cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ks6g0
title: Data from: Recurrent gene deletions and the evolution of adaptive cyanogenesis polymorphisms in white clover (Trifolium repens L.)

description: Understanding the molecular evolution of genes that underlie intraspecific
 polymorphisms can provide insights into the process of adaptive evolution.
 For adaptive polymorphisms characterized by gene presence/absence (P/A)
 variation, underlying loci commonly show signatures of long-term balancing
 selection, with gene-presence and gene-absence alleles maintained as two
 divergent lineages. We examined the molecular evolution of two unlinked
 P/A polymorphisms that underlie a well-documented adaptive polymorphism
 for cyanogenesis (hydrogen cyanide release with tissue damage) in white
 clover. Both cyanogenic and acyanogenic plants occur in this species, and
 the ecological forces that maintain this chemical defense polymorphism
 have been studied for several decades. Using a sample of 65 plants, we
 investigated the molecular evolution of sequences flanking the two
 underlying cyanogenesis genes: Ac/ac (controlling the presence/absence of
 cyanogenic glucosides), and Li/li (controlling the presence/absence of
 their hydrolyzing enzyme, linamarase). A combination of genome-walking,
 PCR assays, DNA sequence analysis, and Southern blotting was used to test
 whether these adaptive P/A polymorphisms show evidence of long-term
 balancing selection, or whether gene-absence alleles have evolved
 repeatedly through independent deletion events. For both loci, we detect
 no signatures of balancing selection in closest flanking genomic
 sequences. Instead, we find evidence for variation in the size of the
 deletions characterizing gene-absence alleles. These observations strongly
 suggest that both of these polymorphisms have been evolving through
 recurrent gene deletions over time. We discuss the genetic mechanisms that
 could account for this surprising pattern and the implications of these
 findings for mechanisms of rapid adaptive evolution in white clover.
description: GenBank Accession
 InformationGenBank accession
 numbers for each submitted sequence3CYP_2.34Sequence alignment for 3CYP_2.34 locus3Li_6.65Sequence alignment for 3Li_6.65 locus
DOI: 10.5061/dryad.42sh717m
title: Data from: Russian wheat aphids (Diuraphis noxia) in China: native range expansion or recent introduction?

description: In this study, we explore the population genetics of the Russian wheat
 aphid (RWA) (Diuraphis noxia), one of the world’s most invasive
 agricultural pests, in north-western China. We have analysed the data of
 10 microsatellite loci and mitochondrial sequences from 27 populations
 sampled over 2 years in China. The results confirm that the RWAs are
 holocyclic in China with high genetic diversity indicating widespread
 sexual reproduction. Distinct differences in microsatellite genetic
 diversity and distribution revealed clear geographic isolation between RWA
 populations in northern and southern Xinjiang, China, with gene flow
 interrupted across extensive desert regions. Despite frequent grain
 transportation from north to south in this region, little evidence for RWA
 translocation as a result of human agricultural activities was found.
 Consequently, frequent gene flow among northern populations most likely
 resulted from natural dispersal, potentially facilitated by wind currents.
 We also found evidence for the long-term existence and expansion of RWAs
 in China, despite local opinion that it is an exotic species only present
 in China since 1975. Our estimated date of RWA expansion throughout China
 coincides with the debut of wheat domestication and cultivation practices
 in western Asia in the Holocene. We conclude that western China represents
 the limit of the far eastern native range of this species. This study is
 the most comprehensive molecular genetic investigation of the RWA in its
 native range undertaken to date and provides valuable insights into the
 history of the association of this aphid with domesticated cereals and
 wild grasses.
description: DRYAD-microsat
 data
DOI: 10.5061/dryad.7mv2b
title: Data from: Partner switching can favor cooperation in a biological market

description: Intraspecific cooperation and interspecific mutualisms can be promoted by
 mechanisms that reduce the frequency with which cooperative organisms are
 exploited by unhelpful partners. One such mechanism consists of changing
 partners after interacting with an uncooperative individual. I used
 McNamara et al.'s (Nature, 451, 2008, 189) partner switching model as
 a framework to examine whether this mechanism can select for increased
 cooperative investment by house sparrows (Passer domesticus) collaborating
 to rear offspring; previous research on this species has shown that
 substantial cooperative investments by both pair members are required to
 achieve high pay-offs from collaborating. I found that the poorer the
 outcome of a breeding attempt relative to the number of eggs the female
 invested, the greater the likelihood of partner switching. The incidence
 of partner switching changed seasonally, with peak switching coinciding
 with an increase in the number of alternative partners available to
 females. After females switched partners, their breeding outcomes rose to
 match those of females that remained with the same partner; this was not
 the case for males that switched partners. Consistent with the
 model's prediction, males in stable partnerships achieved over 25%
 higher than average reproductive success, which was attributable to both
 persistently good breeding outcomes and their older partners' high
 fecundity. These results provide empirical support for the hypothesis that
 partner switching favours increased cooperative investment levels, and
 they demonstrate that variation in the relative value of by-product
 benefits can enhance that process.
description: pswitchmalepswitchprodpswitchfnext
DOI: 10.5061/dryad.2f7h7t6
title: Data from: Flow-ecology relationships are spatially structured and differ among flow regimes

description: 1. In streams, hydrology is a predominant driver of ecological structure
 and function. Providing adequate flows to support aquatic life, or
 environmental flows, is therefore a top management priority in stream
 systems. 2. Flow regime classification is a widely accepted approach for
 establishing environmental flow guidelines. However, it is surprisingly
 difficult to quantify relationships between hydrology and ecology
 (flow-ecology relationships) while describing how these relationships vary
 across classified flow regimes. Developing such relationships is
 complicated by several sources of spatial bias, such as autocorrelation
 due to spatial design, flow regime classification, and other environmental
 or ecological sources of spatial bias. 3. We used mixed moving-average
 spatial stream network models to develop flow-ecology relationships across
 classified flow regimes and to assess spatial patterns of these
 relationships. We compared relationships between fish traits and
 life-history strategies with hydrologic metrics across flow regimes and
 assessed whether spatial autocorrelation influenced these relationships.
 4. Trait-hydrology relationships varied between flow regimes and across
 all streams combined. Some relationships between traits and hydrologic
 metrics fit predictions based on life-history theory, while others
 exhibited unexpected relationships with hydrology. Spatial factors
 described a large proportion of variability in fish traits and different
 patterns of spatial autocorrelation were observed in different flow
 regimes. Synthesis and Applications. Further work is needed to understand
 why flow-ecology relationships vary across classified flow regimes and why
 these relationships may not fit predictions based on life-history
 theories. Managers determining environmental flow standards need to be
 aware that different hydrologic metrics are often important drivers of
 fish trait diversity in different flow-regimes. Flow-ecology relationships
 may therefore be confounded by spatial structure that is inherent in flow
 regime classification and much existing biological data. Complex patterns
 of spatial bias should be considered when managing stream systems within
 an environmental flows framework.
description: Hydrologic
 metricsHydrologic metrics for
 sites used in analysis. Metrics were predicted using hydrologic modelling
 procedure described in Leasure et al. (2016), "Natural Flow Regimes
 of the Ozark–Ouachita Interior Highlands Region". X and Y coordinates
 are provided in meters projected using NAD 1983 Albers.flow_metrics_by_site.csvFish Assemblage DataPresence (1) and absence (0) of fish species across sample sites in AR, USA. Data is compiled samples taken between 1980-2009 by various state and federal agencies, universities, and museums. Data was compiled by the Arkansas GAP analysis project and was obtained from the Nature Conservancy. X and Y coordinates are provided in meters projected using NAD 1983 Albers.fish_by_site.csv
DOI: 10.5061/dryad.fn208
title: Data from: Models for assessing local-scale co-abundance of animal species while accounting for differential detectability and varied responses to the environment

description: We developed a new modeling framework to assess how the local abundance of
 one species influences the local abundance of a potential competitor while
 explicitly accounting for differential responses to environmental
 conditions. Our models also incorporate imperfect detection as well as
 abundance estimation error for both species. As a case study, we applied
 the model to four pairs of mammal species in Borneo, surveyed by extensive
 and spatially widespread camera trapping. We detected different responses
 to elevation gradients within civet, macaque, and muntjac deer species
 pairs. Muntjac and porcupine species varied in their response to terrain
 ruggedness, and the two muntjac responded different to river proximity.
 Bornean endemic species of civet and muntjac were more sensitive than
 their widespread counterparts to habitat disturbance (selective logging).
 Local abundance within several species pairs was positively correlated,
 but this is likely due to the species having similar responses to
 (unmodeled) environmental conditions or resources rather than representing
 facilitation. After accounting for environment and correcting for false
 absences in detection, negative correlations in local abundance appear
 rare in tropical mammals. Direct competition may be weak in these species,
 possibly because the ‘ghost of competition past’ or habitat filtering have
 already driven separation of the species in niche space. The analytical
 framework presented here could increase basic understanding of how
 ecological interactions shape patterns of abundance across the landscape
 for a range of taxa, and also provide a powerful tool for forecasting the
 impacts of global change..
description: data for
 Dryaddetection data, site
 covariates, sampling covariates
DOI: 10.5061/dryad.c2kn2k60
title: Data from: The eco-evolutionary responses of a generalist consumer to resource competition

description: This article explores the combined evolutionary and ecological responses
 of resource uptake abilities in a generalist consumer to exploitative
 competition for one resource using a simple 2-resource model. It compares
 the sizes of ecologically and evolutionarily caused changes in population
 densities in cases where the original consumer has a strong or a weak
 trade-off in its abilities to consume the two resources. The analysis also
 compares the responses of the original species to competition when the
 competitor’s population size is or is not limited by the shared resource.
 While divergence in resource use traits in the resident generalist
 consumer is expected under all scenarios when resources are substitutable,
 the changes in population densities of the resources and resident consumer
 frequently differ between scenarios. The population of the original
 consumer often decreases as a result of its own adaptive divergence, and
 this decrease is often much greater than the initial ecological decrease.
 If the evolving consumer has a strong trade-off, the overlapped resource
 increases in equilibrium population density in response to being consumed
 by a generalist competitor. Some of these predictions differ qualitatively
 in alternative scenarios involving sustained variation in population
 densities or nutritionally essential resources.
description: fitmin_Evolution_archivedThe file is a pdf of a Mathematica (Wolfram Research: version 8) file for integrating the set of differential equations that is explored in the article
DOI: 10.5061/dryad.vn5sq
title: Data from: Anthropogenic environments exert variable selection on cranial capacity in mammals

description: It is thought that behaviourally flexible species will be able to cope
 with novel and rapidly changing environments associated with human
 activity. However, it is unclear whether such environments are selecting
 for increases in behavioural plasticity, and whether some species show
 more pronounced evolutionary changes in plasticity. To test whether
 anthropogenic environments are selecting for increased behavioural
 plasticity within species, we measured variation in relative cranial
 capacity over time and space in 10 species of mammals. We predicted that
 urban populations would show greater cranial capacity than rural
 populations and that cranial capacity would increase over time in urban
 populations. Based on relevant theory, we also predicted that species
 capable of rapid population growth would show more pronounced evolutionary
 responses. We found that urban populations of two small mammal species had
 significantly greater cranial capacity than rural populations. In
 addition, species with higher fecundity showed more pronounced
 differentiation between urban and rural populations. Contrary to
 expectations, we found no increases in cranial capacity over time in urban
 populations—indeed, two species tended to have a decrease in cranial
 capacity over time in urban populations. Furthermore, rural populations of
 all insectivorous species measured showed significant increases in
 relative cranial capacity over time. Our results provide partial support
 for the hypothesis that urban environments select for increased
 behavioural plasticity, although this selection may be most pronounced
 early during the urban colonization process. Furthermore, these data also
 suggest that behavioural plasticity may be simultaneously favoured in
 rural environments, which are also changing because of human activity.
description: cranial capacity and
 body size measurements for all specimensMeasurements of museum
 specimens from the University of Minnesota's Bell Museum of Natural
 History mammal collection. From each specimen we measured the length,
 width and height of the neurocranium and took data on the total body
 length, tail length and hindfoot length from the specimen label. Data also
 included from the specimen database include county where the specimen was
 collected, sex, and taxonomic information. See the manuscript methods for
 more details on measurements and subsequent analyses.Dryad dataset
 final.xls
DOI: 10.5061/dryad.r6s20
title: Data from: Indirect genetic effects from competition in the clonal herb Sedum album (Crassulaceae)

description: Recent years have seen increasing interest in indirect genetic effects,
 i.e. influences on the phenotype that depend on the genotype of other
 conspecific individuals; however, the empirical evidence for such effects
 is still limited, especially in wild plant species. The present study of
 the clonal herb Sedum album assessed direct and indirect genetic effects
 on performance-related traits in a 4-year experiment with clonally
 replicated genotypes, grown in pairs and differing in anthocyanin
 pigmentation to allow separation of individuals during data collection. In
 agreement with the existence of indirect genetic effects, the
 experimentally-paired plants not only expressed their own genotype but
 were also affected by the genotype of their pair mate. The effect of
 neighbour genotype explained up to one-fourth of the variation in
 performance and most likely resulted from competition, imposed by the
 close physical contact between paired individuals and the limiting
 conditions used in the garden environment. Indirect genetic effects from
 competition have the potential to enhance the efficacy of group-level
 selection relative to individual selection, given the nutrient-poor and
 spatially-confined substrate available to plants of S. album in the
 natural habitat.
description: Performance data for
 Sedum album plants in a paired-plant experimentThe present file
 contains data on vegetative and reproductive performance traits (shoot and
 panicle number) measured on Sedum album plants, paired with a genetically
 different or identical individual in a 4-year garden experiment. The
 paired individuals in two-genotype trays differed in anthocyanin
 pigmentation (green vs. red) to allow separation of plants during data
 collection. The data were used to estimate direct and indirect genetic
 effects on plant performance.Sedum
 data.xls
DOI: 10.5061/dryad.jt1fb
title: Data from: Growth responses of a green alga to multiple environmental drivers

description: One feature of global change is that biota must respond not to single, but
 to multiple environmental drivers. By growing a model photosynthetic
 microbe in environments containing between one and eight different
 drivers, including changes in CO2, temperature, and pH, in different
 combinations, we show that the number as well as the identities of drivers
 explain shifts in population growth rates. This is because the biotic
 response to multiple environmental drivers depends on the response to the
 single dominant driver, and the chance of a driver of large effect being
 present increases with the number of drivers. Interactions between drivers
 slightly counteract the expected drop in growth. Our results demonstrate
 that population growth declines in a predictable way with the number of
 environmental drivers, and provide an empirically supported model for
 scaling up from studies on organismal responses to single drivers to
 predict responses to large numbers of environmental drivers.
description: DataDryad_mixed_model_290415Raw data for mixed model analysis, plotting and creating case studies for further analysis. See Read me section in r script "mixed_model_DataDryad_290415.r"All_lines_030515.csv file for plotting case study plot using r script "mixed_model_DataDryad_290415.r"mixed_model_DataDryad_290415R script for mixed model analysis of raw data supplied and plotting.SimulationThe effect of sampling from a finite number of possible environmental drivers was explored using a simulation written in R
DOI: 10.15468/dl.t64xuj
title: Occurrence Download

description: A dataset containing 44286634 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "IucnRedListCategory is one of (LC, DD, NE, NT, VU, EN, CR)",
 "OccurrenceStatus is Present",
 "TaxonKey is Animalia",
 "Year 1850-1995"
 ]
}

 The dataset includes 44286634 records from 1563 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000717-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7910/dvn/t3up6r
title: Replication Data for: Public Gender Egalitarianism: A Dataset of Dynamic Comparative Public Opinion Toward Egalitarian Gender Roles in the Public Sphere

description: Societal attitudes toward gender roles in the workplace and politics play a central part in theorizing on the difficulty women face in achieving political equality, but shortcomings in the available data have prevented direct examination of many implications of these theories. Drawing on recent advances in latent variable modeling of public opinion and a comprehensive collection of survey data, we present the Public Gender Egalitarianism dataset to address this need: comparable estimates of the public’s attitudes on gender equality in the public sphere across more than one hundred countries over time. These PGE scores are strongly correlated with responses to individual survey items and with women’s rates of participation in the labor force and corporate boards. We expect that the PGE data will become an invaluable source for broadly cross-national and longitudinal research on the causes and consequences of collective attitudes toward gender equality in politics and the economy.
DOI: 10.7910/dvn/t8ghts
title: Orange County Annual Survey 1985

description: The Orange County Annual Survey is in its fourth year. The 1985 survey represents the first as a university-based research program with all its funding from external sources. It aims (1) to provide decision makers in the private and public sectors with valid and current information on Orange County residents; (2) to track shifts in important attitudes and population characteristics over time; (3) to study the social, economic, and political issues of Orange County from a nonadvocacy position; and (4) to help establish public discussion and enlightened debate in future public policy. The theme of this year's survey is "Orange County at Mid-Decade." The 1985 survey continues the analysis of attitudes on national issues by considering views towards social welfare spending. This survey analyzes geographical divisions of Orange County that represent distinguishable communities in terms of social, housing, and public policy concerns. The sample size is 1,008 Orange County adult residents.
DOI: 10.7910/dvn/n61eai
title: Replication Data for: Who Lobbies the Lobbyists? State Medicaid Bureaucrats' Engagement in the Legislative Process

description: Research on bureaucratic power typically focuses on rulemaking and policy implementation, while bureaucrats’ participation in in the legislative process remains underexplored. We theorize and test a specific mechanism by which bureaucrats attempt to sway legislative outcomes, which we term indirect bureaucratic lobbying. Using a novel survey of state-based health lobbyists in 25 states, we show that state Medicaid agency staff routinely request lobbying assistance from provider associations and consumer advocates. We also provide the first systematic evidence of the conditions under which indirect bureaucratic lobbying is likely to occur. Our results suggest that individual-level policy agreement interacts with institutional factors, most notably agency capacity and gubernatorial power, to increase the likelihood that bureaucrats will use this strategy to attempt to influence legislative deliberations.
DOI: 10.7910/dvn/nm3gke
title: Food Safety Domain: Defining the flow and food safety behaviors of actors in the Cambodian vegetable value-chain

description: This dataset was created from results of a stakeholder survey of a total of n=102 farmers, n=21 collectors, n=30 distributors, and n=100 vendors from two rural Provinces, in Cambodia. The dataset includes sex disaggregated data, Provential disaggregate data, horticulture crops cultivated, self reported food safety and hygiene practices, and observational information on food safety practices in informal markets Data was collected November 30- December 7, 2018. Policy makers, research, and other stakeholders can use this data to identify potential points of contamination along the vegetable value-chain in Cambodia, and identify potential interventions for controlling contamination. This dataset was collected through research of the project "Integrated Horticulture Livestock Systems" lead by Kansas State University, in partnership with the Royal University of Agriculture, as a part of the Feed the Future Innovation Lab for Horticulture.