miraflorensis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 136 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002220-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.1jwstqjrd
title: Weekly reported measles cases and code

description: The nigerm folder includes the data on reported measles cases and the
 yearly estimates of the population at district level in the subfolder
 "data" the code used for the analysis presented as a R package.
 The resolution of the weekly reported measles cases has been reduced. The
 data shared here are at the department level instead of the district level
 because the original data are not publicly available. The package does not
 include the additional datasets already freely available. They remain
 available using the URLs provided in the manuscript.
DOI: 10.7291/d1w093
title: How climate impacts the composition of wolf killed-elk in northern Yellowstone National Park

description: 1. While the functional response of predators is commonly measured, recent
 work has revealed that the age and sex composition of prey killed is often
 a better predictor of prey population dynamics because the reproductive
 value of adult females is usually higher than that of males or juveniles.
 2. Climate is often an important mediating factor in determining the
 composition of predator kills, but we currently lack a mechanistic
 understanding of how the multiple facets of climate interact with prey
 abundance and demography to influence the composition of predator kills.
 3. Over 20 winters, we monitored 17 wolf packs in Yellowstone National
 Park and recorded the sex, age, and nutritional condition of kills of
 their dominant prey – elk – in both early and late winter periods when elk
 are in relatively good and relatively poor condition, respectively. 4.
 Nutritional condition (as indicated by percent marrow fat) of wolf-killed
 elk varied markedly with summer plant productivity, snow water equivalent
 (SWE) and winter period. Moreover, marrow was poorer for wolf-killed bulls
 and especially for calves than it was for cows. 5. Wolf prey composition
 was influenced by a complex set of climatic and endogenous variables. In
 early winter, poor plant growth in either year t or t-1, or relatively low
 elk abundance, increased the odds of wolves killing bulls relative to
 cows. Calves were most likely to get killed when elk abundance was high
 and when the forage productivity they experienced in utero was poor. In
 late winter, low SWE and a relatively large elk population increased the
 odds of wolves killing calves relative to cows, whereas low SWE and poor
 vegetation productivity one year prior together increased the likelihood
 of wolves killing a bull instead of a cow. 6. Since climate has a strong
 influence on whether wolves prey on cows (who, depending on their age, are
 the key reproductive component of the population) or lower reproductive
 value calves and bulls, our results suggest that climate can drive wolf
 predation to be more or less additive from year to year.
DOI: 10.5061/dryad.9s4mw6mc6
title: Impacts of environmental heterogeneity on natural selection in a wild bird population

description: Natural selection has been studied for several decades, resulting in the
 computation of thousands of selection estimates. Although the importance
 of environmental conditions on selection has often been suggested,
 published estimates rarely take into account the effects of environmental
 heterogeneity on selection patterns. Here, we estimated linear and
 non‐linear viability selection gradients on morphological traits of 12
 days‐old nestlings in a wild population of tree swallows (Tachycineta
 bicolor) across a large‐scale heterogeneous study system in southern
 Québec, Canada. We assessed the environmental drivers of nestling survival
 and evaluated their effects on strength and direction of selection
 gradients. Separate analyses of environmental variables showed that high
 temperatures and heavy rainfall caused stronger positive linear selection
 on morphological traits. Weaker linear selection was also measured in more
 extensively cultivated areas. Both strength and shape of non‐linear
 quadratic and correlational components of selection were modified by
 environmental variables. Considering all environmental variables revealed
 that precipitation since hatching affected patterns of linear selection on
 traits, while temperatures since hatching shaped nonlinear selection
 patterns. Our study underlines the importance of quantifying linear and
 non‐linear natural selection under various environmental conditions and
 how the evolutionary response of traits may be affected by ongoing
 human‐induced environmental changes.
DOI: 10.5066/p1yrcp97
title: Bsal Not Detected After Pet Release in Western Massachusetts Pond

description: These data have been collected by the United States Geological Survey’s Northeast Amphibian Research and Monitoring Initiative (USGS NEARMI) scientists. We collected these data to examine if Bsal was introduced to a site where there was a known pet release in Western, Massachusetts.
DOI: 10.5061/dryad.0vt4b8gvt
title: Ancient hybridization with an unknown population facilitated high altitude adaptation of canids

description: Genetic introgression provides material for adaptive evolution, but also
 confounds our understanding of evolutionary history. This is particularly
 true for canids, a species complex in which genome sequencing and analysis
 has revealed a complex history of admixture and introgression. Here, we
 use newly sequenced genomes of high-altitude Tibetan and Himalayan wolves
 to explore the evolutionary history and adaptation of this group. We find
 that Tibetan and Himalayan wolves are closely related to each other, and
 that approximately 39-49% of their nuclear genome are derived from an
 as-yet unrecognized wolf-like lineage that is deeply diverged from living
 Holarctic wolves and dogs. The EPAS1 haplotype, which is present at high
 frequencies in Tibetan dog breeds and wolves and confers an adaptive
 advantage to animals living at high altitudes, was probably derived from
 this ancient lineage. Our study suggests the complexity of canid evolution
 and demonstrates how admixture and introgression shape the evolutionary
 trajectories and adaptation of species.
description: We <i>de novo</i> assembled mitochondrial genomes for
 HAW using NOVOPlasty2.7.2 (Dierckxsens, et al. 2017) using with dog mitochondrial genome (GenBank accession: NC_002008.4 ) as a seed sequence. K-mer of 31 was used to perform the assembly independently. These mitogenomes and those downloaded from NCBI-Genbank are aligned together using MUSCLE. Genotypes for dog and wolf in this study were got using BWA-GATK pipeline.
description: In this dataset, genotype with more than 10% missing rate
 among these samples was removed. Mitochondrial genomes
 are partially assembled and control regions contain missing
 bases.
DOI: 10.5061/dryad.jm63xsj6w
title: Land use impacts poison frog chemical defenses through changes in leaf litter ant communities

description: Much of the world’s biodiversity is held within tropical rainforests,
 which are increasingly fragmented by agricultural practices. In these
 threatened landscapes, there are many organisms that acquire chemical
 defenses from their diet and are therefore intimately connected with their
 local food webs. Poison frogs (Family Dendrobatidae) are one such example,
 as they acquire alkaloid-based chemical defenses from their diet of leaf
 litter ants and mites. It is currently unknown how habitat fragmentation
 impacts chemical defense across trophic levels, from arthropods to frogs.
 We examined the chemical defenses and diets of the Diablito poison frog
 (Oophaga sylvatica), and the diversity of their leaf litter ant
 communities in secondary forest and reclaimed cattle pasture. Notably,
 this research was performed in collaboration with two high school science
 classrooms. We found that the leaf litter of forest and pasture frog
 habitats differed significantly in ant community structure. We also found
 that forest and pasture frogs differed significantly in diet and alkaloid
 profiles, where forest frogs contained more of specific alkaloids and ate
 more ants in both number and volume. Finally, ant species composition of
 frog diets resembled the surrounding leaf litter, but diets were less
 variable. This suggests that frogs tend to consume particular ant species
 within each habitat. To better understand how ants contribute to the
 alkaloid chemical profiles of frogs, we chemically profiled several ant
 species and found some alkaloids to be common across many ant species
 while others are restricted to a few species. Our experiments are the
 first to link anthropogenic land use changes to dendrobatid poison frog
 chemical defenses through variation in leaf litter communities, which has
 implications for conservation management of these threatened amphibians.
description: frog alkaloids: alkaloid extraction described in manuscript and
 GC/MS ant alkaloids: alkaloid extraction described in
 manuscript and combination of GC/MS and LC/MS frog
 stomach contents: CO1 sequenced individual arthropods using Sanger
 sequencing, no pooling of specimens  
description: Please see the README file