cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m1m50
title: Data from: Do polycultures promote win-wins or tradeoffs in agricultural ecosystem services? A meta-analysis

description: 1. Agriculture comprises the largest global land use, makes it a leading
 cause of habitat loss. It is therefore critical to identify how to best
 construct agricultural systems that can simultaneously provide food and
 other ecosystem services. This challenge requires that we determine how to
 maximize win-win relationships and minimize trade-offs between services.
 2. Through meta-analysis, we tested whether within-field crop
 diversification (polyculture) can lead to win-win relationships between
 two ecosystem services: yield of a focal crop species and biocontrol of
 crop pests. We selected only studies that recorded both services (N = 26
 studies; 301 observations), allowing us to better determine the underlying
 mechanisms of our principal findings. We calculated log-response ratios
 for both ecosystem services in mono- and polycultures. 3. We found win-win
 relationships between per-plant yield of the primary crop and biocontrol
 in polyculture systems that minimized intraspecific competition via
 substitutive planting. Additionally, we found beneficial effects on
 biocontrol with no difference in per-unit area yield of the primary crop
 in polyculture fields at high cropping densities (additive planting) where
 legumes were used as the secondary crop. These results suggest that there
 is a strong potential for win-win relationships between biocontrol and
 per-unit area yield under certain scenarios. Our findings were consistent
 across geographical regions and by type of primary crop. We did not find
 evidence that biocontrol had an effect on yield, but rather, both were
 independently affected by polycultural cropping. 4. Synthesis and
 applications. We show that well-designed polycultures can produce win-win
 outcomes between per-plant, and potentially per-unit area, primary crop
 yield and biocontrol. Biocontrol services are consistently enhanced in
 polycultures, so polyculture management that focuses on yield optimization
 is likely to be the best strategy for maximizing both services. In doing
 so, we suggest that practitioners utilize polycultures that decrease
 plant–plant competition through a substitution of relatively large
 quantities of the primary crop for compatibly harvestable secondary crops.
 Additionally, if planting at high cropping densities, it is important that
 legumes be the secondary crop.
description: Log response ratios of
 observations included in meta-analysisLog response ratios of
 biocontrol and primary crop yield for every observation included in
 meta-analysis.Iverson_et_al_datasubmitted.xlsx
DOI: 10.5061/dryad.9sj18
title: Data from: Resident-invader phylogenetic relatedness, not resident phylogenetic diversity, controls community invasibility

description: A central goal of invasion biology is to elucidate mechanisms regulating
 community invasibility. Darwin’s naturalization hypothesis, one of the
 oldest hypotheses in invasion biology, emphasizes the importance of
 phylogenetic relatedness (PR) between resident and invader species for
 predicting invasibility. Alternatively, a recent extension of the
 diversity-invasibility hypothesis predicts that phylogenetic diversity
 (PD) of resident communities influences invasibility. Neither of these
 hypotheses has undergone rigorous experimental testing, and the relative
 contributions of PR and PD, whose effects tend to be confounded with each
 other, to community invasibility are unknown. Here we consider both
 perspectives together by independently manipulating PR and PD in
 laboratory bacterial assemblages. We found that while invader abundance
 declined significantly as PR increased, it was unaffected by PD. Likewise,
 we found that resident-invader functional similarity, not functional
 diversity of resident communities, was a significant predictor of invader
 abundance. Nevertheless, invader abundance was better predicted by PR than
 functional similarity. These results highlight the importance of
 considering species evolutionary relationships, especially the
 phylogenetic relatedness between resident and invader species, for the
 prediction, prevention and management of biological invasions.
description: Resident community
 structure and invader abundanceData.xlsx
DOI: 10.5061/dryad.6g33308
title: Data from: Abiotic and habitat drivers of tick vector abundance, diversity, phenology and human encounter risk in southern California

description: The distribution, abundance and seasonal activity of vector species, such
 as ticks and mosquitoes, are key determinants of vector-borne disease
 risk, and are strongly influenced by abiotic and habitat conditions.
 Despite the numerous species of tick vectors in the heavily populated
 North American West Coast, all but Ixodes pacificus, the primary vector of
 the Lyme disease spirochete, is poorly characterized with regard to
 seasonal activity patterns and fine scale drivers of distribution and
 abundance, particularly in heavily populated regions of southern
 California. This lack of knowledge inhibits both scientific understanding
 and public health efforts to minimize vector exposure and risk of pathogen
 transmission to humans. Here we address this gap by characterizing the
 abiotic and habitat drivers of the distribution, abundance, and diversity
 of the vector tick community using fine scale temporal surveys over two
 seasons (2014 and 2015) across coastal and inland regions of Santa Barbara
 County, CA. We also characterize patterns of seasonal activity of the more
 common vector species to understand seasonality in risk of vector
 exposure, and specifically focus on human encounter risk using
 standardized tick drags as our method of collection. Leveraging plot-level
 habitat and abiotic variables in partial least squares regression
 analysis, we find the seven different vector species collected in this
 study have divergent drivers of activity and abundance. For example, I.
 pacificus is strongly associated with dense forest habitats and cool and
 moist microclimates, while Dermacentor occidentalis and Dermacentor
 variabilis, competent vectors of Rocky Mountain Spotted Fever, were found
 to be more tolerant of higher average temperatures and more open habitats.
 These results suggest that I. pacificus may be expected to experience
 reductions in geographic distribution and seasonal activity under
 projected land cover and climate change in coastal southern California,
 while D. occidentalis may experience more limited effects. We discuss
 implications for changing tick-borne disease risk associated with
 pathogens transmitted by Ixodes as well as Dermacentor species ticks in
 the western US, and contrast these predictions with eastern North America.
description: Tick host-seeking
 seasonality by species, Santa Barbara CountyAll_Ticks_Seasonality_Dryad.csvAverage and maximum adult tick abundance by species, Santa Barbara County, CATotal_Plot_Data_PLS_A_All_Sp_Dryad.csvAverage and maximum nymphal tick abundance by species, Santa Barbara County, CATotal_Plot_Data_PLS_N_All_Sp_Dryad.csvAverage and maximum larval tick abundance by species, Santa Barbara County, CATotal_Plot_Data_PLS_L_All_Sp_Dryad.csv
DOI: 10.5061/dryad.34q3p09
title: Data from: Evolution without standing genetic variation: change in transgenerational plastic response under persistent predation pressure

description: Transgenerational phenotypic plasticity is a fast nongenetic response to
 environmental modifications that can buffer the effects of environmental
 stresses on populations. However, little is known about the evolution of
 plasticity in the absence of standing genetic variation although several
 nongenetic inheritance mechanisms have now been identified. Here, we
 monitored the pea aphid transgenerational phenotypic response to ladybird
 predators (production of winged offspring) during 27 generations of
 experimental evolution in the absence of initial genetic variation (clonal
 multiplication starting from a single individual). We found that the
 frequency of winged aphids first increased rapidly in response to
 predators and then remained stable over 25 generations, implying a stable
 phenotypic reconstruction at each generation. We also found that the high
 frequency of winged aphids persisted for one generation after removing
 predators. Winged aphid frequency then entered a refractory phase during
 which it dropped below the level of control lines for at least two
 generations before returning to it. Interestingly, the persistence of the
 winged phenotype decreased and the refractory phase lasted longer with the
 increasing number of generations of exposure to predators. Finally, we
 found that aphids continuously exposed to predators for 22 generations
 evolved a significantly weaker plastic response than aphids never exposed
 to predators, which, in turn, increased their fitness in presence of
 predators. Our findings therefore showcased an example of experimental
 evolution of plasticity in the absence of initial genetic variation and
 highlight the importance of integrating several components of nongenetic
 inheritance to detect evolutionary responses to environmental changes.
description: data_sentis et
 alExperimental evolution
 data
DOI: 10.5061/dryad.qd740
title: Data from: Wild ungulate decision-making and the role of tiny refuges in human-dominated landscapes

description: Wildlife conservation in human-dominated landscapes requires that we
 understand how animals, when making habitat-use decisions, obtain diverse
 and dynamically occurring resources while avoiding risks, induced by both
 natural predators and anthropogenic threats. Little is known about the
 underlying processes that enable wild animals to persist in densely
 populated human-dominated landscapes, particularly in developing
 countries. In a complex, semi-arid, fragmented, human-dominated
 agricultural landscape, we analyzed the habitat-use of blackbuck, a large
 herbivore endemic to the Indian sub-continent. We hypothesized that
 blackbuck would show flexible habitat-use behaviour and be risk averse
 when resource quality in the landscape is high, and less sensitive to risk
 otherwise. Overall, blackbuck appeared to be strongly influenced by human
 activity and they offset risks by using small protected patches (~3 km2)
 when they could afford to do so. Blackbuck habitat use varied dynamically
 corresponding with seasonally-changing levels of resources and risks, with
 protected habitats registering maximum use. The findings show that human
 activities can strongly influence and perhaps limit ungulate habitat-use
 and behaviour, but spatial heterogeneity in risk, particularly the
 presence of refuges, can allow ungulates to persist in landscapes with
 high human and livestock densities.
description: Blackbuck indirect signs
 and habitat variables.Collected in the field
 and processed using Mircosoft Office Excel. Column headings,
 'drywt' refers to dry weight of forage, and 'Dist'
 refers to Distance from Protected Area (PA) boundary (Negative values
 refer to points inside the PA).Manuscript_Data.csv
DOI: 10.5061/dryad.hd8gs614
title: Data from: Diversity of S-alleles and mate availability in 3 populations of self-incompatible wild pear (Pyrus pyraster)

description: Small populations of self-incompatible plants may be expected to be
 threatened by limitation of compatible mating partners (i.e. S-Allee
 effect). However, few empirical studies have explicitly tested the
 hypothesis of mate limitation in small populations of self-incompatible
 plants. To do so, we studied wild pear (Pyrus pyraster), which possesses a
 gametophytic self-incompatibility system. We determined the S-genotypes in
 complete samplings of all adult trees from three populations using a
 PCR-RFLP approach. We identified a total of 26 different S-alleles,
 homologous to S-alleles of other woody Rosaceae. Functionality of
 S-alleles and their Mendelian inheritance were verified in artificial
 pollination experiments and investigations of pollen tube growth. The
 smallest population (N = 8) harboured nine different S-alleles and showed
 a mate availability of 92.9%, while the two larger populations harboured
 18 and 25 S-alleles and exhibited mate availabilities of 98.4% and 99.2%,
 respectively. Therefore, we conclude that even small populations of
 gametophytic self-incompatible plants may exhibit high diversity at the
 S-locus and are not immediately threatened owing to reduced mate
 availability.
description: S-allele sequences in
 NEXUSAllignment of 21
 S-allele sequences of Pyrus pyraster in NEXUS formatSequencesNEXUS.txt
DOI: 10.5061/dryad.45q7h
title: Data from: Brain size evolution in pipefishes and seahorses: the role of feeding ecology, life history and sexual selection

description: Brain size varies greatly at all taxonomic levels. Feeding ecology, life
 history and sexual selection have been proposed as key components in
 generating contemporary diversity in brain size across vertebrates.
 Analyses of brain size evolution have, however, been limited to lineages
 where males predominantly compete for mating and females choose mates.
 Here, we present the first original data set of brain sizes in pipefishes
 and seahorses (Syngnathidae) a group in which intense female mating
 competition occurs in many species. After controlling for the effect of
 shared ancestry and overall body size, brain size was positively
 correlated with relative snout length. Moreover, we found that females, on
 average, had 4.3% heavier brains than males and that polyandrous species
 demonstrated more pronounced (11.7%) female-biased brain size dimorphism.
 Our results suggest that adaptations for feeding on mobile prey items and
 sexual selection in females are important factors in brain size evolution
 of pipefishes and seahorses. Most importantly, our study supports the idea
 that sexual selection plays a major role in brain size evolution,
 regardless of on which sex sexual selection acts stronger.
description: Syngnathid brain
 sizeThe file consists of
 three parts. First, the data for brain mass and body length for 339
 individuals across 23 species are presented. Then, head shape of 23
 species as described with 12 homologous landmarks are presented in NTS
 format. Finally, a nexus format description of molecular-morphological
 phylogeny (see paper for details) is provided. Uses needs to separate
 these three parts of this file with appropriate file extensions (.txt,
 .NTS and .nex) to repeat the analyses presented in the paper. Questions
 will be answered by Masahito Tsuboi
 (masa.tsuboi@gmail.com).
DOI: 10.5061/dryad.qn370
title: Data from: Epistasis between antibiotic resistance mutations and genetic background shape the fitness effect of resistance across species of Pseudomonas

description: Antibiotic resistance often evolves by mutations at conserved sites in
 essential genes, resulting in parallel molecular evolution between
 divergent bacterial strains and species. Whether these resistance
 mutations are having parallel effects on fitness across bacterial taxa,
 however, is unclear. This is an important point to address, because the
 fitness effects of resistance mutations play a key role in the spread and
 maintenance of resistance in pathogen populations. We address this idea by
 measuring the fitness effect of a collection of rifampicin resistance
 mutations in the β subunit of RNA polymerase (rpoB) across 8 strains that
 span the diversity of the genus Pseudomonas. We find that almost 50% of
 rpoB mutations have background-dependent fitness costs, demonstrating that
 epistatic interactions between rpoB and the rest of the genome are common.
 Moreover, epistasis is typically strong, and it is the dominant genetic
 determinant of the cost of resistance mutations. To investigate the
 functional basis of epistasis, and because rpoB plays a central role in
 transcription, we measured the effects of common rpoB mutations on
 transcriptional efficiency across 3 strains of Pseudomonas.
 Transcriptional efficiency correlates strongly to fitness across strains,
 and epistasis arises because individual rpoB mutations have differential
 effects on transcriptional efficiency in different genetic backgrounds.
description: Vogwill Background
 summary dataFitness and
 transcription data used in this manuscript.
DOI: 10.5061/dryad.3k019
title: Data from: Variation in gut microbial communities and its association with pathogen infection in wild bumble bees (Bombus)

description: Bacterial gut symbiont communities are critical for the health of many
 insect species. However, little is known about how microbial communities
 vary among host species or how they respond to anthropogenic disturbances.
 Bacterial communities that differ in richness or composition may vary in
 their ability to provide nutrients or defenses. We used deep sequencing to
 investigate gut microbiota of three species in the genus Bombus (bumble
 bees). Bombus are among the most economically and ecologically important
 non-managed pollinators. Some species have experienced dramatic declines,
 probably due to pathogens and land-use change. We examined variation
 within and across bee species and between semi-natural and conventional
 agricultural habitats. We categorized as ‘core bacteria’ any operational
 taxonomic units (OTUs) with closest hits to sequences previously found
 exclusively or primarily in the guts of honey bees and bumble bees (genera
 Apis and Bombus). Microbial community composition differed among bee
 species. Richness, defined as number of bacterial OTUs, was highest for B.
 bimaculatus and B. impatiens. For B. bimaculatus, this was due to high
 richness of non-core bacteria. We found little effect of habitat on
 microbial communities. Richness of non-core bacteria was negatively
 associated with bacterial abundance in individual bees, possibly due to
 deeper sampling of non-core bacteria in bees with low populations of core
 bacteria. Infection by the gut parasite Crithidia was negatively
 associated with abundance of the core bacterium Gilliamella and positively
 associated with richness of non-core bacteria. Our results indicate that
 Bombus species have distinctive gut communities, and community-level
 variation is associated with pathogen infection.
description: data1Data file contains the
 main dataset used for analyses
DOI: 10.5061/dryad.23h06
title: Data from: Residency time as an indicator of reproductive restraint in male burying beetles

description: The cost of reproduction theory posits that there are trade-offs between
 current and future reproduction because resources that are allocated to
 current offspring cannot be used for future reproductive opportunities.
 Two adaptive reproductive strategies have been hypothesized to offset the
 costs of reproduction and maximize lifetime fitness. The terminal
 investment hypothesis predicts that as individuals age they will allocate
 more resources to current reproduction as a response to decreasing
 residual reproductive value. The reproductive restraint hypotheses
 predicts that as individuals age they will allocate fewer resources to
 current reproduction to increase the chance of surviving for an additional
 reproductive opportunity. In this study, we test for adaptive responses to
 advancing age in male burying beetles, Nicrophorus orbicollis. Burying
 beetles use facultative biparental care, but the male typically abandons
 the brood before the female. Previous work in male burying beetles has
 suggested several factors to explain variation in male residency time, but
 no study has observed male behavior throughout their entire reproductive
 lifetimes to determine whether males change residency time in an adaptive
 way with age. We compared residency time of males that reproduced
 biparentally, uniparentally, and on different-sized carcasses to determine
 if they used an adaptive reproductive strategy. Males did not increase
 residency time as they aged when reproducing biparentally, but decreased
 residency time with age when reproducing uniparentally. A decrease in
 parental care with age is consistent with a reproductive restraint
 strategy. When female age increased over time, males did not increase
 their residency time to compensate for deteriorating female condition. To
 our knowledge, this is the first test of adaptive reproductive allocation
 strategies in male burying beetles.
description: Abandonment Data for
 AnalysisThis data file includes
 data for male residency time in Nicrophorus orbicollis. Within the data
 set, each male and female are given ID numbers. Treatment 1 is the 20g
 carcass treatment and treatment 2 is the 30g carcass treatment. Male and
 female age correspond to the number of the reproductive attempt for that
 data point. Residency time is the number of days the male remained on the
 carcass after larvae arrived on the carcass. Pronotum width is a measure
 of individual body size. Parental type is either biparental (B) or
 uniparental (U). Initial brood size is the number of first instal larvae.
 Male mass change is the amount of mass gained or lost during that
 reproductive attempt.
DOI: 10.5061/dryad.sv26t
title: Data from: Age, state, environment and season dependence of senescence in body mass

description: [No abstract entered]
description: Data file in csv
 formatBMdata.csvRcode
DOI: 10.5061/dryad.4df03
title: Data from: Field studies demonstrate bivoltinism in the mountain pine beetle (a reply to Bentz and Powell)

description: [No abstract entered]
description: Air temperature data
 used by Mitton and FerrenbergAir temperature and
 growing degree day calculations for Mitton and Ferrenberg's reply to
 Bentz and Powell. This temperature data was pulled from raw data for
 1953-present are available through the University of Colorado's
 Institute for Arctic and Alpine Research. The data presented are from the
 C-1 climate station located at the Niwot Ridge LTER site, 3018 m above sea
 level in Boulder County, Colorado, USA.Mitton_Ferrenberg_Data.csv
DOI: 10.15468/dl.2z2ey8
title: Occurrence Download

description: A dataset containing 1218 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((120.08242 23.2933,120.22427 23.2933,120.22427 23.40709,120.08242 23.40709,120.08242 23.2933))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Aves",
 "Year is 2024"
 ]
}

 The dataset includes 1218 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014636-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.24vz4k
title: Occurrence Download

description: A dataset containing 59 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Quipuanthus epipetricus",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 59 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008266-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.