cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6wwpzgmtr
title: Learning‐induced switching costs in a parasitoid can maintain diversity of host aphid phenotypes although biocontrol is destabilized under abiotic stress

description: Aphid populations frequently include phenotypes that are resistant to
 parasitism by hymenopterous parasitoid wasps, which is often attributed to
 the presence of ‘protective’ facultative endosymbionts residing in aphid
 tissues, particularly Hamiltonella defensa. In field conditions,
 under parasitoid pressure, the observed coexistence of aphids with and
 without protective symbionts cannot be explained by their difference in
 fitness alone. Using the cereal aphid Rhopalosiphum padi as a
 model, we propose an alternative mechanism whereby parasitoids are more
 efficient at finding common phenotypes of aphid and experience a fitness
 cost when switching to the less common phenotype. We construct a model
 based on delay differential equations and parameterise and validate the
 model with values within the ranges obtained from experimental studies. We
 then use it to explore possible effects on system dynamics under
 conditions of environmental stress, using our existing data on the effects
 of drought stress in crops as an example. We show the ‘switching penalty’
 incurred by parasitoids leads to stable coexistence of aphids with and
 without H. defensa and provides a potential mechanism for
 maintaining phenotypic diversity amongst host organisms. We show that
 drought-induced reduction in aphid development time has little impact.
 However, greater reduction in fecundity on droughted plants of
 symbiont-protected aphids can cause insect population cycles when the
 system would be stable in the absence of drought stress. The stabilising
 effect of the increased efficiency in dealing with more commonly
 encountered host phenotypes is applicable to a broad range of
 consumer-resource systems and could explain stable coexistence in
 competitive environments. The loss of stable coexistence when drought has
 different effects on the competing aphid phenotypes highlights the
 importance of scenario testing when considering biocontrol for pest
 management.
description: This file contains R code for the delay differential equation
 models described in the manuscript 'Learning-induced switching costs
 in a parasitoid can maintain diversity of host aphid phenotypes although
 biocontrol is destabilised under abiotic stress'. In addition the
 code used to generate the figures has been included in plotfunctions.r
 file The single stage model source code is contained in
 SingleStageModelCode.r and associated parameters in
 SingleStageParameters.R, the stage-structured model code is contained in
 StageStructureModelCode.r and associated parameters are in
 StageStructureParameters.R.
description: The Model utilises the StagePop R package and this should be
 pre-installed. Source code and parameter files should
 be stored in the same folder Default output for
 stagePop is in timesteps which are the time for 1 unit of reproduction -
 this can be converted back into the original measure of time by dividing
 by the reproductive rate so "mod$time/r"
DOI: 10.5061/dryad.0cfxpnvxx
title: The geographic distribution of the imperiled Barrens Darter, Etheostoma forbesi, and threats of hybridization with the closely related Fringed Darter, Etheostoma crossopterum.

description: The Barrens Darter, Etheostoma forbesi, is one of the most
 geographically restricted freshwater fish species in North America, with a
 distribution limited to headwater portions of nine streams in the western
 part of the upper Caney Fork, a tributary of the Cumberland River in
 Tennessee. This limited geographic distribution makes E.
 forbesi especially vulnerable to potential threats posed by human
 alterations to rivers and streams, and the risk of ecological competition
 and introgressive hybridization with the closely related Fringed
 Darter, E. crossopterum. Museum collection records and targeted
 surveys conducted since its description suggest that E.
 forbesi’s present-day range does not include several streams it
 previously inhabited– some as recently as 15 years ago. We investigate the
 geographic distribution and variation in meristic traits of
 both E. forbesi and E. crossopterum in
 the upper Caney Fork system through the examination of all available
 museum vouchers, and assess phylogeographic patterns among populations
 using mitochondrial DNA sequence data. We report a newly discovered
 population of E. forbesi from the upper Collins River,
 and present evidence that E. crossopterumhas
 displaced E. forbesi in the Hickory Creek system and Mud
 Creek in the upper Barren Fork River system. Meristic differences between
 the species are slight, but and fin ray counts can provide a visual means
 of identifying species and potential hybrid individuals. Analysis of mtDNA
 variation indicates gene flow between E.
 forbesi and E. crossopterum. Our results suggest that
 sympatry of the two species in the western upper Caney Fork system is a
 potential threat to the persistence of E. forbesi.
description: Meristic data description:  Meristic data
 tables for both Etheostoma forbesi and Etheostoma crossopterum are
 attached ("E_forbesi_meristic_data.csv" and
 "E_crossopterum_meristic_data.csv"). Data are presented as one
 row of data representing each individual. Museum identification numbers
 for each individual examined are listed in column 1 of each table. The
 locality information for each museum lot number from column 1 of the
 meristic data tables can be found in the corresponding locality data files
 ("E_forbesi_meristic_locality_data.csv",
 "E_crossopterum_meristic_locality_data.csv").
 Genetic data description: Supplementary
 Materials A and B (files "Supplementary_Material_A.csv" and
 "Supplementary_Material_B.csv") are tables listing the Genbank
 accession numbers, tissue and whole-body museum accession numbers, and
 geographic collection locality information for each DNA sequence used in
 this study.  Alignments of mitochondrial cytb and
 nuclear S7 sequence data are provided in nexus file format (files:
 "spottail_cytb_alignment.nex" and
 "spottail_s7_alignment.nex").
DOI: 10.5061/dryad.gf1vhhmk7
title: Multiscale drivers of phytoplankton communities in north-temperate lakes

description: Multiple factors operating across different spatial and temporal scales
 affect beta-diversity—the variation in community composition among sites.
 Disentangling the relative influence of co-occurring ecological drivers
 over broad biogeographic gradients and time is critical to developing
 mechanistic understandings of community responses to natural environmental
 heterogeneity as well as predicting the effects of anthropogenic change.
 We partitioned taxonomic beta-diversity in phytoplankton communities
 across 75 north-temperate lakes and reservoirs in Alberta, Canada, using
 data-driven, spatially-constrained null models to differentiate between
 spatially-structured, spatially-independent, and spuriously correlated
 associations with a suite of biologically relevant environmental
 variables. Beta-diversity was largely independent of space, indicating
 spatial processes (e.g. dispersal limitation) likely play a minor role in
 structuring freshwater phytoplankton communities at the regional scale.
 Our findings also identified seasonal differences in the importance of
 environmental factors, suggesting a general shift towards greater
 relevance of local, in-lake (e.g. nutrients and Secchi depth) over
 regional, atmospheric and catchment-level (e.g. monthly solar radiation
 and grassland coverage) drivers as the open-water growing season
 progressed. Several local and regional variables explained taxonomic
 variation jointly, reflecting climatic and land-use linkages (e.g. air
 temperature and water column stability or pastureland and nutrient
 enrichment) that underscore the importance of understanding how
 phytoplankton communities integrate—and may serve as sentinels of—broader
 anthropogenic changes. We also discovered similar community composition in
 natural and constructed water bodies, demonstrating rapid filtering of
 regional species to match local environmental conditions in reservoirs
 comparable to those in natural habitats. Finally, certain factors related
 to human-footprint (e.g. cropland development) explained the composition
 of bloom-forming and/or toxic cyanobacteria more than the overall
 phytoplankton community, suggesting their heightened importance to
 integrated watershed management.
DOI: 10.15468/dl.4p8asu
title: Occurrence Download

description: A dataset containing 25 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "PublishingOrg is one of (c2ecae57-6701-485e-9ebd-5f87b2945cb2, f9b67ad0-9c9b-11d9-b9db-b8a03c50a862, 6ea87510-0561-11d8-b851-b8a03c50a862)",
 "TaxonKey is Melanoplus chattahoochee",
 "Year 1900-2026"
 ]
}

 The dataset includes 25 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002151-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7sqv9s4pg
title: Harbour porpoise (Phocoena phocoena) reaction to a 3D seismic airgun survey in the North Sea

description: The most common cetacean in the North Sea is the harbor porpoise (Phocoena
 phocoena). Underwater noise is increasingly recognized as a source of
 impact on the marine environment and seismic airguns were one of the first
 man-made high intensity sound source to receive attention with respect to
 potential impact on marine mammals. In this study, we investigate the
 effects of a 3D seismic survey on harbor porpoise echolocation
 activity in the Danish sector of the North Sea. This was achieved by
 deploying porpoise click detectors (C-PODs) and sound recorders (SM2M and
 SM3M) both inside and adjacent to the seismic survey area, before, during
 and after the survey over a total duration of 9 months. Three echolocation
 parameters were analyzed: number of clicks per minute, minutes with
 porpoise echolocation click trains and feeding buzz frequency in relation
 to all minutes with click trains. Decreases in echolocation signals were
 detected up to 8–12 km from the active airguns, which may indicate
 temporary displacement of porpoises or a change in porpoise echolocation
 behavior. However, no general displacement of harbor porpoises away from
 the seismic survey area could be detected when comparing to reference
 stations 15 km away from any seismic activity. Our results add to the
 understanding that underwater noise has the potential to affect
 temporarily foraging efficiency in porpoises. While the effect of seismic
 surveys on harbor porpoise behavior was smaller than what has been found
 for pile-driving, the cumulative effect of anthropogenic impacts could be
 assessed by evaluation of potential population level consequences.
DOI: 10.5061/dryad.jsxksn05s
title: Life history predicts flight muscle phenotype and function in birds

description: 1. Functional traits are the essential phenotypes that underlie an
 organism’s life history and ecology. Although biologists have long
 recognized that intraspecific variation is consequential to an animals’
 ecology, studies of functional variation are often restricted to
 species-level comparisons, ignoring critical variation within species. In
 birds, interspecific comparisons have been foundational in connecting
 flight muscle phenotypes to species-level ecology, but intraspecific
 variation has remained largely unexplored. 2. We asked how age- and
 sex-dependent demands on flight muscle function are reconciled in birds.
 The flight muscle is an essential multifunctional organ, mediating a large
 range of functions associated with powered flight and thermoregulation.
 These functions must be balanced over an individual’s lifetime. 3. We
 leveraged within- and between-species comparisons in a clade of small
 passerines (Tarsiger bush-robins) from the eastern edge of the
 Qinghai-Tibet Plateau. We integrated measurements of flight muscle
 physiology, morphology, behavior, phenology, and environmental data,
 analyzing trait data within a context of three widespread, adaptive
 life-history strategies – sexual dichromatism, age and sex-structured
 migration, and delayed plumage maturation. This approach provides a
 framework of the selective forces that shape functional variation within
 and between species. 4. We found more variation in flight muscle traits
 within species than has been previously described between species of birds
 under 20 g. This variation was associated with the discovery of mixed
 muscle fiber types (i.e. both fast glycolytic and fast oxidative fibers),
 which differ markedly in their physiological and functional attributes.
 This result is surprising given that the flight muscles of small birds are
 generally thought to contain only fast oxidative fibers, suggesting a
 novel ecological context for glycolytic muscle fibers in small birds.
 Within each species, flight muscle phenotypes varied by age and sex,
 reflecting the functional demands at different life-history stages and the
 pressures that individuals face as a result of their multi-class identity
 (i.e. species, age, and sex). 5. Our findings reveal new links between
 avian physiology, ecology, behavior, and life history, while demonstrating
 the importance of demographic-dependent selection in shaping functional
 phenotypic variation.
DOI: 10.5061/dryad.cz8w9gj0c
title: Continent-wide effects of urbanization on bird and mammal genetic diversity

description: Urbanization and associated environmental changes are causing global
 declines in vertebrate populations. In general, population declines of the
 magnitudes now detected should lead to reduced effective population sizes
 for animals living in proximity to humans and disturbed lands. This is
 cause for concern because effective population sizes set the rate of
 genetic diversity loss due to genetic drift, the rate of increase in
 inbreeding, and the efficiency with which selection can act on beneficial
 alleles. We predicted that the effects of urbanization should decrease
 effective population size and genetic diversity, and increase
 population-level genetic differentiation. To test for such patterns, we
 repurposed and reanalyzed publicly archived genetic data sets for North
 American birds and mammals. After filtering, we had usable raw genotype
 data from 85 studies and 41,023 individuals, sampled from 1,008 locations
 spanning 41 mammal and 25 bird species. We used census-based urban-rural
 designations, human population density, and the Human Footprint Index as
 measures of urbanization and habitat disturbance. As predicted, mammals
 sampled in more disturbed environments had lower effective population
 sizes and genetic diversity, and were more genetically differentiated from
 those in more natural environments. There were no consistent relationships
 detectable for birds. This suggests that, in general, mammal populations
 living near humans may have less capacity to respond adaptively to further
 environmental changes, and be more likely to suffer from effects of
 inbreeding.
description: <strong>Schmidt_etal_README.txt</strong>
 <strong>Data_S1.xlsx</strong> List
 of all results from systematic searches. 
 <strong>synthesized_geneticdiversity_dryad.csv</strong> Raw data used for analyses (gene diversity, allelic richness, effective population size, population-specific FST). Note coordinates for sensitive sites were removed.
DOI: 10.5061/dryad.bk3j9kd74
title: Predation and competition induce variable organ size tradeoffs in larval anurans

description: Inducible-defenses allow organisms that live in variable environments to
 invest energy into defense when necessary.  These responses are
 common in aquatic organisms and are particularly notable in larval
 anurans, which tend to develop deeper tails under sit-and-wait
 macroinvertebrate predation threat.  Although tradeoffs between
 defense and growth have been well-studied, tradeoffs with internal organ
 sizes have rarely been considered.  The purpose of our study was
 to investigate the effects of predation and competition on tradeoffs
 associated with total length (body + tail), tail size, and internal organ
 size (gut, pancreas, liver, and fat body) in two larval anurans, red-eyed
 treefrogs (Agalychnis callidryas) and gray treefrogs (Hyla
 versicolor).  In two separate experiments, we reared larvae in
 outdoor mesocosms with and without competition in the presence and absence
 of a caged predator.  We subsampled larvae from each mesocosm and
 measured tail and internal organ sizes.  Both competition and
 predation exerted strong effects on total length and morphology, although
 each experiment produced unique results.  Competition increased
 gut size in both species, supporting a previously reported tradeoff
 between gut and tail size.  Competition also reduced total length
 in both experiments: gray treefrogs balanced total length with lipid
 deposition, and red-eyed treefrogs favored total length at the expense of
 lipid reserves.  Predation threat elicited an increase in tail
 depth but a reduction in tail muscle size in gray treefrogs, which may
 have allowed larvae to maintain pancreas size and total length. 
 Conversely, red-eyed treefrogs developed larger tails with more muscle
 area, allocating resources in a way that sacrificed both liver and
 pancreas size, as well as total length.  Although the specific
 tail response was different, both species prioritized larger guts over
 tail modifications when faced with both competition and predation, as
 large gut sizes were maintained in competitive environments even when
 predators were present.
DOI: 10.5061/dryad.3bk3j9kfd
title: Sequence-capture phylogenomics of true spiders reveals convergent evolution of respiratory systems

description: The common ancestor of spiders likely used silk to line burrows or make
 simple webs, with specialized spinning organs and aerial webs originating
 with the evolution of the megadiverse “true spiders” (Araneomorphae). The
 base of the araneomorph tree also concentrates the greatest number of
 changes in respiratory structures, a character system whose evolution is
 still poorly understood, and that might be related to the evolution of
 silk glands. Emphasizing a dense sampling of multiple araneomorph lineages
 where tracheal systems likely originated, we gathered genomic-scale data
 and reconstructed a phylogeny of true spiders. This robust phylogenomic
 framework was used to conduct maximum likelihood and Bayesian character
 evolution analyses for respiratory systems, silk glands, and aerial webs,
 based on a combination of original and published data. Our results
 indicate that in true spiders, posterior book lungs were transformed into
 morphologically similar tracheal systems six times independently, after
 the evolution of novel silk gland systems and the origin of aerial webs.
 From these comparative data we put forth a novel hypothesis that
 early-diverging web building spiders were faced with new energetic demands
 for spinning, which prompted the evolution of similar tracheal systems via
 convergence; we also propose tests of predictions derived from this
 hypothesis.
DOI: 10.6078/d18t2s
title: Partial migration alters population ecology and food chain length: evidence from a salmonid fish

description: Many migratory species, from monarch butterflies to wildebeest, express
 partial migration, where only a subset of a population migrates. This
 intraspecific variation is likely to have large ecological consequences.
 We studied the ecological consequences of partial migration in a salmonid
 fish, Oncorhynchus mykiss, in coastal streams in California, USA. One
 ecotype, steelhead trout, migrates to the ocean, whereas the other,
 rainbow trout, completes its lifecycle in freshwater. Migration has a
 strong genetic basis in O. mykiss. In one stream, we found differences in
 the frequency of migration-linked genotypes below and above a waterfall
 barrier (migratory allele frequency of 60% below vs. 31% above). Below the
 waterfall, in the migratory-dominated region, the density of young fish
 (&lt;1 year old) was approximately twice that in the
 resident-dominated region above the waterfall (0.46 vs 0.26
 individuals/m2, respectively), presumably reflecting the higher fecundity
 of migratory females. Additionally, there were half as many older fish
 (&gt;1 year old) in pools downstream of the waterfall (0.05 vs. 0.13
 individuals/m2). In a second stream, between-year variation in the
 dominance of migratory vs. resident fish allowed us to explore differences
 in fish density and size structure through time, and we found a consistent
 pattern. In brief, when migratory genotypes dominated, we found higher
 densities of young fish and lower densities of older fish, resulting in a
 simpler size structure, compared to when resident genotypes dominated.
 Moreover, large resident trout had a slightly higher trophic position than
 young fish (3.92 vs. 3.42 in one creek and 3.77 vs. 3.17 in the other),
 quantified with stable isotope data. The difference in fish size structure
 did not generate trophic cascades. Partial migration is widespread among
 migratory populations, as is phenotypic divergence between resident and
 migratory forms, suggesting the potential for widespread ecological
 effects arising from this common form of intraspecific variation.
description: See methods in Kelson et al. 2020, Partial migration alters
 population ecology and food chain length: evidence from a salmonid fish,
 Ecosphere. 
description: See read me files for each data file.
DOI: 10.5061/dryad.zw3r2284z
title: Bottom-up when it is not top-down: Predators and plants control biomass of grassland arthropods

description: 1) We investigate where bottom-up and top-down control regulates
 ecological communities as a mechanism linking ecological gradients to the
 geography of consumer abundance and biomass. We use standardized surveys
 of 54 North American grasslands to test alternate hypotheses predicting
 100-fold shifts in the biomass of four common grassland arthropod
 taxa—Auchenorrhyncha, sucking herbivores, Acrididae, chewing herbivores,
 Tettigoniidae, omnivores, and Araneae, predators. 2) Bottom-up models
 predict that consumer biomass tracks plant quantity (e.g. productivity and
 standing biomass) and quality (nutrient content) and that ectotherm access
 to food increases with temperature. Each of the focal trophic groups
 responded differently to these drivers: the biomass of sucking herbivores
 and omnivores increased with plant biomass; that of chewing herbivores
 tracked plant quality; and predator biomass did not depend on plant
 quality, plant quantity, or temperature. 3) The exploitation ecosystem
 hypothesis (EEH) is a top-down hypothesis that predicts a shift from
 resource limitation of herbivores when plant production is low, to
 predator limitation when plant production is high. In grasslands where
 spider biomass was low, herbivore biomass increased with plant biomass,
 whereas bottom-up structuring was not evident when spiders were abundant.
 Furthermore, neither predator biomass nor trophic position (via stable
 isotope analysis) increased with plant biomass, suggesting predators
 themselves are top-down limited. 4) Stable isotope analysis revealed that
 trophic position of the chewing herbivore and omnivore increased
 significantly with plant biomass, suggesting these groups increased
 scavenging and meat consumption in grasslands with higher carbohydrate
 availability. 5) Taken together, our snapshot sampling documents gradients
 of food web structure across 54 grasslands, consistent with multiple
 hypotheses of bottom-up and top-down regulation. 10-Jan-2020
description: Variable descriptions are provided on the first tab of the excel
 sheet.